Comprehensive database of pathogen genomic epidemiology research from PubMed, automatically updated daily
McEwan Callum, Eghrari Donya, Ferdinand Angeline S. · BMC Global and Public Health
Annual pathogen genomic epidemiology publication count
Search Strategy:
Papers were retrieved from PubMed using the following query, which requires papers to have (1) genomic methods AND (2) pathogens AND (3) epidemiological context:
("Whole Genome Sequencing"[MeSH] OR "Genomics"[MeSH] OR "Bacterial Typing Techniques"[MeSH] OR "Molecular Typing"[MeSH])
AND
("Bacteria"[MeSH] OR "Viruses"[MeSH] OR "Fungi"[MeSH] OR "Parasites"[MeSH] OR "Communicable Diseases"[MeSH] OR "Bacterial Infections"[MeSH] OR "Virus Diseases"[MeSH] OR "Genome, Bacterial"[MeSH] OR "Genome, Viral"[MeSH] OR "Genome, Fungal"[MeSH])
AND
("Epidemiology"[MeSH] OR "Disease Outbreaks"[MeSH] OR "Public Health Surveillance"[MeSH] OR "Contact Tracing"[MeSH] OR "Disease Transmission, Infectious"[MeSH] OR "Infection Control"[MeSH] OR "Cross Infection"[MeSH])
NOT
("Genome-Wide Association Study"[MeSH] OR "Polymorphism, Single Nucleotide"[MeSH] OR "Genetic Predisposition to Disease"[MeSH] OR "Pharmacogenetics"[MeSH] OR "Neoplasms"[MeSH]) Date Range:
2010-present (updated daily)
Exclusions:
Human genome-wide association studies (GWAS), single nucleotide polymorphism studies, genetic predisposition studies, pharmacogenetics, and cancer genomics are excluded to focus specifically on pathogen genomic epidemiology.
To Reproduce:
Visit PubMed and paste the query above into the search box. Add date filter: AND 2010:3000[PDAT]
Note: Papers are fetched automatically via PubMed E-utilities API and cached daily. Total retrieved: 10,652 papers.
Genomic pathogen surveillance is a powerful tool for public health and research, but is costly and unachievable in low-resource settings. Most sub-genomic typing methods sacrifice resolution whilst remaining costly. We developed "Phylo-Plex", a novel approach that identifies information-rich genomic...
Cholera remains endemic in India, with outbreaks frequently intensifying during the monsoon due to flooding and disruption of water and sanitation systems. Recent floods in Delhi have raised concerns regarding changing epidemiology, antimicrobial resistance (AMR) and circulation of virulent Vibrio c...
The monophasic Salmonella Typhimurium variant (1,4,[5],12:i:-) is a growing global public health and food safety concern. This study analyzed 60 such isolates collected in Huzhou (2023-2025), including 16 outbreak strains. All isolates belonged to ST34 and carried 211 virulence genes. Antimicrobial...
The study investigates the epidemiological and clinical characteristics of the resurgence of human adenovirus (HAdV) infections among Korean military personnel following the easing of the coronavirus disease 2019 restrictions, with a focus on serotype distribution and healthcare utilization. We cond...
Foot-and-mouth disease (FMD) is among the most important transboundary animal diseases, causing widespread economic losses due to decreased productivity, trade restrictions, and costly disease management efforts. This study aimed to characterize circulating FMDV serotypes and quantify within-farm tr...
We report the detection and genomic characterization of chikungunya virus, an arbovirus, during a 2025 outbreak in Bolivia. We identified the circulating chikungunya virus lineage and the transmission dynamics by using genomic surveillance and phylogenetic analyses. Our findings highlight the utilit...
Transmission is the primary driver of tuberculosis (TB) and drug-resistant TB (DR-TB) in high-burden countries; however, where and between whom spread occurs is poorly understood. We conducted universal whole genome sequencing (WGS) to evaluate the role of casual contact in Mycobacterium tuberculosi...
is an opportunistic pathogen responsible for severe hospital-acquired infections, including bloodstream infections (BSIs). Although major epidemic clones and resistance mechanisms have been described, integrated analyses combining clinical features, patient outcomes and genomic characteristics of BS...
We aimed to identify genomically defined strain transmission events of carbapenem-resistant Gram-negative bacteria (CRGNB) in hospitals, estimate species-specific transmission rates and identify risk factors for transmission. The study included 708 patients from a Japanese prospective multicentre co...
Despite remarkable progress towards measles elimination in Burundi, the country has seen a resurge in cases since 2019. Epidemiological investigations have been performed; however, it remained unclear if all measles cases involved in recent outbreaks were linked or caused by multiple independent eve...
Tuberculosis (TB) remains a global public health concern. In Australia, TB incidence is low, but remains elevated among overseas-born individuals. This study investigates a TB cluster in a non-clinical hospital setting during the COVID-19 pandemic, highlighting transmission dynamics and the public h...
Enteric bacterial pathogens are a major cause of diarrhoeal disease in low-income and middle-income countries, with complex transmission pathways involving human, animal and environmental reservoirs. Conventional epidemiological and microbiological approaches provide important insights into pathogen...
Nosocomial infections are a major health problem worldwide. The increasing time patients spend in hospitals has led to an increase in mortality. Acinetobacter baumannii is an opportunistic pathogen that is a significant factor in nosocomial infections. The main aim of the current study was to invest...
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) remains a significant challenge to clinical management, particularly in critically ill hospitalized patients. The present study aimed to investigate the prevalence and molecular epidemiology of bla among 50 Pseudomonas aeruginosa isolates causing bl...
infections cost Australian society an estimated 140 million Australian Dollars (AUD) per year circa 2019. Salmonellosis is caused by , with over 2,500 serotypes of S. enterica identified. Knowledge of the epidemiology of serotypes may facilitate traceback from strains detected in human cases to ide...
is a serovar with limited published literature on its reservoirs and epidemiology. In April 2024, the Gold Coast Public Health Unit (GCPHU) identified an outbreak of Waycross at a childcare centre in Queensland, Australia, following notifications of acute enterocolitis in children under five years...
Seasonal influenza causes significant global morbidity, mortality, and economic burden. Ongoing viral evolution can lead to vaccine mismatch and the emergence of antiviral resistance, highlighting the importance of genomic surveillance. The 2024-2025 influenza season was characterized by high incide...
Asymptomatic carriage of diarrheagenic Escherichia coli (DEC) in kindergarten children without diarrhoea symptoms represents an important yet underexplored component of community transmission. This study aimed to investigate the prevalence, genomic epidemiology, and antimicrobial susceptibility of D...
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a critical threat to global public health due to limited therapeutic options. This situation is magnified by CRKP strains with elevated virulence. This study aimed to characterize the virulome, resistome, and bla genetic contex...
The chikungunya virus (CHIKV) poses a significant public health threat in China, driven by travel-related introductions and local outbreaks. A comprehensive understanding of the spatiotemporal dynamics, viral genetic diversity, and origins of these outbreaks is imperative for surveillance and contro...
Carbapenem-resistant Enterobacterales (CRE) causing healthcare-associated infections (HAI) represent a growing public health threat. We conducted a large-scale multicenter study to characterize CRE isolates from ICU patients in Egypt. Non-repetitive CRE clinical isolates were collected from infected...
Autochthonous dengue transmission is increasingly being reported in temperate regions of Europe, particularly in areas with established Aedes albopictus populations and high population mobility. We describe a locally acquired dengue outbreak identified in Vila-seca (Tarragona, north-eastern Spain),...
Vancomycin-resistant Enterococcus faecium (VREfm) bloodstream infection (BSI) remains associated with substantial mortality, and timely active therapy may be critical. We evaluated factors associated with 14-day mortality, focusing on anti-VRE therapy, and described contemporaneous molecular epidemi...
Klebsiella pneumoniae is a common cause of hospital-associated pneumonia, bloodstream infection, urinary tract infection, and drainage- or device-related infection. In clinical practice, its significance depends on resistance profile, lineage background, virulence-associated genes, specimen source,...
This study aimed to characterize the frequency of asymptomatic group A (GAS) carriage and respiratory virus detection, and to assess the utility of GAS nucleic acid amplification tests (NAATs) as a microbiological screening method during pharyngitis outbreaks. In this observational cross-sectional...
In 2021, the Los Angeles County (LAC) Department of Public Health suspected a leptospirosis outbreak in LAC affecting over 200 client-owned dogs. We aimed to characterize the outbreak and describe microbiologic findings, risk factors, diagnostic test performance, and outcomes in dogs diagnosed with...
(Group A , GAS) remains a formidable global public health challenge. In this study, we conducted a high-resolution genomic epidemiology study on 176 non-invasive throat GAS isolates collected from pediatric patients in Beijing, China, between June 2024 and March 2025. Whole-genome sequencing was emp...
Dengue virus (DENV) poses a growing risk in Tanzania, yet its genetic diversity in mosquito populations remains poorly understood. Using Nanopore sequencing, we recovered full coding sequences from six DENV-2 positive mosquito pools collected in Dar es Salaam outside recognized outbreak periods. Phy...
is a major opportunistic pathogen in China, yet the molecular epidemiology of quinolone resistance remains poorly characterized. This study analyzed 2,433 clinical isolates from 37 Chinese hospitals (2018-2022). The overall levofloxacin-non-susceptible (NS) rate was 53.60%, with urinary tract isolat...
In April 2020, an outbreak of diarrhea occurred in lactating cows at a dairy farm in the Tottori Prefecture. Five cows died, and Listeria monocytogenes was isolated from the liver, spleen, kidney, and jejunum of one affected cow that was subjected to bacteriological examination. Pathological examina...
Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body...
National and international travel drives the spread of antimicrobial resistance in high-priority pathogens, including Neisseria gonorrhoeae. Border closures and travel restrictions in response to the COVID-19 pandemic had wide-reaching impacts on infectious disease epidemiology, including the transm...
Citrobacter freundii is an emerging nosocomial pathogen, yet its transmission dynamics remain poorly characterized. We conducted a retrospective genomic and epidemiological study to investigate the transmission chains of extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing C. freundii...
Klebsiella pneumoniae is the leading cause of sepsis among neonates in low- and middle-income countries (LMICs) in Africa and Asia, contributing substantially to the overall burden of antimicrobial-resistant infections and mortality among neonates globally. Pathogen sequencing has been used to inves...
A marked resurgence of macrolide-resistant Mycoplasma pneumoniae (MP) was observed in China following relaxation of COVID-19 nonpharmaceutical interventions (NPIs). We characterized the molecular and genomic features of macrolide-resistant isolates in hospitalized children. We retrospectively analyz...
Yellow fever is a major public health concern in Brazil, transmitted in sylvatic cycles by Haemagogus and Sabethes mosquitoes. Among them, Haemagogus janthinomys and Hg. capricornii occur in sympatry in the Atlantic Forest and females are morphologically indistinguishable, complicating vector identi...
is a well-recognized cause of antibiotic-associated colitis. The highly pathogenic PCR ribotype(RT)027/sequence type(ST)1 strain has been prevalent since 2002, particularly in Europe and the United States, whereas strains detected in Japan primarily comprise RT018/ST17, RT369/ST81, and RT002/ST8. Co...
Carbapenemase-producing (CPK) is a major threat in North Africa, yet long-term genomic surveillance efforts remain scarce. To address this, we analyzed 1,013 CPK clinical isolates collected at Habib Bourguiba Hospital (Sfax, Tunisia) from 2009 to 2022. Given limited genomic resources, clinical micr...
The epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) varies across different countries, with a steady global increase. In Portugal, however, epidemiological data on clinical VREfm have been scarce since the early 2000s. This long-term study investigates VREfm isolates from human inf...
Chikungunya virus (CHIKV) and dengue virus (DENV) frequently co-occur in Myanmar and present with overlapping symptoms, complicating diagnosis. During the 2019 dengue outbreak in Yangon, Myanmar, molecular data on CHIKV were limited among dengue-suspected patients and there were no publicly availabl...
The World Health Organization has identified ST23 carbapenem-resistant hypervirulent (CR-hvKP) as a critical public health threat. Through China's national surveillance system (BRICS), we identified and characterized ST23 CR-hvKP bloodstream isolates from 2019-2023. Among 1069 CRKP bloodstream isol...
The role of Muscidae flies as vectors of bacterial pathogens with veterinary and public health significance necessitates accurate species identification and distribution mapping. This review analysed records from the Barcode of Life Data Systems (BOLD) and the South African National Biodiversity Ins...
Respiratory syncytial virus (RSV) infections have a high prevalence in young children, immunocompromised adults, and elderly, raising global concerns. Global RSV surveillance infers an 8%-27% mortality rate in preterm-born children, with 2.8 million/year. Continuous surveillance studies, coupled wit...
The evolutionary trajectory of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has progressed through several distinct phases since its zoonotic emergence, transitioning from initial human adaptation to an era of rapid antigenic drift and complex immune evasion. As of early 2026, the gl...
Japanese encephalitis (JE), caused by mosquito-borne Japanese encephalitis virus (JEV), presents significant public health challenges. To facilitate effective prevention and control, this study conducted an epidemiological and genomic characterization of JEV in mosquitoes across China during the per...
. Carbapenem-resistant (CRKP) strains harbouring and are prevalent in China, while -positive CRKP remains uncommon. This study reports one of the first outbreaks of a nosocomial infection caused by ST101 -positive CRKP in China.. We conducted a retrospective molecular epidemiological study of...
Rates of multidrug resistance (MDR) in Gram-negative bacteria (GNB), particularly those harbouring extended-spectrum beta-lactamases (ESBL) and/or carbapenemases, are increasing globally. Intensive care unit (ICU) patients are vulnerable to healthcare-associated infection (HCAI). Surveillance for ca...
Molecular analysis of Treponema pallidum subsp. pallidum is limited by culture difficulties. We conducted a study using prospectively collected clinical whole-blood specime applying multi-locus sequence typing (MLST) to whole blood to assess strain distribution and macrolide resistance in a cohort o...
Chikungunya virus (CHIKV) is an arthropod-borne Alphavirus of the family Togaviridae. In this study, four CHIKV whole-genome sequences (JH01/China Jinhua/2025 to JH04/China Jinhua/2025) were obtained from a clustered outbreak in Jinhua City, China, using Nanopore sequencing. Phylogenetic relationshi...
The AFROSCREEN initiative, implemented in 13 countries, has strengthened regional genomic surveillance through investments in sequencing infrastructure, workforce training, and cross-country coordination, evolving from a SARS-CoV-2-focused effort into a multi pathogen platform. By building local cap...
No abstract available
In December 2025, Madagascar reported its first confirmed cases of mpox, coinciding with the regional expansion of human monkeypox virus (MPV) Clade Ib across Central and East Africa. To characterize this outbreak, we generated the first near-complete MPV genome sequences from Madagascar using an am...
Advances in molecular epidemiology and computational modeling have improved our ability to track pathogen evolution, but accurate reconstruction of spatiotemporal transmission remains essential for epidemic preparedness and response. Structured coalescent models offer a phylogeographic framework by...
Antimicrobial resistance (AMR) poses a major global health challenge, and wildlife has increasingly been recognized as an important sentinel for monitoring the environmental circulation of clinically relevant resistant bacteria. In this study, we report the phenotypic, genomic, and phylogenomic char...
Acinetobacter baumannii is one of the most important antibiotic-resistant bacterial pathogens. While human clinical isolates have been extensively studied, genomic information from non-human sources remains limited. Here, gathering a dataset of > 23,000 genomes from many sources, we provide a compre...
Chikungunya virus (CHIKV) poses a significant global health threat. Effective genomic surveillance of CHIKV is critical for tracking transmission and evolution. To define an optimal framework, we systematically evaluated four next-generation sequencing (NGS) configurations combining second-generatio...
Klebsiella pneumoniae complex (Kp) is a relevant neonatal pathogen colonizing preterm infants. While outbreak investigations often focus on multidrug-resistant strains, the epidemiology and genomic dynamics of wild-type Kp in nonoutbreak neonatal intensive care unit (NICU) settings remain elusive. W...
is a pathobiont bacterium of the upper respiratory tract in cattle and is associated with acute bovine respiratory disease (BRD). Despite research into bacterial pathogens and their associations with BRD, little is known about how bacterial variant dynamics interplay with disease progression. Theref...
Modern knowledge regarding 'healthy bacterial carriers' traces back to the legacy of typhoid Mary, who unknowingly infected >50 people with enteric fever. Yet, the intricacies of typhoidal Salmonella carriage, inclusive of Salmonella Typhi and Paratyphi A/B, remain largely unknown. Using data collec...
Influenza viruses are segmented negative-sense RNA viruses with high genetic variability, causing seasonal epidemics and pandemics. Whole-genome sequencing from clinical specimens is often hindered by low viral loads and host background, necessitating enrichment-based next-generation sequencing (NGS...
Duck hepatitis B virus (DHBV), a member of the Avihepadnavirus genus, serves as an important model for human hepatitis B virus (HBV) due to shared genomic and replication features. Although typically asymptomatic in adult ducks, DHBV infection is associated with substantial economic losses in commer...
serovar Infantis has emerged as a globally relevant non-typhoidal (NTS) serovar, due to its increasing prevalence in foodborne outbreaks, level of multidrug resistance (MDR), and persistence in poultry production systems. Despite extensive genomic surveillance, few studies have integrated genome-wi...
Multidrug-resistant Klebsiella pneumoniae is spreading rapidly worldwide. The emergence of high-risk clones reinforces the vital need for genomic surveillance to monitor emerging antimicrobial resistance. In this study, we characterized 19 non-duplicate ESBL-producing and carbapenem-non-susceptible...
Clostridioides difficile (CD) is the leading cause of antimicrobial-associated diarrhea (AAD) and causes a spectrum of disease with high recurrence, morbidity, and mortality. CD pathogenicity is primarily driven by toxins A and B, and, in some strains, by the binary toxin. This study evaluated antim...
The coronavirus disease 2019 (COVID-19) pandemic profoundly disrupted global respiratory virus circulation, with sharp declines during 2020-2021, followed by a resurgence after the relaxation of public health measures. In South America, post-pandemic respiratory virus dynamics remain insufficiently...
Arboviruses such as dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) are transmitted by mosquitoes and mainly circulate in tropical and subtropical regions. With global warming, their geographic range is expanding, increasing their threat to public health. Yunnan Province, Chin...
Antimicrobial resistance (AMR) represents a global health crisis, driven largely by the mobility of resistance determinants through mobile genetic elements (MGEs). These include plasmids, integrons, insertion sequences, transposons, integrative and conjugative elements (ICEs), and prophages, which t...
is a ubiquitous foodborne and zoonotic pathogen responsible for necrotizing enteritis, food poisoning, and gas gangrene in humans and livestock, with mortality reaching 100% in specific subtypes. The Qinghai-Tibetan Plateau, with its high altitude, hypoxia, large temperature fluctuations, and strong...
Influenza viruses are the most common causative agents of acute respiratory infections (ARIs), known for their frequent genomic changes, which necessitate close genetic monitoring to track emerging strains. This study aims to determine seasonal trends of H3N2 from 2019 to 2023 and to molecularly cha...
This study evaluated wastewater-based epidemiology (WBE) for monitoring dengue virus (DENGV) and chikungunya virus (CKV) during Brazil's most severe arbovirus epidemic, focusing on the city of Belo Horizonte, Minas Gerais. From March 2022 to August 2024, 24-hour composite raw sewage samples were col...
Ticks serve as key vectors for a diverse range of bacterial pathogens that affect humans and animals worldwide. In Thailand, a comprehensive understanding of tick-associated bacterial diversity remains limited. This scoping review synthesises published data on tick-borne bacteria across Thailand fro...
In 2022, mpox clade IIb disseminated around the world, causing outbreaks in more than 117 countries. Despite the decay of the 2022 epidemic and the increased immunity within sexual networks, mpox continues to persist in North America without extinction, raising concerns of future outbreaks. We combi...
Pathogen genomics has increasingly been integrated into infectious disease surveillance, outbreak detection, and response globally. However, formal evaluation of pathogen genomic surveillance systems has been a major gap. In Australia, the AusTrakka platform was established and deployed nationally t...
is a critical opportunistic pathogen increasingly linked to hospital-acquired infections due to its ability to acquire multidrug resistance (MDR). Its persistence in clinical environments and resistance to nearly all major antibiotic classes make it a formidable challenge for infection control and t...
To investigate the extent of environmental contamination around carbapenem-resistant Acinetobacter baumannii (CRAB)-positive patients and to explore the role of environmental factors in the pathogen's transmission dynamics. Prospectively collected CRAB-positive specimens from intensive care unit (IC...
Zoonotic transmission and viral spillover events pose severe threats to public health, as underscored by recent pandemics. Mitigating these risks requires robust genomic surveillance systems, supported by the growing availability of openly accessible viral genome sequences through dedicated resource...
Enterococcus faecalis has emerged as a significant nosocomial pathogen with increasing relevance at the human-animal interface. This study investigated the antimicrobial resistance (AMR) profiles and genomic characteristics of E. faecalis isolated from cattle farms in Punjab, India. A total of 288 s...
Lassa virus (LASV), a zoonotic, bi-segmented arenavirus endemic to West Africa, causes seasonal epidemics with substantial morbidity and mortality. Increasing frequency of exported cases emphasizes the need for near real-time genomic surveillance to support outbreak response and clinical decision-ma...
Carbapenem-resistant Enterobacter hormaechei (CR-Eh) represents a critical global health threat, especially when carrying mobile antimicrobial resistance genes (ARGs) like bla and mcr. This study characterized three clinical CR-Eh isolates in the context of global genomic datasets, identifying disti...
The pressure of the coronavirus disease 2019 (COVID-19) pandemic on global healthcare systems and societies was unprecedented in the modern era. Social restrictions, containment measures, and disruptions in antimicrobial prescriptions and consumption during the pandemic have been reported to alter t...
Carbapenem-resistant (CRAB) is a critical pathogen associated with severe hospital infections and high antimicrobial resistance. Despite the global significance of , there are limited data from Costa Rica regarding the resistance rate and genomic characteristics of CRAB. : This study aimed to provi...
Nirsevimab is a recombinant monoclonal antibody used to prevent lower respiratory tract infections caused by respiratory syncytial virus (RSV) in infants under one year of age. In Spain a universal immunization program for all children under one year is in place since October 2023. Our goal was to d...
Airborne transmission of respiratory viruses in healthcare settings is often underestimated because conventional epidemiologic methods provide limited insight into aerosol dynamics and ventilation performance. Integrating aerosol simulations with viral genomic data may support the plausibility of ai...
Mpox virus (MPXV) is a zoonotic Orthopoxvirus that has recently gained attention due to outbreaks. In the presence of these constantly changing global health threats, genomic surveillance of the MPXV is no longer a choice but a necessity. The MPXV has diversified through mutation and adaptation, giv...
Acute encephalitis syndrome (AES) caused by Chandipura virus (CHPV) is a rapidly progressive and often fatal neurological illness predominantly affecting children in India. However, limited research on CHPV disease progression and viral genomics has hindered a comprehensive understanding of its tran...
Monkeypox virus (MPXV) is a zoonotic pathogen known to be endemic to the Congo basin and West Africa, and which causes characteristic lesions disseminated on all skin surfaces of infected cases. Multiple MPXV outbreaks have been reported in the Central African Republic (CAR), a country in the Congo...
SARS-CoV-2 continues to cause recurrent waves in the post-pandemic period, yet genomic data from Southeast Asia remain limited for several emerging Omicron lineages, including NB.1.8.1. In this study, routine acute respiratory infection (ARI) surveillance performed in Bangkok, Thailand, from January...
The evolution of SARS-CoV-2 has been driven by successive globally circulating waves, including the Alpha and Delta lineages, early Omicron (BA.1-BA.5), XBB, and the recently dominant JN.1 lineages. Although the marked advantage in fitness of early Omicron over Delta lineages has been recognized, th...
ILTV remains a highly contagious respiratory pathogen causing substantial economic losses on the global poultry industry. Despite the long-term implementation of routine vaccination programs, recurrent outbreaks in vaccinated flocks suggest that the virus's genomic flexibility, driven by both geneti...
We describe a prolonged outbreak of serotype Poona ( Poona) sequence type (ST) 308, which comprised 13 cases occurring intermittently in North West England between 2016 and 2021. Whole genome sequencing (WGS) results indicated potential exposure to a single source but a lack of good quality data fr...
The Bali Provincial Health Office reported 921 cases of suspected chikungunya disease (20.6 incidences/100,000 population) from Oct-2021 to Jun-2022. Sixty-eight samples were collected during the outbreak and underwent further molecular and serological investigations to confirm chikungunya virus (CH...
The human T-cell leukemia virus type 1 (HTLV-1) is a neglected oncogenic retrovirus responsible for adult T-cell leukemia/lymphoma (ATLL) and autoimmune diseases that disproportionately affects marginalized populations worldwide. Peru reports the highest global ATLL incidence, yet comprehensive geno...
Mobile phones are integral to modern clinical workflows and increasingly bridge clinical and private environments. Yet, their role as portable high-touch surfaces in infection prevention remains insufficiently characterized. We hence assessed prevalence and molecular epidemiology of multidrug-resist...
Identifying key biomarkers from multi-omics data is essential for advancing COVID-19 diagnosis and understanding disease mechanisms. Quantum machine learning approaches, particularly the quantum support vector machine, offer potential for biomarker analysis. This study aimed to assess the applicabil...
Neomycin is widely used in livestock to control colibacillosis. Resistance among clinical Escherichia coli is increasing, likely driven by the use of this aminoglycoside following the European restrictions on zinc oxide and colistin. The aim of this study was to investigate the genetic epidemiology...
Zoonotic diseases involve pathogen transmission between humans and animals, with most research focused on animal-to-human spillover. However, reverse zoonosis-the transmission of pathogens from humans to animals-remains understudied despite its potential ecological and epidemiological consequences....
No abstract available
Ocular infections have a substantial impact on global visual health. Despite their association with severe vision impairment, very few studies have systematically monitored antimicrobial resistance (AMR) over time using whole genome sequencing approaches. In the current study, we assembled 291 high-...
Streptococcosis is an emerging bacterial disease in freshwater aquaculture that poses a substantial threat to animal health and production sustainability. In this study, the etiological agent responsible for a "whirling disease" outbreak in yellow catfish (Pelteobagrus fulvidraco) was isolated and c...
Newly renamed anaerobic bacterium Christensenella hongkongensis is an emerging pathogen associated with high mortality. Antimicrobial susceptibility profile and pathogenesis of C. hongkongensis are yet to be fully elucidated. Since its first description from Hong Kong and Canada in 2007, 20 Christen...
The multi-country Mpox (monkeypox) outbreak remains an important issue of global public health, with reported cases of 44,299 and 180 deaths, respectively, in 93 countries by September 2025. Although Africa remains the epicentre, with almost 40,000 cases within countries such as the Democratic Repub...
is a major public health concern and is classified as a priority pathogen by the World Health Organization (WHO) with the global rise of methicillin-resistant (MRSA) infections. Community-associated MRSA (CA-MRSA) strains have become increasingly important in both community and healthcare settings....
Environmental pressures and repeated exposure to antimicrobials drive microbial evolution, often through genomic changes or acquisition of mobile genetic elements that enhance fitness and resistance. This has critically influenced the control of cholera, particularly with the emergence of multidrug-...
Respiratory syncytial virus (RSV) transmission between 2020 and 2025 was impacted by COVID-19-related public health measures, resulting in unprecedented genomic bottlenecks, and postpandemic surges in clinical cases. We performed whole-genome sequencing of 100 infant RSV cases in Sydney during the 2...
The global rise of carbapenem-resistant (CRPA) poses a significant threat to public health. Through active surveillance conducted between 2021 and 2022, we collected 92 distinct CRPA isolates and identified a clonal shift toward high-risk lineages ST235* and ST292. Whole-genome sequencing and phylo...
Candida auris is a globally emerging multidrug-resistant fungus. Its dissemination is driven by patient movement and asymptomatic carriers. However, molecular epidemiological studies linking imported cases to local strains in large metropolitan areas remain limited. To analyse the molecular epidemio...
A comprehensive molecular epidemiological study was conducted on a vancomycin-resistant Enterococcus faecium (VR-Efm) outbreak in Guangdong, China, with the aim of analyzing transmission routes and antimicrobial resistance patterns, developing specific diagnostic tools for early detection, and eluci...
Genomic surveillance of pathogens important to public health, such as (Mtb), offers the opportunity to characterize the geographic movements of pathogens on a range of spatial and temporal scales and to explore the consequences of these inferred movements on the impacts of public health interventio...
Foodborne disease outbreaks, particularly those associated with antimicrobial-resistant (AMR) bacterial pathogens, have become an issue of severe public health concern owing to increased globalisation and active food trade among countries. These disease outbreaks include listeriosis, which can cause...
is a leading cause of healthcare-associated infections worldwide, yet its population structure and transmission dynamics remain largely uncharacterized in New Zealand hospitals. We conducted a 15-month prospective genomic surveillance pilot at Wellington Regional Hospital, embedding Oxford Nanopore...
() is an important cause of healthcare-associated infections (HAIs). In low- and middle-income countries, HAI due to disproportionately affects neonates. In this study, we investigated the genomic changes that occurred during long-term circulation of a sequence type (ST) 39 clone, causing a dispro...
We describe a community outbreak of Panton-Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus (MRSA) during November 2023-June 2024 in the Netherlands. We identified a massage center as the source. Case-patients experienced skin infections and abscesses. This study highlights...
We conducted a retrospective genomic surveillance study of St. Louis encephalitis virus (SLEV) in Texas, USA, to determine the genotypes circulating in the region. By using a custom tiled-amplicon assay with Oxford Nanopore sequencing, we generated 63 genomes from SLEV-positive mosquito pools and vi...
Enterovirus D68 (EV-D68) represents a continuing public health concern, given its association with severe respiratory illness and neurologic complications. In this study, we analyzed EV-D68 circulation and genetic evolution during 2014-2024 using data from 18 countries in Europe. Of 61,297 enterovir...
Prior to 2024, highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses circulated predominantly in wild birds and poultry. In 2024 and 2025, 2.3.4.4b genotypes B3.13 and D1.1 were detected in United States dairy cattle. Using whole-genome and segment-specific phylodynamic inference, we estimat...
Carbapenem-resistant (CRAB) represents a formidable nosocomial pathogen, with healthcare environments acting as critical reservoirs for its dissemination. In this study, we investigated the prevalence, antimicrobial resistance profiles and genomic characteristics of CRAB isolates collected from hos...
Multidrug-resistant (MDR) () represents a growing public health threat worldwide. We performed genomic analyses of carbapenem- and/or colistin-resistant isolates recovered from hospitalized patients at Meram Hospital in Konya, Turkey. Forty-four isolates were identified by matrix-assisted laser de...
In August 2023, 74 symptomatic patients developed Shiga toxin-producing (STEC) O157 infection after consuming raw horse meat processed at a meat shop in Yamagata, Japan. To investigate the outbreak, we conducted multilocus variable-number tandem-repeat analysis (MLVA), whole-genome sequencing (WGS)...
Dengue fever is one of the most widely distributed vector-borne infectious diseases globally, prevalent in tropical and subtropical regions. An estimated 3.9 billion people in 128 countries are at risk of infection globally, and the 2024 outbreak was the most severe. As a tropical region, Hainan Pro...
Antimicrobial resistance (AMR) is a growing global concern within the One Health framework, yet the role of synanthropic wild birds in harboring and disseminating resistant bacteria remains underexplored. This study investigated the seasonal diversity and antibiotic resistance profiles of coliform b...
Wastewater-based epidemiology (WBE) is a cost-effective, unbiased, and time-efficient tool for public health surveillance. Although widely adopted since the COVID-19 pandemic, WBE remains underutilized in genomic epidemiology, as most tools are limited to lineage-level resolution and focus only on e...
() is an important opportunistic zoonotic pathogen, ubiquitous in nature, causing food poisoning, enteric disease, and histotoxic infections in humans and animals. Genomic investigation of from animal-derived food product chains remains limited. In current study, 33 isolates were analyzed and phylo...
: is a Gram-negative bacterium that is found in human microbiota and in diverse environments. This opportunistic pathogen exhibits a highly variable genetic background and is responsible for a broad range of hospital- and community-acquired, multidrug-resistant infections worldwide. To track transm...
Despite its role in healthcare delivery and accessibility, the potential of bioinformatics to transform disease diagnosis in SSA remains unknown. This narrative review aims to assess the current status of bioinformatics initiatives in SSA and evaluate the role of bioinformatics in transforming diagn...
Porcine reproductive and respiratory syndrome virus (PRRSV) remains a major cause of economic losses in the global swine industry, and the emergence of recombinant strains further complicates control efforts, particularly where modified-live vaccines (MLVs) are used. In March 2024, a commercial farr...
Middle East respiratory syndrome coronavirus (MERS-CoV) remains a persistent zoonotic threat more than a decade after its first detection, with Saudi Arabia continuing to be the global epicenter of human infections and the main reservoir interface through dromedary camels. Despite ongoing surveillan...
The emergence of antimicrobial resistance (AMR) is a global threat, with livestock antibiotic use proposed as a significant contributor. We investigated a multidrug-resistant porcine pathogen, as a potential source of AMR gene dissemination to human-associated streptococci in Aragón, Spain. Among 9...
The exact role played by Nigeria in the global monkeypox virus (MPXV) outbreak of 2022 remains unclear, despite exported cases to Singapore, the United Kingdom (UK), the United States of America (USA), and Israel from 2018 to 2022. We sought to resolve the origin of the 2022 MPXV global outbreak. Al...
Hypervirulent Klebsiella pneumoniae (hvKp) has emerged globally as a major public health concern, often associated with severe community-acquired and healthcare-associated human infections. Despite alerts from PAHO/WHO on convergent hvKp strains with multidrug resistance in Latin America, comprehens...
This study aimed to investigate the global genetic diversity, evolutionary relationships, and antimicrobial resistance (AMR) profiles of by performing a comprehensive pan-genome and phylogenetic analysis across worldwide isolates. A total of 72,057 genomes were retrieved from the NCBI database, fr...
Genome sequencing provides an exceptional window into the evolutionary and epidemiological dynamics of endemic and emerging pathogens, and thus allows for better, more targeted, public health interventions. Online genomic surveillance platforms can provide near real-time insight into these dynamics....
Mosquitoes transmit numerous infectious diseases, with climate change expanding their global distribution through warmer environments. Next-generation sequencing offers significant advantages for mosquito genomic surveillance and potential early warning systems. In this study, a portable metagenomic...
Tuberculosis (TB) is a global public health problem, and community outbreaks occur. We report an outbreak of TB with an unusual MPT64 negative status, first detected in North Queensland, Australia, in 2017-2018. A retrospective epidemiological and laboratory investigation into potentially linked cas...
The wide adoption of whole genome sequencing has enabled the implementation of genomics-based systems, which provide unparalleled resolution for the surveillance and outbreak investigation of bacterial pathogens. To fully exploit the wealth and complexity of genomics data, bioinformatics methods nee...
Piperacillin-tazobactam (TZP) resistance in involves diverse mechanisms with unclear prevalence and phenotypic impact. To elucidate these mechanisms, we analyzed clinical isolates resistant to TZP but susceptible to cefotaxime and cefepime. Among 53 isolates, 14 were further studied by MIC testing...
African swine fever (ASF) is a contagious viral disease that causes severe economic losses in the global swine industry. Since its introduction to Vietnam in 2019, ASFV has evolved rapidly, with genotype II strains dominating initially and recombinant I/II variants emerging by 2023. Live attenuated...
Klebsiella pneumoniae strains that combine multidrug resistance and enhanced virulence pose a growing global public health threat. Understanding the genetic basis of these high-risk lineages is critical for surveillance and mitigation. We isolated K. pneumoniae JU-BAEC-01 from treated effluent of an...
is a leading pathogen associated with orthopedic infections, particularly in resource-limited settings where clinical management is complicated by antimicrobial resistance. To characterize the phenotypic and genomic features of associated with orthopedic infections in rural China, 80 isolates were...
Bacillus cereus is an emerging cause of fulminant nosocomial bacteremia in premature infants. Here we aimed to report the successful management of two successive waves of contamination, colonization and infections caused by this pathogen in one neonatal intensive care unit (NICU). This study reports...
Anthrax is one of the most significant zoonotic diseases in Albania due to its endemic presence in livestock, the potential for occupational exposure, and human cases. Although the implementation of risk-based livestock immunization, animal movement restrictions, and appropriate carcass disposal, th...
Air travel plays a key role in the global spread of many diseases, including COVID-19. Surveillance of international travelers is useful for the detection of emerging viruses and variants of concern, especially in a context of global relaxations in testing policy. We aimed to assess the feasibility...
Toscana virus (TOSV) is an arthropod-borne virus, transmitted by sandflies, which represents a major cause of aseptic meningitis in Mediterranean countries during summer months. Despite its epidemiological importance, recent genomic data on circulating Italian strains remain limited. We performed co...
The accelerating frequency of emerging infectious diseases (EIDs) in livestock poses a significant threat to global food security, as well as to animal and public health. While wastewater-based surveillance (WBS) has advanced significantly for human health surveillance, its application to livestock...
This review highlights recent advances in understanding the role of environmental surfaces in healthcare-associated infections, focusing on pathogens like Clostridioides difficile, carbapenem-resistant Enterobacteriaceae, and vancomycin-resistant Enterococci. It emphasizes the importance of effectiv...
Neonatal sepsis due to Gram-negative bacteria remains a clinical challenge. This study aimed to characterize the current epidemiology, genetic diversity, and antimicrobial resistance of invasive Escherichia coli and Klebsiella pneumoniae infections in infants under 90 days old in Taiwan and Korea. C...
KPC and NDM co-producing carbapenem-resistant Klebsiella pneumoniae (KN-CRKP) is an escalating global health threat with limited treatment options. Here, we conducted a multicentre retrospective case-control study on KN-CRKP in China (2020-2025), collecting 3012 non-duplicated CRKP isolates, of whic...
Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the K1 capsule are considered the most common cause of such neonatal invasive infections. This assumption of K1 dominance, and indeed the population geno...
Respiratory viruses circulate yearly with strain-specific patterns. Although SARS-CoV-2 and Influenza A/B genomic surveillance is well-developed, most respiratory viruses are unevenly monitored, lacking geographical diversity to capture wider population dynamics. Consequently, insights into respirat...
Limited evidence exists on the prescription patterns of combination antiretroviral therapy (cART) and their effectiveness in achieving HIV-1 viral suppression. This study evaluated pre-conflict prescription patterns of cART and their virological effectiveness among HIV-1 patients. A retrospective, c...
Human noroviruses are a leading cause of acute gastroenteritis worldwide, with GII.4 Sydney 2012 [P16], being the predominant circulating genotype in Italy in recent years. Outbreaks in pediatric hospital wards represent a major public health concern. Eight stool samples collected between November 2...
Pathogen genome analysis helps characterize transmission between population groups. The information carried by pathogen sequences comes from the accumulation of mutations within their genomes; thus, the pace at which mutations accumulate should determine the granularity of transmission processes tha...
A substantial and rapid increase, followed by a sharp decline in -type vancomycin-resistant (VRE), occurred in Germany in the late 2010s. This unusual epidemiological trend prompted detailed genomic investigations to explore the underlying dynamics at a German university hospital. We retrospectivel...
Fungal meningitis outbreaks are rare and entail high mortality rates. Beginning May 2023, we investigated fungal meningitis caused by Fusarium solani species complex occurring in US patients who received epidural anesthesia in Matamoros, Mexico. Early epidemiological information suggested US patient...
To synthesize updated epidemiological, genomic, clinical, and policy evidence on mpox, with emphasis on the emergence of Clade I sub-lineage "Clade Ib" and its implications for One Health-based preparedness. This narrative, non-systematic state-of-the-art review draws on literature indexed in PubMed...
Following an extended period of declining prevalence of the epidemic ribotype 027 (RT027) in Portugal, a genetically distinct, multidrug-resistant (MDR) RT027 strain with reduced susceptibility to vancomycin has emerged, causing a 15-month outbreak. This investigation provides epidemiological and g...
H11 avian influenza viruses (AIVs) circulate globally among wild bird populations, yet their evolutionary pathways and risks for zoonotic transmission remain insufficiently characterized. In the current study, analysis of 1,179 H11 hemagglutinin (HA) sequences revealed that dispersal patterns closel...
Methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) are major causes of hospital-acquired infections worldwide. However, their genomic features remain underexplored in many regions, particularly in low- and middle-income countries (LMICs). Here, we investigated the genomic diversity, an...
Streptococcus agalactiae was confirmed as the etiologic agent of streptococcosis in Nile tilapia (Oreochromis niloticus) from Campeche, Mexico, during a cross-sectional investigation of eight semi-intensive farms (2021-2022) that yielded virulent strains in a challenge assay. Standard bacteriology,...
The relatively slow mutation rates of bacterial pathogens impose severe limitations on phylodynamic analysis of bacterial outbreaks. However, whole-genome sequencing may enable accurate inference of bacterial transmission dynamics in health-care settings. We simulated the epidemic dynamics of a Stap...
Influenza B virus (IBV) undergoes continuous genetic mutations that can affect vaccine effectiveness and immune evasion. Although considerable research on IBV epidemiology exists globally, understanding of its genetic behavior in Saudi Arabia remains limited. This study characterized the molecular e...
Vibrio parahaemolyticus is a major foodborne pathogen transmitted mainly through contaminated seafood. This study analyzed 157 isolates collected from Nantong, China, during 2023-2024 through antimicrobial susceptibility testing and whole-genome sequencing. Compared with 2018-2021 data, ampicillin r...
Infections caused by carbapenem-resistant Escherichia coli (CREC) pose a serious global public health threat due to limited therapeutic options. This study aimed to investigate the molecular epidemiology and the susceptibility to novel β-lactam/β-lactamase inhibitor combinations in clinical CREC iso...
This study investigate the molecular epidemiology and population characteristics of 184 Acinetobacter baumannii clinical isolates collected in Zhejiang (2015-2020), shedding light on the persistence and success of ST208-KL2 lineage. Whole-genome sequencing and bioinformatic analysis characterized th...
Synanthropic cockroaches, especially and , are persistent pests of human dwellings, healthcare facilities, food establishments, farms, and transport infrastructure. Accumulating field and laboratory studies indicate that synanthropic cockroaches carry clinically important bacteria, fungi, and paras...
Sandfly-borne phleboviruses cause febrile illness and neuroinvasive disease in humans. While infections are reported in the Mediterranean region, the discovery of previously unknown phleboviruses in sandflies from Kenya suggests a wider geographic distribution. Detection and characterization of nove...
Pandemics often involve complex transmission dynamics in which epidemiological surveillance is essential but not sufficient for containment, as resurgence may be driven by emerging or imported variants. Rapidly evolving pathogens produce complex disease dynamics driven by emerging variants often dif...
Transmission of antimicrobial resistance genes between bacteria increases the threat posed by antimicrobial resistance worldwide. In 2019, three hospitals in Limburg (the Netherlands) detected multidrug-resistant Enterobacteriaceae with similar phenotypes. We investigated whether these similar resis...
We report a coding-complete genome sequence of a lumpy skin disease virus (LSDV) isolate (SAUVM-78) collected on 11 October 2021, during a clinical outbreak in Rajshahi, Bangladesh. This resource supports ongoing genomic surveillance of Capripoxviruses in South Asia.
Nipah virus (NiV) is a zoonotic pathogen causing severe respiratory and neurological disease in humans, with high fatality rates, primarily transmitted from fruit bats to humans through bat-tainted raw date palm sap and fruits. NiV outbreaks have occurred almost annually across 34 of 64 districts in...
is a World Health Organization priority pathogen because of its rapidly accumulating resistance to multiple drug classes. Over-expression of the AcrAB and OqxAB Resistance-Nodulation-Division (RND) efflux pumps is a key mechanism, yet genomic data on these systems in Peruvian strains are scarce. Six...
Despite being a major epidemic potential pathogen with recurrent emergence, chikungunya virus (CHIKV) remains neglected in Bangladesh, with poor characterization of long-term epidemiology, reemergence patterns, and prevention policy. We screened epidemiologic, clinical, and genomic data on CHIKV out...
Highly pathogenic influenza A viruses of the H5 subtype continue to diversify worldwide through mutation and genetic reassortment, generating novel variants with unpredictable consequences under the One Health approach. Between 2024 and 2025, five outbreaks of avian influenza A viruses were detected...
is an important zoonotic intestinal protozoon causing diarrhea in humans and animals, threatening public health and livestock farming. This study aimed to investigate the infection and genotype distribution of in black goats in Fujian, southeastern China. A total of 539 fecal samples were collected...
We aimed to investigate a nosocomial outbreak of Mycobacterium abscessus subspecies massiliense (MAM) and to track its transmission route via genomic analyses and environmental surveys at a hospital in Osaka, Japan. The outbreak was initially detected in two patients (M1 and M2) with severe disabili...
Genotyping is essential for identifying the relatedness of multidrug-resistant organisms (MDROs), particularly in outbreak situations. This study outlines the genotypic antimicrobial resistance (AMR) characteristics of Gram-negative bacteria (GNB) isolated from bloodstream infections (BSI) in paedia...
Asymptomatic tuberculosis (TB) poses a major challenge to global TB control. Quantifying its contribution to transmission remains a critical question. Although modelling studies have attempted to address this issue, empirical evidence from real-world settings is scarce. In this study, we estimated t...
HIV-1 CRF01_AE exhibits multiple distinct sub-subtypes (01_C1-C8) with different transmission dynamics across China. Understanding their geographical distribution, transmission patterns, and key affected populations is critical for optimizing targeted interventions. We conducted a comprehensive mole...
Mpox is an infectious disease caused by the Monkeypox virus, which is divided into two main genetic clades: Clade I and Clade II. A large-scale outbreak linked to Clade IIb emerged in 2022 and rapidly spread to more than 100 countries worldwide. Here, we describe the first and only documented Mpox o...
Escherichia coli is a ubiquitous bacterium that acts both as a commensal and a pathogen, serving as a major reservoir of antimicrobial resistance genes (ARGs). The global spread of ARGs, particularly those conferring resistance to last-resort antibiotics such as carbapenems and colistin, poses a ser...
Rifampicin resistance continues to pose a challenge to successful tuberculosis (TB) control, mainly driven by mutations in the rpoB gene of Mycobacterium tuberculosis. Although most diagnostic tools, such as Xpert MTB/RIF, Xpert Ultra, and line probe assays, focus on the standard 81-bp rifampicin re...
Respiratory syncytial virus (RSV) is a leading cause of respiratory infections in infants and older adults, with epidemiological patterns shaped by viral evolution and diversity. To investigate the molecular epidemiology of RSV before and after the COVID-19 pandemic, we conducted genomic surveillanc...
Classical swine fever virus (CSFV) remains a major threat to global swine production due to its high transmissibility, genetic diversity, and continued outbreaks despite vaccination and control programs. Although whole-genome sequencing provides the most reliable framework for phylogenetic inference...
Acute respiratory infections (ARIs) remain a common cause of morbidity and mortality in children, especially in sub-Saharan Africa, where countries such as Ghana are severely affected. This review presents recent data on ARI etiology, clinical burden, and antimicrobial resistance (AMR) from Ghana, s...
Norovirus genogroup II (GII) is a common gastrointestinal pathogen that can cause spatially and temporally linked outbreaks due to its resistance to disinfectants and desiccation. Despite this threat, routine whole-genome sequencing has rarely been systematically applied to Norovirus. We performed w...
Enterococci are commensals of the human gut that opportunistically cause over 10% of hospital-acquired infections. Vancomycin-resistant enterococci (VRE) are often treated with linezolid; however, resistance to linezolid has emerged, most commonly mediated by the optrA gene. Bacterial strain typing...
Mosquito-borne virus surveillance is pivotal for investigating mosquito viromes, facilitating understanding of viral evolutionary histories and genetic diversity. Natural viral communities in mosquitoes include not only insect-specific viruses (ISVs) but also viruses infecting symbiotic microorganis...
The misuse of broad-spectrum antibiotics has facilitated the emergence of carbapenem-resistant subsp. (CRSE). This study aims to investigate the genomic characteristics and epidemiological patterns of two strains isolated from pediatric patients, along with 21 CRSE strains collected from humans wo...
Infectious disease dynamics result from the complex interplay of epidemiological, ecological and evolutionary (epi-eco-evo) processes. Accurately modelling these coupled processes is crucial for understanding pathogen spread and informing public health strategies. However, existing genomic epidemiol...
Linezolid is a critical last-resort antimicrobial for multidrug-resistant , particularly against vancomycin-resistant lineages where therapeutic options are severely limited. While resistance has historically arisen through chromosomal mutations, the global emergence of transferable resistance mech...
Heartland virus (HRTV) is an emerging tick-borne virus capable of causing severe illness and death. The burden of disease is likely underestimated due to limited seroprevalence studies, lack of commercially available diagnostic tests, and an overlapping clinical syndrome with more commonly diagnosed...
Tuberculosis (TB), caused by the Mycobacterium tuberculosis complex (MTBC), remains a pressing global health challenge, with a high burden in West Africa, including The Gambia. Understanding the genetic diversity of circulating MTBC strains is essential for improving diagnosis, surveillance and trea...
Streptococcus agalactiae sequence type (ST) 283 is an emerging, hypervirulent lineage predominantly identified in Southeast Asia and strongly associated with foodborne transmission linked to raw freshwater fish consumption. While ST283 was responsible for the 2015 outbreak in Singapore, no human inf...
Methicillin-resistant Staphylococcus aureus (MRSA) remains a major public health challenge due to its multidrug resistance and diverse virulence factors, which make it difficult to manage and represent a significant cause of hospital-associated infections. In this study, MRSA strain PSU20 was isolat...
Dengue virus (DENV) transmission in Bolivia has historically been restricted to tropical lowland regions, where the primary vector Ae. aegypti is endemic. In recent years, however, the vector has expanded into high-altitude areas. In 2024, Cochabamba, located at ~ 2,550 m above sea level, experience...
In countries where Dengue virus is endemic, the occurrence of outbreaks and epidemic events is strongly associated with viral genomic evolution. In addition, the introduction of a new agent, such as Zika virus, in a naive population and its concomitant circulation may increase mutations and virulenc...
Unprecedented global increases in Mycoplasma pneumoniae respiratory infections began in late summer 2023. Although a predominance of p1 subtype 1 associated with alarmingly high rates of macrolide resistance was reported in Southeast Asia, data from Europe remain limited. We aimed to characterise th...
Traveller's diarrhoea (TD) remains one of the most prevalent health concerns affecting individuals visiting low- to middle-income countries. Among the primary infectious agents, two pathogenic variants of Escherichia coli are especially prominent: enteroaggregative E. coli (EAEC) and enterotoxigenic...
Introduction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been one of the most significant pandemics of the modern era. This coronavirus has a high mutation rate, resulting in variants with changes in the spike protein, which hinder containment efforts. Genomic surveillance is c...
This study aimed to investigate the prevalence and underlying mechanisms of colistin resistance among 557 non-duplicate CRPA isolates collected from a tertiary hospital in Jiangxi, China, between 2021 and 2024. Antimicrobial susceptibility testing, whole-genome sequencing, bioinformatic analyses, si...
Diphtheria is a severe, vaccine-preventable infection caused mainly by , but other species within the complex, including , can also carry the diphtheria toxin (DT) coding gene (). Strains classified as “nontoxigenic toxin-gene bearing” (NTTB) harbor the gene but do not produce functional DT, altho...
Dengue virus (DENV) is a major global health threat whose expansion into temperate regions has been facilitated by climate change and vector adaptation. Despite recurrent epidemics in Brazil, genomic surveillance in mosquito vectors remains limited, particularly in southern regions, constraining our...
Dengue is a major global health challenge, yet no commercially validated molecular kits currently provide both serotyping and viral load quantification in a single integrated format. To address this gap, we developed and internally validated a one-step multiplex real-time RT-PCR assay that simultane...
is a leading foodborne pathogen worldwide, posing significant public health concerns. However, its prevalence in mountainous regions in China remains unclear. This study analyzed 384 strains isolated from 2,540 samples collected between 2017 and 2024 from humans, food, and environmental sources in...
Shiga toxin-producing (STEC) serotype O157:H7 emerged in the 1980s as a cause of foodborne outbreaks of infectious intestinal disease. Over the last decade, whole-genome sequencing (WGS) has replaced phage typing (PT) as the typing method of choice to detect outbreaks and monitor trends of STEC O15...
We describe an outbreak of carbapenemase-producing that occurred in February-March 2025 in a tertiary care hospital in Rome, Italy. Ten patients in two adjacent critical care units were found colonised or infected with strains co-producing NDM-1 and OXA-48 carbapenemases. Nine of these had acquired...
Leptospirosis is an important zoonotic disease globally, which is most prevalent in tropical regions. This disease is endemic in Sri Lanka, where the complex ecology of spp., reservoir animals and environmental and occupational factors has resulted in a public health problem. Although genomic analy...
We describe a large and prolonged outbreak of Enteritidis in the Netherlands. Between June 2023 and September 2025, we identified 227 outbreak cases (110 males, 114 females, three with missing information of sex; median age 43 years). Outbreak cases were individuals whose isolates belonged to the o...
Stenotrophomonas maltophilia is an opportunistic bacterial pathogen found in healthcare settings. During May 2022-September 2023, an acute care hospital in northern California, USA, identified 13 S. maltophilia bloodstream infections among intensive care unit patients. Whole-genome sequencing showed...
MPOX has been declared endemic in Central Africa by WHO in 2017. More recently (2018-2021), MPOX cases have been reported in various regions (endemic as well as non-endemic) all over the world. The sudden, unexpected and simultaneously emerging cases at geographically disparate areas indicate the pr...
(recently renamed ) is an emerging multidrug-resistant fungal pathogen, first identified in Japan in 2009. exhibits remarkable persistence on human skin and inanimate surfaces, resistance to multiple antifungals, notably fluconazole, and biofilm formation, which hinders infection control and leads...
Indigenous populations in the USA experience disproportionately high rates of invasive disease, yet the drivers of this disparity remain unclear. To investigate the role of bacterial population structure, we conducted whole-genome sequencing of 589 invasive isolates and 125 carriage isolates colle...
Global interconnectedness and rapid urbanization intensify the spread of infectious diseases, underscoring the critical need for effective and scalable surveillance. Wastewater-based epidemiology (WBE) has proven to be a practical and cost-effective approach for monitoring community-level pathogen p...
is a major human pathogen responsible for invasive pneumococcal diseases (IPDs). We utilized whole-genome sequencing to assess the impact of pneumococcal conjugate vaccines (PCVs) on the pneumococcal population causing IPD in Lebanon. isolates collected between 2003 and 2025 (=273) were sequenced...
This study describes the genomic and phenotypic characteristics of a Panton-Valentine Leukocidin (PVL)-positive methicillin-resistant Staphylococcus aureus (MRSA)-ST88, causing ventilator-associated pneumonia (VAP) in Brazil. The MRSA-ST88 isolate (SQ684) was recovered from a tracheal aspirate of a...
Orf virus (ORFV), a zoonotic member of the genus Parapoxvirus, causes contagious ecthyma in sheep and goats and poses significant economic and public health concerns. Despite frequent outbreaks, molecular data on ORFV circulating in Tanzania remain scarce. This study aimed to confirm ORFV infection...
Chapare virus (CHAPV) is an emerging New World arenavirus that causes Chapare haemorrhagic fever (CHHF), a severe and often fatal illness. First identified in Bolivia in 2003, CHAPV remains geographically limited but has shown potential for nosocomial transmission. It causes symptoms similar to othe...
Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a formidable healthcare-associated pathogen, particularly in intensive care units, where it causes severe infections associated with prolonged hospitalization, limited treatment options, and high mortality. This review provides an in...
Candidatus Borrelia kalaharica was proposed as bacterial species in 2016 using DNA extracted from a traveller returning from Southern Africa. We investigated DNA of three soft ticks collected in the Kalahari Game Reserve near Maun, Botswana via PCR. One of the DNA extracts yielded positive results f...
Mpox is a zoonosis caused by the monkeypox virus. Here, we report Mali's index Mpox case, which was clinically identified at the Mali-Guinea border by the national telemedicine center and confirmed by PCR. The library prepared with NextGenPCR™ MPXV Sequencing Library Prep and sequenced on Minion MK1...
The emergence of azole-resistant Candida tropicalis poses a significant threat in healthcare settings. It contributed to high morbidity and mortality, particularly in those undergoing chemotherapy for haematological diseases. In this study, we investigated a suspected outbreak in the haematology war...
Dengue is the leading mosquito-borne viral cause of human illness and death. More than four billion people globally are at risk of dengue virus (DENV) infection, and most infections are asymptomatic or present with a non-specific febrile illness. We characterise the first complete DENV-2 genome from...
Rocio virus (ROCV), a neurotropic arbovirus of the genus, caused Brazil’s largest encephalitis outbreak in the 1970s but has since been rarely detected. We report the first ROCV encephalitis clinical case after nearly 40 years and isolated and sequenced the virus from CNS tissue of a horse. Metatra...
Human adenoviruses (HAdVs) are important respiratory pathogens that circulate globally and frequently cause outbreaks, particularly among pediatric populations. Despite their clinical relevance, recent data on genome-wide evolution and recombination of circulating HAdVs in Korea remain limited. In t...
Transmission of human respiratory pathogens to wild, human-habituated great apes has been repeatedly documented within research and tourism projects. While the implementation of hygiene measures has significantly reduced the risk of pathogen introduction, vigilant surveillance remains essential to e...
Genomic epidemiology has transformed the way public health scientists detect, monitor, and respond to infectious disease threats such as SARS-CoV-2 on a global scale. Early in the COVID-19 pandemic, vast inequities in whole-genome sequence data availability between high- and low-income countries wer...
Mosquitoes and sandfly species are well-known vectors of viral pathogens of public health concern. However, the diversity and ecology of viruses within mosquitoes, including those responsible for clinical and sub-clinical infections in humans, remain poorly understood. In this study, we investigated...
Healthcare-associated infections (HAIs) in Europe affect millions of patients annually, driving antimicrobial resistance and imposing significant economic burdens. Carbapenem-resistant Enterobacterales (CRE) are particularly concerning due to their ability to spread, making genomic surveillance esse...
Severe febrile illness (SFI), a major cause of child mortality in Sub-Saharan Africa (SSA), is frequently caused by bloodstream infections (BSI), increasingly caused by antimicrobial-resistant organisms. However, antimicrobial resistance (AMR) prevalence and patterns in this population are largely u...
Bordetella pertussis continues to circulate globally despite widespread vaccination, with a notable epidemic in 2024. Its resurgence is confounded by the emergence of pertactin-deficient, macrolide-resistant B pertussis strains in Asia and Europe, which are under-recognised by conventional diagnosti...
Nosocomial infections in Neonatal Intensive Care Units (NICU) are a major concern due to the vulnerability of premature and immunocompromised infants. Serratia marcescens is an opportunistic pathogen often involved in these infections, contributing significantly to morbidity and mortality. Integrati...
Klebsiella pneumoniae is an important nosocomial pathogen, considered a critical threat to public health, but its genomic data are scarce in Brazil. Therefore, the aim of this study was to identify the mechanisms of virulence and antimicrobial resistance and to evaluate the molecular epidemiology of...
Dengue virus (DENV) serotyping is essential for epidemiological surveillance, clinical risk assessment, and vaccine evaluation, as the four dengue serotypes differ in pathogenicity, immune interactions, and population dynamics. Existing subtyping methods largely rely on sequence alignment and phylog...
To identify enriched pathogens and characterise the viral community associated with epidemic disease outbreaks in the freshwater mussel Hyriopsis cumingii, we performed metatranscriptomic sequencing combined with VirID-driven RNA-dependent RNA polymerase (RdRP) mining and phylogenetic analysis using...
Regional genomic surveillance is essential for tracking viral evolution and informing targeted public health responses. During the COVID-19 pandemic, we established a collaborative genomic surveillance pipeline for SARS-CoV-2 in Southeast Michigan to support national surveillance efforts and guide l...
Here we report a case of late onset neonatal invasive meningococcal disease that was vertically transmitted, with maternal vaginal swab at the time of delivery and neonatal cerebrospinal fluid culture positive for . Whole genome sequencing of meningococcal isolates in the neonatal cerebrospinal flui...
Respiratory viral infections remain a global health concern, particularly among children, the elderly, and immunocompromised individuals. Although real-time polymerase chain reaction (RT-PCR) is the diagnostic gold standard, its limitations in strain-level typing and mutation tracking highlight the...
Neisseria meningitidis is a major pathogen of septicemia and meningitis, with a fatality rate of 10%-15%. Cefotaxime resistance in N. meningitidis remains rare, and has not yet been reported in internationally disseminated serogroup Y (MenY) ST-23 clonal complex (cc23) strains. This study aimed to c...
: Hypervirulent (hvKp) is an emerging global pathogen that causes severe liver abscesses and metastatic infections. Despite rising concerns regarding multidrug-resistant convergence, molecular data in Romania remain limited. This study characterizes the epidemiological, clinical, and genomic profil...
Understanding epistatic interactions, where mutations collectively influence viral fitness, is critical for predicting pathogen evolution. We present a hidden Markov model (HMM) framework that captures the temporal dynamics of epistatic relationships in SARS-CoV-2, addressing limitations of static n...
Tomato spotted wilt virus (TSWV) is distributed globally and causes considerable economic losses in plant production. However, the molecular epidemiology of TSWV remains poorly understood. In this study, we inferred the phylodynamics of TSWV using the most extensive and comprehensive dataset of TSWV...
The accurate inference of pathogen movements among locations during an epidemic is crucial for measuring infectious disease spread and for informing effective control strategies. Phylogeographic methods can reconstruct historical patterns of disease dissemination by combining the evolutionary histor...
O157:H7 is one of the several zoonotic bacteria that causes food-borne disease, has socioeconomic sphere and public health impacts. Cattle are an important reservoir of O157:H7, and shed in their feces as well as contaminate animal-origin food products, sometimes leading to transmission to humans....
Oropouche virus (OROV) is an emerging vector-borne pathogen endemic to the Americas, which causes acute febrile illness (AFI) in humans. Starting in late 2023, surges in OROV infections were reported across Latin America, including an outbreak in Iquitos, a city in the Eastern Peruvian Amazon, where...
Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic pathogen causing outbreaks in humans and ruminants across Africa and the Arabian Peninsula. Originally restricted to the Great Rift Valley, RVFV has expanded geographically, prompting its classification by WHO as a pathogen of pandemic pote...
In 2024, Andalusia (Southern Spain) reported its largest recent West Nile virus (WNV) outbreak, with 106 confirmed human cases and 16 deaths. Genomic analysis of 27 WNV isolates revealed the co-circulation of multiple WNV lineage 1 clades, including both endemic and recently introduced strains, refl...
The COVID-19 pandemic has disproportionately affected immunocompromised individuals, who remain at risk for severe disease despite widespread vaccination efforts. Poor vaccine-induced humoral responses in this population necessitate additional preventive strategies. Sipavibart (AZD3152) is a next-ge...
Genomic surveillance is a cornerstone of pandemic response; it has helped guide public health interventions worldwide. However, North Africa stands between limited surveillance resources and efforts to address the data gap in this strategic geographic region that links sub-Saharan Africa and Europe....
In 2024, a highly fatal outbreak of equine salmonellosis occurred in a Hungarian equine referral hospital, resulting in the death or euthanasia of four out of five affected horses. () subsp. serovar Typhimurium was identified as the primary causative agent from equine faecal, reflux, and post-mor...
Antimicrobial resistance (AMR) is a major public health threat, especially in low- and middle-income countries (LMICs), where large datasets linking antimicrobial susceptibility testing (AST) with genomic data remain limited. We analyzed AST results and whole genomes from 266 resistant bacterial iso...
Respiratory pathogens are a significant source of global morbidity, mortality, and economic burden, with the COVID-19 pandemic driving increased interest in and funding for respiratory disease surveillance. Syndromic panel multiplex nucleic acid amplification tests (NAATs) such as the BioFire Respir...
Carbapenem-resistant Enterobacterales, driven by New Delhi metallo-β-lactamases (NDMs), severely restrict treatment options and are increasingly detected outside hospitals. Yet, integrated genomic-phenotypic data on NDM-positive colonizing the pediatric gut in China remain scarce. Antimicrobial sus...
Tomato spotted wilt virus (TSWV) is a globally important pathogen of peanut, characterized by rapid evolution, broad host range, and capacity to overcome resistance. In this study, we performed deep sequencing of TSWV isolates from two peanut cultivars (GA-06G and Bailey II) and two induced allotetr...
Dengue is one of the most rapidly expanding mosquito-borne viral diseases worldwide, posing a persistent public health challenge across tropical and subtropical regions. Here, we report the re-emergence of dengue virus serotype 3 (DENV-3) in Paraguay following approximately 15 years without confirme...
The systemic establishment of the strictly human-adapted pathogen Salmonella Typhi critically depends on functional interplay between its virulence effectors and the host gut microbiome. Organized within a "colonization-toxicity-immunity- microecological intervention" framework, this review synthesi...
This study was conducted to expand the limited knowledge regarding the detection, molecular characterization, and epidemiology of feline calicivirus (FCV) in Türkiye by examining viral pathogens associated with ulcerative stomatitis in cats. Analysis of forty clinical samples revealed twelve FCV-pos...
, the causative agent of infectious coryza (IC), is an important respiratory pathogen of chickens with growing prevalence in commercial and backyard flocks. Current strain-typing methods, including classical serotyping and molecular approaches, such as ERIC-PCR or single-locus HPG2 typing, lack suff...
Orf virus (ORFV), a member of the genus, is commonly associated with a highly infectious skin disease primarily affecting sheep and goats, with a reported zoonotic potential. Initially identified in the 18th century, ORFV has been sporadically reported in other species, including humans. The presen...
No abstract available
Enterobacter vonholyi isolate E323169 represents a rare case of co-carriage of the antimicrobial resistance genes (ARGs) bla and mcr-10.2, recovered from a clinical rectal swab. E323169 represents one of only 11 known E. vonholyi genomes. To date, within the NCBI Pathogen Detection resource, bla is...
Whole-genome sequencing of can be a valuable tool for TB surveillance and treatment, providing insights into transmission patterns and comprehensive drug susceptibility testing. However, the slow growth of means traditional culture-based sequencing methods can take weeks to return results, which h...
Cholera, caused by , remains a significant diarrheal disease, especially in coastal regions of developing countries. In Malaysia, cholera is largely non-endemic except in Sabah, which has had recurrent outbreaks accounting for ∼75% of national cases between 2004 and 2014. To understand the origin an...
Cholera remains a significant public health burden in many countries in sub-Saharan Africa, though the exact mechanisms of bacterial emergence and spread remain largely undefined. We generated genomic data from 763 Vibrio cholerae O1 isolates predominantly collected between 2019-2024 to create the l...
Myroides odoratimimus is an emerging opportunistic pathogen increasingly implicated in infections across human and animal populations. We previously reported the first outbreak of pneumonia in post-weaning piglets associated with M. odoratimimus, marking a significant shift in its recognized host ra...
Staphylococcus aureus is a leading cause of severe infections in neonatal intensive care units (NICUs). We present results of precision surveillance of S. aureus carriage and invasive infection in a cohort study of high-risk infants in the NICU with the goal of identifying novel strategies for preve...
Current methods are insufficient alone for outbreak detection in hospitals. Real-time genomic surveillance offers the potential to detect otherwise unidentified outbreaks. We initiated and evaluated the Enhanced Detection System for Healthcare-associated Transmission (EDS-HAT), a real-time genomic s...
Cases of melioidosis have been recorded for many years in Vietnam though it is still not a nationally reportable disease in Vietnam. More research is needed to understand the disease ecology and public health impacts of melioidosis in the country. To this aim, broadening the knowledge base of strain...
In July 2024, an outbreak of acute febrile illness occurred in Chassi village, Gombe State, Nigeria, affecting over 30 individuals, primarily children, with symptoms including fever, jaundice, abdominal pain, and mucosal bleeding. The cause remained unidentified after conventional diagnostics exclud...
Human metapneumovirus genotype B (HMPV-B) is an important respiratory pathogen, requiring detailed elucidation of the evolutionary and antigenic features of its () gene. Using 500 sequences collected between 1982 and 2024, we investigated the molecular evolution, phylodynamics, and structural epito...
is a pathogen responsible for invasive pneumococcal disease (IPD) among young children, the elderly, and immunocompromised individuals. The polysaccharide capsule is a main virulence factor that defines pneumococcal serotypes, among which serotype 3 is highly invasive and associated with severe clin...
While pathogen genomics using next-generation sequencing (NGS) has been recommended by the WHO as an essential tool for national communicable disease surveillance programmes, procurement and supply chain management (PSM) systems for this new technology are still evolving. To assess the status of PSM...
Staphylococcus aureus, particularly methicillin-resistant S. aureus (MRSA), poses a persistent global health challenge. Genomic surveillance is essential but often hindered by the bioinformatics complexity of integrating multiple, disparate analysis tools. To address this, we developed StaphScope, a...
Norovirus is a major cause of acute gastroenteritis (AGE) globally. GII.17[P17] has been reported in the last decade as a prevalent norovirus genotype worldwide. We documented the circulation of norovirus GII.17[P17] isolates during an AGE outbreak occurring in western Romania, in 2024. Norovirus wh...
Despite the persistent global threat of seasonal influenza viruses such as A(H1N1)pdm09 and A/H3N2, their epidemiological and genetic characteristics in China following the implementation of COVID-19 non-pharmaceutical interventions (NPIs) remain poorly characterized. Between September 2020 and Dece...
Carbapenemase-producing (CP-Ec) has emerged as an important contributor to the global crisis of antimicrobial resistance. Although less prevalent than carbapenemase-producing , CP-Ec exhibits marked genomic plasticity, efficient plasmid-mediated dissemination, and increasing involvement in bloodstr...
Chikungunya virus (CHIKV) poses an increasing global public health threat, as evidenced by the significant 2025 Foshan outbreak in China. Rapid, whole-genome sequencing (WGS) is critical for outbreak response but is challenged by primer mismatches across diverse lineages and a lack of direct sequenc...
Antimicrobial resistance (AMR), driven by the extensive use of antibiotics in human and animal health, poses a significant global threat. In Ghana, the contribution of poultry farming to the high prevalence of AMR remains underexplored. This study investigates the genomic characteristics and prevale...
Through vaginal colonization, group B (GBS) causes severe outcomes including neonatal sepsis and meningitis. Although intrapartum antibiotic prophylaxis (IAP) has reduced neonatal disease rates, GBS can persist in the genitourinary tract even after antibiotic administration. To determine if IAP sel...
Emerging and re-emerging infectious diseases continue to pose significant threats to lower-middle-income countries (LMICs), particularly in Africa, where health systems are often resource-constrained and prone to disruptions. Drivers such as climate change, antimicrobial resistance, urbanization, ci...
is a leading cause of extensively drug-resistant (XDR) infections in intensive care units (ICUs), with global concern due to its resistance to nearly all antimicrobials. In 2024, the WHO reaffirmed carbapenem-resistant as a critical-priority pathogen. In Peru, over 97% of clinical isolates are car...
Pathogen genotyping via polymerase chain reaction (PCR) amplicon sequencing (AmpSeq) is an informative disease surveillance tool. Several large AmpSeq panels containing > 100 multiplexed PCR amplicons have been developed as alternatives to whole-genome sequencing (WGS) methods for the Plasmodium spp...
The evolution of the viruses is rapidly becoming a global challenge to the creation of vaccines since the new variants are often capable of escaping the immune system and decreasing the vaccine efficacy. The traditional methods of genomic epidemiology rely on the retrospective phylogenetic analysis,...
Equine influenza virus (EIV) H3N8 is a highly contagious respiratory pathogen that poses significant health and economic risks to equids globally. In southeastern Nigeria where equids are sold and slaughtered, limited data exist on EIV epidemiology and circulating lineages. To address this gap, an a...
Mosquito-borne viruses (MBVs) remain a significant public health concern in Northern Queensland, Australia, with dengue virus (DENV), Ross River virus (RRV), and Barmah Forest virus (BFV) representing the most common pathogens. Wolbachia-based biological control programs have made notable contributi...
Proteus mirabilis has emerged as an important multidrug-resistant opportunistic pathogen, with the production of metallo-β-lactamases (MBLs) being a major contributor to its broad-spectrum resistance. Although the aztreonam-avibactam (ATM-AVI) combination represents a key therapeutic option against...
West Nile virus (WNV), a mosquito-borne orthoflavivirus, represents an increasing public health threat in Europe. In July 2025, WNV lineage 2 (WNV-L2) was associated with the first autochthonous cases ever detected in the metropolitan area around Paris, France; understanding the dispersal dynamics a...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical nosocomial pathogen with limited therapeutic options. This study aimed to describe clonal relationships among CRAB isolates and genomic insights from representative clusters. A total of 128 non-duplicate CRAB isolates were included in...
Phylodynamic methods are widely used to infer the population dynamics of viruses between and within hosts. For HIV-1, these methods have been used to estimate migration rates between different anatomical compartments within a host. These methods typically assume that the genomic regions used for rec...
Diarrheagenic Escherichia coli (DEC) is a leading cause of pediatric diarrhea, with antimicrobial resistance (AMR) complicating treatment. This study analyzed 350 E. coli isolates (175 DEC and 175 non-DEC) to determine molecular pathotypes, resistance patterns, and therapeutic targets. Polymerase ch...
African swine fever is a transboundary disease of wild boar and domestic pigs that is caused by the African swine fever virus (ASFV), with a mortality rate of 100 % in naïve animals. The ongoing spread poses a significant threat to food security and economic stability globally. In Nigeria, frequent...
Accurate and efficient whole-genome sequencing (WGS) is crucial for clinical diagnostics and surveillance of bacterial infections. Here, we investigate the potential of a new Oxford Nanopore Technologies (ONT) workflow for WGS of clinically relevant bacterial isolates. Specifically, we assess the pe...
Influenza B virus (IBV) contributes to seasonal epidemics, but its molecular evolution is less defined than influenza A. We analyzed IBVs collected in Japan and Myanmar (2016-2020) to investigate lineage dynamics, reassortment, and genetic mismatch with vaccine strains. Respiratory specimens from pa...
Candida (Candidozyma) auris is an emerging yeast that poses a significant global health threat due to its multidrug resistance and ability to cause healthcare-associated outbreaks. Genomic surveillance is essential for monitoring spread, transmission and antifungal resistance. To report the first id...
With an unexpected increase of human metapneumovirus (hMPV) cases in northern China since late 2024, concerns arose whether novel hMPV variants triggered this epidemic. Utilizing the Beijing Respiratory Pathogen Surveillance System (RPSS), we conducted a genomic evolutionary analysis spanning 2014-2...
Viral detection occurs frequently in critically ill patients. Patients with multiple viremic events had a higher ICU mortality. The highly sensitive mNGS technology has significantly enhanced viral pathogen detection rates. We enrolled 134 critically ill patients with severe infections who underwent...
is an opportunistic pathogen and a growing cause of healthcare-associated infections, characterized by multidrug resistance and the emergence of global high-risk clones. However, regional genomic surveillance data remain limited. Here, we sought to characterize the population structure, transmission...
Plant surfaces host diverse microbial communities acting as reservoirs for pathogenic lineages, yet the ecological dynamics and evolutionary consequences of such reservoirs remain underexplored. We conducted landscape-scale genomic surveillance of Pseudomonas syringae on symptomless leaves of cultiv...
Global dissemination of emergent multidrug-resistant (MDR) Infantis (ESI) is of great public health concern. ESI exhibits increased virulence and MDR phenotypes, features conferred by a conjugative megaplasmid (pESI-like). In Mexico, the potential circulation of ESI clones has been overlooked. This...
Genomic surveillance of human seasonal influenza viruses is an essential component of the Global Influenza Surveillance and Response system (GISRS) and informs the recommendations for the seasonal influenza vaccine composition. Phylogenetic analysis of viral genome sequences is used to identify grou...
Swine enteric coronaviruses (SECoVs), including transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), are major enteric pathogens causing severe diarrhea, dehydration, high neona...
is an emerging opportunistic yeast that is important because of its multidrug resistance, persistence in healthcare environments and ability to cause outbreaks. Since its discovery in 2009 in Japan, it has rapidly spread worldwide and is now recognized as a major global public health threat and was...
Until December 2025, 18 African swine fever outbreaks have occurred in domestic pig holdings in Germany. However, nine of them emerged in western Germany in 2024, representing a separate spatial and temporal cluster. Thus, the current study is limited to the remaining nine outbreaks. We aimed to ill...
remains an urgent public health threat due to the many life-threatening diseases it causes, wide dissemination of multidrug resistant strains, and ability to survive and persist on hospital surfaces. Its accessory genome, composed of genes present in a subset of strains, may provide a clue to its su...
The H1N1pdm09 influenza virus, which emerged in 2009 following a unique reassortment of swine-origin gene segments, rapidly replaced the seasonal H1N1 strain and triggered the first influenza pandemic of the twenty-first century. In Brazil, the virus initially spread through intense community transm...
Vancomycin-resistant (VREfm) is an emerging pathogen responsible for healthcare-associated infections. For this reason, 44 VREfm isolates collected during 2021-2023 were characterized using phenotypic and genomic approaches. VREfm isolates were identified by MALDI-TOF and antimicrobial susceptibili...
: Carbapenem-resistant (CRAB) is classified as an urgent-threat pathogen because of its resistance to nearly all available antibiotics, resulting in high morbidity and mortality rates. However, data on the molecular epidemiology of CRAB isolates in southern Thailand are limited. This study aimed to...
Globally, the trajectory of COVID-19 has been shaped by viral evolution, widespread vaccination and immunity from prior infections. We assessed the epidemiological and clinical patterns of COVID-19 in Lebanon between 2020 and 2024, identified the predominant SARS-CoV-2 clades and evaluated risk fact...
Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP) represent major clinical threats globally. Genomic epidemiological data remain scarce in low- and middle-income countries, limiting a comprehensive understanding of antimicrobial-resistant patho...
Identifying the genetic relatedness of resistant bacterial pathogens in healthcare settings can help identify undetected transmission events and outbreaks. However, current methods are time- and resource-intensive. We evaluated a rapid neighbor typing method paired with long-read sequencing for asse...
In mid-2023, Nepal experienced a significant outbreak of conjunctivitis, affecting over 60% of outpatients in eye hospitals and prompting school closures. The outbreak, peaking in August, predominantly impacted children and individuals with compromised immunity. Clinical manifestations included sudd...
is one of the leading causes of ventilator-associated pneumonia (VAP) and ventilator-associated tracheobronchitis (VAT), with a worldwide spread of difficult-to-treat high-risk clones. This study aimed to investigate the virulence potential and to characterize phenotypic and genotypic antimicrobial...
Staphylococcus aureus is a major pathogen in commercial rabbit farming, causing significant economic damage and animal welfare concerns. Staphylococcosis have been associated with a limited number of clones, particularly the highly virulent ST121 and the low-virulence ST96. However, in recent years,...
The hospital environment is a recognized reservoir for multidrug-resistant (MDR) bacteria, and inadequate hygiene practices by healthcare workers (HCWs) may contribute to the transmission and persistence of healthcare-associated infections (HAIs), particularly in ICUs. This study investigated the pr...
The global dissemination of extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Escherichia coli sequence type 131 (ST131), particularly clade C, represents a major public health concern. However, the clade-specific genomic features underlying the long-term persistence and internationa...
Klebsiella pneumoniae is an opportunistic pathogen responsible for both hospital and community-acquired infections. It is broadly classified into classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp), with the latter being linked to increased mortality owing to its capacity for invasi...
Tuberculosis (TB) remains a major global health concern, particularly in low-income countries where the impact is greater. The lack of proper surveillance tools in these countries is a big impediment to effective TB control. Whole-genome sequencing (WGS) has successfully been integrated into routine...
Genomic sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely instituted during the coronavirus disease 2019 (COVID-19) pandemic to track the emergence and spread of new lineages. While this powerful tool can influence public health decisions and therapeutic deve...
This study aimed to investigate the potential for dog-to-human transmission of Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) and characterize viral shedding patterns in naturally infected dogs. We conducted genomic analysis of SFTSV strains isolated from an infected dog and its owner usi...
The emergence and sustained spread of H5N1 in US dairy cattle since 2024 have demonstrated that highly pathogenic avian influenza (HPAI) is capable of establishing long-term transmission in livestock. Genomic surveillance has clarified national patterns of spatial diffusion, interspecies transmissio...
Healthcare-associated infections are a major concern in intensive care units (ICUs), where early detection of transmission cluster is critical. Whole-genome sequencing remains the reference method for outbreak investigation but is limited by cost and turnaround time. The IR Biotyper (IRBT) provides...
The 2018-2020 Ebola virus disease (EVD) epidemic facilitated the emergence of viral mutations, enhancing the potential for host adaptation during sustained human transmission. Here, we identified the Ebola virus (EBOV) glycoprotein V75A (GP-V75A) substitution as a dominant variant during the epidemi...
infections resurged globally in 2023-2024 following a significant decline during the coronavirus disease 2019 (COVID-19) pandemic. To understand the genomic epidemiology of this resurgence in China, a nationwide 1-year genomic surveillance identified 9907 patients infected with , resulting in an ove...
Trichophyton species cause the greatest burden of dermatophytosis worldwide, with the Trichophyton mentagrophytes species complex being particularly associated with the emergence of new aggressive infections. One emerging species, Trichophyton indotineae is notable for its clinical resistance to ter...
Community-acquired and hospital-acquired bloodstream infections (CA-BSI and HA-BSI) caused by Gram-negative bacteria (GNB) pose major clinical risks, but differences in their molecular epidemiology and prognostic etiologic factors remain unclear. A genomic epidemiology study analyzed 933 CA-BSI and...
This study aims to elucidate the genomic characteristics of three strains isolated from stool specimens of healthy individuals co-carrying (X4) and gene, which confer resistance to tigecycline and carbapenems, respectively. Whole-genome sequencing (WGS) and bioinformatic analysis were conducted to...
Vancomycin is a critical glycopeptide antibiotic for treating severe infections caused by Gram-positive bacteria, particularly MRSA and Clostridioides difficile, by inhibiting cell wall synthesis through binding to D-Ala-D-Ala termini of peptidoglycan precursors. Resistance has emerged in Enterococc...
Pseudomonas aeruginosa is a leading cause of multidrug-resistant (MDR) infections, for which the polymyxin antibiotic colistin has been a treatment of last resort. The emergence of colistin-nonsusceptible strains thus poses a serious therapeutic challenge. In this study, we performed whole-genome se...
West Nile virus (WNV) is an endemic arthropod-borne virus that has routinely caused seasonal outbreaks in the United States since it was first detected in 1999. While phylogenetic studies have shown how WNV has diversified and undergone genotype replacement since introduction, more geographically fo...
The 2022 multi-country mpox (formerly monkeypox) outbreak, driven by mpox virus (MPXV) Clade IIb poses renewed threat to global public health. The cessation of smallpox vaccination has created large immunologically naïve cohorts, with uncertain implications for contemporary MPXV susceptibility. To a...
New SARS-CoV-2 variants arise frequently with different viral properties that can impact the effectiveness of the vaccines. Updating estimates of vaccine effectiveness (VE) in public health surveillance can be limited by the necessity of conducting a distinct study that entails analysis of prospecti...
: is an opportunistic pathogen frequently implicated in healthcare-associated infections, particularly ventilator-associated pneumonia and other device-related infections. The global emergence of carbapenem-resistant (CRPA) represents a major clinical challenge due to its limited therapeutic optio...
Klebsiella pneumoniae is a major cause of bloodstream infections worldwide and is increasingly associated with multidrug resistance, particularly to carbapenems and colistin, which severely limits treatment options. This study investigated the genomic epidemiology of K. pneumoniae bloodstream infect...
There is still little emphasis within One Health on building linkages between human health, changes in biodiversity, and ecosystem perturbation. We use the Great Plains, a system of substantial One Health concern, to illustrate a persistent data challenge to this issue, through the lens of small mam...
(1) Background: (Lm) is recognized by the World Health Organization (WHO) as one of the four principal foodborne pathogens. This study aimed to investigate the molecular characteristics of Lm isolates from Jiaxing, China, using whole-genome sequencing (WGS) to enhance our understanding of their mol...
Advanced genotyping technologies for understanding the genetic intricacies of fungal pathogens have broad applications in crop protection. Here, we introduce a novel genotyping-by-target sequencing (GBTS) chip, a versatile tool designed for comprehensive genetic analysis of fungal populations. This...
In recent years, arboviral infections have surged dramatically because of the geographic expansion of Aedes and Culex mosquitoes, their main vector mosquitoes. Despite significant efforts to uncover arbovirus-host interactions and viral protein effector functions in mammals, systematic studies aimin...
is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR...
Antimicrobial resistance (AMR) is an urgent threat to public health, but gaps in surveillance limit the detection of emergent novel threats and knowledge about the global distribution of AMR genes. International travelers frequently acquire AMR organisms (AMROs) and thus may provide a window into AM...
Tecovirimat (TPOXX) is an antiviral authorized for the treatment of mpox infections in Canada, but recent clinical trials found it has no impact on symptom duration. We conducted a prospective cohort study of individuals diagnosed with mpox in Toronto, Canada. Skin lesion swabs were collected weekly...
This study evaluated the in vitro activity of sulbactam/durlobactam and comparators against carbapenem-resistant Acinetobacter baumannii (CRAB) bloodstream isolates from Italy and investigated genomic mechanisms underlying resistance. A total of 110 consecutive CRAB isolates (2021-2023) were tested...
Dengue fever, a major mosquito-borne viral disease, is transmitted by Aedes mosquitoes and poses a significant global health burden. Despite extensive research, the spatiotemporal dynamics of dengue virus (DENV) lineages in Colombia remain understudied. Here, we analyze 11,443 complete genome sequen...
The global molecular epidemiology of (MP) and its associations with macrolide resistance and disease severity remain unclear. Studies reporting MP genotypes distribution by P1 typing, multiple locus variable number tandem repeat analysis (MLVA), or multilocus sequence typing analysis (MLST) among M...
This study investigates the evolutionary dynamics of norovirus GII.4 lineages circulating in the Amazon region of Brazil, with a particular focus on the recently emerged GII.4 San Francisco variant. A molecular descriptive design was employed, analyzing 615 stool samples from gastroenteritis patient...
is a major foodborne pathogen, and its increasing antimicrobial resistance poses a significant public health challenge. In this study, we conducted a comprehensive genomic epidemiological investigation of isolates recovered from meat products across multiple provinces in China. A total of 141 isola...
Tomato spotted wilt virus (TSWV) is a harmful pathogen that causes severe disease in tomato, pepper, and other horticultural and agronomic crops. Its genome comprises three linear single-stranded RNA molecules (segments L, M, and S), which are unequally packed in nucleocapsids. Although its genome s...
Emerging infectious diseases have risen significantly in the twenty-first century as ecological disruption, climate change, expanding human-animal interfaces, and global mobility intensify opportunities for pathogen transmission. This review synthesizes historical and contemporary evidence across vi...
To investigate and determine the cause of an increase of isolation of Mycobacterium mucogenicum in broncho-alveolar lavage samples in a tertiary hospital. Outbreak investigation including 30 patients who underwent bronchoscopy procedures in a minor procedural area of a university-affiliated, tertiar...
The diagnosis of bovine mastitis relies predominantly on conventional microbiological methods optimized for common pathogens, potentially ignoring environmental bacteria with complex antimicrobial resistance profiles. This pilot study combined conventional identification with whole genome sequencing...
Marburg virus (MARV) is the primary cause of Marburg virus disease (MVD), a severe hemorrhagic fever with a high case-fatality rate. The first reported MVD outbreak in Tanzania occurred in 2023, followed by a second outbreak in 2025, both within the Kagera region. During those MVD outbreaks, 174 sus...
The emergence of the JN.1 variant of SARS-CoV-2 has heightened global health concerns. Here, we aimed to evaluate viral characteristics, epidemiology, transmissibility, infectivity, immune evasion, effectiveness of current antiviral therapies, immunization options, genomic surveillance and public aw...
As genomic surveillance is key to detecting novel respiratory viruses or variants, the highly unequal global distribution of respiratory virus sequencing infrastructure raises concerns about preparedness for future threats. Using mathematical models and global epidemic simulations, we demonstrate th...
Multidrug resistance (MDR) in Gram-negative bacteria is a global issue and needs to be addressed urgently. MDR can emerge through genetic mutations and horizontal gene transfer and deteriorate under antibiotic selective pressure. The emergence of resistance to last-resort antibiotics, which are used...
Whole genome sequencing (WGS) via next-generation sequencing (NGS) platforms offers a powerful approach for investigating viral genetic diversity. Orbiviruses are an economically important group of arboviruses with a double-stranded RNA (dsRNA) genome consisting of 10 segments. Traditional approache...
To characterize the early spatiotemporal transmission dynamics of SARS-CoV-2 following the Chinese government's adjustment of the long-standing "zero-COVID" policy in December 2022, focusing on both overseas importation and subsequent domestic dissemination, and to identify key factors driving these...
Dengue and associated complications are spreading to non-endemic regions of Pakistan. Vector control, the foremost and widely adopted strategy for managing dengue has been implemented through various measures in Pakistan. Biological control through the use of Wolbachia, a bacterium naturally present...
Wastewater-based genomic surveillance (WWGS) has proven effective for monitoring SARS-CoV-2 and other viruses within communities. It enables rapid detection of known and emerging mutations and provides insights into circulating lineages. Despite its advantages, WWGS faces challenges in sample proces...
Pathogen whole-genome sequencing (WGS) has significant potential for improving healthcare-associated infection (HAI) outcomes. However, methods for integrating WGS with epidemiologic data to quantify risks for pathogen spread remain underdeveloped. To identify analytic strategies for conducting WGS-...
Foot-and-mouth disease (FMD) continues to impose significant constraints on livestock health and productivity in Egypt due to the persistent circulation, evolution, and transboundary introduction of antigenically diverse foot-and-mouth disease virus (FMDV) serotypes and lineages. Since the 1950s, Eg...
Non-pigmented Serratia marcescens - bacteria otherwise known for occasional reddish pigmentation and frequent outbreaks in neonatal intensive care units (NICUs) - were recently reclassified to novel species: S. sarumanii and S. bockelmannii. This raised questions about possible differences regarding...
Réunion island just experienced a massive chikungunya virus outbreak in 2024-2025, with more than 54,000 confirmed cases. This is the second major chikungunya outbreak on the island, following the first one that peaked 20 years ago. It has been assessed that this new outbreak finds its origin in a s...
The yeast Candidozyma auris has emerged globally as a major threat to public health. Outbreaks are frequently reported and difficult to control. In the Netherlands, C. auris is rarely detected although national surveillance has been set up. Here, we present all Dutch C. auris cases reported from Mar...
SARS-CoV-2 continues to diversify under the selective pressure of population immunity, with recombination increasingly contributing to the emergence of new lineages. The recombinant lineage XFG (“Stratus”), detected in early 2025, has attracted attention because it combines genetic features from dis...
Klebsiella pneumoniae rapidly disseminates in clinical environments and is frequently responsible for hospital outbreaks. The present study highlights an under-recognized and concerning nosocomial transmission route involving intravenous contrast dye, after a cluster of seven patients became acutely...
The 2022 global mpox outbreak showed that surveillance systems were not ready to quickly detect or adapt to the new dynamic of human-to-human spread. While many lessons were learned, ongoing mpox outbreaks underscore the need for focused attention on enhancing mpox surveillance systems. This review...
Burkholderia cepacia complex (BCC) is a cause of health care-associated infections in immunocompromised patients and people with cystic fibrosis (PwCF). This report summarizes a B contaminans pseudo-outbreak related to improper laboratory processes affecting surgical specimens from immunocompetent i...
Phylodynamic analysis has been instrumental in elucidating epidemiological and evolutionary dynamics of pathogens. Bayesian phylodynamics integrates out phylogenetic uncertainty, which is typically substantial in phylodynamic datasets due to limited genetic diversity. Phylodynamic inference does not...
While drinking water disinfection can significantly reduce bacterial populations it does not eradicate all the bacteria present as many cells enter varying levels of dormancy including the viable but non-culturable (VBNC) state. We posit that the VBNC state represents a continuum, with lower and gre...
Influenza D virus (IDV), an emerging orthomyxovirus with zoonotic potential, infects diverse hosts, causes respiratory disease, and remains poorly characterized in China despite its global expansion. From October 2023 to January 2025, we collected 563 nasal swabs from cattle across 28 farms in Jilin...
Peru recorded one of the world's highest COVID-19 mortality rates, with nearly 4.5 million reported cases and 220,000 deaths by March 2024. Understanding the emergence and spread of SARS-CoV-2 variants in this context is key to informing effective public health responses. This study describes the ge...
Accurate molecular epidemiology relies on recovering from clinical specimens and is essential for informing public health responses, characterizing strains that cause disease, and tracking strain prevalence. We performed a cross-sectional study of the recovery of isolates from test-positive stools...
Q fever, caused by the gram negative obligate intracellular bacterium Coxiella burnetii, remains a globally relevant but underappreciated zoonosis in the 21st century. Despite decades of research, the disease continues to pose diagnostic, epidemiological, and clinical challenges that hinder timely r...
Shiga toxin-producing (STEC) are zoonotic, foodborne pathogens that cause outbreaks of infectious gastrointestinal disease, including haemolytic uraemic syndrome (HUS) which can be fatal. In November 2023, a foodborne outbreak of STEC serotype O26:H11 , involving 40 cases (54% female and 76% aged 0...
The objective of this study was to determine the association between viral subtype/clade and disease severity. Multicentre retrospective cohort study. This study used data from the Global Influenza Hospital Surveillance Network (GIHSN). The dataset comprised hospitalised influenza patients with vira...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines reduced severe coronavirus disease 2019, but variants like Delta and Omicron caused widespread breakthrough infections (BIs). Mexico, offering diverse vaccines, and its Yucatán region, a major travel hub, provide a unique setting...
The COVID-19 pandemic caused by SARS-CoV-2 has had a significant impact on global social and economic activities. The continuous emergence of new SARS-CoV-2 variants has made the global pandemic of COVID-19 difficult to predict. Therefore, it is of great significance to closely monitor the SARS-CoV-...
Inferences from population genomic data provide valuable insights into the demographic history of a population. Likewise, in genomic epidemiology, pathogen genomic data provide key insights into epidemic dynamics and potential sources of transmission. Yet, predicting what information will be gained...
Gonorrhoea, caused by Neisseria gonorrhoeae, is a significant public health challenge due to the rising incidence of antimicrobial resistant (AMR) strains. The Valencian Region, one of the top tourist destinations in Eastern Spain, has witnessed an increase of over 200% in the number of cases in rec...
Infections caused by XDR Pseudomonas aeruginosa significantly limit treatment options. Although ceftolozane/tazobactam and ceftazidime/avibactam have emerged as promising alternatives, increasing resistance has been reported. This study describes three critically ill patients with ventilator-associa...
The emergence and expansion of methicillin-resistant (MRSA) clones in healthcare facilities pose a significant public health concern due to their adaptability and resistance to commonly used antibiotics. In this study, the genomic and epidemiological characteristics of 81 MRSA isolates collected be...
Yaws, a neglected tropical disease caused by Treponema pallidum subspecies pertenue (T p pertenue), has evaded eradication, in part due to a high proportion of asymptomatic cases. Repeated mass drug administration (MDA), whereby an entire population is repeatedly treated irrespective of disease, cou...
Klebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both virulence factors and antimicrobial resistance genes (ARGs) have raised serious public health concerns. The aim of this study is to describe the glob...
Advances in genomic technologies have revolutionised practices for hospital infection prevention and control programmes. In this Personal View, we describe a genomic epidemiology service called the Rapid Response (RR) programme at University of California, San Francisco, a large academic medical cen...
SARS-CoV-2 transmission studies involving children in Thailand have been relatively limited to the early waves with the alpha and delta variants. Our study aims to address these gaps by examining household transmission in Chiang Mai, northern Thailand, during the Omicron wave in a post vaccination p...
Viral genome sequencing is critical for understanding viral biology, identifying strain mutations, and managing public health during pandemics. Although sequencing technologies have progressed over the years in terms of throughput and cost, a portable platform that integrates sample processing, libr...
MicrobeTrace is a free, secure, browser-based bioinformatics tool to integrate and visualize epidemiologic, laboratory, and molecular data for outbreak investigations, with over 14,000 users from 127 countries. Regular testing, user feedback, and comparison with other bioinformatics tools identified...
Next Generation Sequencing is widely deployed in cholera-endemic regions, yet an end-to-end reproducible pipeline that unifies read QC, filtering, reference mapping, variant calling/annotation, recombination screening, and extraction of parsimony informative sites/variant codons, phylogenetic infere...
Untargeted, also known as metagenomic, nanopore sequencing is a powerful tool for virus genomic surveillance, particularly in resource-limited settings and when paired with the portability of the MinION device (Oxford Nanopore Technologies, ONT). However, a major bottleneck for global access is the...
The emergence of a high-risk New Delhi metallo-β-lactamase 14-producing Klebsiella pneumoniae sequence type 147 clone is of public health concern because of its rapid international spread. We report cross-border emergence and rapid dissemination of that clone in the Canary Islands, Spain, during 202...
In 2019, an outbreak of acute haemorrhagic diarrhoea (AHD) in dogs in Norway was linked to . A marked increase in diarrhoeal cases in dogs during the autumn, along with the frequent identification of in affected dogs, supports its role as a causative agent in seasonal diarrhoea in dogs in Norway. P...
The epidemiology of SARS-CoV-2 is marked by the continuous emergence of new lineages. Early detection and assessment of their transmissibility can be challenging for surveillance systems that rely solely on case time series data. Genomic surveillance, focusing on identifying and characterizing circu...
BACKGROUNDCarbapenemase-producing Enterobacterales (CPE) cause infections, particularly nosocomially, with limited treatment options. NDM-1-producing cases have substantially increased since 2022, associated with the Ukraine war.AIMWe aimed to investigate transmission patterns using Germany's Integ...
The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderat...
A sudden increase in the number of Mpox virus (MPXV) cases worldwide prompted the WHO to declare a Public Health Emergency of International Concern in 2022 and again in 2024. Public health genomic surveillance of MPXV in impacted areas is ongoing to inform national and international situational awar...
Pathogen genomic surveillance is globally recognized as a pillar of public health. This field has expanded rapidly following the onset of the coronavirus disease 2019 (COVID-19) pandemic, and there is an urgent need to ensure the quality, comparability and reliability of the results of genomic analy...
Shigellosis is a gastrointestinal illness caused by bacteria belonging to one of four species of . Sexually transmissible (ST) shigellosis was first reported in 1974, but recently there has been a global increase in the transmission of extensively drug-resistant (XDR) strains. Here, we sought to cha...
This study investigates the genetic diversity and evolutionary mechanisms driving polymyxin resistance in Klebsiella pneumoniae, a critical priority pathogen. By analysing mgrB, phoPQ and pmrAB genes in susceptible (PM-S) and resistant (PM-R) populations through neutrality tests (Tajima D, Fu & Li's...
resistant to third-generation cephalosporins (3GCs) is a WHO priority pathogen due to its antimicrobial resistance (AMR). In high-income countries, such as Australia, 3GC-resistant are a common cause of extra-intestinal infections in both healthcare and community settings. Long-term targeted survei...
Coronavirus disease 2019 (COVID-19) caused increased intensive care unit admissions, invasive procedures, and antimicrobial use, potentially worsening bacterial infections and multidrug resistance. Retrospective studies have found that Klebsiella pneumoniae co-infections in COVID-19 patients were si...
Vibrio parahaemolyticus (VP) is a major pathogen causing foodborne diseases, and Liaoning Province, a coastal region with high seafood consumption and production, faces a notable risk of VP-associated foodborne infections. Clarifying the molecular epidemiological characteristics of VP in this region...
(MP) is one of the major pathogens that causes respiratory tract infections, including community-acquired pneumonia (CAP). The aim of the current study was to conduct molecular genetic surveillance of an outbreak of pneumonia caused by MP in various regions of the Russian Federation between January...
Infections caused by clinical carbapenem-resistant (CRAB) are associated with an increased risk of mortality and present a significant challenge for hospitals worldwide. This study aims to analyze the molecular epidemiological characteristics, drug resistance traits, and virulence features of CRAB...
(Group B Streptococcus, GBS) is a major pathogen of neonatal infections worldwide, with significant geographical variation in its prevalent sequence types (STs). In Shanxi, China, ST10 has emerged as the dominant lineage in perinatal infections, yet the mechanisms underlying its regional dominance r...
The Amazon Basin is one of the most biologically diverse regions on Earth, yet its viral diversity remains poorly characterized. Mosquitoes are important vectors and reservoirs of RNA viruses, but little is known about the composition and structure of their viromes in remote areas of the Amazon. In...
In 2024, Chile experienced an outbreak of invasive group A (iGAS) infections. Although increasing reports of GAS outbreaks have been described worldwide, it remains unclear whether these events are driven by increased virulence of circulating lineages or by lineage replacement. In parallel, the bur...
Objective: This study investigated the antimicrobial resistance profile of carbapenem-resistant (CRPA) and its association with the T3SS, aiming to provide evidence for managing highly resistant and virulent CRPA and to guide the optimization of infection control strategies. Retrospective cohort st...
This study provides a comprehensive overview of SARS-CoV-2 genomic surveillance in Central America and the Dominican Republic from February 2020 to January 2023, highlighting the collaborative efforts of the Pan American Health Organization (PAHO), and the Council of Ministers of Health of Central A...
This study aimed to demonstrate the benefits of using SaTScan (Boston, MA, USA), a cluster-detection software programme, and whole genome sequencing to investigate a suspected outbreak of infections in a tertiary government hospital in the southern Philippines. The hospital is part of the national...
Chikungunya fever (CHIKF) is a mosquito-borne viral disease characterized by fever, rash, and severe joint pain. However, these classical descriptions are based overwhelmingly on the Indian Ocean and Caribbean lineages. With the recent introduction and spread of the Middle Africa lineage (MAL) into...
Mosquitoes are critical vectors in tropical regions where arboviruses like dengue and Zika are prevalent. This study focuses on characterising the RNA virome of mosquitoes in the Colombian Caribbean, emphasising the core regional virome and its role in the dynamics of arboviruses. The objective was...
causes severe bloodstream infections (BSIs), and methicillin-resistant (MRSA) poses a major clinical threat due to strong antimicrobial resistance and limited therapeutic options. This retrospective study analyzed 96 isolates from nosocomial BSIs in a tertiary hospital in central China from 2020 t...
Biofilm-related infections significantly contribute to bacterial diseases, with estimates suggesting that at least 80% of such infections are associated with biofilms. These infections often involve opportunistic pathogens, which not only influence the type of infection but also impact the microenvi...
Vancomycin-resistant Enterococci (VRE) are major pathogens causing nosocomial infections globally. This study investigated the genetic characteristics of vancomycin-resistant Enterococcus faecium (VREfm) in Thailand between June and November 2022. Fifty-two clinical VREfm isolates from Bangkok hospi...
Elizabethkingia meningoseptica is an emerging nosocomial pathogen with complex antimicrobial resistance. We conducted a retrospective study in intensive care units (August 2022-December 2024) involving thirteen patients (ten adults, three paediatric). Universal resistance to piperacillin/tazobactam,...
Genomic surveillance has emerged as a fundamental tool in the global response to dengue virus (DENV), enabling the rapid detection of viral strains, monitoring of transmission dynamics, and assessment of evolutionary changes that may impact disease control strategies. This chapter examines the criti...
Plant viruses pose a persistent and escalating threat to global agriculture and food security, inflicting over $30 billion in annual losses - a challenge acutely felt in Saudi Arabia as it strives for agricultural self-sufficiency under Vision 2030. This is the first comprehensive review which prese...
Carbapenem-resistant (CRKP) has become a significant global health concern. The convergence of carbapenem resistance and elevated virulence potential has led to increasingly difficult-to-treat strains. Among these, ST15 is an expanding global high-risk clone, yet variants with elevated virulence p...
has emerged as a major opportunistic pathogen, with rising antimicrobial resistance representing a critical public health concern. This study investigated the genomic characteristics, transmission dynamics, and evolutionary relationships of CRKP isolates from Gansu Province, China, to inform regiona...
Antimicrobial-resistant species are important causes of hospital-acquired infections, yet genomic surveillance data from Yichang, China, are lacking. Between February 2023 and December 2024, 150 antibiotic-resistant isolates were collected from five hospitals in Yichang. Antimicrobial susceptibili...
In June 2022, a case of non-bacillary pulmonary tuberculosis (TB) was reported in a 10-year-old girl attending a primary school in Barcelona. A second pediatric case from the same school was identified in October 2022, prompting the declaration of a TB outbreak and the initiation of an epidemiologic...
Non-typhoidal (NTS) and thermotolerant remain leading causes of bacterial gastroenteritis worldwide, with a disproportionate burden in low- and middle-income regions. This updated review synthesizes current evidence on their epidemiology, antimicrobial resistance (AMR) dynamics, and the role of ge...
The incursion of Chikungunya (CHIKV) and Zika (ZIKV) viruses into Latin America and the Caribbean (LAC) after 2013 created complex epidemics with high attack rates, severe complications, and persistent transmission. While individual aspects have been studied, a synthesized understanding of the inter...
The ongoing global spread of highly pathogenic avian influenza (HPAI) continues causing major impacts on poultry, wildlife, and public health. Among the most affected countries in Europe, Italy experienced three major epidemic waves in 2016-23, caused by 2.3.4.4b H5N8 and H5N1 subtypes. Yet, the und...
Hepatitis E virus (HEV) is a globally prevalent zoonotic pathogen posing major public health risks. Swine, a major meat source, carry HEV strains genetically similar to those in humans, highlighting the risk of zoonotic foodborne transmission. This study aimed to investigate the evolutionary history...
(KP), a Gram-negative bacterium of the Enterobacteriaceae family, is a major opportunistic pathogen responsible for severe infections, particularly urinary tract infections (UTIs). The increasing incidence of KP infections poses a significant challenge to global healthcare systems. In this study, we...
Rapid and accurate detection of respiratory pathogens is essential for timely diagnosis, effective treatment, and outbreak monitoring in both human and veterinary medicine. We evaluated the Microbe Finder (MiFi) software for detection of nine RNA viruses of human and veterinary clinical importance....
(Group B Streptococcus, GBS) is a Gram-positive opportunistic pathogen and a leading cause of invasive infections in neonates and pregnant women worldwide. Pathogenicity and transmission dynamics are shaped by capsular serotypes, clonal backgrounds, and virulence and resistance determinants, which v...
Genomic surveillance is critical for outbreak control and pathogen intelligence, yet protocols such as the Illumina Viral Surveillance Panel (VSP) remain under-evaluated in low-resource and mobile laboratory settings. A key operational question is whether sample pooling can increase throughput witho...
The emergence and spread of resistance to last-resort antibiotics such as tigecycline is of great concern globally which can pose a potential threat to public health due to limited treatment options. In this study, we first identified and characterized the genomic features of a food-acquired strain...
Africa continues to bear a disproportionate burden of infectious diseases, particularly antimicrobial-resistant (AMR) infections, which significantly affect public health and socio-economic development. Addressing these complex health threats requires innovative approaches to data analysis, pathogen...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance is crucial for understanding viral evolution and guiding public health responses. However, many countries, particularly in Central America, have limited sequencing capacity, resulting in scarce and delayed data. This s...
Delta SARS-CoV-2 triggered a devastating wave of COVID-19 in India, infecting approximately 26% of the population (~357 million people) within four months, with ~0.4 million new cases per day, and around 250,000 reported deaths. In contrast, Pakistan experienced a much milder Delta wave, recording o...
is a global urgent-threat pathogen, with prevalence and clinical impact varying over time and across regions. This study aims to elucidate the landscape of infection (CDI) and its causative strains in Southwest China after the COVID-19 pandemic. This retrospective study enrolled CDI patients hospit...
Dengue is the most prevalent mosquito-borne viral disease worldwide and constitutes a major public health concern in Colombia. The disease is caused by four antigenically distinct dengue virus serotypes (DENV-1 to DENV-4), which share more than 65% genome identity. Although all four serotypes co-cir...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of COVID-19 has significantly challenged the public health landscape in late 2019. After almost 3 years of the first ever SARS-CoV-2 case, the World Health Organization (WHO) declared the end of this global health em...
Hypervirulent (hvKp) of the K1/ST23 lineage is an emerging global threat associated with invasive community-acquired infections. Increasing reports of virulence-resistance convergence highlight the need for genomic surveillance, particularly within Europe where data remain limited. This study chara...
Hepatitis B virus (HBV) persists as a major global public health burden, with hyperendemic prevalence in sub-Saharan Africa. Populations with elevated exposure to percutaneous transmission risks, including incarcerated individuals and healthcare workers demonstrate heightened HBV susceptibility. Des...
Staphylococci are major opportunistic pathogens of companion animals and an important reservoir of antimicrobial resistance genes with zoonotic relevance. Otitis externa is one of the most common conditions requiring antimicrobial therapy in veterinary practice, yet data integrating phenotypic and g...
Most urinary tract infections in all populations are caused by gram -negative, facultative anaerobic, uropathogenic (UPEC). Multidrug resistance (MDR) to first line antibiotics recommended for treatment of UTI is a global health problem. The misuse of antimicrobial agents for UTI treatment can lead...
This Technical Resource presents genome sequence data for three strains of the bacterial pathogen pv. () collected in Serbia. We isolated these strains from pepper crops showing bacterial spot symptoms in 2016 at the municipality of Irig, in the Srem district. The presented data comprise raw seque...
Mpox and buffalopox are zoonotic viral infections which demonstrate distinct clinical and immune profile. This study examines the clinical presentation with genomic and immunological characteristics among three confirmed cases of Mpox Clade IIb-A.2.1 and Clade Ib infections and a buffalopox from Mal...
is a Gram-negative, facultatively anaerobic member of the Enterobacteriaceae that functions both as a gut commensal and a major opportunistic pathogen implicated in severe hospital and community-acquired infections. The rapid global expansion of antimicrobial-resistant lineages, particularly ESBL-...
African Swine Fever virus has become a primary concern for veterinarian health agencies and pig producers worldwide. The current panzootic of the virus genotype II is having a devastating impact on pig production in Africa, Europe, Asia, Oceania, and Hispaniola (Caribbean). Due to its high persisten...
High numbers of reported mpox cases and recent identification of multiple sustained human outbreaks of mpox virus (MPXV) have highlighted the need for robust, best-practice genomic surveillance tools. In light of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, many labs ac...
Over the past decade, porcine circoviruses (PCVs) have continued to pose a significant threat to global swine health, and pivotal discoveries have significantly reshaped our understanding of their biology and control. Extensive genomic surveillance has expanded porcine circovirus 2 (PCV2) genotyping...
The environmental spread of antibiotic-resistant bacteria is a growing global health concern, particularly in low- and middle-income countries where limited wastewater treatment infrastructure may facilitate the dissemination of multidrug-resistant (MDR) organisms. and spp. are clinically signific...
Lumpy skin disease (LSD) is a rapidly spreading transboundary viral disease of cattle and water buffalo that poses a significant threat to livestock health and economies of Bangladesh. Calf mortality is steadily increasing over time. This study documented fatal calf mortality with vasculitis-driven...
STREPTOCOCCUS DYSGALACTIAE SUBSP: equisimilis (SDSE) is an emerging pathogen with similarities to S. pyogenes, with limited Indian molecular epidemiological data. This study characterized 55 SDSE isolates via MALDI-TOF and whole genome sequencing for emm typing, MLST, virulence, and antimicrobial re...
Escherichia coli is a major pathogen in bloodstream infections (BSIs), with increasing concern over antimicrobial resistance (AMR) and the evolving pathogenic potential of phylogroups traditionally considered commensal. This study investigates the genetic characteristics of E. coli isolates causing...
Future research on Mycobacterium tuberculosis (Mtb) proteins is essential for advancing tuberculosis (TB) diagnosis, treatment, and control amid rising drug resistance and global health challenges. Recent studies focus on elucidating protein structures and interactions critical to bacterial survival...
Dengue is a mosquito-borne viral disease that poses a global public health problem, particularly in tropical and subtropical regions. It is caused by the dengue virus (DENV), which comprises four antigenically distinct serotypes. The clinical manifestations of the disease overlap with those of other...
Dengue has long been considered a neglected disease since its emergence. However, in recent years, the number of cases has increased significantly, particularly in tropical countries across Latin America. This study aims to describe the evolution of dengue during the 2023 outbreak in Peru. Here, we...
Vancomycin-resistant (VREfm) poses a significant public health threat due to increasing antimicrobial resistance and virulence factors associated with severe infections. The primary objective was to investigate the genetic and phenotypic characteristics of 46 VREfm clinical isolates obtained from t...
Mosquitoes harbor diverse viral communities, including both medically important arboviruses and insect-specific viruses, yet the viromes of mosquito populations in northern temperate regions remains poorly characterized. In this study, we used metagenomic sequencing to analyse pools of archived mosq...
Whole genome sequencing (WGS) is increasingly used to support infection prevention and control. However, its application for routine regional surveillance of vancomycin-resistant Enterococcus faecium (VREfm) across multiple healthcare facilities is still evolving. This study describes the implementa...
is an emerging opportunistic pathogen in humans and belongs to a genus that has shown great genomic diversity. has shown relevant traits in antimicrobial resistance because of its intrinsic resistance to multiple antibiotics and its ability to acquire resistance genes that limit therapeutic options...
The monkeypox virus (MPXV) is an emerging zoonotic pathogen responsible for mpox, a disease characterized by some smallpox-like symptoms, typically mild but occasionally fatal. The largest mpox recorded global outbreak began in May 2022, with over 162,000 cases across 140 countries. Herein, we have...
Novel duck reovirus (NDRV) is an emerging infecting domestic waterfowl, particularly (Muscovy duck), and is associated with arthritis, immunosuppression, and economic losses. Despite its circulation in Southeast Asia, whole-genome data from Vietnam are lacking, restricting molecular surveillance a...
Pasteurella multocida is a zoonotic bacterium commonly found in the oropharyngeal microbiota of cats; despite its clinical relevance, molecular data on feline isolates in Iran remain limited. This study aimed to provide molecular and phenotypic characterization of P. multocida isolates obtained from...
Valley fever, a disease caused by spp., is a fungal respiratory disease with an expanding range. Methods to culture the pathogen from soil, especially , are very challenging, limiting the genomics knowledge of environmental strains. In this study, we designed and tested a targeted DNA capture and e...
Dengue fever is one of the most globally significant arthropod-borne viral diseases. In 2024, more than 14 million cases and 10,000 deaths were reported across 92 tropical and subtropical countries. Dengue virus (DENV), endemic in Sub-Saharan Africa including Kenya, comprises four serotypes (DENV-1...
Tuberculosis (TB) remains a major public health challenge in China. Meigu County, in Liangshan Yi Autonomous Prefecture, Sichuan Province, is severely affected by a high TB burden, a situation exacerbated by its geographic isolation and socioeconomic constraints. This study used DNA microarray techn...
Cholera, caused by , remains endemic in many developing countries, including Pakistan. The extensive use of antibiotics has led to the emergence of antimicrobial resistance in , limiting available treatment options. In this study, we performed molecular characterisation of antibiotic-resistant sero...
Emerging and re-emerging viruses continue to pose major threats to public health. Their ability to adapt, cross species barriers, and spread rapidly can trigger severe outbreaks or even pandemics. Strengthening preparedness with comprehensive and efficient strategies is therefore essential. Here, we...
The recent global outbreak of Monkeypox virus since 2022, particularly outside Africa, has underscored its significant threat to public health. Genomic surveillance from multiple countries has revealed diverse genetic variations among circulating Monkeypox virus strains. Notably, a common F13L (E353...
, a causative agent of Lyme disease, was first reported in South Korea in 2018, yet no complete genome sequence has been described. Here, we present the first whole-genome characterization of strain KW3, isolated from in the Kangwon region of South Korea. Genome assembly was achieved using a hybri...
Multidrug-resistant gram-negative bacteria (MDR-GNB) are one of the main challenges in intensive care units (ICUs), mainly extended-spectrum β-lactamase-producing (EKP), carbapenemase-producing Enterobacterales, carbapenem-resistant (CR) and CR spp. The objectives were to determine the prevalence...
Chemical disinfectants and water-wash methods are widely employed in sanitizing broiler chicken barns. Studies showed that disinfectants affect environmental microbial composition and antibiotic resistance genes (ARGs). However, little is known regarding how barn disinfection treatments impact the c...
: () remains a leading cause of invasive bacterial disease in children worldwide. In Tunisia, the 10-valent pneumococcal conjugate vaccine (PCV10) was introduced into the national immunization program in 2019 for children under two years of age. This study aimed to assess molecular epidemiology, an...
Since its introduction to Europe in 2004, West Nile Virus Lineage 2 (WNV-2) has become endemic, with Italy reporting the highest number of cases each season. In 2022, WNV infections in Italy exceeded those recorded during the major 2018 outbreak-the largest ever reported in Europe. This study invest...
The present study was carried out to analyze the complete genome sequences of infectious bursal disease virus (IBDV) isolates obtained from field outbreaks in the southern regions of India. Bursal tissue samples were collected and screened by RT-PCR, targeting the VP2 gene. Positive samples were sub...
This study investigated the molecular epidemiology, genomic characteristics, and phylogenetic relationships of methicillin-resistant (MRSA) clonal complex 398 (CC398) isolates recovered from clinical infections in Taiwan. Fourteen CC398 MRSA isolates were identified between 2018 and 2022 from patie...
A multicenter cross-sectional study was conducted across six Chinese hospitals between September 2023 and April 2024 to investigate the prevalence, molecular epidemiology, antimicrobial resistance (AMR) and genetic relatedness of in pediatric populations. Among 1,442 stool samples collected, 242 i...
Respiratory syncytial virus (RSV) infection is one of the leading causes of hospitalisation in infants, the elderly and immunocompromised patients, with significant morbidity and mortality rates. Despite its global impact, epidemiological surveillance of RSV in Switzerland has historically been limi...
Traditional typing methods, such as pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and Whole genome sequencing (WGS) have limitations in terms of labor intensity, cost, and delayed results. This study evaluates Fourier transform infrared spectroscopy (FTIR), particularly...
Enterococcus faecalis is one of the leading causes of bacterial infectious diseases. Describing this infection-inducing pathogen can facilitate evidence-based infection prevention and control. Yet clinical isolates of E. faecalis are difficult to structurally distinguish from non-clinical isolates,...
Influenza and other respiratory viruses pose significant public health threats among SARI patients, yet comprehensive surveillance data remain limited in Pakistan. This prospective, multi-center study characterized the burden, distribution, and molecular evolution of respiratory viruses among hospit...
Estimate bacterial pathogen contamination of healthcare workers' (HCW) long-sleeved attire. Prospective observational study. Tertiary care hospital. HCWs wearing long-sleeved attire providing direct inpatient care. Sampling of both sleeves of HCWs wearing long-sleeved attire was performed using a sw...
The emergence and spread of mobile colistin resistance () genes pose a significant challenge in controlling multidrug-resistant Gram-negative pathogens. Understanding the epidemiology of -carrying plasmids is essential for mitigating their dissemination across humans, animals, and the environment. T...
Malaria has caused over 15.7 million deaths in the 21 century and was responsible for ~600 thousand deaths globally in 2023 alone. Although many effective antimalarial drugs have been developed and widely adopted to reduce the occurrence and severity of the disease, recurrent resistance to the front...
Traditional COVID-19 forecasting often misses the rapid dynamics of viral competition, limiting timely ublic health responses. This study demonstrates the value of incorporating SARS-CoV-2 variant data into recurrent neural networks, using an interpretable, data-driven approach to improve accuracy i...
The re-emergence of monkeypox virus (MPXV), renamed mpox, as a global health emergency in 2022 has intensified the search for robust therapeutic interventions. This review summarizes the virological, structural, and pharmacological dimensions of MPXV, with a focus on the virus's lifecycle from host...
Proteus mirabilis has emerged as a clinically significant multidrug-resistant (MDR) pathogen, yet the genomic drivers and dissemination mechanisms of its antimicrobial resistance (AMR) remain poorly characterized. To address this gap, we conducted a pangenome analysis of 2,013 P. mirabilis genomes,...
The 2022 dengue outbreak in Karachi, Pakistan, posed a severe threat to the region, yet no study has investigated the origins of the causal strain. This study aimed to trace the origins and transmission route of the dengue virus serotype 1 (DENV-1) strain responsible for the 2022 epidemic through ge...
Wastewater surveillance at airports has gained interest as a tool for early pathogen detection, but current evidence remains largely feasibility-focused and provides limited guidance on where sampling efforts should be prioritised. In this study, we go beyond feasibility assessments and present a co...
According to the World Health Organization, methicillin-resistant Staphylococcus aureus (MRSA) is classified as a "High" priority pathogen on its Global Priority Pathogens List. The aim of this study is to perform a comprehensive genome-based in silico analysis of S. aureus to elucidate the evolutio...
Rabies, a neglected tropical zoonotic disease caused by the rabies virus (RABV), results in fatal encephalitis in both humans and animals. India, a high-burden country, accounts for nearly 30% of global rabies-related deaths. Robust surveillance combined with large-scale genomic sequencing of RABV i...
subsp. (SDSE) has historically been recognized as a human pathogen, yet β-hemolytic streptococci consistent with SDSE have been documented in pigs for nearly a century. To investigate the population structure of porcine SDSE and the phylogenetic relationships between swine and human strains, we cha...
In carbapenem-resistant , the co-occurrence of carbapenem resistance genes poses a significant threat to global public health. This study investigated the phenotypic and genotypic characteristics of a clinical carbapenem-resistant strain B5, which harbors both and . Antimicrobial susceptibility te...
During an outbreak, infectious disease can spread among populations through host movement, potentially fueling local outbreaks with their own epidemiological dynamics. However, it is difficult to know how often infections between populations are transmitted by diseased travelers infecting healthy re...
The continuous emergence of SARS-CoV-2 variants represents a major public health concern. Next-generation sequencing (NGS) enables genomic surveillance, facilitating the detection and monitoring of mutations that impact viral evolution. In this study, full-length SARS-CoV-2 genomes were analyzed be...
is a Gram-negative pathogen frequently associated with swine and pork products. Despite its global importance, little is known about the genomic characteristics of in Brazil. Furthermore, the antimicrobial resistance (AMR) in has been associated to be driven by horizontal gene transfer, especially...
Mosquito saliva plays a key role in arbovirus transmission and pathogenesis. It was shown that saliva contains several molecules that are essential for blood feeding. Recently, bacteria were also reported to be present in the saliva of Aedes albopictus and Anopheles mosquitoes. Nevertheless, informa...
Avian Influenza (AI) remains a critical threat to livestock production in Oceania, with recent outbreaks of Highly Pathogenic Avian Influenza (HPAI) H7 subtypes in Australia and New Zealand. Historically, AI detections in these countries were largely confined to wild birds. However, since 2024, mult...
The evolutionary, demographic, and phylogeographic histories of viral pathogens can be inferred from their genomic sequence data. Bayesian phylogeographic approaches, for example, can be used to reconstruct the spatial dynamics of pathogen transmission. Although a range of tools is available for evo...
Vectoring tomato spotted wilt virus (TSWV) by two well-known thrips species, Pergande and Trybom (Thysanoptera: Thripidae), is facilitated in different ways. Symbiotic bacteria positively influence thrips fitness, but the interaction between these bacteria and tospovirus inside the thrips' body re...
Uropathogenic Escherichia coli (UPEC) poses a significant public health challenge due to increasing antimicrobial resistance (AMR) and severe infections. This study aimed to investigate the genetic heterogeneity and AMR mechanisms of a clinical UPEC strain associated with a fatal healthcare-associat...
The viromes of maternal peripheral blood (MPB) and umbilical cord blood (UCB) provide crucial insights into mother-to-infant transmission and the associations of maternal health with early-life viral colonization. Using viral metagenomic sequencing of 433 MPB and 426 UCB samples, we assembled 57 nea...
Monitoring and understanding the transmission and evolution of SARS-CoV-2 remains a significant pub-lic health priority. Within-host genetic variation provides insight into viral evolution during infection and may help infer transmission events. In this study, we analyzed intrahost variation in SARS...
Hypervirulent and carbapenem-resistant (hv-CRKP) poses a major clinical threat. Colistin is a last-resort agent against hv-CRKP, yet resistance driven by chromosomal mutations remains poorly characterized in its prevalence and functional impact. From 2020 to 2023, 239 non-duplicate clinical hv-CRKP...
Yellow fever virus remains a major public health threat in Brazil, where recent resurgence risks affecting both forest and periurban populations. Understanding viral movement across ecological settings is critical to support early detection and prevent outbreaks. We performed genomic surveillance in...
is a Gram-negative enteric bacterium responsible for the foodborne and waterborne disease salmonellosis, which was the second most reported foodborne gastrointestinal infection in humans in the European Union in 2023. Animals represent the principal reservoir of this pathogen, with animal-derived fo...
Porcine circovirus types 2 (PCV2) and 3 (PCV3) are major pathogens affecting swine health and productivity, yet important gaps remain in understanding their evolution and circulation in Europe, particularly within wild boar populations that may serve as reservoirs. This study examined the genetic di...
ESKAPE bacteria are a major global threat due to their rapid antibiotic resistance acquisition and severe healthcare-associated infections. Effective countermeasures require epidemiological surveillance and resistance transmission studies, particularly for antimicrobial-resistant (AMR) colonization...
SARS-CoV-2 genome sequencing, genomic characterization, and global data sharing are recommended to facilitate countermeasures against COVID-19. This study involved whole genome sequencing and phylo-evolutionay analysis of SARS-CoV-2 variants circulating in Osun State, Nigeria between January and Jun...
The global emergence of extended-spectrum β-lactamase-producing (ESBL-Kp), especially antimicrobial-resistant high-risk clones, is a public health concern. However, data on their molecular epidemiology in Japan remain limited. In this study, we conducted molecular analysis of 119 ESBL-Kp clinical i...
has emerged as an important multidrug-resistant pathogen implicated in hospital-acquired infections. However, detailed genomic insights into the genetic contexts and dissemination mechanisms of carbapenemase and extended-spectrum β-lactamase (ESBL) genes in this species remain limited. This study ai...
Yellow fever, a zoonotic arboviral disease, has reemerged in Colombia, triggering a major outbreak in the country. During 2024 through mid-2025, a total of 132 human cases and 68 infections in nonhuman primates were confirmed, primarily in the department of Tolima, historically considered a low-risk...
Outbreaks of hemorrhagic septicemia (HS) caused by serogroup B are endemic in Kazakhstan. These outbreaks have repeatedly led to mass mortality events among wild saigas and economic losses to farms. The aim of this study was to conduct the first whole-genome sequencing (WGS) and analysis of genome...
Mammaliicoccus sciuri (formerly known as Staphylococcus sciuri) are Gram-positive bacteria that were previously considered as commensals but has since been reported to cause mild to severe infections in both animals and humans. Since very little is known regarding M. sciuri isolates from Malaysia, t...
Aedes aegypti is not only the primary vector of medically important arboviruses worldwide, but also a host of a wide range of arthropod-specific viruses (ISVs), whose genomic and biological diversity remains largely unknown across most regions of Colombia. Investigating its associated microbiota inc...
Foot-and-mouth disease virus (FMDV) poses a major threat to the global livestock economy. In this study, we analyzed 951 complete genome sequences of FMDV from 66 countries/regions reported from 1958 to 2023, using phylogenomics, recombination detection, and entropy analysis to elucidate its evoluti...
Viral infections continue to pose major challenges to pig health, farm productivity, and global food security. Early and accurate diagnosis is the cornerstone of disease prevention, surveillance, and control in swine populations. In recent years, remarkable progress has been achieved in molecular, s...
Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with reg...
Nosocomial pneumonia (NP), including hospital-acquired (HAP) and ventilator-associated pneumonia (VAP), remains a leading cause of morbidity, mortality, and antimicrobial resistance worldwide. Data from Eastern Europe and the Caucasus are scarce, limiting region-specific infection control strategies...
This study aims to investigate the genomic epidemiological characteristics of enteric adenovirus types F40 and F41 circulating in Yantai from August 2022 to August 2023, with a focus on genetic diversity, recombination events, and their potential implications for public health and vaccine developmen...
Infections caused by carbapenemase-producing organisms are a global health threat. IMP carbapenemases are one of the key drivers of these infections but little is known regarding their global epidemiology. We analyse three decades of bla gene spread using sequence data from 4556 genomes collected be...
Chikungunya virus (CHIKV) caused more than 10,000 infections in Foshan, Guangdong, in 2025. Using plasma from acute-phase patients, we successfully isolated infectious CHIKV, confirmed by focus-forming assay and transmission electron microscopy. Whole-genome sequencing revealed that all isolates bel...
Infectious bronchitis virus (IBV), a highly contagious avian coronavirus, remains a major threat to global poultry production due to its rapid genetic evolution and frequent antigenic shifts. During a nationwide surveillance program in South Korea (2024-2025), we identified a previously unrecognized...
is intrinsically resistant to several antibiotic classes, and acquisition of further restricts treatment options. This study aimed to characterize NDM-producing isolates from a small hospital cluster in Russia and to place them within the global genomic context. Four isolates recovered between Ju...
Plasmids play a critical role in bacterial evolution and represent major drivers of the emergence and dissemination of antimicrobial resistance. As primary mobile genetic elements (MGEs), plasmids facilitate the horizontal transfer of resistance determinants alongside genes associated with virulence...
Newcastle Disease (ND) remains a major threat to poultry production worldwide, particularly in regions where it is endemic, like Southern Asia. The disease is caused by virulent forms of avian paramyxovirus-1, commonly termed Newcastle Disease Virus (NDV), a highly contagious virus with significant...
The H9N2 subtype of avian influenza virus (AIV) is widely distributed in poultry and occasionally infects humans, posing a potential public health risk. While most infections are mild, severe disease can occur in vulnerable individuals. We describe a case of H9N2 infection in a lung transplant recip...
Salmonella enterica serovar Derby is a foodborne pathogen that poses an increasing threat to global public health due to its widespread distribution and increasing antimicrobial resistance (AMR). Herein, a comprehensive genomic overview of 2628 S. Derby strains isolated from 27 countries between 190...
To investigate the genotype and epidemiological characteristics of Human Coronavirus NL63 (HCoV-NL63) epidemic strains in Shanghai, China. Whole genome sequencing of HCoV-NL63 was performed with the nucleic acid-positive specimens collected from the acute respiratory infection surveillance system i...
Carbapenem-resistant isolates harbouring double carbapenemases, from patients in a surgical and transplantation ICU, were investigated to better understand the dispersion of the pathogen. Twenty-three carbapenem-resistant isolates harbouring at least two different carbapenemases (by immunochromato...
, the causative agent of diphtheria, remains a public health concern, especially in regions with low vaccination coverage. While advances in genomic typing, such as core-genome Multi-Locus Sequence Typing (cgMLST), have improved our ability for strain identification, a standardized and stable genomi...
Immunocompromised patients with prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may serve as reservoirs for viral evolution, with suboptimal immune responses facilitating the accumulation of adaptive mutations. This study aimed to characterize the drivers of SARS-Co...
Serratia marcescens may cause rare central nervous system infections. The growing antibiotic resistance in these isolates makes treatment challenging. S. marcescens (MIID-C14) was isolated from the cerebrospinal fluid of a 56-year-old female patient admitted to Salmaniya Medical Complex, Bahrain. Du...
The convergence of artificial intelligence and synthetic biology is innovating and accelerating the design of novel viral genomes, expanding both therapeutic opportunities and dual-use risk. This review articulates a countermeasure strategy for emerging and engineered viruses leveraging the programm...
The circulating strain in the recent Chikungunya fever outbreak in Guangdong Province belongs to the East/Central/South African (ECSA) genotype. However, the specific mutations in the viral genome remained unclear. This study conducted whole-genome sequencing of viral sequences from clinical samples...
Serratia marcescens is a known cause of nosocomial outbreaks in neonatal intensive care units (NICUs). In early 2021, an outbreak occurred in our NICUs, prompting the implementation of rigorous infection control measures. This study aimed to assess whether the outbreak strain was eliminated or persi...
Bussuquara virus (BSQV), an orthoflavivirus discovered in Brazil in 1956, has been detected throughout the Americas in diverse mosquito and vertebrate species, including humans. Critical gaps in BSQV knowledge include its capacity for urban transmission and clinical pathogenesis outcomes, with insuf...
Artificial intelligence (AI) is driving a profound transformation across the healthcare landscape, with the potential to enhance diagnostic accuracy, optimize clinical decision-making, improve resource allocation, and advance personalized medicine. In public health, AI is redefining infectious disea...
Porcine circovirus 2 (PCV2) remains a globally important swine pathogen, and its genetic diversity is central to understanding disease dynamics and control. We estimated a pooled prevalence of 42% (95% CI: 33-52%) by conducting a systematic review and meta-analysis of 53 studies reporting sequencing...
International, multidrug-resistant (MDR) high-risk clonal Klebsiella pneumoniae lineages are a frequent cause of outbreaks, posing a serious public health threat. Tracking, understanding and containing such outbreaks remain a challenge for infection control. In this study, we evaluated Fourier-trans...
Diphtheria remains a major public health threat in areas of the world where diphtheria toxoid-containing vaccine programs are not successfully implemented or maintained. In countries with high vaccine coverage, diphtheria is well-controlled with occasional travel-related cases eliciting a robust pub...
Phlebotomine sand flies are vectors of various pathogens, most notably Leishmania spp. Symbiotic bacteria have recently gained considerable attention owing to their effects on hosts and on other organisms co-infecting the same host. In this study, we investigated the natural Wolbachia infection stat...
The leafhopper Euscelidius variegatus is a laboratory vector of the phytoplasma associated to Flavescence dorée, a severe grapevine disease that threatens viticulture in Europe. Transcriptomic studies have already provided valuable insights into the mechanisms of insect-phytoplasma interactions, but...
Evolutionary forecasting models inform seasonal influenza vaccine design by predicting which current genetic variants will dominate in the influenza season 12 months later. Forecasting models depend on hemagglutinin sequences from global public health networks to identify current genetic variants (c...
Chikungunya virus (CHIKV) poses a significant public health threat, and its continuous evolution necessitates high-resolution genomic surveillance. Current methods lack the speed and resolution to efficiently discriminate sub-lineages. To address this, we developed CHIKVGenotyper, an interpretable m...
is an obligate human pathogen causing gonorrhea the second most reported bacterial sexually transmitted infection. High level genomic plasticity of this pathogen requires whole genome sequence (WGS) analysis for epidemiological investigations. The absence of genomic data from Bangladesh represents...
No abstract available
Bovine coronavirus (BCoV) is a significant pathogen in dairy cattle, but its strain-specific adaptation and antigenic variability in China are poorly understood. This study investigated the prevalence, genetic evolution, and structural-functional characteristics of the BCoV S1 protein across three l...
Duodenoscope-associated infections are typically linked to multidrug-resistant organisms (MDROs) and detected during outbreak investigations. However, the true burden of transmission involving non-MDRO pathogens remains largely underestimated. This study reports a prolonged episode of silent Pseudom...
Nearly half of the human genome consists of transposable elements, among which endogenous retroviruses, remnants of ancient retroviral infections, represent some of the most evolutionarily intriguing due to their paradoxical functional duality. While research has documented functional ERV exaptation...
This dataset comprises raw signal data from a multicenter study evaluating the accuracy of bacterial whole-genome genotyping using Oxford Nanopore long-read sequencing. The raw data comprises 79 isolates across six bacterial species, including 12 triplicates from three different laboratories (totall...
Hepatitis C virus (HCV) remains a public health concern in the United States, particularly in rural communities where the opioid epidemic accelerates transmission among people who use drugs (PWUD). Despite this growing burden, the genetic features and transmission dynamics of HCV in these settings a...
is a rare emerging, multidrug-resistant, opportunistic pathogen known to cause nosocomial outbreaks associated with hospital water sources and medical devices. In June 2024, the microbiology laboratory of Lausanne University Hospital alerted the Infection Prevention and Control Unit following the de...
Cholera, caused by , remains a priority public health concern, particularly in developing countries. The first cholera outbreak in Zambia was documented in the 1970s, with recurring epidemics reported since then. In 2023, a cholera outbreak affected Zambia, particularly in districts bordering Malawi...
Lactococcosis is a major bacterial disease impacting rainbow trout production in South Africa and Southeast Asia, particularly during summer. In this study, 15 isolates from affected aquaculture facilities were characterised, revealing Lactococcus petauri (n = 12) as the predominant species, rather...
Enterobacter hormaechei, a prominent species within the Enterobacter cloacae complex, is a significant cause of nosocomial infections and is frequently associated with multidrug resistance. Rapid genomic comparison helps guide timely infection control measures. This study aimed to develop a simple a...
Genomics has revolutionized epidemiology and disease surveillance by providing powerful tools for identifying, tracking, and analyzing pathogens at the molecular level. This exploratory analysis examines the integration of genomic with traditional epidemiological approaches, highlighting the role of...
remains a major pathogen causing invasive diseases in children worldwide. Although pneumococcal conjugate vaccines (PCVs) have significantly reduced the disease burden, non-vaccine serotypes and antimicrobial resistance continue to be of concern. The epidemiology of paediatric invasive pneumococcal...
The burden of respiratory syncytial virus (RSV) remains a major global health concern in early childhood, responsible for substantial morbidity, hospitalizations, and deaths, particularly in infants under 6 months. For over two decades, palivizumab was the only monoclonal antibody (mAb) available fo...
Rift Valley fever virus (RVFV) is a mosquito-borne phlebovirus that causes severe febrile and hemorrhagic illness in humans. In September 2025, an outbreak in northern Senegal led to 119 confirmed infections and 15 deaths as of October 7, 2025. We performed rapid genomic sequencing to characterize t...
is a foodborne pathogen of major concern due to its link with severe neonatal infections through powdered infant formula (PIF). However, its genomic epidemiology in Bangladesh remains uncharacterized. We report the first whole-genome analysis of three isolates from PIF. Two isolates (S41_PIFM and S4...
Dengue has emerged as a public health challenge in Brazil since the early 1980s, and it is currently one of the most affected regions and an epicenter of the disease. The country faced its worst dengue epidemic on record, with the co-circulation of different dengue virus (DENV) serotypes alongside g...
Raoultella ornithinolytica is recognized as an emerging opportunistic pathogen, with sporadic reports of multidrug resistance. However, comprehensive analyses of carbapenem-resistant isolates remain limited. This study investigated the molecular features and plasmid-mediated transmission of bla amon...
Many hospital laboratories have the technical capacity to perform microbial whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates delays that can be highly detrimental to outbreak responses. The Wellington Regional Hospi...
The continued evolution of SARS-CoV-2 Omicron sublineages requires ongoing genomic and epidemiological surveillance. This study investigated the genomic epidemiology, national trends, and clinical aspects of SARS-CoV-2 in Taiwan from November 2023 to February 2025. We analyzed the molecular and clin...
Shiga toxin-producing (STEC) are zoonotic pathogens with significant public health implications. The interplay between humans, domestic animals, wildlife, and environmental reservoirs such as water bodies influences their circulation. This study aimed to evaluate the role of the environment in the...
Arboviruses continue to threaten global health because of their rapid geographical expansion and significant disease burden. Of the over 500 recognized arboviruses, approximately 150 affect humans, and around 50 affect domestic animals and wildlife. The spread and impact of these viruses have increa...
We investigated the genetic characteristics of non-IMP type carbapenemase-producing Enterobacterales isolates detected in Japan. The isolates were found to carry diverse plasmids with high sequence similarity to those previously reported in other countries, underscoring the critical imperative for c...
Salmonella is a major foodborne pathogen, frequently linked to poultry and posing serious food safety and public health risks. To investigate its epidemiology in retail chicken in Shaanxi Province, China, we conducted a comprehensive study integrating whole-genome sequencing (WGS), Clusters of Ortho...
Highly pathogenic avian influenza (HPAI) A/H5N1, clade 2.3.4.4b, has spread globally, with the first outbreak in a commercial poultry farm in Brazil reported in 2025. This study aimed to genetically characterize A/H5N1 samples from multiple Brazilian regions using whole-genome next-generation sequen...
Acute respiratory infections (ARIs) remain a leading cause of global morbidity and mortality, disproportionately affecting vulnerable populations such as children, the elderly, and immunocompromised individuals. Despite the availability of traditional diagnostic tools, including viral culture and hi...
Face masks are widely recognized as a key intervention to limit SARS-CoV-2 transmission, yet the distribution and persistence of viral RNA across different mask regions and layers remain poorly understood. To address this, we analyzed 185 masks collected from 60 SARS-CoV-2-positive individuals in Ri...
Carbapenem-resistant (CRKP) represents a critical global health threat, with ST101 identified as a major circulating clone in Saudi Arabia. We used whole genome sequencing and plasmid reconstruction to investigate the molecular characteristics of CRKP ST101 isolates from Saudi Arabia (2018-2021), a...
Traditional infectious disease surveillance systems face significant limitations, including delayed detection, underreporting of asymptomatic cases, and inequitable health care access. Wastewater-based epidemiology (WBE), enhanced with genomic analysis, offers a noninvasive and cost-effective altern...
Metallo-β-lactamases (MBLs)-producing Enterobacterales infections represent a serious threat in clinical practice due to high mortality rates associated and the limited therapeutic options available. Given their increased dissemination across Europe and their involvement in hospital outbreaks, furth...
An outbreak of /ST82 was detected through prospective genomic surveillance at a military treatment facility. Twenty-one of twenty-six patients had confirmed epidemiological links to grappling sports. One case resulted from household transmission. The benefits of routine surveillance extend beyond t...
Methicillin-susceptible Staphylococcus aureus (MSSA) remains a major pathogen in neonatal intensive care units (NICUs), with colonization and infection posing significant risks. MSSA colonization occurs in up to 42.8% of neonates, while 12-41% of healthcare personnel also carry MSSA, contributing to...
Human metapneumovirus (HMPV) is a major viral cause of acute respiratory tract infections, especially in young children and older adults. However, data on its molecular epidemiology in the Middle East remain scarce. As the COVID-19 pandemic may have altered the circulation and molecular epidemiology...
The MERS-COV virus is a zoonotic coronavirus that emerged in 2012 in KSA and caused viral illness with a case fatality rate up to 35 %. Over a decade later, the virus is still evolving and circulating. The aim of this review is to discuss the current epidemiology of MERS-COV both in humans and anima...
Isolate characterization and comparison are central aspects in foodborne outbreak investigation and is nowadays regularly performed using whole genome sequencing (WGS). Despite its high accuracy, WGS is relatively expensive, time-consuming, and requires specific expertise for data analysis. Therefor...
The COVID-19 pandemic posed unprecedented challenges to public health surveillance frameworks. In response, the Provincial Public Health Laboratory (PPHL), Sindh, contributed to early detection, large-scale diagnostic testing, and genomic surveillance from February 2020 to June 2025. This study revi...
Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but the rate and directionality of this process is unknown. Here, we explore within-host diversity as w...
Enterovirus D68 (EV-D68) is an important respiratory pathogen occasionally linked to acute flaccid myelitis. While recombination drives enterovirus evolution, recombinant EV-D68 strains have been rarely documented. As part of 2025 genomic surveillance in Maryland, 115 EV-D68 genomes were sequenced u...
Despite global improvements in water, sanitation, and rotavirus vaccination, rotavirus-associated diarrhea continues to cause significant morbidity and mortality among children in low-to-middle-income countries. Genomic surveillance is essential for evaluating vaccine efficacy and detecting emerging...
Carbapenem-resistant (CREC), particularly strains producing New Delhi metallo-β-lactamase-9 (NDM-9), pose a growing threat as agents of nosocomial infections. Despite their emergence since 2013, a comprehensive global phylogeographic and genetic characterization of -carrying CREC is lacking. Throug...
This study systematically characterizes the genetic diversity, phylogenetic relationships, recombination events, and structural variations of human adenovirus serotypes 40 and 41 (HAdV-F40/41) circulating in Shandong Province, China, between 2017 and 2019. A total of 2,221 stool samples were collect...
Urinary tract infections (UTIs) impose a substantial health care burden with increasing antimicrobial resistance and treatment failure rates. is a challenging UTI pathogen due to intrinsic resistances coupled with formation of crystalline biofilms. We combined pangenome analysis, antimicrobial resi...
Chickenpox is a highly contagious viral infection caused by varicella-zoster virus (VZV) whose clinical manifestations mimic mpox posing challenges for diagnosis without laboratory confirmation. Here, we investigated VZV among the mpox-suspected cases, May to October 2022, in Ethiopia. Samples were...
HIV infection can affect SARS-CoV-2 infection dynamics through prolonged viral replication and altered immune responses, but population-level genomic evidence from HIV-endemic settings is limited. Botswana, a country with high HIV prevalence and an established genomic surveillance infrastructure, pr...
KL57 Klebsiella pneumoniae (K. pneumoniae) is an emerging serotype with epidemiological characteristics and pathogenic mechanisms that remain incompletely understood. This study comprehensively analyzed the genomic features of KL57 K. pneumoniae strains isolated in Wuxi from 2016 to 2023, and invest...
Plant viruses account for nearly half of emerging and re-emerging plant disease epidemics, leading to significant crop losses, and are of great concern due to their severe impact on global food security. Host shifting, which results in dead-end infections until viruses completely adapt to the new ho...
This multicentre study investigated the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates across Xinjiang, China. We aimed to characterise resistance phenotypes, genotype distributions, virulence gene profiles, and regional variations to inform precise pr...
The COVID-19 pandemic underlined the need to focus on women's health, particularly during pregnancy. Recent studies have shown that maternal SARS-CoV-2 infection during pregnancy may increase obstetrical risks. However, intraamniotic SARS-CoV-2 infection has been understudied. Here, we conduct inclu...
Bloodstream infections and sepsis necessitate rapid, sensitive, and clinically relevant diagnostics to minimize treatment delays and improve clinical outcomes. Next-generation sequencing enables culture-independent pathogen detection, antimicrobial resistance profiling, and genome-informed epidemiol...
Stenotrophomonas maltophilia is an environmental opportunistic pathogen that affects immunocompromised patients. Its genomic heterogeneity led to definition of the S. maltophilia complex, including different subpopulations (genogroups) with unknown respective dissemination potential. This study aime...
Enteritis is a common and recurrent disease in shrimp aquaculture, causing significant economic losses and management challenges. However, its specific causative pathogen remains unclear. Here, a pathogen strain, VSP1, was directly isolated from shrimp with enteritis, and its pathogenicity and geno...
Antimicrobial resistance (AMR) is a growing global health concern with profound implications for ophthalmology, where it compromises the management of ocular infections such as bacterial keratitis, conjunctivitis, endophthalmitis, and postoperative complications. Resistance in common ocular pathogen...
This study aimed to characterize the molecular epidemiology, antimicrobial resistance, virulence profiles, and clinical outcomes of Methicillin-resistant Staphylococcus aureus (MRSA) infections among intensive care unit (ICU) patients in southern China. A total of 104 non-duplicate MRSA isolates wer...
To investigate the genetic diversity in OXA-48-producing Escherichia coli ST131 in a New Zealand community outbreak, and to characterize the mobile genetic elements carrying bla, with emphasis on the gene's global dissemination. Forty outbreak isolates underwent short-read sequencing; 36 also underw...
A nationwide collection of Pseudomonas aeruginosa bacteraemia isolates was assembled during a wild-type P. aeruginosa ST3875 outbreak affecting approximately 400 patients across 40 hospitals in Norway in 2021-2022. To investigate the molecular epidemiology of P. aeruginosa in Norway through a multi-...
Nontyphoidal Salmonella (NTS) is a major foodborne pathogen, and rising antimicrobial resistance (AMR) threatens treatment efficacy. Salmonella remained the leading cause of bacterial foodborne outbreaks in Hong Kong, but data regarding its prevalence in retail meats are limited. This study investig...
Enterococcus faecium is a major cause of hospital-acquired infections, particularly bloodstream infections, which are associated with high mortality rates. This study aimed to characterize the molecular epidemiology, antimicrobial resistance profiles, and virulence determinants of E. faecium isolate...
Asymptomatic carriers of antimicrobial-resistant organisms (AMROs) can unwittingly transmit these pathogens in hospitals, contributing to the burden of healthcare-associated infections (HAIs). Surveillance in hospitals can involve different types of observations; however, a framework to coherently s...
Antimicrobial resistance in healthcare-associated infections represents one of the greatest threats to global health. The COVID-19 pandemic disrupted infection control and antimicrobial stewardship, potentially affecting the prevalence of pathogens and the development of resistance. This study aimed...
(), the etiologic agent of gonorrhea, is the second most reported bacterial sexually transmitted infection globally. In the USA, nucleic acid amplification tests (NAATs) are considered the gold standard for diagnosis. Although NAATs are sensitive and offer high throughput, cross-reactivity with comm...
We describe an atypical case of mpox virus (MPXV) infection in a Polish patient, with a focus on clinical presentation, virological characterisation, and the phylogenetic placement of the viral isolate within the emerging C.1 lineage of Clade IIb. The report aims to contribute to a better understand...
German cockroaches (Blattella germanica) are prevalent indoor pests that have long been associated with the spread of enteric human pathogens. Recent work investigating the relationship between these insects and Salmonella enterica serovar Typhimurium (S. Typhimurium), a model pathogen of global con...
is a spirochete associated with Lyme borreliosis and is widely distributed across Eurasia. Although its genomic features have been well characterized in Europe, genomic data from East Asian isolates remain limited. Two strains, HN13 and HN18, were isolated from a wild rodent () in South Korea and s...
Aedes aegypti is the primary vector of arboviruses worldwide, including dengue, Zika, chikungunya, and yellow fever. It is believed to have originated in Africa and migrated to the Americas during the sixteenth and seventeenth centuries, subsequently spreading to Asia and Oceania between the ninetee...
Carbapenem-resistant (CRAb) has emerged as a major and often fatal cause of bloodstream infections among hospitalized patients in low- and middle-income countries (LMICs). CRAb outbreaks are hypothesized to arise from reservoirs in the hospital environment, but outbreak investigations in LMICs are...
Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using...
In the neonatal intensive care unit (NICU), outbreaks caused by methicillin-susceptible (MSSA) are less commonly described than outbreaks caused by methicillin-resistant (MRSA) despite the increased burden of MSSA infections. To investigate a NICU MSSA outbreak utilizing whole-genome sequencing (W...
Acinetobacter baumannii is an opportunistic pathogen associated with healthcare-acquired infections. This study examined the clonal relatedness and drug resistance of 38 clinical isolates of A. baumannii from three hospitals in Poland and five isolates from pig manure. PFGE analysis identified seven...
The rise of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) strains represents a major clinical threat, particularly in Asia. These strains possess both extensive drug resistance and enhanced virulence traits, leading to high morbidity and mortality. This study aimed to characteri...
Shiga toxin-producing (STEC) is a zoonotic pathogen that can be transmitted to humans through contaminated food or contact with infected animals. Here, we aim to characterize the population diversity and genome characteristics of the clinical STEC population in New York State collected over a span...
Outbreak investigation and control are critical for preventing the spread of infectious diseases in healthcare settings. Traditional methods rely on manual processes, which are time-consuming and limited in scope. Whole genome sequencing (WGS) surveillance improves outbreak detection but still requi...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major threat to public health and is a common cause of nosocomial outbreaks. To describe the genetic epidemiology of CRAB from both clinical and hospital environments in a network of hospitals in Hong Kong. A collection of 185 CRAB strains fro...
The IR Biotyper (IR-BT) was evaluated for its performance in typing Candida parapsilosis strains, in comparison to a short tandem repeat analysis. Although the IR-BT offers advantages such as speed and ease of use for routine applications, it demonstrated lower discriminatory power and concordance w...
With the introduction of novel antimicrobial agents, the threat posed by multidrug-resistant organisms has rapidly emerged. Among these, metallo-β-lactamase-producing carbapenem-resistant Enterobacterales (MBL-CRE) represent a significant challenge, severely limiting therapeutic options for clinicia...
Vancomycin-resistant enterococci (VRE), particularly Enterococcus faecium, represent a significant nosocomial threat worldwide. In Saudi Arabia, limited genomic data exist to support phenotypic surveillance findings, impeding the understanding of resistance mechanisms, clonal diversity, and plasmid...
Since its emergence in late 2019, SARS-CoV-2 has demonstrated remarkable genetic diversity driven by mutations and recombination events that shaped the course of the COVID-19 pandemic. Continuous genomic monitoring is essential to track viral evolution, assess the spread of variants of concern (VOCs...
Whole-genome sequencing provides the highest resolution for characterizing pathogen evolution, epidemiology, and diagnostics. Genome assemblies contain information on the identity and potential phenotypes of a pathogen. Likewise, variant calling can inform on transmission patterns and evolutionary r...
Colonization of pregnant women with Streptococcus agalactiae is the main risk factor for vertical transmission to neonates and the occurrence of early onset neonatal disease. Screening for maternal carriage is used to guide the administration of intrapartum antibiotics and can significantly reduce d...
Genome annotation, alignment and phylogenetics are at the centre of most studies in evolutionary genomics. These techniques function best when rooted in prior work. Genes are mined from new genomes using evidence from old gene models. These genomes are aligned to well-worn references to create matri...
Postoperative infections following spinal surgery are typically caused by skin flora or hospital-acquired pathogens. This article reports a novel outbreak of Enterobacter kobei infections linked to a collagen-based adhesion barrier. To identify the source of increased surgical site infections in lum...
The 2022 mpox outbreak highlighted the threat of emerging infectious diseases and the value of genomic epidemiology, emphasizing the need to strengthen laboratory and data-sharing capacities. This manuscript presents strategies to develop and enhance genomic tools and infrastructure for monitoring m...
Information on the molecular epidemiology of and antimicrobial resistance mechanisms is still limited in some South American countries. This study aims to decipher the population structure of 111 extensive drug-resistant isolates from a national study conducted in Bolivia during 2023-2024. The ant...
has evolved over the years into predominant nosocomial multidrug-resistant (MDR) pathogen, especially associated with ventilator-associated pneumonias (VAPs). About one-third of VAPs can cause bloodstream infections. MDR causing VAP is associated with significant longer hospital stays and mortality...
Health-care-associated infections (HAIs) are a global threat. Microbial whole-genome sequencing (WGS) can strengthen HAI prevention strategies by enabling high-resolution detection and tracking of pathogen transmission and predicting clinically relevant phenotypic traits, such as antibiotic resistan...
The re-emergence of COVID-19 in India and South Asia, driven by the Omicron variant (NB. 1.8.1), poses an urgent challenge to global pandemic preparedness amid waning citizen awareness and reduced monitoring. This review aims to examine the variant's characteristics, assess its public health impact,...
Novel SARS-CoV-2 variants demonstrating considerable intra-host evolution emerged throughout the pandemic. The persistent infections thought to give rise to these variants, however, have been difficult to identify at scale. This study sought to detect and characterize persistent infection cases in C...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a significant global public healthchallenge. A total of 63,099 KP genomes was available in the NCBI Genome database, and assembly quality was further assessed using QUAST. Antibiotic resistance genes (ARGs), virulence factors (VFs), an...
Carbapenem-resistant Gram-negative bacteria (CR-GNB) are rapidly spreading pathogens that increase morbidity and mortality in hospital settings and significantly restrict available treatment options worldwide. The lack of molecular epidemiological data and the limited use of next-generation sequenci...
During the COVID-19 pandemic, the spread and diversity of SARS-CoV-2 was monitored non-invasively in more than 99% of Dutch households by a comprehensive wastewater-based epidemiology (WBE) programme which analysed viral RNA in wastewater samples taken at every household wastewater-treatment plant (...
Rabies is a zoonosis primarily transmitted through bites from infected animals. The rabies virus (RABV) remains a significant public health concern in some countries and causes substantial economic losses in livestock farming. In Brazil, around 45,000 cattle die annually due to rabies, resulting in...
Listeria monocytogenes, a major foodborne pathogen, causes invasive listeriosis with a high mortality rate. Its distribution and genomic diversity in livestock products in Korea remain poorly understood. This study investigated the prevalence and genomic characteristics of L. monocytogenes across Ko...
The COVID-19 pandemic has profoundly influenced healthcare systems and infection control worldwide, with important implications for the epidemiology of antimicrobial resistance. This study examined the prevalence and characteristics of carbapenem-resistant Enterobacterales (CRE) isolates in Southeas...
During the COVID-19 pandemic, large-scale pathogen sequencing generated millions of SARS-CoV-2 genomes deposited in repositories like GenBank and GISAID. However, most of these records lack detailed patient metadata, such as demographics and clinical outcomes, which limits their utility for large-sc...
Methicillin-resistant (MRSE) is a major opportunistic pathogen associated with high morbidity and mortality. However, its transmission dynamics and molecular characteristics in high-risk populations such as men who have sex with men (MSM) remain poorly understood. A community-based cross-sectional...
Extended-spectrum β-lactamase (ESBL)-producing is among the most important multidrug-resistant pathogens causing bloodstream infections (BSIs). Cefotaximase (CTX-M) enzymes are the most common and highly diverse ESBL family in . CTX-M-15 in group CTX-M-1 and CTX-M-14 in group CTX-M-9 are the most e...
is considered one of the emerging bacterial agents causing healthcare-associated infections (HAIs) in hospital environments. This microorganism has been identified as multidrug-resistant, capable of forming mature biofilms-an ability that promotes adherence to surfaces and invasive medical devices,...
Chronic infections in cystic fibrosis (CF) patients are often driven by adaptive and drug-resistant bacterial lineages. Understanding sequence types (STs) and phenotypic adaptations such as small colony variants (SCVs) can guide more effective clinical management. Seventeen bacterial isolates from r...
Phylogenetics has a central role in evolutionary biology and genomic epidemiology. Assessing phylogenetic confidence and reliability is therefore crucial and the methods that do this, such as those derived from Felsenstein's bootstrap, are among the most widely used in modern science. However, these...
To evaluate mandated infection control measures to reduce SARS-CoV-2 introduction and transmission in skilled nursing facilities, we characterized outbreak duration by the number of lineages identified. Median outbreak duration among outbreaks with multiple lineages identified was 35 days compared w...
Candidozyma (Candida) auris is a multi-drug-resistant fungal pathogen associated with protracted, costly hospital outbreaks. Conventional patient-level screening is resource-intensive and may not be cost effective. Wastewater surveillance may offer a pragmatic, ward-level approach to early detection...
Norovirus (NoV) is one of the leading causes of acute gastroenteritis worldwide, being responsible for millions of cases each year. We report a large NoV outbreak occurred in a Northern Italy school complex, and the genomic characterization of the outbreak strain. Stool samples from 105 subjects inv...
Clostridium perfringens is one of the leading causes of food-borne outbreaks (FBO). This study explores the epidemiological and genomic features of a major FBO occurred in a Spanish school in 2023. Through genomic analysis, the virulence factors and relatedness of C. perfringens strains involved in...
Intensive care units (ICUs) face high risks of methicillin-resistant Staphylococcus aureus (MRSA) transmission, yet how accessory gene regulator (agr) dysfunction drives strain adaptation remains unclear. This study investigated MRSA epidemiology in a new ICU, focusing on post-COVID-19 clonal dynami...
West Nile virus (WNV) has emerged as a public health concern in Germany since its first detection in 2018, with evidence of expanding geographic spread. Genomic surveillance is critical for tracking viral evolution, identifying introductions, and monitoring local transmission. However, genome recove...
Sheeppox virus (SPPV) and Goatpox virus (GTPV), members of the genus Capripoxvirus, cause transboundary pox diseases in sheep and goats. Although disease is mostly host-specific, uncertainty of cross-infection always exists under mixed farming practices. A comprehensive genome-wide plasticity and ph...
The WHO African Region bears a disproportionately high burden of hepatitis B and C virus infections, yet molecular diagnostic capacity remains limited, impeding accurate detection, treatment monitoring, and surveillance. This Letter highlights the critical role of molecular diagnostics, including nu...
Listeria monocytogenes is a globally relevant foodborne pathogen and a major public health concern because of its ability to cause severe invasive disease and persist in food processing environments. This study aimed to characterize the genomic diversity of L. monocytogenes isolates collected in Uru...
Dengue fever, a major mosquito-borne viral disease, is transmitted by mosquitoes and poses a significant global health burden. Despite extensive research, the spatiotemporal dynamics of dengue virus (DENV) lineages in Colombia remain understudied. Here we analyze 11,443 complete genome sequences fr...
Antimicrobial resistance (AMR) in enterica serotype Kentucky ( Kentucky) is a global challenge, with increasing resistance to cephalosporins, ciprofloxacin, and carbapenems significantly limiting treatment strategies, yet its worldwide dissemination patterns and AMR profiles remain unclear. Therefo...
Plasmids are extrachromosomal mobile genetic elements that often carry genes responsible for antimicrobial resistance. Plasmid epidemiology aims to track the evolution and spread of plasmids, but the field currently faces significant barriers that make practical implementation using whole genome seq...
We report the first detection of bla gene in Africa carried in a carbapenem-resistance Acinetobacter baumanii clinical isolate. In this study, an Acinetobacter baumannii isolate cultured from a purulent open septic ulcer on the right breast in a 58-year-old female patient in Kenya was characterized....
Corynebacterium striatum (C.striatum) is an emerging multidrug-resistant opportunistic pathogen frequently isolated in intensive care units (ICUs). Accurate strain typing is critical for identifying transmission routes and implementing effective infection control strategies. This study aimed to comp...
Mpox is a reemerging infectious disease caused by monkeypox virus (MPXV). Whole-genome sequencing provides comprehensive surveillance of MPXV but is challenging in resource-limited outbreak settings and on clinical samples with low viral load. We developed a low-cost, high-throughput partial-genome...
In July-October 2025, two concurrent outbreaks (clones ST49#3 and ST52#4) with 112 notified cases were detected through Denmark's whole genome sequencing surveillance programme. The outbreaks were clinically severe: 45 (40%) infected individuals were hospitalised and 16 (14%) had bacteraemia. We es...
Routine use of pneumococcal conjugate vaccines (PCV) in South Africa caused a decline in vaccine-associated invasive pneumococcal disease (IPD), followed by the emergence of non-PCV serotypes, driven mainly by pre-existing lineages. We determined the molecular epidemiology of isolates causing IPD am...
BACKGROUND has emerged globally as a major threat to public health due to its outbreak causing capacity and antifungal resistance. Outbreaks have proven difficult to control despite enhanced infection prevention measures. Thus, national surveillance is warranted.AIMWe aim to characterise the epidemi...
We describe the emergence of vancomycin-resistant (VREfm) ST612 in Switzerland from 2018 to 2024 that resulted in a national outbreak investigation. This clone has predisposing genetic alterations associated with reduced daptomycin susceptibility. The National Nosocomial Outbreak Investigation Cen...
In Spain during March-April 2024, an outbreak of invasive meningococcal disease (IMD) occurred in four young adults, exhibiting high case fatality with two deaths. Cases 1 and 4 were confirmed by isolation of from blood samples, while Cases 2 and 3 were PCR-confirmed from cerebrospinal fluid (CSF)....
There is growing interest in the molecular surveillance of the respiratory syncytial virus (RSV) and data concerning the virus molecular epidemiology in high-risk pediatric patients in Italy are still limited. A total of 127 RSV-positive swabs collected in 2022-2023 season were analyzed. Whole genom...
The influenza A H1N1pdm09 virus continues to pose a significant zoonotic threat, with implications for both animal and human health. Italy, which hosts one of the largest swine populations in Europe, is strategically positioned to monitor the evolution of influenza viruses in livestock. This study a...
Methicillin-resistant (MRSA) surveillance in regions with mass gatherings presents unique challenges for public health systems. Saudi Arabia, hosting millions of pilgrims annually, provides a distinctive setting for studying how human mobility shapes bacterial populations, yet comprehensive genomic...
No abstract available
With the large-scale use of antibiotics, the detection rate and mortality of carbapenem resistant Escherichia coli (CR-EC) have gradually increased. This study investigated the molecular characteristics and prevalence of CR-EC in order to supplement the isolated data of CR-EC in Hangzhou, China. The...
Drug-resistant Acinetobacter baumannii poses a global health crisis, especially in Asia. It has a propensity to become clonally endemic in healthcare settings. However, its clonal distribution in a broad geographic area is unclear. The clonality of A. baumannii was characterized nationwide by collec...
The continuous evolution of SARS-CoV-2 and its variants poses persistent challenges to global public health. As a sublineage of the XDV.1 variant, NB.1.8.1 has rapidly emerged as a dominant strain worldwide, triggering a new wave of infections. Representing a product of viral adaptation, this varian...
, the causative agent of melioidosis, is a neglected tropical pathogen that has been increasingly encountered in Europe through travel-related infections. Clinical manifestations range from localized abscesses to life-threatening sepsis, posing diagnostic challenges in non-endemic regions. We report...
Feed additives are an alternative to improve fish performance and health (without compromising growth) during farming conditions. To determine the physiological effects of two hydrolyzed Debaryomyces hansenii yeasts (LAN4 and LAN6 from Lallemand SAS) on the gut of post-smolts Atlantic salmon (Salmo...
Methicillin-resistant Staphylococcus aureus (MRSA) outbreaks in neonatal intensive care units (NICUs) continue to pose serious challenges. Despite the importance of active surveillance, molecular typing, and decolonization for containment, Japan lacks national implementation guidelines. This study r...
Since 2022, the Zinder region has been facing an epidemic of diphtheria. The objective of this study was to investigate the epidemiological and virulence characteristics of the diphtheria epidemic in the Zinder region. This was a cross-sectional study conducted from 2022 to 2024 in the Zinder region...
The Alto Pantanal is a key yet unexplored Brazilian wetland for studying vertebrate viral profiles. This study presents viral taxonomic profiles from vertebrate sera sampled in May, June and October of 2019 in Porto São Luiz and Pirizal, Alto Pantanal. A total of 13 frogs, 19 bats, 23 caimans, 36 eq...
spp. are critical pathogens causing diarrheal diseases. This study analyzed the epidemiological characteristics, antimicrobial resistance profiles, virulence factor profiles, and molecular patterns of isolates in Pudong New Area, Shanghai, from 2013 to 2024. Antimicrobial susceptibility of isolat...
To understand the prevalence and phylogeny of methicillin-resistant (MRSA) in Chinese hospitals and identify the dominant MRSA lineages causing hospital infections, we collected 101 . isolates from multiple centers across China, tested their antibiotic sensitivity, and performed whole-genome seque...
Surgical site infections (SSIs) caused by pose significant challenges in healthcare, particularly in low and middle-income countries (LMICs). Understanding the genomic characteristics and antimicrobial resistance profiles of isolates is crucial for informing appropriate treatment and guiding infec...
Whole-genome sequencing is revolutionizing bacterial outbreak investigation, but its application to the clinic remains limited. In 2020, prospective and retrospective surveillance detected a outbreak with 253 isolates collected from 82 patients in 26 wards of a hospital. Its origin was dated to the...
Newcastle disease (ND) is a major viral infection of poultry caused by virulent strains of avian paramyxovirus type 1, resulting in considerable global economic losses. In Ethiopia, ND outbreaks persist despite vaccination efforts, and the genetic diversity of circulating Newcastle disease virus (ND...
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the virus's remarkable ability to evolve and adapt in diverse hosts. Despite the observation of recurrent mutations and convergent evolution in the viral genome, the mechanisms driving these p...
spp. infections present an urgent and significant global public health challenge. This study offers a genomic characterization of spp. isolates from human samples and chicken-origin food sources in Italy during 2023. Whole-genome sequencing, cluster analysis, genomic comparison of human and food of...
Introduction Multidrug-resistant (MDR) poses significant treatment challenges, particularly in intensive care settings. Ceftazidime-avibactam (CZA) has emerged as a key option against extended-spectrum beta-lactamase (ESBL) and carbapenemase (KPC) producing strains; however, increasing resistance,...
African swine fever (ASF) is a severe viral haemorrhagic disease affecting domestic pigs, maintained by ASF virus within an ancient sylvatic cycle involving Ornithodoros ticks that inhabit warthog burrows. This study aimed to develop and optimise a multiplex polymerase chain reaction (PCR) assay to...
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is one of the important opportunistic pathogens causing nosocomial infections. This study aims to investigate a suspected outbreak of CRPA in a kidney transplant ward. Clinical data of 6 kidney transplant recipients with positive CRPA tests from Sep...
The early months of the COVID-19 pandemic were characterized by high transmission rates and mortality, compounded by the emergence of multiple SARS-CoV-2 lineages, including Variants of Concern (VOCs). This study investigates the phylodynamic and spatio-temporal trends of VOCs during the peak of the...
Antimicrobial resistance (AMR) in high-altitude environments remains understudied despite its growing global concern. This study investigates the molecular epidemiology of the optrA gene, which confers resistance to oxazolidinones and phenicols, in Enterococcus species isolated from herders and yak...
Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is a...
Typhoid fever results from systemic infection with Salmonella enterica serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial-resistant (AM...
Coccidioidomycosis (Valley fever), caused by the fungal pathogen , is increasing in incidence across the western United States and parts of the Americas. However, genomic data from low-incidence regions remain scarce, limiting our understanding of the pathogen's dispersal and evolution. To address t...
Most US carbapenem-resistant Acinetobacter baumannii (CRAB) isolates harbour carbapenem-hydrolysing class D β-lactamases. Other carbapenemases, such as New Delhi metallo-β-lactamase (NDM), are uncommon but emerging. We describe the epidemiology of NDM-producing CRAB reported to the US Centers for Di...
Since July 2025, an outbreak of mosquito-borne chikungunya fever has occurred in Foshan City, Guangdong Province, China. This was the second large-scale local outbreak in China after the one that occurred in Dongguan City, Guangdong Province, in 2010. As of 23 August, more than 10,000 human cases ha...
is a multidrug-resistant opportunistic pathogen that poses critical challenges in hospital settings due to its environmental resilience and high resistance to antibiotics. Genomic surveillance has become essential for identifying transmission patterns, guiding antimicrobial stewardship, and informin...
Infectious bronchitis virus (IBV) is a genetically diverse avian coronavirus that significantly impacts global poultry production. While IBV evolution and spread have been widely studied, most analyses lack global scope and statistical evaluation of dispersal drivers. This study investigates the pop...
Shigellosis is a leading cause of diarrheal mortality worldwide. is one of four species that contributes to this burden, however studies on are limited. Here we combined epidemiological and genomic data to better understand circulating both in Australia and globally. Between 1991 and 2019, there...
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) has emerged as a critical threat in bloodstream infections (BSIs), with rising global prevalence and elevated mortality rates. Traditional surveillance methods often lacks resolution for resistance-virulence-transmission interplay, highlighting the...
Rapidly growing non-tuberculous mycobacteria (NTM) are increasingly recognized as causative agents in healthcare-associated infections. , first described in 1999, has been associated with post-traumatic and post-operative wound infections. We report a case of pacemaker pocket infection and lead end...
Patients in burn intensive care units (BICUs) are at high risk of infections caused by multidrug-resistant pathogens, which can lead to hospital outbreaks. To investigate an outbreak caused by carbapenem-resistant Acinetobacter baumannii (CRAB) in a BICU at a tertiary care hospital in Madrid, Spain,...
is a coagulase-negative staphylococcal species and an opportunistic pathogen associated with hospital-acquired infections. The aim of this study was to use whole-genome sequencing (WGS) to characterize a novel multidrug-resistant (MDR) strain, DUEML1 (ST-184), isolated from a respiratory infection...
The Mississippi Public Health Laboratory conducts active surveillance of carbapenem-resistant Enterobacterales (CRE) infections as part of the Antimicrobial Resistance Laboratory Network (ARLN) program implemented by the United States Centers for Disease Control and Prevention (CDC). Here, we descri...
Whole genome sequencing provides the highest resolution for characterizing pathogen evolution, epidemiology, and diagnostics. Genome assemblies contain information on the identity and potential phenotypes of a pathogen. Likewise, variant calling can inform on transmission patterns and evolutionary r...
: , a member of complex, has emerged as an opportunistic pathogen for human infection; however, antimicrobial resistance and hypervirulent characteristics of have rarely been investigated in South Korea. : We analyzed 76 clinical isolates collected from 12 hospitals between September 2022 and Oct...
The fluorescent brighteners (FBs) utilized in microscopic morphological examination of clinical microorganism exhibit suboptimal performance due to fluorescence instability and unfavorable chromatic properties. Here we provide an alternative strategy by one-pot hydrothermal synthesis of green fluore...
Carbapenem-resistant (CRAb) is among India's leading bacteria responsible for hospital-acquired infections (HAIs). The CRAb causing intra-facility and inter-facility (or importation) HAI transmissions may differ phylogenetically. For control and prevention of CRAb-associated HAIs within and across...
The escalating prevalence of carbapenem-resistant (CR) enteric pathogens elicits significant challenges to public health management and effective antimicrobial therapy. While carbapenem resistance is rare in O1 (VC), the recent emergence of CR strains reveals a concerning shift in their antimicrobi...
The identification of antibiotic resistance genes (ARGs), virulence genes, and pathogens in animal slaughterhouses poses a major threat to human health. However, limited data is available about the contamination and dissemination of ARGs in commercial pig slaughterhouses before and after disinfectan...
Serratia marcescens is an opportunistic AmpC β-lactamase-producing Enterobacterales associated with intensive care unit outbreaks, causing high morbidity and mortality. The spatiotemporal dynamics of Serratia species and their implications for hospital infection prevention and control remain underst...
During 2018-2022, a resurgence of hepatitis A occurred in Florida, with 5491 cases reported. Genotyping was performed on a convenience sample of cases through amplification and sequencing of the hepatitis A virus VP1-P2B junction region. Virus isolates from 1190 cases (22%) were genotyped; 69% were...
Antimicrobial resistance (AMR) surveillance in low- and middle-income countries (LMICs) often relies on poorly resourced laboratory processes. Centralized sequencing was combined with cloud-based, open-source bioinformatics solutions for national AMR surveillance in Cambodia. Blood cultures growing...
As Nigeria has the sixth-highest population in the world and a significant amount of inbound and outbound travel, the characterization of SARS-CoV-2 genomic diversity across the country is critical for understanding novel pandemic dynamics. We describe the genomic diversity of SARS-CoV-2 in Nigeria...
Measles, once considered under control in many high-income countries, has experienced a notable resurgence in recent years due to declining vaccination rates, increased vaccine hesitancy, and gaps in public health preparedness. This study provides an overview of the current measles outbreaks in two...
Carbapenem-resistant Klebsiella pneumoniae is an opportunistic pathogen causing outbreaks in healthcare settings. In hospitals with high K. pneumoniae prevalence, identifying outbreaks is particularly difficult because of recurrent carbapenem-resistant strains. To describe K. pneumoniae circulation...
This study outlines the investigation into an outbreak of infections involving 17 cases undergoing hip or knee surgeries at two ambulatory surgery centers (ASCs) in Tennessee from January 2023 to November 2024. Notably, the outbreak could not be attributed to contaminated water sources, which are t...
With increasing reports about , its role as an emerging human pathogen is been recognized. However, few studies have explored the genomic epidemiology of . in China. A total of 263 isolates collected in various specimens from 2021 to 2022 were analyzed from a tertiary hospital in China. Nearly all...
Monkeypox (Mpox), a zoonotic disease caused by the monkeypox virus, has gained global attention due to rising incidence and the emergence of new clades. Understanding the epidemiology, transmission dynamics, and diagnostic challenges associated with the two major clades, Clades I and II, is crucial...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is relentlessly evolving, with emerging variants exhibiting heightened transmissibility and immune escape capabilities. Understanding the genetic diversity and seasonal transmission dynamics of SARS-CoV-2 in Thailand is crucial for impleme...
Chicken anemia virus (CAV) is a highly infectious pathogen that causes severe immunosuppression and significant economic losses in poultry, with limited genomic data in Bangladesh hindering effective disease control. This study characterizes a CAV strain from a field outbreak in Bangladesh through c...
Burkholderia cepacia complex (BCC) is an aerobic Gram-negative bacillus commonly isolated from aqueous environments. In May 2024, we identified two cases who developed BCC infections within one month following fronto-orbital advancement (FOA) procedures in the paediatric surgery ward. To identify th...
Viral metagenomic next-generation sequencing (vmNGS) has transformed our capacity for the untargeted detection and characterisation of (re)emerging zoonotic viruses, surpassing the limitations of traditional targeted diagnostics. In this review, we critically evaluate the current landscape of vmNGS,...
Aminoglycoside resistance mediated by 16S rRNA methyltransferases poses a growing threat in both human and veterinary medicine. Here, we conducted a retrospective genomic study of Enterobacterales isolates ( = 789) collected from clinical samples at a veterinary teaching hospital in Spain between 20...
Nipah virus (NiV) is a highly virulent zoonotic pathogen capable of triggering severe outbreaks with pandemic potential. This review consolidates current knowledge on its biology, transmission, pathogenesis, and clinical presentation, alongside recent progress in diagnostics, therapeutics, and vacci...
The breach of an interspecies barrier by RNA viruses has facilitated the emergence of lethal hCoVs, particularly SARS-CoV-2, resulting in significant socioeconomic setbacks and public health risks globally in recent years. Moreover, the high evolutionary plasticity of hCoVs has led to the continuous...
sequence type (ST)-1047 is emerging globally as a carbapenemase-rich lineage, yet its evolutionary history and population structure are not known. Here, we performed a comprehensive genomic and epidemiological investigation of 141 ST-1047 isolates from 15 countries, integrating short- and long-read...
The measles vaccine, introduced over 60 y ago, has been proven to be both safe and effective. Despite the genetic diversity of the measles virus, eradication is considered possible with near-complete coverage of the two-dose vaccination schedule. However, real-world data show that this level of cont...
Integrated genomic surveillance, combining whole genome sequencing (WGS) of bacterial isolates with patient movement data, promises improved detection and prevention of pathogen transmission. However, evidence on its cost-effectiveness and clinical utility remains limited, not least because the full...
Phlebotomine-borne diseases, transmitted by sand flies, cause significant public health burdens worldwide. In Morocco, is a primary vector for and phleboviruses. Despite extensive research in other countries, entomopathogenic parasite investigations in have not been conducted in Morocco until now...
Mpox (formerly called monkeypox) is a zoonotic viral disease caused by the monkeypox virus (MPXV) that has recently emerged as a notable global health issue by spreading beyond its typical geographical zones in Central and West Africa. In this study, we conducted a phylogenetic and evolutionary inve...
primarily recognized as an environmental bacterium, has emerged as an opportunistic pathogen associated with nosocomial infections. is well-adapted to oligotrophic and humid environments, harbors intrinsic resistance to both disinfection measures and antimicrobial therapies and possesses the abilit...
Respiratory syncytial virus (RSV) remains a leading cause of lower respiratory tract infections in young children, older adults, and immunocompromised individuals worldwide. In 2023, the first RSV vaccines and the widespread use of monoclonal antibodies were approved, underscoring the need for genom...
The emergence and global dissemination of Infantis carrying the pESI megaplasmid is a growing public health concern owing to its association with multidrug resistance (MDR), enhanced virulence, and increased environmental adaptability. This study investigated the molecular epidemiology and transmis...
Linezolid resistance in Gram-positive cocci has been reported in clinical settings but it is still a rare phenomenon. This study investigated the molecular epidemiology of linezolid-resistant Enterococcusfaecalis strains and the genetic environment of linezolid-resistance genes, in immunocompromised...
In July 2025, China witnessed its most significant chikungunya virus (CHIKV) outbreak since 2010. As of August 1, with over 6,000 cases reported in Foshan city, Guangdong Province. Although the clinical manifestations have been relatively mild, the rapid transmission within communities warrants our...
Information on the epidemiology, transmission dynamics, and public health impact of enteroaggregative Escherichia coli (EAEC) infection in schoolchildren from high-income countries is scarce. This study investigated the occurrence of EAEC infections in apparently healthy children (0-12 years) attend...
Duck virus hepatitis (DVH) is highly fatal disease that predominantly affects young ducklings, causing substantial losses due to its high morbidity and mortality rates. A severe outbreak occurred in young Pekin ducklings on a commercial farm in Benha, Egypt. The affected birds exhibited neurological...
The 2024 Oropouche virus (OROV) outbreak in Brazil raised public health concerns due to its unprecedented rapid spread, high incidence, and potential neurological complications. OROV symptoms overlap with locally endemic arbovirus diseases, like dengue virus (DENV), complicating diagnosis. The study...
Crimean-Congo hemorrhagic fever (CCHF) is prevalent in Africa, Asia, and Europe and poses a serious and long-standing public health burden. Europe, especially Russia, Turkey, and the Balkan region, has been a hotspot for the disease, with the most confirmed reports. Crimean-Congo hemorrhagic fever v...
Dengue's true burden on the African continent is likely underestimated. The majority of cases originate from West Africa, mostly from Burkina Faso. We report here the detection in Guinea of two imported cases of dengue in travelers returning from Côte d'Ivoire, one fatal (case 1) and one mild (case...
Since 2022, the global epidemiology of Mpox (MPXV) has transformed, with Clade IIb driving widespread transmission in non-endemic regions and Clade I resurging across Central Africa. Genomic adaptations, such as APOBEC3 mutations, and increasing human-to-human transmission have raised public health...
is a major source of both hospital- and community-acquired infections worldwide. Advances in whole-genome sequencing (WGS) technologies have recently generated large volumes of WGS data. The timely classification of WGS data using genomic typing technologies has the potential to describe detailed...
In recent years, the detection of Klebsiella pneumoniae (KLPN) producing New Delhi metallo-β-lactamase (NDM), particularly NDM-1, has increased in Germany. Plasmids play a crucial role in the dissemination of NDM-1, facilitating its persistence in both clinical and environmental reservoirs. Between...
Respiratory syncytial virus (RSV) remains a leading cause of pneumonia in young children in Mexico and worldwide. To investigate RSV dynamics in Mexico, we conducted a multicenter study from August 2021 to July 2023 in six hospitals across five States, analyzing respiratory samples from children und...
Antimicrobial resistance (AMR) has emerged as a serious public health threat with a sharply increasing burden globally. Resource limited countries like Nepal are facing difficulties in the fight against AMR. This has been further worsened due to the lack of adequate molecular data. Ciprofloxacin res...
Multidrug-Resistant Organism (MDRO) refers to bacteria that are Resistant to three or more types of antibiotics in clinical use. The global health threat posed by multidrug-resistant (MDR) bacterial pathogens and their cross-species transmission necessitates rigorous Surveillance. This urgency is am...
A large multi-country outbreak of Oropouche virus (OROV), a segmented negative-sense RNA virus, is emerging in Latin America. By analyzing publicly available whole-genome sequences spanning 1955 to 2024, this study reveals accelerated spatiotemporal evolution of OROV, cooperatively driven by genome...
Metagenomic sequencing (mGS) is a useful tool for identifying pathogens in patient samples. During nosocomial outbreaks of respiratory viruses, mGS allows for the identification of viral strains and provides insight into their genetic relatedness. Multiple bioinformatics analysis assembler are avail...
An outbreak of an ertapenem-resistant clone occurred in a specialist children's hospital in Liverpool, United Kingdom (UK), from April 2022 to February 2023. Carbapenem-resistant is unusual in the UK, and identification of two isolates exhibiting ertapenem resistance in the same ward in December 2...
Cholera epidemics due to O1 El Tor have been occurring in Iran since 1965, but the incidence of this disease has declined significantly over time. We found that multiple sublineages of the seventh pandemic O1 El Tor lineage have caused cholera outbreaks in Iran, suggesting recurrent introductions...
Finland experienced three invasive pneumococcal disease (IPD) outbreaks among shipyard workers at the same shipyard, in 2019, 2023 and 2025. During the latest outbreak (30 April-6 June 2025), 13 cases were reported, with six confirmed. All five isolates from blood culture-positive cases were serotyp...
Notifications of Strathcona infections increased in Europe in 2023 prompting a multi-country outbreak investigation. We aimed to describe the epidemiology of . Strathcona infections in 17 European countries 2011-2024, investigate the genetic relatedness of . Strathcona isolates and identify the veh...
Between 1 November and 12 December 2019, a Legionnaires' disease (LD) outbreak occurred in the Strasbourg metropolitan area, France. Epidemiological, environmental and genomic investigations (nested sequence-based typing and whole genome sequencing (WGS)) were undertaken to locate the outbreak sourc...
spp. are an important cause of healthcare-associated bloodstream infections that are uncommonly reported in Africa. This study utilized whole-genome sequencing to characterize spp. from hospitals in Nigeria's antimicrobial resistance surveillance system. Bloodstream spp. isolates from six sentinel...
The global rise of antimicrobial resistance (AMR), exacerbated by the COVID-19 pandemic, has led to a surge in infections caused by multidrug-resistant (MDR) bacteria. A key driver of this phenomenon is co-selection, where exposure to one antimicrobial promotes resistance to others via horizontal ge...
The unprecedented number of (the pneumococcus) genomes sequenced in recent years has accelerated the discovery of novel serotypes and highlighted the genetic diversity both between and within each serotype. A novel serotype should demonstrate a distinct locus, capsular structure and serological pr...
Acinetobacter baumannii is widely recognized as a multidrug-resistant pathogen, although most public genome datasets are biased toward hospital-derived isolates. Little is known about A. baumannii isolates from healthy individuals in the community. This study analyzed genome sequences from nine A. b...
is a major foodborne bacterial pathogen that has become increasingly resistant to clinically important antimicrobials. Of particular concern is the emergence of (B)-mediated macrolide resistance, which has been increasingly documented across isolates from diverse ecological reservoirs. In this stud...
, the main aetiological agent of diphtheria, is a re-emerging bacterial pathogen of public health concern, yet remains largely understudied globally. In this study, we analysed the population structure and antimicrobial resistance (AMR) of 210 . isolates from Victoria, Australia, including 103 hist...
This article summarizes a genomic investigation of a 4-fold increase in disseminated gonococcal infections in Minnesota, USA, in 2024. We detected the emergence of a Neisseria gonorrhoeae strain of a rarely observed sequence type, which carries a porB1a allele previously associated with disseminated...
Vancomycin-resistant (VREfm) is an important nosocomial pathogen. The recent emergence of the highly virulent clonal complex 17 (CC17) is posing a challenge for both therapeutic interventions and hospital infection control measures. Hence, prompt discrimination of CC17 VREfm from unrelated and less...
This study characterizes the molecular epidemiology of Sporothrix species in Shanxi Province, a low-prevalence region in China, providing real data on genetic profiles and antifungal susceptibility patterns. Clinical records of sporotrichosis cases from a tertiary hospital in Shanxi (2019-2024) were...
Between 2018 and 2023, a genomic study was conducted in a military camp in Djibouti to investigate the molecular epidemiology of Panton-Valentine Leukocidin-producing Staphylococcus aureus. Among 43 isolates, Sequence Type 152 was predominant (72%), mainly associated with spa types t355 and t4235. C...
Atypical Porcine Pestivirus (APPV) is an emerging pathogen in pigs. The virus causes diseases associated with neurological disorders, such as congenital tremors (CT) Type A-II in piglets, leading to economic losses in the swine industry. This study investigated an outbreak of Atypical Porcine Pestiv...
Since 2020, the outbreak of high pathogenicity avian influenza (HPAI) H5N1 virus clade 2.3.4.4b has turned into the largest documented panzootic . Here, we describe its arrival into the Indian Ocean sub-Antarctic archipelagos of Crozet and Kerguelen, where we first detected the virus in October 2024...
Reports of severe infections caused by Panton-Valentine leukocidin (PVL)-positive community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) are increasing. Pediatric infections caused by CA-MRSA, including in children without known risk factors, are on the rise worldwide. In recent ye...
Campylobacter is the leading cause of foodborne bacterial gastroenteritis globally. The cfr(C) gene encodes a 23S rRNA methyltransferase conferring cross-resistance to multiple classes of antibiotics. Here, we identified three novel cfr(C) variants in C. coli of swine origin. Compared to the origina...
The Enterobacter cloacae complex (ECC) are important nosocomial pathogens involved in hospital outbreaks. They present a significant challenge for accurate species identification, hindering outbreak detection and investigation. Nevertheless, many clinical laboratories report identification of these...
Klebsiella pneumoniae (Kp) is a major cause of bloodstream infections (BSI) globally. Yet, detailed characterization of invasive isolates, particularly from datasets not biased toward resistance, remains limited. This baseline study, conducted prior to the expansion of carbapenemase producers in Por...
The emergence of linezolid-resistant enterococci has become a significant global health concern. This study aimed to investigate the molecular characterization and resistance mechanisms in clinical isolates in a tertiary hospital in China. The VITEK®2 Compact system, VITEK® MS, and whole-genome sequ...
The etiologic pathogen is unknown for many pediatric community-acquired pneumonia (CAP) cases. We aimed to identify the causes of CAP of unknown etiology (CAP-UKN) using broad-panel targeted next-generation sequencing (tNGS). A prospective surveillance study was conducted across 26 hospitals in Kore...
Since its initial detection among men who have sex with men (MSM) in Nanjing, CRF119_0107 has rapidly emerged as the third most prevalent HIV-1 subtype. To elucidate its transmission dynamic, spatial characteristics, and the prevalence of transmitted drug resistance (TDR), we conducted a joint genom...
Pertussis (whooping cough), a highly contagious respiratory disease caused by Bordetella pertussis, has resurged worldwide and requires increased attention. This study aimed to characterize the molecular epidemiology and antimicrobial susceptibility profiles of B. pertussis isolates circulating in G...
The multidrug resistant NRCS-A clone of Staphylococcus capitis (SC) has spread globally in neonatal intensive care units (NICUs) where it causes neonatal sepsis and colonisation of infants, fomites and staff. Whole genome sequencing (WGS) of international isolates has suggested a putative origin of...
Drug-resistant remains a significant global public health threat. While whole-genome sequencing (WGS) holds immense promise for understanding transmission dynamics and drug resistance mechanisms, its integration into routine surveillance remains limited. Additionally, insights from WGS are increasi...
Whole-genome sequencing (WGS) is essential for monitoring the genetic diversity of influenza A virus (IAV) across host species. We optimized a multisegment RT-PCR (mRT-PCR) protocol to enhance amplification of all eight IAV segments using modified RT and PCR conditions. Additionally, we introduced a...
Bacterial infections pose a global health threat across clinical and community settings. Over the past decade, the alarming expansion of antimicrobial resistance (AMR) has progressively narrowed therapeutic options, particularly for healthcare-associated infections. This critical situation has been...
The spread of infectious diseases is shaped by spatial and temporal aspects, such as host population structure or changes in the transmission rate or number of infected individuals over time. These spatiotemporal dynamics are imprinted in the genomes of pathogens and can be recovered from those geno...
Community-acquired urinary tract infections (UTIs) are a significant health concern in older adults. However, few studies have investigated the epidemiology of uropathogens across diverse settings where older adults reside. In this study, we whole-genome sequenced urinary isolates of , species, and...
Limited information is available regarding the global molecular epidemiology of Serratia spp. with carbapenemases. We characterized carbapenemase-producing Serratia spp. (n = 56) using short read whole genome sequencing (WGS) obtained from global surveillance programs (2015-17). KPC (54%), VIM (16%)...
Avian influenza viruses (AIVs) represent an ongoing threat to global health due to their capacity for genetic evolution, zoonotic transmission, and pandemic emergence. This review highlights recent progress in understanding the molecular mechanisms underlying AIV infection, including viral immune ev...
Invasive cases of have been found in Europe, and beyond, and have been associated with the use of heater-cooler units necessary to regulate the temperature of blood in extracorporeal circulation during cardiac surgery, mostly due to contamination of patients by aerosol coming from the water in the...
New York City (NYC) was a major hotspot during the 2022 multi-country Mpox virus (MPXV) outbreak in the U.S. To investigate the genomic characteristics of MPXV in NYC, we sequenced 1138 specimens from 758 individuals using PrimalSeq and Illumina technology and performed phylogenomic analyses alongsi...
The Flaviviruses Dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), and Yellow Fever virus (YFV), are mosquito-borne viruses that represent a persistent challenge to global health due to the emergence and re-emergence of outbreaks of significant magnitudes. Their positive-sense RNA genom...
Antimicrobial resistance (AMR) in livestock represents a significant and growing One Health concern, with Escherichia coli acting as a major reservoir of resistance and virulence determinants. The present study analysed the whole-genome sequences of 172 E. coli strains of dairy cattle origin from 7...
Streptococcus pneumoniae (pneumococcus) is a major pathogen globally, responsible for an estimated one million deaths annually and contributing significantly to the global burden of antimicrobial resistance. Ongoing surveillance of its vaccine antigen (i.e. serotypes), antimicrobial resistance, and...
•A century-scale analysis of 208,000 + genomes reveals accelerating global antimicrobial resistance (AMR).•Multidrug-resistant outbreaks are rising worldwide, endangering food safety and public health systems.•Fluoroquinolone- and cephalosporin-resistant are WHO-prioritized threats, demanding gen...
During the COVID-19 pandemic, a significant increase in the spread of healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) was observed. , particularly carbapenem-resistant strains, poses a serious threat in intensive care units (ICUs). This study aimed to genetically character...
is a major zoonotic bacterial pathogen that causes a broad spectrum of human and animal diseases, including skin infections, sepsis, endocarditis, and bovine mastitis. In the geographically isolated setting of New Zealand, the population structure of exhibits a distinct genomic profile. Globally, b...
Carbapenem-resistant (CRPM), largely driven by dissemination of , poses a growing global threat, yet its phylogeographic and genetic patterns remain understudied. We analyzed 16 -harboring CRPM clinical isolates from a tertiary hospital in China (2017-2024) using antimicrobial susceptibility testin...
To analyze the molecular epidemiology of () isolates from bloodstream infections, and to investigate preliminarily the underlying mechanisms of fluconazole resistance. Clinical isolates were collected from bloodstream infections at West China Hospital, Sichuan University and other hospitals in Sic...
Enteroinvasive Escherichia coli (EIEC) is a diarrhoeagenic E. coli pathotype that shares key virulence traits with Shigella, including the invasion plasmid (pINV). In Thailand, an outbreak caused by the EIEC serotype O8:H19-the first reported in the country-occurred in 2023, affecting over 150 patie...
The COVID-19 pandemic has given us an unprecedented opportunity to study the clinical and molecular epidemiology of Streptococcus pneumoniae infections during this period, when its incidence was at its record low and started to rise again when social distancing restriction policies were lifted. A to...
is a nosocomial pathogen increasingly associated with multidrug resistance and hospital outbreaks. Despite its growing clinical relevance, no standardized core genome multilocus sequence typing (cgMLST) scheme has been available for high-resolution epidemiological analyses. Here, we developed and va...
Broad and unregulated antibiotic use in livestock production, particularly poultry farming, has increased the development and persistence of multidrug-resistant (MDR) bacterial strains in animals. These resistant pathogens and their antibiotic resistance genes (ARGs) can spread to humans through env...
To assess the homology of Escherichia coli between pregnant women and neonates and to identify the vertical transmission risk factors. Pregnant women in 35-37 gestational weeks who underwent prenatal checkups between May 1st, 2015, and April 30th, 2016 were screened for Escherichia coli. Paired swab...
The SARS-CoV-2 Omicron variant has exhibited a rapid progression around the world, but its molecular insights in North Africa remain understudied. This study characterizes the genetic diversity, dynamics, and evolutionary trends of the Omicron variant in Tunisia over a 33-month period (December 2021...
Carbapenem-resistant (CRPA) represents a critical-priority pathogen capable of causing life-threatening, multidrug-resistant infections. We performed susceptibility testing, whole-genome sequencing, and bioinformatic analyses on 137 CRPA isolates from a Guangdong hospital. We found that the major s...
Kyasanur Forest Disease Virus (KFDV) is a tick-borne flavivirus endemic to the Western Ghats region of India, with increasing reports of geographic expansion. This study employs phylogenetic analysis and spatial diffusion modeling to understand the evolutionary dynamics and transmission patterns of...
AHPN disease, caused by Vibrio parahaemolyticus, poses a significant threat to global shrimp farming. Here, we investigated the epidemiological relationships of the AHPND- causing Vp CGVP22, isolated from the 2016 AHPND outbreak in Pyeongtaek, Korea, through whole-genome sequencing (WGS). Initially...
Senegal has witnessed the emergence and spread of carbapenem-resistant (CRE), which often cause deadly infections. Accordingly, this study aimed to determine the antimicrobial susceptibility and prevalence of carbapenemases, as well as to perform a whole-genome sequence analysis of clinical CRE iso...
The Oropouche virus (OROV) is an arthropod-borne virus that causes an acute febrile illness, like other arboviral diseases. In 2024, Oropouche cases sharply increased in several countries of the Americas, including Bolivia. Here, we investigate the origin and spread of OROV in the Bolivian Amazon re...
Lumpy Skin Disease Virus (LSDV) is a transboundary pathogen that affects cattle, causing significant economic losses, particularly in Africa and Asia. While the virus was originally endemic to sub-Saharan Africa, it has rapidly spread to Europe, the Middle East, and Asia, necessitating comprehensive...
Monkeypox (Mpox) has reemerged globally, with thousands of confirmed cases reported in China. However, limited data exist on the genomic variations and transmission patterns of monkeypox virus (MPXV) in southwestern China. Clinical samples from Mpox cases and sewage samples from wastewater treatment...
Salmonella enterica serovar Paratyphi A (S. Paratyphi A) has emerged as a significant global health concern due to the progressive development of antimicrobial resistance and its broader geographic distribution. In Taiwan, paratyphoid fever was historically rare and predominantly associated with imp...
Enterotoxigenic (ETEC), a leading cause of diarrhea, is defined by heat-stable (ST) and/or heat-labile (LT) toxins and associated colonization factors (CFs). However, there is still a knowledge gap in understanding ETEC's evolution, particularly in endemic regions like Bangladesh. This study invest...
The effectiveness of travel restrictions in mitigating the spread of novel viral variants remains understudied, particularly in regions with sparse genomic surveillance. We evaluated the efficacy of these restrictions in Western Asia, where countries sequenced less than one percent of SARS-CoV-2 cas...
is a commensal bacterium that colonizes the gut of humans and animals and is a major opportunistic pathogen, known for causing multidrug-resistant healthcare-associated infections (HAIs). Its ability to thrive in diverse environments and disseminate antimicrobial resistance genes (ARGs) across ecolo...
Methicillin-resistant Staphylococcus aureus (MRSA) remains a global health threat, with livestock-associated (LA-)MRSA ST398/t011 emerging in regions with human-animal contact. This study reports the first detection of ST398/t011 in clinical isolates from Bojnurd, northeastern Iran, alongside the ho...
Ongoing viral evolution in immunocompromised individuals with persistent infection may facilitate the evolution of SARS-CoV-2 and emergence of variants of concern (VOC). This study was conducted in the Western Cape Province of South Africa where the HIV prevalence is around 8%, with limited informat...
The sub-Saharan African region bears the highest burden of rotavirus-associated morbidity and mortality, with substantial genetic diversity observed in circulating strains despite vaccine introduction. The G8 genotype, originally predominant in bovine strains, has increasingly become prevalent in hu...
As of September 2024, Mexico had reported over 7.6 million confirmed cases of COVID-19 and 334,785 deaths. Genomic surveillance has been essential, with 94,799 SARS-CoV-2 genomes sequenced nationwide, 38.5% by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex). Analyze the genomic diversi...
Antimicrobial resistance (AMR) in livestock production systems has emerged as a major global health concern, threatening not only animal welfare and agricultural productivity but also food safety and public health. The widespread, and often poorly regulated, use of antimicrobials for growth promotio...
The spread of monkeypox virus (Orthopoxvirus monkeypox) clade Ib from the Democratic Republic of the Congo to neighbouring countries has raised global concerns, leading to WHO declaring mpox a public health emergency on Aug 14, 2024. We applied genomic epidemiology to investigate the causes of recur...
In mid-2021, a global surge in cholera cases was reported. This study characterized Vibrio cholerae O1 isolates obtained from faecal samples of cholera-positive cases during the 2022 cholera outbreak in Kenya. A total of 202 V. cholerae were confirmed through serogroup and serotype characterization...
is an opportunistic pathogen, a member of the ESKAPE group, associated with nosocomial infections and foodborne illnesses due to its production of various toxins. This study conducted a comprehensive genomic characterization of isolates producing toxic shock syndrome toxin (TSST-1) using a comparat...
Whole genome sequencing (WGS) has emerged as a powerful tool to facilitate the study of existing and emerging infectious diseases. WGS-based genomic surveillance provides information on the genetic diversity and tracks the evolution of important viral pathogens, including respiratory syncytial virus...
End 2023, the UK Health Security Agency sent an alert about a new hypervirulent PCR ribotype, ribotype 955 (RT955), causing slowly progressing infection clusters in hospitals in the Midlands. Between March 2018 and February 2022, surveillance of infections (CDI) was performed in southern Serbia wi...
Recent evidence of vertical transmission of Tonate virus (TONV) during early pregnancy and its association with fetal neurological anomalies highlights its potential public health threat. TONV is an understudied alphavirus endemic to French Guiana. The growing presence of in Europe raises concerns...
Extended-spectrum beta-lactamases (ESBLs) producing Gram-negative bacteria are public health threats. This study aims to characterize ESBL-producing Gram-negative bacteria (GNB) isolated from surgical site infection patients. A multicenter cross-sectional study was conducted at four hospitals locate...
Data on the population-scale impact of dolutegravir (DTG)-based HIV regimens in sub-Saharan Africa are extremely limited. We used data from a surveillance cohort in southern Uganda to assess viral suppression and antiretroviral (ART) resistance over 10-years alongside DTG scale-up. Consenting partic...
In Cote d'Ivoire, the incidence rate of acute respiratory infections (ARIs) rose from 165 cases per 1000 children in 2014 to more than 200 cases per 1000 children in 2015. The genetic diversity, transmission dynamics, and epidemiology of human metapneumovirus (hMPV), a causative agent of ARIs, in Co...
To investigate the genetic diversity, evolutionary dynamics, and phylogeography of DENV strains circulating in Saudi Arabia. We conducted serotyping, whole-genome sequencing, and phylogeographic analyses of DENV strains collected across Saudi Arabia between 2021 and 2023. A total of 20 full genomes...
Conventional surveillance methods may miss healthcare-associated pathogen transmission, particularly for common, drug-susceptible organisms. It is unclear if prospective genomic analyses can help identify otherwise silent transmission events and inform prevention efforts. We sequenced methicillin-su...
The incidence of gonorrhoea has increased significantly in Norway over the past 10 years. The emergence of antimicrobial resistance and potential for increased rates of future treatment failure make epidemiological surveillance of a top priority. Here, we combine epidemiological data and genomic an...
emerged in Chicago, IL, USA, in 2016 and has since become endemic. We used whole-genome sequencing (WGS) of 494 isolates, epidemiologic metadata and patient transfer data to describe the transmission of among Chicago healthcare facilities between 2016 and 2021. In total, 99% of isolates formed a si...
Respiratory infection outbreaks pose a threat to the readiness of the United States and allied armed forces. Predicting and preventing such outbreaks requires understanding of the epidemiology of potential respiratory pathogens in communities where service members live and work. We conducted pan-vir...
remains a leading respiratory pathogen for children and the elderly. In Taiwan, a national PCV13 catch-up vaccination programme for children began in March 2013. This study investigates the population structure and antimicrobial profiles of pneumococcal isolates in Taiwan from 2006 to 2022. A total...
There are currently no standardized guidelines for genomic surveillance of One Health antimicrobial resistance (AMR). This project aimed to utilize metagenomics to identify AMR genes present in a companion animal hospital and compare these with phenotypic results from bacterial isolates from clinica...
In 2025, Pune, India, witnessed an unprecedented surge in Guillain-Barré Syndrome (GBS) cases, raising urgent public health concerns. GBS, a rare neurological condition often linked to infections, demanded immediate epidemiological and molecular scrutiny. Evidence from earlier studies points to infe...
Since the onset of the COVID-19 pandemic, the Republic of Korea has experienced continuous waves of SARS-CoV-2 variants. The current study aimed to analyze the long-term trends of variant prevalence and associated changes in immune responses within the country. Whole-genome sequencing was performed...
Colistin resistance in carbapenem-resistant (CRKP) poses a significant global health challenge, as colistin remains the last-resort antibiotic for treating multidrug-resistant infections. This study aimed to investigate the prevalence and molecular mechanisms underlying colistin resistance in CRKP...
Highly pathogenic avian influenza (HPAI) clade 2.3.4.4b H5Nx viruses are a major zoonotic concern. Clade 2.3.4.4b was first reported in India during the HPAI H5N8 outbreaks in zoological parks, in 2016. Recently, in June 2024, clade 2.3.4.4b HPAI H5N1 virus outbreaks were reported from Kerala. The g...
A comprehensive analysis of the molecular epidemiology of SARS-CoV-2 in the Kandy District of Sri Lanka from November 2020 to March 2022 was conducted to address the limited genomic surveillance data available across the country. The study investigated the circulating SARS-CoV-2 lineages, their temp...
A major cause of lameness in turkeys is reoviral arthritis, driven by turkey reovirus (TRV) infection. In the U.S., TRV was first isolated in the 1980s but re-emerged as a significant pathogen causing arthritis in 2011. Since then, TRV outbreaks have spread nationwide across turkey-producing regions...
: While enteroviruses (EVs) are recognized causes of diverse illnesses, little is known about the epidemiology and molecular characteristics of uncommon enterovirus C (EV-C) types, including EV-C104, EV-C105, and EV-C109. : We conducted genomic surveillance of EVs at the Johns Hopkins Health System...
Influenza B virus (IBV) contributes significantly to morbidity and mortality during Influenza seasons annually. However, IBV genomic surveillance occurs unevenly across the globe, particularly within the African region, obscuring its epidemiology. This study aims to elucidate the epidemiological dyn...
This study investigated the prevalence and genomic epidemiology of SARS-CoV-2 variants as part of the TQT-COVID-19 Project, which aimed to expand COVID-19 testing, quarantine, and telemonitoring strategies. A total of 177 samples were analyzed between July 2022 and April 2023 from patients of 17 Pri...
This systematic review, conducted according to PRISMA guidelines, provides a comprehensive synthesis of epidemiological data on Coxiella burnetii, the causative agent of Q fever, in humans and animals worldwide. A total of 1321 publications were identified, of which 166 met the inclusion criteria. Q...
This study aims to systematically investigate the molecular epidemiology and genomic characteristics of Enterobacter cloacae complex (ECC) strains globally harbouring bla and mcr, as well as the co-existence of drug resistance genes. The goal is to provide insights and recommendations for monitoring...
ESBL-producing Escherichia coli and Klebsiella pneumoniae are major causes of infections, including urinary tract, abdominal, nosocomial pneumonia, diabetic foot and bloodstream infections. This study examines trends in their prevalence, genotypes and antibiotic susceptibility and identifies at-risk...
Microbial whole genome sequencing (WGS)-based methods have replaced conventional methods for genomic relatedness analysis in the investigation of or surveillance for infectious outbreaks. Analysis of WGS by core genome multi-locus sequence typing (cgMLST) has been proposed for standardized strain co...
Dengue virus (DENV) remains a significant public health concern in Pakistan, with recurrent outbreaks necessitating continuous genomic surveillance. The 2024 dengue outbreak prompted an investigation into circulating serotypes and genomic diversity. The National Institute of Health (NIH), Pakistan,...
Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (ov...
Clostridioides difficile is the most common cause of health care-associated infections in the United States. The persistence of C difficile as a significant cause of morbidity and mortality is a testament to significant gaps remaining in our understanding of how and where it spreads, and pathways le...
infections can cause life-threatening meningitis and septicemia. In Europe, serogroup B (MenB) is the leading cause of invasive meningococcal disease (IMD), particularly in young children. Genomic surveillance of circulating MenB strains through whole genome sequencing (WGS) provides a powerful tool...
: Vancomycin-resistant (VREfm), particularly -positive strains, represents a growing threat in hospital settings worldwide. These bacteria are able to survive under severe environmental conditions, including high temperatures and saline concentrations. High genome plasticity and advanced ability of...
Pertussis, a highly contagious respiratory disease caused by Bordetella pertussis (BP), poses challenges due to genomic variation that may contribute to its persistence in vaccinated populations and the development of antimicrobial resistance. In this study, we characterized 27 BP isolates collected...
Core-genome multi-locus sequence typing (cgMLST) is a well-established and standardized method for genomics-based cluster detection and phylogenomic analysis of bacteria. The reduced error rate of Oxford Nanopore Technologies (ONT) R10 sequencing has prompted many laboratories to explore incorporati...
In August 1995, necropsies on post-weaning piglets from the CA-CART farm in the province of Cartago, Costa Rica, revealed respiratory lesions, pleuritis, peritonitis, and arthritis. Skin lesions were also observed, progressing to scabs. A subsequent outbreak in 1996 prompted antibiotic administratio...
is endemic among Enterobacterales in the USA. While present on diverse plasmids, burden is often associated with the clonal spread of multi-drug resistant (MDR) epidemic lineages. In this study we sought to determine the relative contributions of clonal spread and plasmid transfer to burden acro...
Bacterial species cultured from sputum change during treatment or observation for non-tuberculous mycobacterial pulmonary disease; however, strain-level changes remain unrecognized. Variable number tandem repeat typing is a standard technique for strain identification; nonetheless, its labor-intensi...
Duck enteritis virus (DEV) was identified as the etiological agent responsible for an outbreak of morbidity and mortality in adult ducks on a farm in Jiangsu, China. Diagnostic approaches confirmed that the outbreak was caused by the highly pathogenic DEV-JS2024 isolate. The clinical progression of...
In 2023-2024, measles cases progressively increased in Europe. Multiple outbreaks were reported and viral strains with three-nucleotide mutations potentially compromising diagnostic testing were identified. We analyzed the first cases of measles reported in Lazio (Central Italy) from September 2023...
Acute gastroenteritis (AGE) remains a significant global health concern, with noroviruses among the most prevalent viral pathogens. However, other enteric viruses also contribute substantially to the public health burden. This study provides the first molecular characterization of a co-infection inv...
The global emergence of multidrug- and pandrug-resistant poses a critical threat to public health, particularly in hospital settings. This study describes a nosocomial outbreak caused by in a tertiary-care hospital in Mexico and provides a comprehensive genomic analysis of six clinical isolates. A...
Salmonella Derby (S. Derby) is transmitted to humans through contaminated pork products. S. Derby ST40, with multidrug resistance (MDR) and extensive drug resistance, poses major food safety and public health challenges. By integrating antimicrobial susceptibility testing, phylogenetic analysis, phy...
is the most common cause of bacterial foodborne illness in the EU, primarily linked to poultry. To better understand its transmission dynamics, we applied whole-genome sequencing (WGS) to isolates collected at slaughterhouses over a two-year period from broilers originating from 26 Danish farms. Th...
The persistent evolution of SARS-CoV-2 highlights the crucial role of genomic surveillance in tracking emerging variants and guiding public health interventions. We performed whole-genome sequencing on 235 SARS-CoV-2-positive samples collected across Morocco between 2021 and 2024 to characterize vir...
Klebsiella pneumoniae is an opportunistic pathogen associated with nosocomial infections, known for its multidrug resistance (MDR) and biofilm-forming abilities. ST48 is a particularly concerning sequence type and an emerging international clone linked to global spread and MDR infections. This study...
Salmonella Enteritidis infections started to appear in fox farms in Finland in 2002, but it was not until 2014 when S. Enteritidis emerged on cattle and swine farms. S. Enteritidis is also a common finding from dead hedgehogs throughout the country. In this study, we used core genome multilocus sequ...
Bioaerosols are a major transmission route for respiratory infections. Metal oxide materials sterilize air via contact oxidation and reactive oxygen species (ROS). Bacteria rely on autocatalytic network for survival, where a single node change can impact the entire network. However, the bactericidal...
A series of transmission of Pseudomonas aeruginosa ST111 bla, previously undetected by standard surveillance, was discovered in a tertiary care hospital in Northern Germany through molecular genetic monitoring. Hence, environmental sampling was initiated to find the source of infection. First, routi...
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most prevalent bacterial pathogens leading to various kinds of infections, but the characteristics of this superbug with both strong biofilm-producing and intracellular invasive capabilities is rarely reported. This study aimed to inve...
Obtaining complete genomes of bacterial sexually transmitted infections (STIs) directly from clinical samples is challenging due to the presence of human DNA, microbiota, and very low bacterial pathogen loads. Culture is often not an option, as these species are fastidious, and most samples are take...
Lumpy skin disease virus (LSDV), a transboundary pathogen threatening cattle health in South and Southeast Asia, presents growing challenges for disease control. This study combined serological, molecular, and genomic approaches to investigate LSDV in Barura Upazila, Bangladesh. Serological screenin...
Myroides odoratimimus, a non-fermentative Gram-negative bacillus, has increasingly been recognized as a cause of opportunistic healthcare-associated infections, particularly in intensive care units (ICUs). Its intrinsic resistance to multiple antibiotic classes, including carbapenems, aminoglycoside...
African swine fever virus (ASFV) and classical swine fever virus (CSFV) are important transboundary animal diseases (TADs) affecting swine. ASFV is a large DNA virus with a genome size of 170-190+ kilobases (kB) belonging to the family , genus Asfivirus. CSFV is a single-stranded RNA virus with a ge...
Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021...
Carbapenemase-producing (CPEn) has globally emerged to be a severe threat to human health. However, the disease spectrum, impact on affected patients' outcomes, and transmission of CPEn are largely uncharacterized. We performed genome sequencing on a collection of CPEn clinical isolates spanning a...
The increasing zoonotic potential of highly pathogenic avian influenza (HPAI) H5N1 poses a growing threat to global public health. This review examines the molecular and evolutionary mechanisms facilitating H5N1 adaptation in mammalian hosts, focusing on genetic reassortment events, key mutations, a...
Equine influenza (EI) is a highly contagious viral respiratory disease affecting equids, with the potential of causing widespread outbreaks across Europe, the Americas, Asia, and other regions of the world. In Tunisia, in the spring of 2021, an EI virus outbreak occurred in a farm housing purebred A...
The emergence of the Omicron variant in November 2021 marked a significant turning point in the COVID-19 pandemic due to its unprecedented number of mutations compared to previous variants. To better understand its clinical impact and evolutionary trajectory, we conducted a comprehensive genomic epi...
Antimicrobial resistance is an emerging threat, with carbapenemase-producing Enterobacterales (CPE) and vancomycin-resistant enterococci (VRE) posing substantial challenges. This study investigated CPE/VRE acquisition and spread in hospitalized patients by analysing resistance genes and microbiomes...
In Brazil, molecular surveillance expanded after Rotarix™ vaccine introduction, alongside G2P[4] dominance. The G2P[6] genotype, despite sharing the same DS-1-like constellation as G2P[4] strains, remains rare. This retrospective study analyzed eight Brazilian G2P[6] strains (2012-2014) through RT-P...
, the causative agent of plague, has triggered multiple pandemics throughout human history, yet its long-term evolutionary patterns and reservoir dynamics remain poorly understood. Here, we present a global phylogenomic analysis of ancient and modern strains spanning from the Neolithic and Bronze A...
Cystic Fibrosis (CF) Centers worldwide have reported healthcare-associated outbreaks of nontuberculous mycobacteria (NTM). We report a retrospective investigation of shared Mycobacterium abscessus strains among people with cystic fibrosis (pwCF) receiving care at Dell Children's/Ascension combined P...
The highly pathogenic avian influenza H5N1 2.3.4.4b clade virus has caused widespread outbreaks across South America, primarily affecting seabirds, poultry, and marine mammals. The virus likely reached the continent through migratory birds from North America, initially spreading along the Pacific co...
Carbapenem-resistant (CRKP) poses a major threat to global health. The co-production of multiple carbapenemases has emerged as a critical concern, further limiting the effectiveness of last-resort antibiotics such as ceftazidime-avibactam. This study identifies an IncP6 plasmid co-harboring both...
The first PPR outbreak in Greece was laboratory confirmed in the region of Thessaly on the 11th of July 2024. A total of 86 farms in multiple regions were infected and no additional outbreaks have been reported in Greece since 1st of November 2024. To assess the origin of PPRV identified in Greece,...
A quantitative understanding of local transmission dynamics is essential for designing effective prevention strategies. In this study, we developed a computational workflow to identify viral introductions and trace locally circulating clusters. We analyzed over 26,000 SARS-CoV-2 genomes and their as...
Infections caused by KPC-producing Klebsiella pneumoniae (KPC-KP) represent a persistent public health challenge. This prospective study examines ten-year trends, clinical features, and genomic epidemiology of hospital-onset (HOI) and non-hospital-onset (non-HOI, including healthcare-associated [HcA...
While a global downward trend in rotavirus diarrhea cases has been observed following vaccine introduction, reassortment, genetic drift, and vaccine-escaping strains remain a concern, particularly in Sub-Saharan Africa. Here, we provide genomic insights into three equine-like G3P[8] rotavirus strain...
The COVID-19 pandemic has severely impacted Bolivia due to its high social vulnerability and limited healthcare resources. In response to the limited local capacity for genomic surveillance during the pandemic, we characterized the genetic diversity and geographic distribution of SARS-CoV-2 variants...
(former name: ) is the second most common cause of vulvovaginal candidiasis (VVC), but its molecular epidemiology and antifungal resistance in China remain poorly understood. This study analysed 204 isolates from VVC patients in Suzhou, Eastern China, using multi-locus sequence typing (MLST) and mi...
Histoplasmosis, the disease caused by thermally dimorphic fungi in the genus , is usually associated with pulmonary involvement in healthy individuals and a disseminated syndrome in immunocompromised patients. Among African patients, lung disease is less commonly reported than skin, lymph node, or b...
Vancomycin-resistant (VRE) poses a global public health threat, with particularly severe ramifications in low-resource settings. While is commonly a commensal organism in the human gut, the acquisition of vancomycin resistance has contributed to the emergence of VRE as a major cause of hospital-ac...
Past reports of nosocomial outbreak due to human rhinovirus (HRV) in adults are limited. We report a case of nosocomial outbreak of HRV-A34 in a long-term care facility with a literature review. Multiplex real-time polymerase chain reaction assay (Allplex™ RV Essential Assay) was used for the detect...
To evaluate the effect of the selective pressure exerted by nirsevimab on human respiratory syncytial virus (HRSV) in Catalonia (2023-2024) by analysing viral mutations, diversity, and evolutionary dynamics, based on viruses characterised from non-immunised and previously immunised patients. Respira...
In December 2024, human metapneumovirus (hMPV) gained global attention amid rising cases in Chinese hospitals, prompting a World Health, Organization (WHO) statement indicating case numbers remained within expected ranges. To assess whether a variant of public health concern was emerging and to exam...
Multidrug resistance in Pseudomonas aeruginosa, particularly resistance to carbapenem, represents a major challenge for public health. This study investigated resistance mechanisms in three P. aeruginosa isolates: HU63 (blaGES-6 carbapenemase-positive), HU141 (carbapenem-resistant without carbapenem...
The repeated occurrence of SARS-CoV-2 variants, largely driven by virus-host interactions, was and will remain a public health concern. Spike protein mutations shaped viral infectivity, transmissibility, and immune escape. From February 2022 to April 2024, a local genomic surveillance program in Ver...
Next-generation sequencing (NGS) has the potential to transform mosquito-borne disease surveillance but remains under-utilised. This study introduces a comprehensive multi-loci metabarcoding-based MX (molecular xenomonitoring) approach to mosquito and arbovirus surveillance, enabling parallel identi...
Pseudomonas aeruginosa is frequently responsible for hospital-acquired infections. It may be isolated in healthcare environment where it can survive. Between January 2018 and June 2024, a growing number of VIM-producing Pseudomonas aeruginosa (PA-VIM) were isolated from patients hospitalized in our...
Porcine reproductive and respiratory syndrome (PRRS) is a global challenge for swine production. Due to its high variability and limited cross-protection, immune-based control measures are only partially effective, emphasizing the critical role of biosecurity. A prior study on Italy's largest integr...
We report the emergence and evolution of a circulating vaccine-derived poliovirus type 1 (cVDPV1) outbreak in Israel, linked to a vaccine-associated paralytic poliomyelitis case. Whole genome sequencing revealed a strong genetic link between the Sabin-like poliovirus type 1 variant from the case and...
The global spread of SARS-CoV-2 was significantly impacted by the emergence of Variants of Concern (VOC), with Pakistan experiencing similar trends to other countries. To gain a comprehensive understanding of the genomic epidemiology of SARS-CoV-2 strains circulating during Pakistan's third and four...
Candida tropicalis is a clinically significant non-albicans species that has shown increasing azole resistance globally. Despite its growing clinical importance, genotypic and epidemiological data from East Asia, particularly Korea, remain limited. This study aimed to expand the global understanding...
Carbapenems are broad-spectrum antibiotics that are losing effectiveness against infections caused by multidrug-resistant that have acquired carbapenemase genes. The New Delhi metallo--lactamase ( ) is one of the most common carbapenemases in Canada and around the globe. These genes are frequently...
Human respiratory syncytial virus (HRSV), a leading cause of paediatric respiratory infections, is a major contributor to global childhood morbidity. The primary objective of this study was to investigate the epidemiology and phylogenetic characterization of HRSV in paediatric severe acute respirato...
Collaborative genomic and epidemiological investigations identified a tuberculosis outbreak in Vienna as part of a multi-country cluster comprising 57 foreign-born cases of ST215/Beijing 2.2.1 notified 2021-2025. While 14 of 16 cases in Vienna were considered autochthonous, the diverse geographic o...
We sequenced sarbecovirus from Rhinolophus spp. bats in Bandarban District, Bangladesh, in a genomic surveillance campaign during 2022-2023. Sequences shared identity with SARS-CoV-1 Tor2, which caused an outbreak of human illnesses in 2003. Describing the genetic diversity and zoonotic potential of...
Flood-related waterborne diseases are an acute consequence of natural disasters, primarily due to contamination of drinking water supplies. With climate change driving an increase in extreme weather events, such as floods, the risk of waterborne disease outbreak is expected to rise. This report summ...
The Plague of Justinian marked the beginning of the First Pandemic (541-750 CE), yet no genomic evidence of has previously been recovered from the Eastern Mediterranean, where the outbreak was first recorded. This study aimed to determine whether was present in a mid-6th to early 7th century mass...
Typhoid fever results from systemic infection with serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial resistant (AMR) Typhi lineages h...
The emergence of multidrug-resistant (MDR) plasmids poses a significant global public health threat. This study characterized a novel multi-replicon IncN-R MDR plasmid pCUVET19-1426.1, harboring and 12 additional antimicrobial resistance genes (ARGs) in a newly identified sequence type 13037, isol...
Multidrug-resistant continues to challenge healthcare services globally. However, our understanding of its occurrence, genomic characteristics, and epidemiology in low- and middle-income countries (LMICs) remains severely limited. In this study, we report the whole-genome sequencing of an extended-...
Vancomycin-resistant Enterococcus faecium (VREfm) is a significant cause of hospital-acquired infections due to its multidrug resistance, environmental persistence, and high transmissibility. This study aimed to characterize clinical and surveillance VREfm isolates by examining antimicrobial resista...
Persistent SARS-CoV-2 infections in hospitalised immunocompromised individuals are known to facilitate accelerated within-host viral evolution, potentially contributing to the emergence of highly divergent variants. However, little is known about the evolutionary dynamics and transmission risks of p...
Carbapenemase-producing Enterobacterales (CPE) pose a major healthcare challenge. We report the first hospital outbreak of Pseudocitrobacter faecalis carrying blaNDM-1 using an omics-based approach. Short- and long-read sequencing enabled genomic epidemiological investigation to track its spread, ch...
Monkeypox is an emerging infectious disease of unclear zoonotic origin in Africa although increasing evidence suggests that rope squirrels are reservoirs of the monkeypox virus (MPXV). Here, we describe new data on the systematics of rope squirrels (Sciuridae, ). Our molecular phylogeny strongly sup...
Influenza A virus (IAV) remains a global public health concern, causing influenza-like illness and severe respiratory tract infections. Two major subtypes, A/pdm09 H1N1 and A/H3N2, circulate globally, and their epidemics are influenced by multiple factors, especially during the COVID-19 pandemic. Ba...
Hospital environments are critical yet underexamined reservoirs for hazardous antimicrobial resistance (AMR), particularly in lower-middle-income countries (LMICs) where resource constraints often hinder comprehensive surveillance. In this study, we employed 16S rRNA gene sequencing and shotgun meta...
Wastewater-based genomic surveillance is a cost-effective approach for tracking outbreaks like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A 2023 study in Addis Ababa, Ethiopia, revealed two infection waves in March and August, with the latter undetected by clinical surveillance. T...
Molecular fingerprinting analyses of the pathogens isolated from healthcare-associated infections (HAIs) in an off-outbreak period can provide important data which cannot be obtained by prospective surveillance. Such data may indicate unnoticed breaks in infection control measures and guide in deter...
The Crimean-Congo hemorrhagic fever virus (CCHFV) is a single-stranded, segmented RNA virus belonging to the family, and it is rapidly expanding across Africa, Asia, and southern Europe, probably favored by climate change and livestock trade. Its fatality rate in humans reaches up to 40%, and there...
Human respiratory syncytial virus (hRSV) is a one of major cause of severe acute respiratory infection (SARI) in young children and the elderly. Because genomic surveillance of hRSV is essential to understand viral evolution and the genetic variation that may affect transmissibility and pathogenicit...
Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasingly been used for population-scale monitoring of pathogen dynamics, including in low-resource setti...
A collaborative effort by the National Institute of Health, Pakistan and the World Health Organization initiated RSV surveillance in children under 2 years old in 2019 in Pakistan. This study aimed to characterise RSV disease, assess genetic diversity of circulating subtypes, and reconstruct the evo...
Arbovirus transmission by mosquitoes remains a major global health concern. A clearer understanding of the molecular mechanisms enabling mosquitoes to acquire and transmit these pathogens (i.e., their vector competence) is crucial for developing more effective control strategies. This review focuses...
is a major human nosocomial pathogen. Due to this, a significant amount of knowledge has been gained about human clinical isolates over a substantial period of time. More recently, studies have begun to pay attention to non-human isolates of . In reviewing these studies, we highlight some major tren...
Non-typhoidal Salmonella is a globally important bacterial pathogen, typically associated with foodborne gastrointestinal infection. Some non-typhoidal Salmonella serovars can also colonise typically sterile sites in people to cause invasive non-typhoidal Salmonella disease. Salmonella enterica sero...
A notable increase in the incidence of vancomycin-resistant (VREfm) was observed at a hospital in Guangzhou, China, during 2022-2023. We conducted a retrospective cross-sectional study from January 1, 2022, to August 31, 2023, to investigate the clinical and genomic characteristics of VREfm. Clinic...
Multidrug resistant Acinetobacter baumannii remains a global concern with its ability to adhere, disperse and sustain in areas involving suboptimal infection control measures, particularly in war areas. In this study we aimed to evaluate the susceptibility profiles, molecular epidemiology and pathog...
West Nile virus (WNV) is a priority pathogen that poses a high risk for public health emergencies of global concern. Although WNV is endemic to Africa, only few (n=63) whole genomic sequences are available from the continent. In this Review, we examined the status of the molecular testing and genomi...
: , an environmental bacterium, is increasingly recognized as an emerging nosocomial pathogen, particularly in Asia, and is often characterized by multidrug resistance. : This study aimed to investigate the genomic features of clinical isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand, to...
Genomic characteristics and optimal treatment of remain largely unknown. We collected clinical information and performed whole-genome sequencing analysis of the causative strains of six cases of infection at a single hospital over a 9-year period. Additionally, whole-genome sequencing analysis was...
Understanding how pathogens adapt to new hosts is critical to elucidating the evolutionary mechanisms driving disease emergence. This study investigates the evolutionary dynamics of Ostreid herpesvirus 1 (OsHV-1) in two host species-the Pacific oyster Magallana gigas and the European flat oyster Ost...
The COVID-19 pandemic highlighted the urgent need for genomic surveillance to monitor viral evolution and guide public health responses, especially in limited-resource settings. This study describes the establishment and implementation of a SARS-CoV-2 genomic surveillance system by Pasteur Institute...
is a multidrug-resistant (MDR) zoonotic pathogen increasingly implicated in infections in both humans and animals, including avian species. Raptors, particularly peregrine falcons, are vulnerable due to their exposure to diverse environments and intensive management practices. This study aimed to id...
In 2022, consecutive sweeps of highly transmissible SARS-CoV-2 Omicron-derived lineages (B.1.1.529*) maintained viral transmission despite extensive antigen exposure from both vaccinations and infections. To better understand Omicron variant emergence in the context of the dynamic fitness landscape...
Acute gastroenteritis remains a leading cause of morbidity in children under 5 in Pakistan, with rotavirus group A as a major pathogen. The contribution of norovirus is less understood. In 2023, we analyzed stool samples from 248 rotavirus group A-negative pediatric patients hospitalized with acute...
Strangles (Streptococcus equi infection) remains endemic in the UK, with ~300 laboratory diagnoses annually. Sub-clinically infected long-term carriers are considered a key driver of endemicity. Analysing genomes of circulating strains could provide valuable transmission insights of this pathogen. T...
Among the Chlamydia species known to infect snakes, C. serpentis is a recently described pathogen. A first outbreak of C. serpentis in the snake collection of a zoological institution was documented in 2018. In 2023, a wild-caught asp viper (Vipera aspis) tested positive by PCR for C. serpentis, fol...
There is growing concern regarding biofilm-producing methicillin-resistant Staphylococcus aureus (MRSA) due to the sudden rise in infection rates and associated morbidity and mortality. Therefore, epidemiological studies, including molecular typing and correlation analysis, are essential for underst...
The coronavirus disease 2019 (COVID-19) pandemic has highlighted the importance of genomic surveillance and whole genome sequencing (WGS) for identifying mutations and supporting epidemiologic investigations. Healthcare workers (HCWs) face unique risks for COVID-19, potentially amplifying outbreaks...
Unlike genomic data, serological data have not been previously leveraged to evaluate the SARS-CoV-2 variants circulation. In Bolivia, sustained genomic surveillance capacities were lacking, especially at the beginning of the pandemic. In 2021 and 2022 we estimated the prevalence of anti-SARS-CoV-2 a...
In this work, we present an optimized nanopore long-read only sequencing workflow for epidemiologic analysis of clonal outbreaks built with open-source tools. A set of unrelated clinical isolates ( = 10) was chosen for workflow optimization, and sequencing libraries were prepared using a modified r...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a growing threat in Greek hospitals, with increasing reports of multidrug- and pandrug-resistant strains; however, molecular data from regional centers remain limited. This study aimed to investigate the molecular epidemiology, resistance mecha...
In Ukraine, SARS-CoV-2 detection and national genomic surveillance have been complicated by full-scale war, limited resources, and varying levels of public health infrastructure impacted across the country. Following the Spring of 2022, only a paucity of data have been reported describing the preval...
is a highly adaptable opportunistic pathogen with significant clinical relevance in both human and veterinary medicine. Despite its well-documented role in hospital-acquired infections in human healthcare settings, its persistence and transmission within veterinary clinics remain underexplored. This...
The primary objective of this study was to determine if DNA sequences of the mitochondrial (mt) cytochrome oxidase c subunit 1 gene (cox1) and/or the mt 16S ribosomal RNA (rRNA) gene can be used to study the population genetics and phylogeography of the American dog tick, Dermacentor variabilis (Say...
This study aimed to investigate the molecular characteristics of predominant epidemic clusters of FC428-like N. gonorrhoeae in Guangdong, China in 2022. Minimum inhibitory concentrations (MICs) were determined for N. gonorrhoeae isolates collected from the Guangdong Gonococcal Antimicrobial Surveill...
Carbapenemase-producing Citrobacter (CPC) species have recently been recognised as emerging pathogens associated with nosocomial infections in humans. The increased rate of Citrobacter freundii infections is a public health concern and there is a paucity of genomic data regarding its global transmis...
Recent Monkeypox virus (MPXV) outbreaks in non-endemic regions have highlighted the need for genomic surveillance to support epidemiological investigations and monitor viral evolution. In this paper we present the results of genomic characterization and analyses of mechanisms of human adaptation, in...
Monkeypox, a zoonotic illness caused by the Monkeypox virus (MPXV), is a re-emerging disease that has resurfaced as a prominent global public health issue in the 21st century. The 2022 outbreak, previously limited to Central and West Africa, exhibited extraordinary global dissemination, prompting cr...
Many developing countries in Africa and Asia are hotspots and endemic for cholera. Over the past five years, these countries have had steady rises in the incidence of cholera, with case fatality ratios continuously exceeding the WHO recommendation of 1 %. Despite this, there aren't many non-outbreak...
Human adenoviruses (HAdV) comprises a genetically diverse group of double-stranded DNA viruses strongly associated with influenza-like illness (ILI) and acute respiratory illnesses (ARI) outbreaks. This study aimed to elucidate the molecular characteristics of HAdV implicated during ILI outbreaks in...
The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa represents a significant challenge in managing nosocomial infections, particularly in vulnerable populations such as burn patients. This study provides genomic and molecular characterization of MDR...
In this 4-month-long prospective observational study, we explored the colonization rate of extended-spectrum β-lactamase-producing (ESBL-EC) in the patient and ward environment of an intensive care unit (ICU). Additionally, we evaluated the risk factors for colonization and analyzed genomic charact...
Computational multi-scale pandemic modelling remains a major and timely challenge. Here we identify specific requirements for a new class of models simulating pandemics across three scales: (1) pathogen evolution, often punctuated by the rapid emergence of new variants, (2) human interactions within...
is listed by the World Health Organization as an emerging bacterial priority pathogen, the prevalence and multidrug resistance of which have been increasing. This functional genomics study aimed to understand the drug-resistance mechanisms of an extensively drug-resistant (XDR) strain (IRMCBCU95U)...
A prolonged tuberculosis outbreak, linked by whole-genome sequencing, occurred in a Pasifika extended family over 10 years (2013-2022) in Sydney, Australia. Despite Australia's low tuberculosis incidence, social and cultural complexities, and coronavirus disease 2019 (COVID-19) disruptions exacerbat...
Despite the global public health threat posed by carbapenem-resistant Enterobacter spp, clinical and molecular epidemiological studies on international isolates remain scarce. Historically, the taxonomy of Enterobacter has been challenging, limiting our understanding of the clinical characteristics...
Fire blight, a devastating bacterial disease affecting rosaceous plants such as apples and pears, is caused by . The disease, known for its rapid spread and destructive potential, can lead to severe symptoms and often result in the death of infected plants. In Korea, was first recorded in 2015, and...
Categorized as a critical priority pathogen by the World Health Organization (WHO), carbapenem-resistant (CRAB) is a leading cause of healthcare-associated infections (HAIs) worldwide. Although the environmental spread of healthcare-acquired strains through hospital wastewater and urban sewage has...
In 2022, the presumption of monkeypox (mpox) to be of limited epidemiology shifted when a global outbreak was announced. Being a member of the Orthopoxvirus genus in the Poxviridae family, it'd been reported in over 82 countries with over 17 000 confirmed cases by July 2022, thus showing its capabil...
Microgravity, pressure, and temperature variations in the International Space Station (ISS) create conditions leading to the emergence of superbugs. Due to technical issues in spacecraft, astronauts are forced to stay in ISS for extended periods; prolonged stay and exposure in stressful ISS environm...
Urinary tract infections (UTIs), primarily caused by Escherichia coli, pose a global health challenge owing to rising antimicrobial resistance (AMR), particularly carbapenem-resistant (Carb-RT) and extended-spectrum beta-lactamase (ESBL)-producing uropathogenic E. coli (UPEC). This study analyzed AM...
Multidrug-resistant (MDR) Acinetobacter baumannii is a major cause of healthcare-associated infections, which showed a significant increase during the SARS-CoV-2 pandemic, particularly in intensive care units (ICUs). The spread of A. baumannii in these environments is facilitated by contact with con...
Avian metapneumovirus subtype B (aMPV/B) is an economically significant pathogen in poultry, causing respiratory and reproductive disorders. In this study, 167 clinical samples were collected from commercial poultry farms across Thailand to investigate the prevalence, genetic diversity, and evolutio...
While evidence supports co-evolution between Mycobacterium tuberculosis and humans, underlying mechanisms remain unclear. We identified PPE50 as a novel subfamily of PE/PPE proteins comprising eight variants. Surveying 387 M. tuberculosis complex (MTBC) strains representing global phylogeography, we...
Orthohantavirus hantanense (HTNV), a major cause of hemorrhagic fever with renal syndrome (HFRS), remains a public health concern in East Asia. We investigated its evolutionary history, reassortment, and genetic diversity by analyzing 123 complete genomes from the Republic of Korea (1976-2023), comp...
Appropriate antibiotic therapy in patients with carbapenem-resistant (CRKp) infections often requires knowledge of resistance mechanisms. Therefore, we aimed to define the clonal diversity, mechanisms of carbapenem resistance, potential for carbapenem resistance transmissibility, virulence gene rep...
The prevalence of carbapenemase-producing Klebsiella pneumoniae increased significantly during COVID-19 in Argentina, rising from 20 % in 2019 to 30 % in 2021. Additionally, there was a notable increase of K. pneumoniae ST307 co-producing KPC and NDM. We aimed to reveal the genetic structure of the...
Rapidly evolving viral pathogens such as SARS-CoV-2 continuously accumulate amino acid changes, some of which affect transmissibility, virulence or improve the virus' ability to escape host immunity. Since the beginning of the SARS-CoV-2 pandemic, multiple lineages with concerning phenotypic alterat...
In early 2024, an outbreak of acute hemorrhagic conjunctivitis occurred in Mayotte and in Madagascar, two islands in the Indian Ocean. Real-time diagnosis and genotyping identified a different lineage of coxsackievirus A24 variant (CVA24v) from the current Asian outbreak. Although no recombination e...
is a major nosocomial pathogen worldwide and, specifically, in Latin America. Genomic epidemiology has been instrumental in determining the transmission dynamics of in many countries of the world, yet some Latin American countries have conducted no genomic epidemiology studies. Here, we conduct the...
Aedes albopictus mosquitoes are key vectors for arboviruses such as Dengue virus, Zika virus, and Chikungunya virus, posing significant global public health risks. Guangdong Province, a densely populated subtropical region in southern China, has experienced recurrent outbreaks of mosquito-borne dise...
Yersinia enterocolitica is a significant foodborne pathogen causing gastrointestinal illnesses worldwide. This study investigates the prevalence and genomic characteristics of Y. enterocolitica to assess potential health risks in southeastern China, a region lacking mandatory yersiniosis monitoring....
The locus of gram-negative bacteria encodes penicillin-binding protein 3 (PBP3), a common target of β-lactam antibiotics. Recent genomic surveillance of carbapenem-resistant revealed that 17% of strains possessed nonsynonymous substitution in . However, the contribution of nonsynonymous substitut...
The growing threat of emerging infectious diseases necessitates proactive genomic surveillance, particularly, in regions with limited resources and low levels of existing reporting. This study highlights the implementation of a comprehensive genomic surveillance program at the Kigali International A...
To study the risk factors and the molecular epidemiology characteristics for Carbapenem-resistant Enterobacteriaceae(CRE) colonization in neonatal inpatients in Shenzhen region, China, which provide reference for the prevention and control of clinical CRE infection. This study is a prospective case...
The potential for aerosol generation during bronchoscopy to facilitate the transmission of multidrug-resistant bacteria remains incompletely understood. This study aimed to assess the risk of carbapenem-resistant Klebsiella pneumoniae (CRKP) transmission via aerosols during bronchoscopy in an intens...
Clade I monkeypox virus is endemic in DR Congo. We aim to describe the epidemiological trends of the cocirculating subclades Ia and Ib mpox outbreaks in Kinshasa, DR Congo. This retrospective observational study included suspected and laboratory-confirmed mpox cases reported between Jan 1, 2023, and...
The El Tor biotype of caused the seventh cholera pandemic (7CP). Although variants of this biotype frequently emerge, studies on their microevolution and spatiotemporal transmission in epidemics caused by a single clone are limited. During the cholera outbreak in Sichuan Province, China, in the 19...
Since the creation of the Global Polio Eradication Initiative (GPEI) in 1988, significant progress has been made toward attaining a poliovirus-free world. This has resulted in the eradication of wild poliovirus (WPV) serotypes two (WPV2) and three (WPV3) and limited transmission of serotype one (WPV...
Tuberculosis (TB), particularly extremely drug-resistant TB (EDR-TB), remains a significant public health concern worldwide. Understanding the transmission patterns and epidemiological characteristics of EDR-TB is vital for effective disease control. Between 1 January 2006 and 31 December 2018, we c...
The bovine mastitis caused by Klebsiella pneumoniae (K. pneumoniae) infection, lead to high death rate and severe economic loss. Currently, the regional epidemiological characteristics of K. pneumoniae in China are still unclear, especially the surveillance data on prevalence of extended-spectrum β-...
Highly pathogenic avian influenza (HPAI) H5N1, particularly clade 2.3.4.4b, has demonstrated an unprecedented capacity for cross-species transmission, with recent reports confirming its presence in dairy cattle in the United States of America (USA) in 2024. This unexpected spillover challenges tradi...
Clostridioides (Clostridium) difficile transmission between community and healthcare settings has been increasingly reported. We aimed to identify the prevalence and molecular epidemiology of C. difficile colonising adolescents and non-hospitalised children in Cambodia. Stool samples were collected...
The ability of multiple bat species to host zoonotic pathogens without often showing disease has fostered a growing interest in bat immunology to discover the ways immune systems may differ between bats and other vertebrates. However, interspecific variation in immunological diversity among bats has...
Multidrug-resistant (MDR) ESBL-producing K. pneumoniae is widely implicated in community and hospital-acquired infections. Thus, the current study determined the prevalence and clonal relatedness of MDR K. pneumoniae from hospital environments, patients and healthcare workers in a Ghanaian hospital....
Hospital wastewater represents a significant reservoir for antimicrobial-resistant bacteria, including multidrug-resistant (MDR) Bacillus cereus, a pathogen of growing concern due to its potential impact on public health and environmental safety. This study characterizes the genomic features, antimi...
Autopsy workers are known to be at risk of contracting various infectious diseases from dead bodies. However, infections caused by group A Streptococcus (GAS, Streptococcus pyogenes) are rarely reported and often overlooked despite their potential severity. GAS infections can lead to serious complic...
Cholera is an acute diarrhoeal disease caused by . It remains a major public health challenge worldwide, and particularly in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates and spreads in global pandemic waves. However, it remains unclear to wha...
In September 2024, a school-aged child (P1), unvaccinated against diphtheria, was hospitalised with severe respiratory diphtheria caused by toxigenic P1 subsequently died from the disease. The child's mother (P2) had pharyngitis 9 days before the onset of symptoms of P1 and subsequently tested posi...
During the COVID-19 pandemic, next-generation sequencing (NGS) has been instrumental for public health laboratories in tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations and informing responses. Illumina systems and Oxford Nanopore Technologies (ONT) have been primary to...
is a leading pathogen in terms of deaths attributable to or associated with antimicrobial resistance globally. Thus, monitoring antibiotic resistance determinants constitutes a key aspect of surveillance efforts for this microbe. Leveraging publicly available whole-genome sequencing (WGS) data, we a...
K. oxytoca generally has a benign susceptibility profile and low virulence but can cause invasive infections in vulnerable populations, like preterm infants. We aim to describe how whole-genome sequencing (WGS) was used to inform management of a prolonged K. oxytoca outbreak on a neonatal intensive...
We investigated the molecular epidemiology of Vibrio cholerae O1 in Fujian Province, China, during 2009--2023. Sequence type (ST) 75 clonal complex has emerged continuously since 2020, and ST1480 and ST182 have dominated. ST1480 strains appear to have widespread transmission. To monitor V. cholerae...
We analyzed whole-genome sequences of Salmonella enterica serovar Enteritidis isolates in South Korea that had the SEGX01.049 pulsed-field gel electrophoresis pattern. That lineage has emerged and circulated in South Korea since 2020, leading to 2 fatal infection cases. We investigated the genomic c...
Expansion of carbapenemase-producing Klebsiella pneumoniae (CP-Kp) is driven by within-hospital transmission, requiring timely typing data for effective infection control. We evaluated real-time performance and flexibility of our previously developed Fourier-transform infrared (FT-IR) spectroscopy w...
Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic...
In New Zealand, OXA-48-producing Escherichia coli is uncommon and typically associated with international travel. We investigated a cluster of 25 patients without recent travel history from Hutt Valley health district, New Zealand, who had multilocus sequence type 131 OXA-48-producing E. coli during...
To investigate the epidemiology and molecular typing of 307 clinical Wickerhamomyces anomalus isolates collected in China. A total of 307 W. anomalus isolates were collected from CHIF-NET, a surveillance network with nationwide coverage, from 2009 to 2021. Antifungal susceptibility of all W. anomalu...
Enteritidis (SE) cases in humans have increased in the Netherlands, from an annual average of 281 (2017-2019) to 427 in 2023, 401 in 2024 and 209 in 2025 (January-June). This rise is paralleled by a 2.5-fold increase in SE-positive laying hen flocks. Genomic surveillance shows numerous small cluster...
is a leading cause of bovine mastitis, resulting in large economic losses and welfare issues for affected cows. However, relatively little is known about the global distribution and emergence of bovine mastitis-causing lineages and dissemination of antimicrobial resistance or virulence genes in the...
Methicillin-resistant (MRSA) represents a significant public health challenge. In New Zealand, the community-associated MRSA sequence type (ST)5, carrying the staphylococcal cassette chromosome (SCC) type IV genetic element (which confers methicillin resistance), has been predominant since its det...
, a clinically significant pathogen, causes invasive diseases in children and older adults. Pneumococcal conjugate vaccines (PCVs) have substantially reduced the incidence of vaccine serotype (VT) pneumococcal diseases. However, serotype replacement, characterized by the emergence of non-vaccine ser...
In March 2024, the French genomic surveillance of enteric yersiniosis identified a cluster of lineage 2/3-9b isolates, corresponding to bioserotype 2/O:9. An outbreak investigation was conducted to identify the source and implement control measures. A total of 175 confirmed cases were identified in...
Hantaviruses are zoonotic RNA viruses that cause hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome, posing significant public health risks. This study reports the identification and genomic characterization of Ulleung virus (ULLEV), a newly discovered genetic lineage of O...
Given that influenza vaccine effectiveness depends on a good antigenic match between the vaccine and circulating viruses, it is important to assess the antigenic properties of newly emerging variants continuously. With the increasing application of real-time pathogen genomic surveillance, a key ques...
We sequenced Leishmania tropica genomes from 8 human skin samples collected in a newly emerging focus of cutaneous leishmaniasis in the Somali region of Ethiopia. We found a variant with unique genomic signatures of drug resistance. Public health officials should use genomic surveillance to slow exp...
Diarrhea in alpaca crias significantly impacts livestock health in high-altitude regions, with as a common pathogen. This study analyzed 10 isolates from diarrheic and healthy alpacas using whole-genome sequencing to assess genetic diversity, virulence factors, and antibiotic resistance. Predomina...
Salmonella Typhimurium is a significant foodborne pathogen and a leading cause of gastroenteritis in humans and animals. Among its various lineages, the DT104 strain is particularly notable for its high level of antimicrobial resistance, making it a significant global concern. Here, we used whole-ge...
Between 2018 and 2019, Israel experienced one of its largest measles outbreaks in recent decades, with over 4300 reported cases and more than 100 documented importation events. Despite high national vaccination coverage, the prolonged nature of the outbreak posed a risk to the country's measles elim...
No abstract available
Measles continues to pose a serious threat to global public health, fueled by declining vaccination rates, international travel, and persistent immunization gaps. Early outbreak detection and response remain hampered by fragmented surveillance systems, which often lack interoperability and limit dat...
Pakistan experienced a significant outbreak of Acute Hemorrhagic Conjunctivitis (AHC) in 2023. To identify the cause, in the absence of targeted diagnostic tests, the National Institute of Health, Islamabad, studied 15 conjunctivitis patients from Islamabad in September 2023. Metagenomic Next Genera...
India, with over 535 million livestock, is one of the largest and most densely populated countries in Asia in terms of livestock population. Transboundary animal diseases, such as foot and mouth disease (FMD), pose significant constraints on the development of progressive livestock enterprises in de...
Mpox, caused by the Mpox virus (MPXV), is a re-emerging zoonotic disease in the Poxviridae family. Since 2022, sub-Saharan Africa has experienced recurrent outbreaks, with the Democratic Republic of the Congo (DRC) accounting for 96% of the 567 confirmed cases reported in the African region by the W...
The rapid evolution of RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens therefore can contain information about the processes that govern their transmission and dispersal. Landscape phylogeographic approaches use p...
Highly pathogenic avian influenza (HPAI) H5N1 continues to pose a major threat to animal and public health. Since its emergence, clade 2.3.4.4b has become the dominant global lineage, associated with widespread outbreaks in Europe. This study aimed to characterise the H5N1 strains detected in backya...
The emergence of the Omicron variant (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raised global concerns with its highly transmissible nature. To investigate the genomic, clinical, and demographic characteristics of Omicron infections within the early outbreak cluster...
There is little infrastructure for human disease testing apart from rapid malaria diagnostic tests in many low- and middle-income countries of sub-Saharan Africa outside major referral hospitals, and animal testing is also limited. Eight pathogens were studied in wastewater and environmental surveil...
Tusavirus 1 of species (family ) was first identified in humans and later in small ruminants (caprine and ovine). This study reports the full-length coding sequences (~4400-4600 nt) of three novel tusavirus-related protoparvoviruses from ovine ("misavirus", PV540792), for the first time bovine ("si...
In Finland, notable colibacillosis outbreaks occurred in 2015 and 2021, impacting numerous flocks across the country. Diagnostic examinations of broiler carcasses revealed classical colibacillosis indicators such as polyserositis, cellulitis, and femoral head necrosis. Avian pathogenic Escherichia c...
The evolution of pathogen virulence is a central question in evolutionary epidemiology. This review examines the development of these ideas over the last 75 years from an ecological perspective using a mixture of theoretical and empirical studies. I begin with Fenner's work on myxomatosis, which led...
Here, we characterized the first isolates responsible for an outbreak in the intensive care units (ICUs) in a hospital in Argentina. Five isolates recovered from inpatients and sinks at the ICUs of one hospital in Bahia Blanca City were included. Identification and antimicrobial susceptibility test...
Numerous outbreaks of interdigital phlegmon (IP) occurred in Finnish dairy herds country-wide in the 2010s, resulting in significant but varying morbidity and severe clinical signs. These outbreaks increased antibiotic use and caused financial losses on the affected farms. During 2012-2015, we perfo...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a significant cause of severe nosocomial infections in intensive care units (ICUs) worldwide. Various genotyping methods have been employed to study the epidemiology of CRAB. To investigate the genetic diversity of CRAB clinical isolates and det...
Passive sampling provides a cost-effective alternative to conventional auto-sampling and serves as a valuable approach for wastewater surveillance in resource-limited settings. However, the feasibility of passive sampling for SARS-CoV-2 wastewater genomic surveillance (WWGS) remains underexplored in...
In early April 2024, three Nepalese students (Pt1-Pt3) in the morning classes of a Japanese language school in Western Japan were diagnosed with sputum smear-positive pulmonary tuberculosis (TB). The smear status of Pt1 and Pt3 was 3+, whereas Pt2 was scanty positive. This study aims at describing c...
We investigated an outbreak of bla harbouring pathogens lasting over a year, affecting patients in an intensive care unit (ICU) in a tertiary hospital in Bergamo, Italy. To identify transmission routes of pathogens, we combined classical epidemiological investigation with the molecular identificatio...
Accurate genomic characterization of respiratory syncytial virus (RSV) is crucial for studies of epidemiology and viral evolution, including monitoring potential escape from newly authorized vaccines and prophylactic monoclonal antibodies. A viral genome tiling amplicon panel (UW-ARTIC) was adapted...
Outbreaks of infectious diseases contribute significantly to morbidity and mortality in resource-limited settings, yet the capacity to identify their etiology remains limited. We aimed to characterize microbes and antimicrobial resistance (AMR) genes in Tanzanian children affected by an acute febril...
Poverty, disease, and vector ecology intersect to present ongoing health threats, particularly in ecologically sensitive regions. Guizhou Province in China, with its complex karst topography and rich biodiversity, offers a unique environment to study mosquito-borne viral transmission. Despite over 5...
Infections caused by carbapenem-resistant Enterobacterales have steadily multiplied over time, becoming a major threat to healthcare systems due to limited therapeutic options and high case-fatality rates. We studied a patient who, after being discharged from an ICU, developed salmonellosis caused b...
Escherichia coli is a major pathogen responsible for enteric diseases in swine. This study aims to assess the genetic diversity, virulence factors, and antimicrobial resistance genes of E. coli isolated from diarrheic pigs within Spanish integrated production systems. Metadata, including epidemiolog...
Invasive meningococcal disease (IMD) remains a significant public health concern and one of the leading causes of morbidity and mortality worldwide. In Paraguay, IMD continues to pose a serious health challenge. A retrospective, descriptive, cross-sectional observational study was conducted. Whole-g...
Rice yellow mottle virus (RYMV) is a major pathogen of rice in Africa. RYMV has a narrow host range limited to rice and a few related poaceae species. We explore the links between the spread of RYMV in East Africa and rice history since the second half of the 19th century. The phylogeography of RYMV...
Water fixtures can be involved in hospital outbreaks with multi-resistant pathogens. To document an outbreak of a Verona integron-encoded metallo-β-lactamase type 2-producing carbapenem-resistant Pseudomonas aeruginosa (CRPA-VIM) and evaluate infection control measures. Additionally, to overview wat...
Metapseudomonas otitidis was first isolated from human middle ear fluid and has since been detected in both environmental and clinical samples, emerging as an opportunistic pathogen linked to chronic otitis media and other infections. This study reports the first clinical isolate of M. otitidis from...
Streptococcus dysgalactiae subsp. equisimilis (SDSE), a Gram-positive, beta-hemolytic group G Streptococcus, possesses virulence factors such as M protein, streptolysin O, streptolysin S, streptokinase, and hyaluronidase. This study reports a foodborne outbreak caused by SDSE infection recently occu...
This study aimed to investigate the epidemiological characteristics and genomic evolutionary mechanisms of pks-positive Klebsiella pneumoniae (pks KPN), providing theoretical insights for infection prevention and control strategies. A total of 873 non-duplicate K. pneumoniae isolates collected betw...
This article documents the first outbreak of aeromoniasis caused by in farmed European seabass () along the Greek Ionian Sea coast. In late spring 2024, commercially sized fish exhibited anorexia, hemorrhages, and ulcers on the skin, accompanied by elevated morbidity and mortality rates. The outbre...
Carbapenemase-producing carbapenem-resistant Pseudomonas aeruginosa (CP-CRPA) is a major public health threat due to limited treatment options and high transmissibility. Though widespread globally, few instances of locally transmitted New Delhi metallo-β-lactamase (NDM)-producing CP-CRPA have been d...
A major dengue outbreak was reported by the Cuban Ministry of Health in 2022, highlighting the need for strong surveillance, with high pediatric cases showing warning signs. Using phylogenetic and epidemiologic approaches, we provide evidence toward a better understanding of dengue's recent transmis...
Despite recent advances in error rate reduction, until recently, Oxford Nanopore Technologies (ONT) sequences lacked the accuracy required for fine-scale bacterial genomic analysis. Here, recent software improvements of ONT and the ONT-core-genome multilocus sequence typing (cgMLST)-Polisher within...
Phylodynamic analysis has been instrumental in elucidating the epidemiological and evolutionary dynamics of pathogens. The Bayesian approach to phylodynamics integrates out phylogenetic uncertainty, which is typically substantial in phylodynamic datasets due to low genetic diversity. Bayesian phylod...
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is an important antimicrobial-resistant bacterial pathogen. We observed an increase in the detection rate of CRPA isolates at a tertiary children's hospital in Japan. We suspected an outbreak of a clonal CRPA strain and conducted a genetic study to...
Acinetobacter baumannii (A. baumannii) has emerged as a major public health threat in low- and middle-income countries (LMICs), particularly in Egypt, due to its remarkable ability to acquire and transfer resistance genes, as highlighted in the WHO bacterial Priority Pathogens List 2024 classificati...
New Delhi metallo-β-lactamase is endemic in India and the gut may act as a reservoir of carbapenemase-producing Enterobacterales (CPE). Maternal gut colonisation with bla-harbouring CPE increases the risk of neonatal gut colonisation. This study aimed to assess the vertical transmission of CPE from...
Hepatitis C virus (HCV) remains a significant public health concern in the United States particularly in rural communities where the opioid epidemic has accelerated transmission among people who use drugs (PWUD)/ Despite, this growing burden the genetic features and transmission patterns of HCV in t...
Phylodynamic models capture joint epidemiological-evolutionary dynamics during an outbreak, providing a powerful tool to enhance understanding and management of disease transmission. Existing phylodynamic approaches, however, mostly rely on various non-mechanistic or semi-mechanistic approximations...
This study reports increased Enterovirus D68 (EV-D68) circulation in 2024, re-establishing its biennial circulation cycle after its interruption during the COVID-19 pandemic. A total of 1,395 respiratory and cerebrospinal fluid (CSF) samples, positive for rhinovirus/enterovirus, collected from Janua...
Dengue fever, a vector-borne disease caused by four serotypes of dengue virus (DENV), ranges from asymptomatic to severe illness, including hemorrhagic fever and shock syndrome. A 2023 outbreak (August 2023-May 2024) in Mali affected six districts in Bamako, causing 1,422 confirmed cases with a 2.7%...
Salmonella enterica serotype Mbandaka (S. Mbandaka), a multi-host adapted non-typhoidal Salmonella, has emerged as a significant public health concern in recent years. In this study, we isolated S. Mbandaka strains carrying a multidrug-resistant IncHI2A/IncHI2 plasmid from deceased chickens in China...
Clostridioides difficile is a major cause of healthcare-associated infections, contributing to significant morbidity and mortality. This study aimed to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, and temporal dynamics of C. difficile strains isolated from hospit...
In 2022, mpox clade IIb disseminated around the world, causing outbreaks in more than 117 countries. Despite the decay of the 2022 epidemic and the accumulation of immunity within queer sexual networks, mpox continues to persist at low incidence in North America without extinction, raising concerns...
Extended-spectrum beta-lactamase (ESBL)-producing resists broad-spectrum cephalosporins, considered as a critical priority pathogen, and its presence in animals, humans, and the environment highlights its significance as a One Health issue. Dairy farm waste is a potential environmental contaminant...
Forecasting the short-term spread of an ongoing disease outbreak poses a challenge owing to the complexity of contributing factors, some of which can be characterized through interlinked, multi-modality variables, and the intersection of public policy and human behavior. Here we introduce PandemicLL...
Most plant viruses rely on insect vectors for transmission, with insect saliva serving as a critical interface in tripartite virus-vector-host interactions. Southern rice black-streaked dwarf virus (SRBSDV), a destructive pathogen transmitted by the white-backed planthopper (Sogatella furcifera, WBP...
To ameliorate the antibiotic resistance crisis, the drivers of resistance emergence (i.e., evolution) and resistance spread (i.e., cross-transmission) must be better understood. Whole-genome sequencing and susceptibility testing were performed on clinical carbapenem-resistant isolates collected fr...
Necrotizing enterocolitis (NEC), a severe comorbidity of prematurity, is usually sporadic, but occasional outbreaks suggest an infectious cause. Escherichia coli , the most frequent Gram-negative pathogen in preterm infants, historically displays a low inhospital transmissibility. To report the mana...
A surge of cases of infection was observed in reception centers for migrants in Europe beginning in the summer of 2022. Most of the cases were cutaneous, although some respiratory cases as well as one death were reported. A pan-European consortium was created to assess the clinical, epidemiologic,...
Molecular surveillance was widely used during the COVID-19 pandemic to detect rapidly emerging variants and monitor the transmission of SARS-CoV-2 within communities. In 2021, the Czech COVID-19 Genomics Consortium (COG-CZ) was set up to coordinate a new SARS-CoV-2 molecular surveillance network. In...
Serratia marcescens is a frequent cause of outbreaks in high-risk hospital settings such as neonatal intensive care units (NICU). This study investigated a potential S. marcescens outbreak in the NICU of a reference children's hospital using Whole Genome Sequencing (WGS). Additionally, it assessed t...
Salmonella enterica serovar 4,[5],12:i:- (S. 4,[5],12:i:-), the monophasic variant of Typhimurium, is among the most prevalent surface antigen subtypes and most frequent carriers of multidrug-resistance in Salmonella worldwide, therefore becoming a prominent public health threat. Genomic surveillanc...
Accurately estimating the prevalence and transmissibility of an infectious disease is an important task in genetic infectious disease epidemiology. However, generating accurate estimates of these quantities, that make use of both epidemic time series and pathogen genome sequence data, is a challengi...
Effective pathogen surveillance is critical for public health decision-making, with both individual and environmental monitoring playing essential roles. While wastewater (WW) and individual whole genome sequencing (WGS) have been used to monitor SARS-CoV-2 dynamics, their complementary potential fo...
To assess the prevalence of ESBL Enterobacteriaceae among dogs attending a veterinary clinic in Vienna, characterize the isolates in terms of antimicrobial resistance, virulence and phylogenetic relationships. Faecal samples of 88 dogs were streaked on selective plates, species were identified by MA...
Bacillus cereus can cause severe and potentially fatal bloodstream infections in immunocompromised patients, including preterm neonates. When the infection is nosocomial, investigating a potential environmental source is crucial to mitigate the transmission. This study investigated the potential env...
The relentless evolution of K. pneumoniae ST307 into a "superbug" with dual resistance to last-line antibiotics and hospital disinfectants poses an existential threat to infection control. This study characterizes the molecular epidemiology, resistance profiles, and biocide tolerance of ST307 isolat...
The emergence of Serratia marcescens as a significant healthcare-associated pathogen is compounded by its rising carbapenem resistance resulting in a critical global health challenge. This study is the first in Pakistan to comprehensively characterize the antimicrobial resistance patterns and molecu...
Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure populat...
Fluoroquinolone resistance in Shigella is among the serious antimicrobial resistance threats. We investigated the genomic epidemiology of fluoroquinolone-resistant (FQR) strains of S sonnei and S flexneri from 2015 to 2022 in Spain and Portugal. We determined the antimicrobial resistance profiles of...
SARS-CoV-2 transmission and detection on academic campuses in low- to middle-income countries has not been explored. The present study explored wastewater surveillance of SARS-CoV-2 in a campus setting in Pune, Maharashtra, India, offering insights into variant-specific trends and their correlation...
spp., the second leading cause of bacteraemia in the UK, are major nosocomial pathogens. We investigated the epidemiology of extended-spectrum -lactamase (ESBL)-producing spp. in Aberdeen, Scotland and England. Twenty-four ESBL producers underwent whole-genome sequencing and typing using MLST. Sequ...
BACKGROUNDCarbapenemase-producing Enterobacterales (CPE) frequently cause nosocomial outbreaks. To investigate these, tracing focused on patients with related CPE strains and spatiotemporal contact (e.g. contact with each other in a room or on a ward during overlapping periods) has limitations. More...
Campylobacteriosis is the leading cause of gastroenteritis worldwide, and species are the most frequently reported zoonotic, bacterial foodborne pathogens in England. Currently, less than 2.0% of isolates in England undergo strain identification and typing, resulting in limited insight into their...
Chikungunya virus re-emerged on Réunion Island in August 2024, 18 years after a first major outbreak. Analysis of 173 genomes from the current epidemic reveals a monophyletic clade with mutations linked to adaptation to mosquitoes, including E1-A226V. Bayesian inference suggests only brief cryptic...
In the aftermath of 2 extreme weather events in 2022, Malawi experienced a severe cholera outbreak; 59,325 cases and 1,774 deaths were reported by March 31, 2024. We generated 49 Vibrio cholerae full genomes from isolates collected during December 2022-March 2023. Phylogenetic and phylogeographic me...
The emergence of antimicrobial resistance (AMR) in (), particularly to last-line antibiotics such as linezolid, represents a critical challenge in clinical settings. This study investigates the genomic epidemiology of linezolid-resistant , focusing on the distribution and mutational patterns of the...
The risk of bloodstream infections increases in patients undergoing chronic hemodialysis, primarily due to water contamination or improper handling during dialyzer reprocessing. This study aimed to identify virulence factors and gather epidemiological data on the Burkholderia cepacia complex (Bcc),...
In Cali, Colombia, 405,689 COVID-19 cases were reported until March 2023, with 2463 complete genome sequences available for analysis. SARS-CoV-2 genomic data from Cali were analyzed to determine the prevalence of variants as well as the mutation frequencies. This study identified Nextstrain clades,...
African swine fever virus (ASFV) is a highly virulent DNA virus that causes African swine fever, a severe hemorrhagic disease affecting domestic and wild pigs, leading to significant animal health burdens and economic losses. Initially limited to the sub-Saharan African region, ASFV genotype II has...
Soybean mosaic virus (SMV) is one of the most serious viral pathogens, causing reductions in soybean yield worldwide. Using more than 350 time-stamped SMV coat protein encoding gene sequences from more than a dozen countries and regions in Central Asia, East Asia, North America, South America, and W...
During the COVID-19 pandemic, the emergence of multidrug-resistant (MDR) pathogens, driven by heightened antibiotic usage and device-associated infections, has posed significant challenges to healthcare. This study reports an outbreak of producing NDM-5 and CTX-M-15 β-lactamases in a hospital in Bu...
Phylodynamics bridges the gap between classical epidemiology and pathogen genome sequence data by estimating epidemiological parameters from time-scaled pathogen phylogenetic trees. The models used in phylodynamics typically assume that the sampling procedure is independent between infected individu...
Low pathogenicity avian influenza (LPAI) H9N2 has been enzootic in Bangladeshi poultry since 2006. H9N2 outbreaks can decrease egg production and growth and pose a risk to human health. The role of avian hosts in the persistence, evolution, and dispersion of H9N2 is poorly understood in Bangladesh....
Outbreaks of the highly pathogenic small ruminant disease peste des petits ruminants (PPR) were reported in Greece and Romania in July 2024, and central Bulgaria in November 2024. The origin and the link between these outbreaks are not clear. In this study, genome sequences of PPR virus were obtaine...
Ecuador, a tropical country with frequent dengue outbreaks, including a surge from 16,017 cases in 2022 to 61,329 in 2024, was the focus of this study. The study was conducted in Borbon, a semi-urban rural town in the Esmeraldas province. Genomic analysis, alongside entomo-virological surveillance,...
In a Dutch tertiary care hospital, two cases of puerperal sepsis were diagnosed within 16 days in June-July 2022. The subsequent outbreak investigation emphasizes the value of collaboration between hospital infection control, regional public health services (PHS) and a national reference laboratory....
The prevention of vancomycin-resistant Enterococcus faecium (VREfm) infections and transmissions poses a major challenge to hospitals. Vancomycin resistance can be plasmid encoded; however, as the analysis of plasmids is challenging, so far only a few reports have provided a detailed characterizatio...
Clostridioides difficile infections (CDI) present significant health risks and are among the most important nosocomial infections. Ribotype (RT) 027 poses a particular risk due to its proposed "hypervirulence". Traditionally, C. difficile isolates are characterized using PCR-ribotyping. More recentl...
Since November 2021, five genetically distinct SARS-CoV-2 Omicron lineages (BA.1-BA.5) are believed to have emerged in southern Africa, with four (BA.1, BA.2, BA.4, and BA.5) spreading globally and collectively dominating SARS-CoV-2 diversity. In 2023, BA.2.86, a highly divergent BA.2 lineage that r...
The emerging ST80 vancomycin-resistant Enterococcus faecium (VREfm) lineage, linked to the increases of clinical infections in China and Japan, raises concerns about environmental transmission. Hospital wastewater systems are recognized reservoirs for antimicrobial-resistant bacteria, but their role...
Atypical enteropathogenic (aEPEC) mainly causes sporadic diarrhea and occasional outbreaks. However, the genetic determinant of aEPEC causing large outbreaks is still unknown. In June 2022, 171 of 934 people presented with diarrhea and abdominal pain after eating a lunch box in the Kinki region of...
IMP carbapenemases confer extensive drug resistance and are increasingly noted worldwide. Despite this, little is known regarding the global epidemiology of IMP carbapenemases. We comprehensively identified genes in all publicly available bacterial genomes, then systematically analysed the distrib...
We evaluated the prevalence, pathogen profile, and antimicrobial resistance (AMR) patterns of bloodstream infections (BSIs) among 392 children with severe febrile illness who presented (July 26, 2022-September 20, 2023) to a referral hospital in Tanzania. We identified a causative pathogen in 9.8% (...
Acinetobacter baumannii (A. baumannii) is a major multidrug-resistant pathogen, posing serious threats in the healthcare settings. This study provides a comprehensive genomic analysis of nosocomial A. baumannii whole-genome sequences retrieved from NCBI Genome database. Multilocus sequence typing an...
West Nile virus (WNV), a mosquito-borne flavivirus, circulates in an enzootic cycle between birds and mosquitoes, with raptors serving as key amplifying hosts. Despite their importance in WNV surveillance, complete genome sequences from raptors remain limited. This study aimed to investigate the gen...
Corynebacterium ulcerans is an emerging zoonotic pathogen which causes diphtheria-like infections. Although C. ulcerans is found in multiple domestic and wild animal species, most human cases are linked with pets. Our ability to decipher cross-host species transmission dynamics and to understand the...
The emergence of hypervirulent and antibiotic-resistant Klebsiella pneumoniae isolates poses a significant global public health threat, necessitating stringent prevention and control strategies on an international scale. However, current research efforts are often geographically restricted and lack...
Carbapenemase-resistant Pseudomonas aeruginosa (CR-PA) is a WHO priority pathogen posing a serious public health threat. This study reports the first IMP-13-producing P. aeruginosa isolate (150UDEC/24) in Chile, recovered from a bone infection in April 2024. Antimicrobial susceptibility was determin...
Extensive vaccination campaigns against COVID-19 have played a significant role in controlling virus spread and preventing severe illness. This study focused on breakthrough infections in vaccinated individuals, raising concerns about vaccine effectiveness against SARS-CoV-2 variant immune escape, w...
Antimicrobial resistance (AMR) imperils global public health overlooking the epidemiological situation of community-acquired infections, especially in low- and middle-income countries. We conducted this study in a suburban community in West Bengal, India, to comprehend the AMR and bacterial forensic...
This study investigates a nationwide Salmonella outbreak in Norway during October-December 2024 involving four different serovars-S. Newport, S. Typhimurium, S. Kisarawe, and S. Kinondoni. The investigation aimed to assess the outbreak's scope, identify the source, and implement control measures. Ep...
is a prominent zoonotic pathogen with diverse virulence factors and significant antibiotic resistance, particularly in pig farming environments. Pig slaughterhouses are critical points of potential bacterial transmission to humans and the environment. Comprehensive genomic surveillance of in these...
This study investigates two distinct carbapenemase-producing outbreaks involving patients and contaminated sink traps at the University Hospital of Lausanne. It focuses on the diversity and transmission dynamics of plasmids carrying carbapenemase genes. Between 2022 and 2023, 57 carbapenem-resistan...
Shigellosis is a gastrointestinal infection caused by species of Shigella. A large outbreak of Shigella flexneri serotype 2a occurred in Albuquerque, New Mexico between May 2021 and November 2023 that involved humans and non-human primates (NHP) from a local zoo. We analyzed the genomes of 202 New M...
The origin and transmission history of lineage 4 (MTB L4) has been extensively studied. However, different studies yielded different results; thus, the evolutionary history of MTB L4 still remains a subject of debate. Recently, a substantial amount of whole-genome sequencing data of MTB has become...
Invasive aspergillosis, caused by , represents a critical public health concern, particularly due to increasing resistance to triazole antifungals linked to TR/TR 51A haplotypes. In our genomic epidemiology study of 157 . isolates from Dutch environmental hotspots and two clinical centers, we ident...
Prolonged detection of multispecies New Delhi metallo-β-lactamase (NDM)-1-producing Enterobacterales was observed in front of a South Korean hospital. This study aimed to investigate the transmission mechanisms of bla and assess the role of environmental reservoirs in its persistence. Epidemiologica...
Opportunistic premise plumbing pathogens (OPPPs) can establish reservoirs in hospital plumbing and cause healthcare associated infections (HAIs). There is currently no widely accepted protocol for sink drain cleaning to reduce OPPP burden. We implemented a sink cleaning intervention in 12 intensive...
Fourier transform infrared (FT-IR) spectroscopy has emerged as a rapid and reliable method for bacterial typing. In this study, we evaluated FT-IR spectroscopy for characterizing a nosocomial outbreak caused by VIM-1-producing Klebsiella michiganensis (K. oxytoca complex). All K. oxytoca complex iso...
To describe a sink-related outbreak of Klebsiella oxytoca and determine risk factors for acquiring the outbreak strain. Case-control analysis, environmental sampling from sinks, short-read whole-genome sequencing and long-read whole-genome sequencing of selected isolates. Whole-genome sequencing rev...
To describe the epidemiological and molecular characterization and in vitro activity of imipenem/relebactam against imipenem non-susceptible (IPMNS) Klebsiella pneumoniae isolates in China. K. pneumoniae isolates were collected from 16 sites in 5 regions across China during 2019. Antimicrobial susce...
Vancomycin-resistant represents an emerging threat in healthcare settings. The aim of this study was to investigate biomolecular characteristics of 31 isolates from patients in two hospitals of Molise region, central Italy. Particularly, antimicrobial resistance profiles and prevalence of resistan...
: Livestock species, particularly dairy animals, can serve as important reservoirs of , carrying antibiotic resistance and virulence genes under constant selective pressure and their spread in the environment. In this study, we performed the pathogenomic analysis of seven multidrug resistant (MDR)...
Plesiomonas shigelloides, an aquatic Gram-negative bacterium, is increasingly recognized as an emerging pathogen with antimicrobial resistance (AMR) potential. This study provides a genome-based alert on P. shigelloides PSU59, isolated from a patient in Thailand. Whole-genome sequencing (WGS) reveal...
Bacillus paranthracis belongs to Bacillus cereus group, Gram-positive and spore-forming bacteria, has the potential to induce foodborne diseases. However, globally reported outbreaks caused by B. paranthracis remain exceptionally rare and the genomic characteristics of outbreak isolates are seldom c...
The COVID-19 pandemic has illuminated the utility of pathogen genomics and highlighted roadblocks to international data sharing. This article describes the deferred value of pathogen genomics data for secondary use using a set of 10,110 assembled genomes of Vibrio cholerae shared via international r...
As a member of Acinetobacter calcoaceticus-baumannii complex, Acinetobacter pittii has been an emerging concern in nosocomial infection due to its increasing prevalence and multidrug resistance (MDR). However, its population structure remains broadly unknown, hampering efficient tracing of its trans...
A characteristic feature of influenza A viruses is their high capacity for reassortment, significantly increasing their genetic diversity. This can lead to the formation of influenza A virus variants with unique phenotypic characteristics, particularly those with pandemic potential. Representatives...
Dissemination of antimicrobial resistance (AMR) is a growing global public health burden. The aim of this study was to characterize AMR plasmid transmissions within a tertiary care hospital and identify relevant AMR plasmid transmission pathways. During an 18-month observation period, 540 clinical g...
Panama is a clinically relevant serovar isolated from food sources, particularly poultry and swine, being also reported in human gastrointestinal and extraintestinal disease globally. The emergence of broad-spectrum cephalosporin-resistant has been considered a One Health matter that demands contin...
African swine fever (ASF) is a viral pandemic in domestic pigs and wild boars that has recently caused outbreaks across Asia, Europe, and the Caribbean. The Philippines has 90% of its provinces affected, but there is limited information on the current circulating strain. Here, we present a comprehen...
The emergence and spread of antimicrobial resistance (AMR) pose significant challenges to public health worldwide. Understanding the dynamics of AMR within bacterial populations is crucial for devising effective strategies to mitigate its impact. Clonal lineages, representing genetically related gro...
Identifying the sources of pathogenic bacteria causing ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients is crucial for developing effective prevention and treatment strategies. However, the scarcity of reported cases with confirmed sources limits the ability to evaluate an...
Sub-Saharan Africa has made remarkable strides in genomic surveillance, with more than 50% of countries now equipped with an in-country sequencing capacity and 98% actively contributing data to public genomic repositories. Catalyzed by the momentum of the COVID-19 pandemic, these advancements have e...
Toscana virus (TOSV), a Phlebovirus transmitted by sandflies, is a leading cause of aseptic meningitis in the Mediterranean region. Despite its clinical significance, underreporting and limited availability of complete genomic data hinder a thorough understanding of its genetic diversity and evoluti...
CRKP infections are a significant public health threat due to their high mortality and limited treatment options. This study aimed to investigate CRKP colonization and clonal dissemination mechanism in an ICU. From August 2019 to December 2019, 8668 samples were collected from patients and the ICU e...
The emergence and spread of third-generation cephalosporins (3GC) and carbapenem-resistant Klebsiella pneumoniae pose a global critical challenge. Understanding the transmission dynamics within and between hospital environments is crucial to develop effective control strategies. From 2017 to 2019, w...
The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-Co...
To examine the near-complete genomic analysis of norovirus (NoV) subtype GⅡ.17 [P17] outbreaks in Beijing Chaoyang District from 2014 to 2024. Data and specimens related to outbreaks of the NoV aggregation in Beijing's Chaoyang District from 2014 to 2024 were collected. The NoV was identified using...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing ear infections. However, genomic epidemiology and determinants influencing transmission of ear infections associated MRSA (EIA-MRSA) in community remain unknown. In 2020-2021, 105 EIA-MRSA isolates were collected and sequ...
The COVID-19 pandemic demonstrated that fast and accurate analysis of continually collected infectious disease surveillance data is crucial for situational awareness and policy making. Coalescent-based phylodynamic analysis can use genetic sequences of a pathogen to estimate changes in its effective...
Outbreaks with vancomycin-resistant Enterococcus faecium (VRE) are common in hospitals worldwide. Whole-genome MLST (wgMLST) is often used to identify outbreak strains, but VRE typing can still be challenging due to their limited genomic variation. Developing a method for sequence analysis of vancom...
Hospital-acquired infections (HAIs) significantly increase morbidity and mortality worldwide, with Klebsiella pneumoniae (K. pneumoniae) being a leading HAI pathogen requiring targeted eradication in healthcare settings. The growing bacterial tolerance to chemical disinfectants, like chlorhexidine,...
Characterize the colistin-resistance mechanisms, determine the molecular epidemiology, and genomic traits of the colistin-resistant Klebsiella pneumoniae species complex (ColR-KpSC) clinical isolates in Mexico. In this study, 1539 KpSC isolates were collected in Mexico from 2016 to 2021. We conducte...
In Europe, highly pathogenic avian influenza (HPAI) virus circulates in avian wildlife, undergoing frequent reassortment, sporadic introductions in domestic birds, and spillover to mammals. An H5N1 clade 2.3.4.4b reassortant, EA-2023-DG, affecting wild and domestic birds was detected in western Euro...
Circoviruses are relatively new pathogens, and new circoviruses are constantly being discovered, with a growing range of hosts. Recently, canine circovirus (CanineCV) was reported to infect cats and badgers, further broadening its host range. Previous studies on the evolution and dissemination of Ca...
Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics...
This retrospective cross-sectional study examined the epidemiology, clinical presentations, and genomics of Streptococcus pyogenes genotype emm5.23, linked to severe outcomes in Scotland. Between 2014 and 2022, 58 cases of invasive Group A Streptococcus (iGAS) disease associated with emm5.23 were re...
BackgroundOn 29 January 2024, the European Centre for Disease Prevention and Control distributed an alert about a metronidazole-resistant outbreak of PCR ribotype (RT) 955 in England.AimWe aimed to investigate the presence of RT955 in Czech, Slovak and Polish isolates and evaluate different cultur...
We report the detection of a Shigella sonnei outbreak from a small investigation in the San Francisco Bay area, California, USA, in 2024. By combining outbreak investigation with genomic sequencing, we show the utility of phylodynamics to aid outbreak investigations of bacterial pathogens by state o...
In the United States, Shiga toxin-producing Escherichia coli (STEC) outbreaks cause >265,000 infections and cost $280 million annually. We investigated REPEXH01, a persistent strain of STEC O157:H7 associated with multiple sources, including romaine lettuce and recreational water, that has caused mu...
Mitigating antimicrobial resistance (AMR) is a public health priority to preserve antimicrobial treatment options. The Washington State Department of Health in Washington, USA, piloted a process to leverage longitudinal genomic surveillance on the basis of whole-genome sequencing (WGS) and a genomic...
A monkeypox virus genomic surveillance pilot began in King County, Washington, USA, during the 2022 outbreak. Genomic surveillance proved critical in determining local versus international exposure of a case where no known exposures were identified by interview, illustrating the value of genomics in...
Bioinformatic software containerization, the process of packaging software that encapsulates an application together with all necessary dependencies to simplify installation and use, has improved the deployment and management of next-generation sequencing workflows in both clinical and public health...
The role of genomics in outbreak response and pathogen surveillance has expanded and ushered in the age of pathogen intelligence. Genomic surveillance enables detection and monitoring of novel pathogens; case clusters; and markers of virulence, antimicrobial resistance, and immune escape. We can lev...
In May 2022, the Finnish Institute for Health and Welfare observed an increase in Mbandaka cases. Whole genome sequencing (WGS) linked the outbreak strain to a previously reported strain in the United Kingdom. From April 2022 to January 2023, 97 cases were reported across 18 of Finland's 21 hospita...
We investigated genomic evolution of vancomycin-resistant Enterococcus faecium (VREF) during an outbreak in Shenzhen, China. Whole-genome sequencing revealed 2 sequence type 80 VREF subpopulations diverging through insertion sequence-mediated recombination. One subpopulation acquired more antimicrob...
We assessed turnaround times in the national Listeria monocytogenes genomic surveillance system in Australia before and after decentralized sequencing. Using 1,204 samples collected during 2016-2023, we observed statistically significant reductions in median time from sample collection to issuance o...
Airport-based pathogen monitoring is a critical tool that can contribute to early detection and characterization of existing and new pathogen threats. A novel public-private partnership between an airport spa group, a biotech company, and the Centers for Disease Control and Prevention was instrument...
Advanced molecular detection (AMD) refers to the integration of next-generation sequencing, epidemiologic, and bioinformatics data to drive public health actions. As new AMD technologies emerge, it is critical to ensure those methods are used in communities that are most affected by disease-induced...
Enterovirus D68 (EV-D68) is responsible for a plethora of clinical manifestations ranging from asymptomatic infections to severe respiratory symptoms and neurological disorders. EV-D68 was first detected in children with pneumonia in 1962 and, from then, only sporadic cases were reported until 2014,...
Due to the continuous genetic diversification of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) over time, the co-circulation of two different lineages in the same region may lead to co-infections within a host, a situation known to contribute to the emergence of hybrid viral popu...
The objective of this research was to investigate the genomic epidemiology of methicillin-resistant (MRSA) in a pediatric population in Shanghai, China. Whole-genome sequencing was conducted for 492 randomly selected MRSA isolates obtained from a pediatric hospital between 2013 and 2022. ST59 (37.4...
2 (CyHV-2) is the causative agent of herpesviral hematopoietic necrosis in several economically important farmed freshwater fish species of the genus . Despite several CyHV-2 strains being isolated and fully sequenced, there is a lack of detailed characterization and consistent information on strain...
Pigs are recognised as crucial intermediate hosts for the emergence of influenza viruses of pandemic potential. As the largest pork-producing nation, China hosts a complex ecosystem of swine influenza viruses (SIVs). We aimed to investigate the evolutionary processes, spatiotemporal dynamics, and bi...
Multidrug-resistant Klebsiella pneumoniae (MDR K. pneumoniae) is a significant pathogen associated with nosocomial infections, often leading to high morbidity and mortality. This resistance is largely due to the efficient horizontal transfer of mobile genetic elements such as plasmids, which carry r...
Different laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involv...
In 2018, Singapore's National Infection Prevention & Control Committee (NIPC) recommended standard precautions and unrestricted movements for CPE carriers in nursing homes. This study investigates the short-term impact of this intervention on CPE transmission in a nursing home in Singapore. We condu...
Epigenetics offers insight into the mechanisms by which early life HIV infection and HIV exposure in utero affects offspring health. However, due to the widespread use of antiretroviral therapy (ART) during pregnancy/infancy, contemporary studies are unable to disentangle effects of HIV from ART exp...
is an emerging pathogen within the species complex, and its clinical and microbiological characteristics remain poorly understood. This retrospective case-control study analyzed 252 patients with bloodstream infections caused by species complex, including 60 with infection, to elucidate these cha...
Scallop aquaculture is of economic importance along the east coast of the tropical Pacific. However, scallop diseases have been observed and there is limited knowledge about bacterial pathogens, especially in hatcheries. The objective of this study was to identify and characterize one of the predomi...
Respiratory virus transmission in healthcare settings is not well understood. To investigate the transmission dynamics of common healthcare-associated respiratory virus infections, we performed retrospective whole genome sequencing (WGS) surveillance at one pediatric and two adult teaching hospitals...
Lumpy skin disease is a transboundary viral disease affecting bovine species. This disease had never been recorded in Malaysia prior to May of 2021, and had spread to 65 of 92 districts in Peninsular Malaysia by December of the same year. In this study, we conducted a whole-genome sequencing, phylog...
Mikawasima is a rare, mainly environmental serovar. In 2020, an outbreak was observed in neonatal and maternal wards of the University Hospital of Split and was established as an endemic until the end of 2024. Using whole-genome sequencing, this study aimed to analyse the phenotypic and genotypic ch...
-truncated (ATAB) isolates are associated with elevated tigecycline resistance and enhanced virulence, yet its epidemic dynamics and genomic features remain poorly understood. This study aimed to investigate the epidemiology of ATAB isolates, identify infection risk factors, and assess their impact...
Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoide...
The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest. The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coro...
This study presents the development and validation of a genomic surveillance strategy using Whole Genome Sequencing (WGS) on normalized pooled samples to detect and monitor SARS-CoV-2 variants. A bioinformatics pipeline was designed specifically for analyzing pooled WGS data and was validated using...
There has been an unprecedented effort to sequence the SARS-CoV-2 virus and examine its molecular evolution. This has been facilitated by the availability of publicly accessible databases, such as the GISAID (Global Initiative on Sharing All Influenza Data) and GenBank, which collectively hold milli...
Cases of whooping cough (pertussis) have rebounded strongly from the very low incidence observed during the pandemic. This re-emergence is characterized by changes in epidemiology. Here we describe the importance of genomics to monitor and understand the drivers to these changes. Changes in the geno...
Estimating the transmission fitness of SARS-CoV-2 variants and understanding their evolutionary fitness trends are important for epidemiological forecasting. Existing methods are often constrained by their parametric natures and do not satisfactorily align with the observations during COVID-19. Here...
An African Swine Fever (ASF) outbreak was first recorded in the Philippines in July 2019. Since then, the disease has spread across provinces in Luzon, Visayas, and Mindanao, causing severe economic consequences for the country's swine industry. Here, we report the genome sequencing of ASF virus str...
The reference microbiology laboratory of Israel's National Institute for Antibiotic Resistance and Infection Control has established a national repository of isolates analyzed by Fourier-transform infrared (FTIR) spectroscopy and their spectra. Healthcare institutions send antibiotic-resistant isola...
Over the past decade, pathogen genome sequencing has become well established as a powerful approach to study infectious disease epidemiology. In particular, when multiple genomes are available from several geographical locations, comparing them is informative about the relative size of the local pat...
The human parvovirus B19 (B19V) infections cycle occurs in 3- to 4-year periods and is responsible for benign childhood erythema infectiosum. It is also associated with transient aplastic crisis in patients with underlying hemolytic diseases and with severe fetal sometimes fatal infection. This stud...
The Burkholderia cepacia complex (Bcc), a group of environmentally ubiquitous bacteria, are inherently resistant to antiseptics and antibiotics. Bcc can proliferate in pharmaceutical products, resulting in nosocomial outbreaks. However, Bcc is often dismissed as blood culture contaminants, and preci...
Nationwide surveillance was conducted in Japan to clarify the status of pediatric invasive pneumococcal diseases (IPD) after introducing a 13-valent pneumococcal conjugate vaccine (PCV13). Detailed clinical and epidemiologic information of IPD cases in children aged <15 years was collected from 10 o...
Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used for whole genome sequencing of SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess and improve...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a significant global threat due to its high prevalence rates and limited therapeutic options. The primary objective of this study was to investigate the clinical distribution and molecular epidemiology of CRKP collected between 2016 and 20...
Genomic surveillance has been crucial in monitoring the evolution and spread of SARS-CoV-2. In Andalusia (Spain), a coordinated genomic surveillance circuit was established to systematically sequence and analyze viral genomes across the region. This initiative organizes sample collection through 27...
To evaluate genetic changes in respiratory syncytial virus (RSV) between 2019 and 2023, we analyzed RSV strains from Myanmar before and after the COVID- 19 pandemic. Real-time polymerase chain reaction (RT-PCR) positive samples from children presenting with acute respiratory infections at outpatient...
Stakeholder training is essential for handling unexpected crises swiftly, safely, and effectively. Functional and tabletop exercises simulate potential public health crises using complex scenarios with realistic data. These scenarios are designed by integrating datasets that represent populations ex...
Difficult-to-treat resistant Pseudomonas aeruginosa (DTR-PA) is an MDR subset resistant to all first-line antipseudomonal agents. It is particularly concerning in respiratory infections like bronchiectasis, leading to poor outcomes, limited treatment options, and higher healthcare costs. This study...
Group B Streptococcus (GBS) is a leading cause of neonatal meningitis and sepsis and an important cause of disease in adults. Capsular polysaccharide and protein-based GBS vaccines are currently under development. Through national laboratory-based surveillance, invasive GBS isolates were collected f...
We observed a discrepancy between dengue NS1 antigen test and molecular diagnostics, with the emergence of dengue virus (DENV) serotype 3 in Sri Lanka, and sought to understand the cause for the rise in cases and high failure rates of molecular diagnostics. Whole-genome sequencing was carried out in...
Nontuberculous mycobacteria (NTM) cause pulmonary and extrapulmonary infections. Although isolation of NTM from clinical specimens has increased nationally, few studies delineated the molecular characteristics of extrapulmonary NTM. Extrapulmonary isolates were collected by 4 Emerging Infections Pro...
Antimicrobial resistance (AMR) is a critical global public health threat, with bacterial pathogens of primary concern. Pathogen genomics has revolutionized the study of bacterial pathogens and provided deep insights into the mechanisms and dissemination of AMR, with the precision of whole-genome seq...
In recent decades, Acinetobacter baumannii has become a major global nosocomial pathogen, with bloodstream infections (BSIs) exhibiting mortality rates exceeding 60% and imposing substantial economic burdens. However, limited large-scale genomic epidemiology has hindered understanding of its populat...
Mpox is a zoonotic viral infection caused by the monkeypox virus (MPXV) genus Orthopoxvirus. The MPXV, possesses a large and complex double-stranded DNA genome, encoding approximately 190 genes. The virus has gained attention due to recent outbreaks and the emergence of resistant variants. MPXV exis...
Chickenpox, caused by the Varicella Zoster Virus (VZV), presents as varicella (chickenpox) during primary infection and as herpes zoster (shingles) upon reactivation. With a high infectivity rate and transmission through airborne droplets and contact, VZV poses a significant public health challenge....
During the Coronavirus Disease 2019 (COVID-19) epidemic, the strain on intensive care units (ICUs) has increased, which made them more vulnerable to the threat of multidrug-resistant organism (MDRO). This study aims to investigate an outbreak of carbapenem resistant Acinetobacter baumannii (CRAB) in...
Yellow Fever virus (YFV) continues to challenge public health systems across the Americas, despite decades of successful control and the availability of a highly effective vaccine. Following major outbreaks between 2016 and 2022, YFV re-emerged in Brazil in 2023, with a confirmed infection in a non-...
Phylodynamic analyses infer epidemiological parameters from pathogen genome sequences for enhanced genomic surveillance in public health. Pathogen genome sequences and their associated sampling dates are the essential data in every analysis. However, sampling dates are usually associated with hospit...
Salmonellosis due to non-typhoidal (NTS) is a zoonotic infection that has epidemiological uniqueness in different settings. The current study aimed to determine the serotypes and the genetic diversity of human isolates causing infection in Kuwait. Isolates were obtained from feces of healthy adult...
Brucella species are intracellular Gram-negative bacteria that cause brucellosis, a global zoonosis that impacts cattle productivity and public health. Both cattle and buffaloes are susceptible to bovine brucellosis, which can lead to severe degenerative changes in uterine mucosa of non-pregnant ani...
This study focused on genomic epidemiology of metallo-β-lactamase (MBL)-producing Citrobacter spp. in Poland. It included 118 isolates with VIM (n = 100), NDM (n = 17) or IMP (n = 1) enzymes from 2011 to 19, largely C. freundii (n = 94) of 33 sequence types (STs). Three globally-spread STs were more...
Pseudomonas aeruginosa is a major pathogen in cystic fibrosis (CF), where chronic and intermittent infections significantly affect patient outcomes. This study aimed to investigate the molecular epidemiology of P. aeruginosa in CF patients from the Brazilian Amazon, focusing on genotypic diversity,...
Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of healthcare-associated infections in hospitals, which are frequently antimicrobial resistant (AMR). Exacerbating the public health threat posed by K. pneumoniae, some strains also harbour additional hypervirulence determinants...
IncF plasmids are mobile genetic elements found in bacteria from the family and often carry critical antibiotic and virulence gene cargo. The classification of IncF plasmids using the plasmid Multi-Locus Sequence Typing (pMLST) tool from the Center for Genomic Epidemiology (CGE; https://www.genomic...
In May 2018, an outbreak of NDM-5-carrying Escherichia coli (NDM-5-EC) was detected at the hemato-oncology department of a tertiary care center in Austria. This report details the outbreak investigation, control measures and the whole genome sequencing (WGS) data of the outbreak isolates. A total of...
Despite intensive study, gaps remain in our understanding of SARS-CoV-2 transmission patterns during the COVID-19 pandemic, in part due to limited contextual metadata accompanying most large genomic surveillance datasets. We analyzed over 130,000 SARS-CoV-2 genomes, over 85,000 with matched epidemio...
After the relaxation of stringent control measures, nationwide large-scale SARS-CoV-2 surveillance was gradually phased out post-2023, transitioning to focused monitoring of Influenza-like Illness (ILI) through sentinel hospitals and laboratory networks. Nationally, surveillance of respiratory patho...
(ToBRFV) and (ToCV) are emerging viral threats to tomato production worldwide, with expanding global distribution. Both viruses exhibit distinct biological characteristics and transmission mechanisms that influence their spread. This study aimed to reconstruct the complete genomes of ToBRFV and ToC...
Defining the temporal dynamics of invasive Streptococcus pyogenes (group A Streptococcus) and differences between hyperendemic and lower-incidence regions provides crucial insights into pathogen evolution and, in turn, informs preventive measures. We aimed to examine the clinical and temporal lineag...
The global emergence of Jingmen group viruses (JMVs), including Jingmen tick virus (JMTV), Alongshan virus (ALSV), and Yanggou tick virus (YGTV), has significantly broadened our perspective on the potential public health risks posed by segmented flaviviruses. However, the global evolutionary and gen...
This study examined the genetic and evolutionary features of influenza A/H3N2 viruses in Hangzhou (2010-2022) by analyzing 28,651 influenza-like illness samples from two sentinel hospitals. Influenza A/H3N2 coexisted with other subtypes, dominating seasonal peaks (notably summer). Whole-genome seque...
To establish the epidemiological correlation between the study isolates, Indian and World isolates of Acinetobacter baumannii by performing Multilocus Sequence typing. A total of 181 isolates (Sputum (n = 116), lower respiratory tract other than sputum (n = 36), upper respiratory tract (n = 20), Env...
We used metagenomic next-generation sequencing (mNGS) to investigate an outbreak of Fusarium solani meningitis in US patients who had surgical procedures under spinal anesthesia in Matamoros, Mexico, during 2023. Using a novel method called metaMELT (metagenomic multiple extended locus typing), we p...
Identifying the causes of tuberculosis (TB) chronicity in cattle herds in Spain is a complex endeavour, mainly due to the multiple factors involved in persistence and the clonal population structure of the Mycobacterium tuberculosis complex. This study assessed the genomic diversity among M. bovis i...
Mycoplasma gallisepticum (MG) can infect a wide range of birds, seriously jeopardizing the development of the poultry industry. A nested-PCR method was constructed based on mgc2 gene for evaluating the prevalence of MG in duck flocks. A total of 1002 samples were detected from Shandong and Inner Mon...
Staphylococcus aureus is an important zoonotic pathogen that has often been seen in animals through the prism of the MRSA clonal complex (CC) 398 in pigs and in-contact humans. The goal of this study was first to assess the prevalence of MRSA, and second to look for MSSA CC398 in cats, dogs and hors...
The phylodynamic curve (Grenfell . 2004 , 327-332 (doi:10.1126/science.1090727)) conceptualizes how immunity shapes the rate of viral adaptation in a non-monotonic fashion, through its opposing effects on viral abundance and the strength of selection. However, concrete and quantitative model realiz...
The SARS-CoV-2 pandemic presented unprecedented challenges, particularly in understanding its complex spatial transmission patterns. The high transmissibility of the virus led to frequent super-spreading events. These events demonstrated clear spatial clustering patterns, often tied to specific even...
We detected in October 2024 an abnormally high number of Chlamydia pneumoniae diagnoses through real-time surveillance of infections in Southeastern France, which followed significant increases in Mycoplasma pneumoniae and Bordetella pertussis diagnoses. Therefore, we retrospectively analyzed C. pne...
Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due to their variable gene content and order, reference-free methods offer more sensitive d...
serotype Enteritidis (SE) is a common foodborne pathogen that can cause human salmonellosis. Identifying closely related cases is essential to control the pathogen through, e.g. outbreak investigation, but it is often challenging due to the low genetic diversity of SE, particularly with traditional...
Pathogen genomic data are increasingly being used to investigate transmission dynamics in infectious disease outbreaks. Combining genomic data with epidemiological data should substantially increase our understanding of outbreaks, but this is highly challenging when the outbreak under study is only...
In January-February 2025, a community outbreak of serogroup B was reported in Aragón, Spain, with nine confirmed cases. This represents a 27-fold increase vs the previous 3 years. Five cases had respiratory co-infections; seven were attributed to complex CC213. Epidemiological investigations reveal...
Newcastle disease (ND) is a significant viral disease affecting poultry worldwide, with outbreaks persisting despite extensive vaccination efforts. This study characterizes a novel NDV strain, RT40, isolated from poultry farms in northeast Iran for the first time. RT40, classified as genotype VII, s...
are widely distributed in aquatic environments and are major pathogens commonly found in aquaculture environments, playing a significant role in human production activities and maintaining ecological stability. Here, a novel phage, vB_VneS_J26, which infects , was isolated from coastal seawater in Q...
Mutation is one of the most important drivers of viral evolution and genome variability, allowing viruses to potentially evade host immune responses and develop drug resistance. In the context of COVID-19, local genomic surveillance of circulating virus populations is therefore critical. The goals o...
The Gamma and Delta variants of concern (VOCs) of SARS-CoV-2 drove the second and third wave in Brazil and significantly intensified the number of cases and deaths. In this study, we investigate the timeline and origins of the Gamma and Delta variants using a spatiotemporal analysis based on 1508 ge...
BackgroundIntegrated genomic surveillance (IGS), i.e. the integrated analysis of pathogen whole genome sequencing and classical epidemiological data, can contribute substantially to the disease surveillance and infection prevention activities of local public health authorities (LPHAs).AimOur aim was...
Influenza seasons are characterized by a complex interplay of co-circulating strains with high spatial and temporal heterogeneities. Surveillance is crucial for monitoring the spread and evolution of the virus and design effective public health response strategies. We combined epidemiological, virol...
Data on enteric yersinioses in Central America are limited. Genomic characterization of 78 Yersinia enterocolitica isolates from Costa Rica indicated persistent infection-source circulation between animal reservoirs and humans, as well as unusual antimicrobial resistance levels. Our study highlights...
Acinetobacter baumannii, a Gram-negative bacterium, is a public health threat due to its role in nosocomial infections and increasing antibiotic resistance. In Nigeria, data on the molecular epidemiology of A. baumannii is scarce. This study investigates the genetic diversity and the presence of ant...
The main issue of the Klebsiella pneumoniae species complex (KpSC) research in clinical settings is the accurate identification and differentiation of the closely related species within this complex. Moreover, the emergence and spread of carbapenem-resistant K. pneumoniae (CRKP) represent a signific...
The World Health Organization African region has the greatest infectious disease burden in the world. However, many African countries have limited capacity to rapidly detect, report, and respond to public health events. The Centre for Epidemic Response and Innovation (CERI), KwaZulu-Natal Research I...
Oropouche virus (OROV), first detected in Trinidad and Tobago in 1955, was historically confined to the Brazilian Amazon Basin. However, since late 2022, an increasing number of OROV cases have been reported across various regions of Brazil as well as in urban centers in Bolivia, Ecuador, Guyana, Co...
Recommendations on the use of genomics for pathogens surveillance are evidence that high-throughput genomic sequencing plays a key role to fight global health threats. Coupled with bioinformatics and other data types (e.g., epidemiological information), genomics is used to obtain knowledge on health...
In December 2021, an outbreak of the SARS-CoV-2 B.1.640.2 variant, potentially originating from Cameroon, was investigated among schoolchildren in Germany. The index case, an adult who had recently returned from a three-week stay in the Republic of Congo, introduced the variant into a school setting...
The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeogr...
(Group A ; GAS) is a pathogen of global significance. In the pre-antibiotic era, GAS was a major cause of childhood morbidity and mortality, but its spread rapidly declined until the mid-2010s. The continuing increase in GAS infections, associated with the expansion of the M1 lineage, was observed f...
The 2022 global mpox epidemic was caused by transmission of MPXV clade IIb, lineage B.1 through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing phylogeographic analysis of MPXV genomes sampled from 757 individuals in N...
Having spanned thousands of kilometers from Africa through Europe, the Middle East, Central Asia through to the south eastern part of Eurasia in the recent decade, lumpy skin disease virus has now become entrenched in China, Thailand, Vietnam, and South Korea. In light of discovered findings on reco...
In summer 2021, while the Delta variant was predominant in many European countries, Luxembourg experienced a large outbreak of the P.1.17.1 SARS-CoV-2 Gamma variant. This surge coincided with the introduction of digital COVID-19 certificates and eased restrictions prior to national holiday festiviti...
The evolution of COVID-19 pandemic has been characterized by the rapid emergence of new SARS-CoV-2 variants, each of which poses unique challenges to public health. This study analyzes the dispersion profiles during the Pre-Omicron and Post-Omicron phases in different epidemiological contexts. The B...
Since the emergence of Severe Acute Respiratory Syndrome (SARS) in 2002, bats have been recognized as important reservoirs of diverse coronaviruses (CoVs). Despite extensive research on the broad geographic transmission of bat CoVs, there is a notable gap in understanding the transmission dynamics w...
Invasive meningococcal disease (IMD) caused by Neisseria meningitidis can result in life-threatening meningitis and septicaemia. There are twelve serogroups of N. meningitidis, but most cases of IMD are caused by serogroups A, B, C, W, X and Y. In Europe, serogroup B (MenB) accounts for 51 % of docu...
Acinetobacter baumannii is a significant nosocomial pathogen recognized for its multidrug-resistance (MDR) and capacity to endure in hospital settings. This study aims to investigate the clonal relationships of A. baumannii isolates from diverse clinical samples, identify the sequence types of MDR i...
Vancomycin-resistant Enterococcus faecium (VREfm) poses a significant concern in healthcare settings, particularly during outbreaks. Traditional antibiotic susceptibility testing may fail to detect occult vancomycin resistance, and long culture times delay diagnosis. While whole genome sequencing (W...
The surveillance of wildlife viromes is essential for identifying zoonotic threats within the One Health framework. This study analyzed rectal and oral swabs from 88 individuals representing 13 species as felids, wild rodents, marsupials and non-human primates in Southern Brazil using metagenomic se...
The goal of this study is to describe the genome of that was found in clinical mastitis in cattle in Bangladesh. This work will show how strong the bacteria are and how important they are for public health. Whole genome sequencing (WGS) was performed using the Illumina MiSeq platform, followed by c...
Viruses associated with acute febrile illness in Africa cause a spectrum of clinical disease from mild to life-threatening. Routine diagnostic methods are insufficient to identify all viral pathogens in this region. In this study, 1281 febrile Ugandan patients were prospectively recruited as part of...
The CRISPR/Cas system defends bacteria and archaea against invasive pathogens, such as phages, establishing an immunological memory from this interaction. Pseudomonas aeruginosa, an opportunistic pathogen, represents a significant public health concern due to its multidrug resistance. This study con...
Linezolid-non-susceptible (LNSEf) has emerged as a critical clinical concern worldwide, yet data from Latin American settings remain scarce. This study aimed to investigate the molecular epidemiology and mechanisms underlying LNSEf in a Mexican tertiary care university hospital, focusing on clinica...
The Liverpool Epidemic Strain (LES) of Pseudomonas aeruginosa is one of several known strains to be transmissible between persons with cystic fibrosis (CF) (pwCF) and the only known strain to have infected large proportions of CF populations on two continents. Despite its prevalence, efforts to unde...
The genomic epidemiology of has been based on culture-dependent whole-genome sequencing. However, this approach neglects sources that are not amenable to microbial culture. Here, we show that metagenome-assembled genomes (MAGs) are useful in appraising the neglected diversity of from unconventiona...
Spotted fever group (SFG) rickettsioses are increasingly recognized worldwide as threats to public health. Rickettsia rickettsii, Rickettsia parkeri, and Rickettsia rickettsii subspecies californica cause spotted fever rickettsioses, including Rocky Mountain spotted fever. These disease agents are t...
CHIKV infection is transmitted by mosquitoes spp., with considered as the primary vector and playing an important role in sustaining outbreaks in Europe. The ECSA-Indian Ocean Lineage (IOL) strain emerged in Reunion, subsequently spreading to areas such as India, the Indian Ocean, and Southeast A...
The symposium "The New Era Shaped by Environmental Genome Monitoring," held in December 2024 by the Japanese Environmental Mutagen and Genome Society (JEMS), aimed to explore the interdisciplinary collaborations that are essential for the development of new scopes in environmental genome monitoring....
To date, human immunodeficiency virus (HIV) molecular epidemiology has been primarily used to identify clusters of related infections (cluster detection and response) and then address interventions to these clusters. Community groups have raised concern regarding cluster detection and response relat...
Salmonella, a significant threat to public safety, inflicts substantial economic losses on the poultry industry. The unique "parental feeding" breeding model of pigeon farms, against the "all-in & all-out" biosecurity strategy, makes them susceptible to Salmonella infections and subsequent outbreaks...
mcr-10 is among the growing families of newly identified plasmid-mediated mobile colistin-resistance genes. In this study, we identified an mcr-10 gene in a seafood-borne extended-spectrum β-lactamase (ESBL)-producing Enterobacter xiangfangensis. E. xiangfangensis strain, B12-S77, was subjected to w...
Gastrointestinal and bloodstream infections account for a major cause of medical emergency and mortality among pediatric populations. Although is implicated in multiple infections, its virulence and antimicrobial resistance are elusive. Here we aimed to uncover the pathogen associated with diarrhea...
Carbapenem-resistant Citrobacter spp. (CRC) are increasingly recognized as healthcare-associated pathogens, while systematic studies on clinical epidemiology, genetic diversity, and resistant mechanisms of CRC are relatively scarce. The present study provides comprehensive and systematic research on...
The complex (ECC) comprises multiple species that require genomic analysis for precise identification. They produce inducible AmpC β-lactamase and may carry acquired β-lactamases, which are responsible for cefotaxime and cefepime resistance. To determine the molecular epidemiology, antimicrobial re...
is known to be virulent, but there are few large-scale epidemiologic studies of this species to define types of infection, susceptibility patterns, and severity. isolates from any culture at four U.S. tertiary care hospitals between 1 April 2021 and 1 April 2022 were identified. For the first isola...
The convergence of globalization with increased sexual risk behaviours has significantly facilitated the dissemination of multidrug-resistant and extensively drug-resistant clusters of Shigella spp. among men who have sex with men, particularly Shigella sonnei and Shigella flexneri. A cluster of S....
The prevalence of multidrug-resistant Acinetobacter baumannii (MDRA) has rapidly increased and is linked to severe nosocomial infections. MDRA outbreaks in a Japanese hospital were analysed using whole-genome sequencing. Antibiotic susceptibility testing was performed on clinical isolates from hospi...
Hybrid capture-based target enrichment prior to sequencing has been shown to significantly improve the sensitivity of detection for genetic regions of interest. In the context of One Health relevant pathogen detection, we present a hybrid capture-based sequencing method that employs an optimized pro...
In Nepal, dengue is an emerging disease of growing concern as outbreaks are increasing in both size and geographic reach and beginning to affect areas previously thought dengue-free. Dengue genomic surveillance has previously been limited within Nepal; however, with the increase in accessibility to...
Acute Hemorrhagic Conjunctivitis (AHC) is primarily caused by viral infections, with Coxsackievirus A-24v (CV-A24v) being a significant culprit. Enteroviruses, including CV-A24v, are responsible for global AHC outbreaks. Over time, CV-A24v has evolved, and genotype IV (GIV) has become the dominant s...
The H3N2 canine influenza virus (CIV) emerged from an avian reservoir in Asia to circulate entirely among dogs for the last 20 years. The virus was first seen circulating outside Asian dog populations in 2015, in North America. Utilizing viral genomic data in addition to clinical reports and diagnos...
Rabies, a re-emerging zoonosis with the highest known human case fatality rate, has been largely absent from Peru, except for endemic circulation in the Puno region on the Bolivian border and re-emergence in Arequipa City in 2015, where it has persisted. In 2021, an outbreak occurred in the rapidly...
Bacteria that adhere to epithelial cells, form intracellular bacterial communities (IBCs), or transition to filamentous forms are referred to as morphotype-positive bacteria. () with this morphotype plays a critical role in urinary tract infections (UTIs), yet its impact on urine culture outcomes a...
serotype 1 is one of the most prevalent serotypes commonly associated with invasive pneumococcal disease cases and outbreaks worldwide. Several sequence types of this serotype have been identified globally, including those exhibiting both high virulence potential and antimicrobial resistance profile...
Birds are natural hosts for numerous zoonotic viral pathogens, including West Nile virus, which is transmitted by mosquitoes. During migration, birds can act as vectors for the geographic spread of viruses. WNV is endemic in Portugal, causing annual outbreaks, particularly in horses. Here, we report...
is a significant nosocomial pathogen, particularly problematic due to its extensive drug resistance. This study investigates 56 extensively drug-resistant (XDRAB) strains collected from various ICU wards at Jinhua Central Hospital, Zhejiang Province, China. Strains were isolated from diverse clinic...
To describe the analysis, epidemiology, and control of six contemporaneous and linked outbreaks of Salmonella enterica subsp. enterica serovar Infantis on British broiler farms. Salmonella Infantis is a potentially multidrug-resistant foodborne zoonosis and can persistently colonize poultry flocks a...
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we leverage the power of whole genome sequencing (WGS) to screen AmpC- and extended-spectrum beta-lactamase (ESBL)-producing Escheric...
To characterize the recent trends in serogroup W isolates from invasive meningococcal disease (IMD) cases (MenW) in Ontario, Canada since 2015. IMD case isolates in Ontario between January 1, 2015 and June 30, 2024 were examined by phenotypic and genetic methods for possession of vaccine antigen gen...
Human respiratory syncytial virus (HRSV) is a common cause of lower respiratory tract infections globally, and changes in viral epidemiology have been observed in many jurisdictions following the coronavirus disease 2019 (COVID-19) pandemic. Newly licensed vaccines and monoclonal antibodies are anti...
Influenza A outbreak risk is impacted by the potential for importation and local transmission. Reconstructing transmission history with phylogenetic analysis of genetic sequences can help assess outbreak risk but relies on regular collection of genetic sequences. Few influenza genetic sequences are...
The prevalence of multidrug-resistant (MDR) is increasing globally, raising concerns for public health. In 2022, an outbreak of MDR was observed in Tunisia. We aimed to evaluate the genetic profile of isolates during the outbreak, including their clonal relationship, antimicrobial determinants an...
In Ethiopia, dengue virus (DENV) infections have been reported in several regions; however, little is known about the genetic diversity of circulating viruses. We conducted clinical surveillance of DENV during the 2023 nationwide outbreak in Ethiopia. We enrolled patients at 3 sentinel hospital site...
The presence of all five of the virulence-associated genes iucA, iroB, peg-344, rmpA, and rmpA2 is presently the most accurate genomic means for predicting hypervirulent Klebsiella pneumoniae (hvKp-p). With this longitudinal cohort study, we firstly provide novel insights into the clinical and genom...
Plasmids are well-known vehicles of antimicrobial resistance (AMR) gene dissemination. Through conjugation, plasmid-encoded AMR genes are spread among neighbouring bacteria, irrespective of their strain or even their species. This process is very concerning from a public health perspective, as plasm...
Fungicides are used in agriculture to manage fungal infections and maintain crop yield and quality. In Europe, their application on cereals increased drastically starting from the mid 1970s, contributing to a significant improvement in yields. However, extensive usage has led to the rapid evolution...
In the Netherlands, the 7-valent pneumococcal conjugate vaccine (PCV) was introduced to the childhood immunization programme in 2006 and replaced by the 10-valent PCV (PCV10, GSK) in 2011. To describe invasive pneumococcal disease in the era of childhood PCV vaccination on pneumococcal bacteraemia a...
This study aimed to establish a Severity Scale for influenza and other acute respiratory infections (ARI), requiring hospitalization, for surveillance and research purposes (the SevScale). Such a scale could aid the interpretation of data gathered from disparate settings. This could facilitate poole...
Candida auris is an emerging fungal pathogen associated with outbreaks in healthcare settings. We report a multiyear outbreak of C. auris in a burn intensive care unit in Illinois, USA, during 2021-2023. We identified 28 C. auris cases in the unit over a 2-year period, despite outbreak response and...
The evolution of new carbapenemase variants is alarming. We aimed to investigate the genetic context and molecular epidemiology of the emerging OXA-484 carbapenemase in the United Arab Emirates, to decipher its resistance mechanisms and evolutionary relationships. Antimicrobial susceptibility testin...
To analyse the antibiotic resistance, resistance genes and clonal relationship of Escherichia coli in bloodstream infections in Ningxia from 2022 to 2023. We retrospectively analyzed the antibiotic susceptibilities of 257 isolates. PCR was used to detect bla, bla, bla, qnrS, qnrA, qnrB, oqxA, qepA,...
The eastern parts of Ethiopia, including Dire Dawa City, have experienced annual dengue fever (DF) outbreaks since 2013, leading to significant healthcare and economic impacts. However, comprehensive evidence on the specific dengue virus (DENV) serotypes and genotypes involved remains limited. Durin...
Sustaining and expanding genomic surveillance capacity requires broader investment in genomics that target both novel and pandemic pathogens. Currently, there is no standardized methodology to evaluate the cost and benefit of a multi-pathogen surveillance system. We propose a framework for pathogen...
Brucella melitensis is a zoonotic pathogen that poses a worldwide public health challenge. In recent years, whole-genome sequencing has become a widely accepted molecular typing method for the genomic epidemiology of brucellosis. This study reports the genomic characteristics of 24 B. melitensis str...
Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings. Residents of nursing homes are at increased risk of pathogen colonization and infection owing to antimicrobial-resistant bacteria and...
Group A rotavirus (RVA) is the leading cause of acute gastroenteritis in infants and young children worldwide. To elucidate the molecular epidemiology of G2P[4] rotavirus in China and the protective effects of vaccines, whole-genome analysis of 13 G2P[4] RVA strains collected from China in 2022 was...
An outbreak of diarrheal illness related to milk cartons served in school lunches, occurred in June 2021, involving more than 1800 cases from 25 schools. A strain of Escherichia coli OUT (OgGp9):H18 was implicated in the outbreak. This strain does not possess virulence factors typical of other E. co...
Watermelon mosaic virus (WMV) is a major plant pathogen, infecting over 170 plant species, including cucurbits and legumes. Though mostly propagated locally by aphids in a non-persistent manner, long-range dispersal can occur through human-induced plant or vector movements. Understanding patterns of...
Orthoflavivirus denguei (Dengue virus) type 4; (DENV-4) has emerged as a significant public health concern in Brazil, particularly following its reintroduction in the early 21st century. This study provides a comprehensive analysis of DENV-4's genetic characterization and its spatiotemporal dynamics...
Human enterovirus D68 (EV-D68) has been associated with an increase in mild-to-severe pediatric respiratory diseases worldwide. The rate of circulation of this virus is largely underestimated in the population and genetic evolutionary data are usually available only for partial sequences. To achieve...
Blastomycosis is an environmentally acquired fungal infection that can result in severe pulmonary illness and high hospitalization rates. In 2023, a blastomycosis outbreak was detected among workers at a paper mill in Delta County, Michigan. We included patients with clinical and laboratory evidence...
The genomic surveillance of SARS-CoV-2 is challenging in high-volume, resource-limited settings. Faster and less expensive methods are required for the prompt detection of variants of interest. This study aimed to validate and implement the TaqMAMA RT-PCR method for the detection of SARS-CoV-2 varia...
Carbapenem-resistant () poses a major threat to global public health. This study aimed to investigate the genomic characteristics and phylogenetic relatedness of colonization and infection with among intensive care unit (ICU) patients. A total of 61 isolates, including 29 non-ICU-acquired and 32...
Sporadic cases and rare outbreaks of Zika Virus (ZIKV) have been reported in India since 2016. Between June to early September 2024; the city of Pune in western India was affected with a large outbreak of ZIKV. Here we report the analysis of epidemiological; clinical and genomic characteristics of t...
The outbreak of mass mortality of Japanese flounder occurred in an aquaculture farm in Hebei province of China. This study isolated and identified Pseudomonas putida as the dominant bacterium from diseased Japanese flounder (Paralichthys olivaceus) based on morphological, physiological, biochemical...
Carbapenemase-producing Pseudomonas aeruginosa (CPPA) is known to cause outbreaks in healthcare settings. Outbreak investigations, including screening of contact patients and the environment, are key in infection prevention and control (IPC) management to contain them. The aim of this study was to d...
Considerations of the notion of preparedness have come to the fore in the recent pandemic, highlighting a need to be better prepared to deal with sudden, unexpected and unwanted events. However, the concept of preparedness is also important in relation to planned for and desired interventions result...
This study updates the COVID-19 pandemic surveillance in East Asia and the Pacific region that we first conducted in 2020 with 2 additional years of data for the region. First, we aimed to measure whether there was an expansion or contraction of the pandemic in East Asia and the Pacific region when...
In February 2022, the United Kingdom (UK) detected a cluster of monophasic Salmonella Typhimurium based on whole genome sequencing (WGS). Subsequently, several countries reported cases belonging to this cluster. Epidemiological, microbiological and traceability investigations pointed toward a chocol...
The One Health approach aims to balance and optimize the health of humans, animals, and ecosystems, recognizing that shared health outcomes are interdependent. A One Health approach to disease surveillance, control, and prevention requires infrastructure for coordinating, collecting, integrating, an...
We monitored severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in Haiti from 2020 to 2023. Despite Haitian coronavirus disease 2019 (COVID-19) travel restrictions and in the setting of a vaccination rate of 2.7%, the timing and lineage evolution of the Haiti epidemic mirrored wha...
Viral phylodynamics focuses on using sequence data to make inferences about the population dynamics of viral diseases. These inferences commonly include estimation of growth rates, reproduction numbers and times of most recent common ancestor. With few exceptions, existing phylodynamic inference app...
Aedes aegypti mosquitoes transmit numerous viruses that impact human health. Contemporary biological control programs aim to reduce Aedes fertility despite our limited understanding of interactions between the sexes required for reproduction. During mating, males transfer seminal fluid proteins (SFP...
Serratia marcescens, an opportunistic nosocomial Gram-negative bacterium pathogen, has emerged as an important cause of healthcare-associated infections owing to its acquisition of antimicrobial resistance genes (ARGs) and virulence factor determinants. Four carbapenem-resistant S. marcescens strain...
Despite high levels of global concern, little is known about the epidemiology of () infection (CDI) in Cambodia. This study aimed to identify the prevalence and risk factors for CDI, and molecular types of in hospitalized adults at Calmette Hospital, Phnom Penh, Cambodia. Stool samples were colle...
Mosquito-borne viral diseases pose a significant impact on human health, with the potential to cause widespread outbreaks of diseases. Monitoring viral genomes in mosquito populations can lead to informed risk assessment and promote early diagnosis. However, a standardized methodology is lacking to...
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a major contributor to healthcare-associated infections globally. The aim of this study was the impact of the COVID-19 pandemic on the genomic characteristics of P. aeruginosa, particularly clinical CRPA isolates. Clinical data of each patient we...
High rates of resistance to vancomycin are now being reported among invasive isolates of Enterococcus faecium, a major cause of healthcare-associated infections globally. The objective of this study was to generate a better understanding of emerging vanA sequence types (ST) of the pathogen. A tempor...
Genomic surveillance activity is a useful tool in epidemiologic investigations and monitoring of virus evolution. This study aimed to describe the COVID-19 outbreaks through SARS-CoV-2 virus genomic surveillance by whole genome sequencing. A cross-sectional study was conducted using archived clinica...
A sudden mass mortality involving 44 fallow deer () occurred in September 2020 at a game management area near Budapest, Hungary. The die-off affected both sexes and all age classes equally. On postmortem examination of 2 subadults and 1 fawn, we found average body condition, diffuse subcutaneous ede...
Japanese encephalitis is a viral disease caused by the Japanese encephalitis virus (JEV), primarily affecting rural areas of Asia and western Pacific region. China remains one of the main epicenters, experiencing a significant burden of human and animal cases despite vaccination efforts. The ecology...
Global viral threats underscore the need for effective genomic surveillance, but high costs and uneven resource distribution hamper its implementation. Targeting surveillance to international travelers in major travel hubs may offer a more efficient strategy for the early detection of SARS-CoV-2 var...
Fowl typhoid (FT) is a concerning poultry disease caused by Gallinarum.Five Gallinarum lineages (I to V) were demonstrated in South American farms. Gallinarum lineages have specific antimicrobial resistance / virulence genomic profiles.Main FT outbreaks in Brazil have been caused by the specific l...
In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account for the time passing since the divergence of pathogen variants...
Methicillin resistant Staphylococcus aureus (MRSA) is one of the main causes of hospital-acquired infections, but the diagnosis of MRSA pseudomembranous enteritis has faded in recent years. Here, we reported a pseudomembranous enteritis case in a young male patient caused by ST5 MRSA. Clinical data...
Human parainfluenza virus type 2 (HPIV2) is a clinically significant respiratory pathogen, which highlights the necessity of studies on its molecular evolution. This study investigated the evolutionary dynamics, phylodynamics, and structural characteristics of the HPIV2 fusion () gene using a compre...
In September 2023, an ongoing mpox outbreak emerged in South Kivu (Democratic Republic of the Congo) that spread to other regions and countries. Here we describe the epidemiological and genomic evolution of the outbreak between September 2023 and June 2024. Samples were collected from hospitalized p...
This genomic epidemiology study analyzed and isolates from animals and humans in Catalonia, Spain, between 2005 and 2023. Of 42 human tuberculosis (TB) cases, five were phylogenetically linked to livestock outbreaks, suggesting zoonotic transmission. The findings specifically indicate goats as a p...
The global circulation of SARS-CoV-2 has been extensively documented; however, the dynamics within Central America, particularly Nicaragua, remain underexplored. This study characterizes the genomic diversity of SARS-CoV-2 in Nicaragua from March 2020 through December 2022, utilizing 1064 genomes ob...
Vancomycin-resistant Enterococcus faecium (VRE) infections have increased in the last years. Hospital outbreaks have been described with a challenging microbiological diagnosis and control of the transmission. This is a prospective study of a nosocomial outbreak of VRE in a conventional hospitalizat...
Enteritidis (. Enteritidis) stands as a leading cause of human salmonellosis worldwide with a tendency to spread through contaminated foodstuffs and animals. In Hong Kong, a significant proportion of food products are imported, and many cases are often caused by the consumption of contaminated food,...
Klebsiella variicola has been implicated in neonatal intensive care unit (NICU) outbreaks previously and can be misidentified as Klebsiella pneumoniae. An increased incidence of K. pneumoniae bacteremia on the NICU of our institution was notified to the infection prevention and control (IPC) team in...
In this study, we conducted a comprehensive investigation into the Enterobacter cloacae complex (ECC), a group of notorious pathogens responsible for various hospital-acquired infections. We aimed to gain critical insights into antimicrobial resistance profiles and genomic diversity among 17 ECC iso...
Orthohantavirus hantanense (HTNV) poses a substantial global public health threat due to its role in causing hemorrhagic fever with renal syndrome (HFRS). HTNV outbreaks are particularly prevalent in the Gyeonggi and Gangwon Provinces of the Republic of Korea (ROK). This study aimed to evaluate the...
To report the epidemiologic, microbiologic and genetic investigation of a large outbreak of carbapenem-resistant Klebsiella pneumoniae associated with gastrointestinal endoscopy, including infection control interventions. Internal and external audits of reprocessing procedure, systematic microbiolog...
Genomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization. However, its application is limited by the poor cost-efficiency of short-rea...
The rapid sequence typing (ST) of bacterial strains is crucial for effective nosocomial infection control and mitigating the spread of nosocomial pathogens, e.g., . While accurate in identifying strains, current typing methods are often impractical in clinical settings due to their time-consuming n...
Noroviruses represent one of the leading causes of outbreaks and sporadic acute gastroenteritis (AGE) cases across all age groups. Although the GII.4 norovirus has been identified as the primary cause of most AGE outbreaks, the transient predominance of other genotypes has been reported globally. In...
Human rhinoviruses (RVs) primarily cause the common cold, but infection outcomes vary from subclinical to severe cases, including asthma exacerbations and fatal pneumonia in individuals who are immunocompromised. To date, therapeutic strategies have been hindered by the high diversity of serotypes....
Drivers of tuberculosis (TB) transmission in India, the country estimated to carry a quarter of the world's burden, are not well studied. We conducted a genomic epidemiology study to compare epidemiological success, host factors, and drug resistance among the 4 major Mycobacterium tuberculosis (Mtb)...
Shenzhen, a city with a substantial mobile population, was identified as the first discovered region of human immunodeficiency virus-1 (HIV-1) CRF55_01B and epicenter of its severe epidemic. During the implementation of venue-based behavioral interventions and the "treat-all" policy, identifying the...
Antimicrobial resistance in species poses risks to both human and marine mammal health. Whole genome sequencing of spp. can be utilized to screen for antimicrobial resistance genes and allelic variants to provide mechanistic insights in ways that PCR screening and phenotypic interpretation cannot....
Pseudomonas aeruginosa is one of the main causes of hospital infections that are difficult to manage because of multidrug resistance (MDR). The aim of this study was to describe a molecular investigation on 19 clinical and 14 isolates from the environment in the Hub hospital of the Molise region, ce...
To enumerate and describe the effect of whole genome sequencing (WGS) on epidemiological investigations of healthcare-associated transmission of nontuberculous mycobacteria (NTM). Systematic review. We performed a literature search using targeted search terms to identify articles meeting inclusion c...
In 2013, foodborne outbreaks in Japan were linked to non-O1, non-O139 . However, laboratory tests have detected several serogroups, making it difficult to determine the causative agent. Therefore, whole-genome analyses revealed that only serogroup O144 possesses a genomic island with a type III sec...
We conducted 4 years of epidemiologic and genomic surveillance of single-dose effectiveness of a killed whole-cell oral cholera vaccine (kOCV) and Vibrio cholerae transmission in the Democratic Republic of the Congo. We enrolled 1,154 patients with diarrhea; 342 of those had culture-confirmed choler...
Whole-genome analysis has provided insights into the evolution of and, recently, into circulating strains that cause lymphogranuloma venereum (LGV). A large LGV outbreak of a new -genotype, L2b, was first reported in Europe in the early 2000s, primarily affecting men who have sex with men (MSM), an...
continues to pose a significant risk to the health and production of striped catfish () in Vietnam. Whilst recent advances in genomic sequencing provide an insight into the global genomic diversity of this important fish pathogen, genome-wide analysis of Vietnamese isolates recovered over time is la...
The COVID-19 epidemic has shown regional variations in transmission and outcomes. As a primary hotspot in Chad, N'Djamena is crucial for comprehensive epidemiological investigation. Our study employed two methodologies: seroprevalence data collection and whole-genome sequencing of SARS-CoV-2 strains...
Chikungunya virus (CHIKV) is an emerging cause of acute encephalitis syndrome (AES) in India, with limited data on its role in childhood AES in southern India. We systematically evaluated children with AES in southern India during a non-epidemic period for CHIKV. Serum and cerebrospinal fluid (CSF)...
This study investigates the evolution and genetic diversity of SARS-CoV-2 strains circulating in Morocco to track the spread, clade distributions and mutations of the virus across various regions from February 2020 to June 2024. The genome sequences were retrieved from the GISAID database. A total o...
Coronavirus disease 2019 (COVID-19) continues to pose a significant public health threat, requiring epidemiological and genomic surveillance. Next generation sequencing (NGS) is commonly utilized for monitoring viral evolution at a high cost. This study evaluated pooled sequencing as a cost-effectiv...
The emergence of SARS-CoV-2 variants has significantly impacted the global response to the COVID-19 pandemic. This review examines the genetic diversity of SARS-CoV-2 variants, their roles in epidemiological tracking, and their influence on viral fitness. Variants of concern (VOCs) such as Alpha, Be...
Acinetobacter baumannii (A. baumannii) causes severe infections among intensive care units (ICUs) and patients who are mechanically ventilated. According to the European Centre for Disease Prevention and Control data for 2018 the prevalence of A. baumannii in Polish ICUs was higher than in other Eur...
Vibrio cholerae remains a significant public health threat in Sub-Saharan Africa and the East Mediterranean Region, where recurrent outbreaks are driven by inadequate water, sanitation, and hygiene infrastructure, climatic variability, and socio-political instability. This review explores the persis...
Tuberculosis is a global public health concern, and understanding Mycobacterium tuberculosis transmission routes and genetic diversity of M. tuberculosis is crucial for outbreak control. This study aimed to explore the genomic epidemiology and genetic diversity of M. tuberculosis in Ecuador by analy...
Respiratory disease (RD) is a worldwide leading threat to the pig industry, but there is still limited understanding of the pathogens associated with swine RD. In this study, we conducted a nationwide genomic surveillance on identifying viruses, bacteria, and antimicrobial resistance genes (ARGs) fr...
Clinical re-breaks of PRRSV on sow farms are a frustrating reality for producers and practitioners. The underlying mechanisms allowing for a single viral variant to persist and cause repeated clinical outbreaks within a herd that should have strong immunity, through recent exposure to a highly simil...
Since the onset of the pandemic, many SARS-CoV-2 variants have emerged, exhibiting substantial evolution in the virus' spike protein, the main target of neutralizing antibodies. A plausible hypothesis proposes that the virus evolves to evade antibody-mediated neutralization (vaccine- or infection-in...
Several areas of the world suffer a notably high incidence of Shiga toxin-producing . To assess the impact of persistent cross-species transmission systems on the epidemiology of O157:H7 in Alberta, Canada, we sequenced and assembled O157:H7 isolates originating from collocated cattle and human po...
The unprecedented sequencing efforts during the COVID-19 pandemic paved the way for genomic surveillance to become a powerful tool for monitoring the evolution of circulating viruses. Herein, we discuss how a state-of-the-art artificial intelligence approach called protein language models (pLMs) can...
Bacterial typing at whole-genome scales is now feasible owing to decreasing costs in high-throughput sequencing and the recent advances in computation. The unprecedented resolution of whole-genome typing is achieved by genotyping the variable segments of bacterial genomes that can fluctuate signific...
Human Parvovirus B19 (hB19V) is a widespread virus, causing in children and several clinical manifestations from acute to persistent infections in adults. In early 2024, ECDC reported an increased human Parvovirus B19 circulation in 14 European countries. A hB19V outbreak was also reported in Tusca...
The phylogeographic inference approach aims to connect genomic data with epidemiology to understand the spread and evolution of pathogens using visualization of spatiotemporal reconstructions. Orthohantavirus hantanense (HTNV), the causative agent of hemorrhagic fever with renal syndrome (HFRS), rep...
Ceftriaxone-resistant Enterobacterales remain a public health threat; contemporary data investigating their molecular epidemiology are limited. Five hundred consecutive ceftriaxone-resistant (MIC ≥ 4 µg/mL) Enterobacterales bloodstream isolates were collected between 2018 and 2022 from three Marylan...
Whole genome sequencing (WGS) and clinical review were used to characterize 14 cases of central line-associated bloodstream infection (CLABSI) due to . WGS, which demonstrated disparate strains, suggested that 42.9% of CLABSI cases were due to contamination, while clinical review suggested that 57....
Staphylococcus aureus is one of the most common pathogens that colonizes human skin/mucous membranes, where it causes local infection that can progress to invasive infection, resulting in high morbidity and mortality worldwide. This study aimed to investigate the antibiotic susceptibility and molecu...
The SARS-CoV-2-induced disease, COVID-19, remains a worldwide public health concern due to its high rate of transmission, even in vaccinated and previously infected people. In the endemic state, it continues to cause significant pathology. To elu- cidate the viral mutational changes and screen the e...
Mixed infection with multiple strains of the same pathogen in a single host can present clinical and analytical challenges. Whole genome sequence (WGS) data can identify signals of multiple strains in samples, though the precision of previous methods can be improved. Here, we present MixInfect2, a n...
Interactions between microbial communities and the host can modulate mosquito biology, including vector competence. Therefore, future vector biocontrol measures will utilize these interactions and require extensive monitoring of the mosquito microbiome. Metabarcoding strategies will be useful for co...
Emerging human pathogens of animal origin have become an increasing public health concern in recent years. The aim of this study was to investigate the transmission of group B streptococcus (GBS) clonal complex (CC) 61 strains in the southern Chinese population and analyze their genetic characterist...
(CHPV) is an arthropod-borne virus linked to encephalitis in humans, primarily in India. Its evolutionary dynamics and transmission pathways remain poorly understood due to limited genomic data. This study analyzed 23 publicly available CHPV genomes, including isolates from humans, sandflies, and a...
causes life-threatening infections in immunocompromised hosts, including hospitalized neonates. This pathogen is intrinsically resistant to fluconazole, while uncommon strains resistant to multiple antifungal drugs, including voriconazole, amphotericin B, and echinocandins, have also been reported...
Recombination, a process of genetic exchange between distinct organisms, has played a critical role in the emergence of SARS-CoV-2 variants such as the XEC recombinant. This study provides a detailed genomic and structural characterization of XEC, derived from the recombination of lineages KP.3.3 (d...
Kalamari is a resource that supports genomic epidemiology and pathogen surveillance. It consists of representative genomes and common contaminants. Kalamari also contains a custom taxonomy and software for downloading and formatting the data.
The coronavirus disease 2019 (COVID-19) pandemic, driven by the rapid evolution of the SARS-CoV-2 virus, has led to the emergence of multiple variants with significant impacts on global health. This study aims to analyze the evolutionary trends and mutational landscape of SARS-CoV-2 variants circula...
Despite over four decades since its emergence, canine parvovirus type 2 (CPV-2) remains a relevant disease for dogs. Few studies, primarily only recent ones based on phylodynamic and phylogeography approaches, have highlighted the impact of rapid and long-distance transport of dogs on the CPV-2 spre...
Salmonella enterica serovar Enteritidis (S. Enteritidis) is a commonly reported pathogen which adapts to multiple hosts and causes critical disease burden at a global level. Here, we investigated a recently derived epidemic sublineage with multidrug resistance (MDR), which have caused extended time-...
are opportunistic pathogens which can cause mastitis in dairy cattle. mastitis often has a poor cure rate and can lead to the development of chronic infection, which has an impact on both health and production. However, there are few studies which aim to fully characterize by whole-genome sequenci...
Humanity faces an ongoing battle at the microscopic level to identify, contain, and treat outbreaks of numerous pathogens each year. Global genomic surveillance is the first step in monitoring outbreaks, but high-throughput methods are expensive and time-consuming. To solve this problem, we designed...
Given the rapid cross-country spread of SARS-CoV-2 and the resulting difficulty in tracking lineage spread, we investigated the potential of combining mobile service data and fine-granular metadata (such as postal codes and genomic data) to advance integrated genomic surveillance of the pandemic in...
African swine fever (ASF), a severe and highly contagious haemorrhagic viral disease of pigs, is becoming a major threat not only in Malaysia but around the world. The first confirmed case of ASF in Malaysia was reported in February 2021. Despite the emergence of ASF in Malaysia, genetic information...
In dengue hyperendemic regions, the evolution of the virus is marked by frequent virus introduction/reintroduction and clade replacement events, occasionally linked to an epidemic outbreak. From 2023 onwards, an increase in the detection of DENV-3 cases has been reported in different regions of Braz...
Infections by carbapenem-resistant Enterobacterales (CRE) in hospitals represent a severe threat but little is known on outbreaks in rehabilitation wards caused by Klebsiella pneumoniae producing Klebsiella pneumoniae Carbapenemase (KPC-Kp). We report an outbreak by KPC-Kp, in a neurorehabilitation...
Group A Streptococcus (GAS) has recently reemerged as a leading cause of both mild and severe invasive infections worldwide, with recent upsurges in invasive disease among children and adults. Notwithstanding a partial synchronicity with the COVID-19 pandemic, this rapid global dissemination of more...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is recognized as a common clinical conditional pathogen with bla gene-mediated multidrug-resistance that is a significant threat to public health safety. Timely and effective infection control measures are needed to prevent their spread. We conduct...
Genomic surveillance is extensively used for tracking public health outbreaks and healthcare-associated pathogens. Despite advancements in bioinformatics pipelines, there are still significant challenges in terms of infrastructure, expertise, and security when it comes to continuous surveillance. Th...
Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen affecting the pig industry, is an RNA virus with high genetic diversity. In this study, 12,299 clinical samples were collected from northern China during 2021-2023 to investigate the molecular epidemiological characte...
The growing issue of drug resistance, particularly multidrug-resistant TB (MDR-TB), has exacerbated this problem. The rise of drug resistance TB is a severe global health concern. In Thailand, a persistent community outbreak of primary MDR-TB has been confirmed in the Tha Maka district of Kanchanabu...
Human noroviruses are the leading cause of non-bacterial shellfish-associated gastroenteritis. In 2022, a multi-jurisdictional norovirus outbreak associated with contaminated oysters occurred that involved hundreds of illnesses. Here, we conducted genetic analysis on 30 clinical samples associated w...
The etiological agent for the coronavirus disease 2019 (COVID-19), the SARS-CoV-2, caused a global pandemic. Although mRNA, viral-vectored, DNA, and recombinant protein vaccine candidates were effective against the SARS-CoV-2 Wuhan strain, the emergence of SARS-CoV-2 variants of concern (VOCs) reduc...
In high-income countries, dogs and cats are often considered members of the family. Because of this proximity, it has been suggested that pets and humans might exchange bacterial species from their gut microbiota, with multidrug resistant bacteria being of particular concern. The aim of this study w...
This research delves into the evolving dynamics of antibiogram trends, the diversity of antibiotic resistance genes and antibiotic efficacy against Vibrio cholerae strains that triggered the cholera outbreak 2022 in Odisha, India. The study will provide valuable insights managing antimicrobial resis...
Brucellosis, a zoonotic disease caused by Brucella spp. globally, is of great significance not only to livestock but also to public health. The most significant of the twelve species is Brucella melitensis. This article is devoted to the endemic region of Iran and aims to uncover the molecular epide...
The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for data analysis methods and bioinformatics expertise, which can be a bottleneck for many laboratories. At Sciensano, the Belgian national public health institute, an intuitive a...
Immunoinformatics, an integrative field consisting of bioinformatics and immunology, has showcased its potential in addressing zoonotic diseases, as evidenced during the Coronavirus disease 2019 (COVID-19) pandemic. However, its application in livestock health remains largely untapped. This opinion...
Pertussis (or whooping cough) has experienced a global resurgence despite widespread vaccine efforts. In China, the incidence of pertussis has rapidly increased, particularly following the COVID-19 pandemic. Whole-genome sequencing analysis was performed on 60 strains isolated in Beijing from 2020-...
Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are highly prevalent in long-term care (LTCF) settings. In order to estimate the acquisition rate of ESBL-producing Escherichia coli and Klebsiella pneumoniae in LTCF settings, and identify clinical and environmental risk fact...
New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could improve our understanding of viral biology and highlight new variants that warrant further study. Here we develop a generic, anal...
Streptococcus suis (S. suis) is a major pathogen for pigs, causing large economic losses to the swine industry. Moreover, this bacterium has a zoonotic potential, being capable of infecting humans in close contact with pigs or, less frequently, through contact with pork products. Given its importanc...
The major histocompatibility complex (MHC) is a cluster of functionally related genes encoding proteins which, among other functions, mediate immune system activation. While the MHC of many vertebrates has been extensively studied, less is known about the amphibian MHC. This represents an important...
Between April and November 2023, 27 unexplained human deaths that presented with swelling of the arms, skin sores with black centers, difficulty in breathing, obstructed swallowing, headaches, and other body aches were reported in Kyotera District, Uganda by the Public Health Emergency Operations Ce...
Epizootic hemorrhagic disease (EHD) is a noncontagious viral infection that can cause important economic losses on dairy farms. This study aimed to identify epidemiological and genetic factors influencing the susceptibility and severity of EHD in Holstein dairy cattle during the 2023 outbreak in Spa...
The infections of bacterial origin represent a significant problem to the public healthcare worldwide both in clinical and community settings. Recent decade was marked by limiting treatment options for bacterial infections due to growing antimicrobial resistance (AMR) acquired and transferred by var...
This paper presents an update on the content, accessibility and analytical tools of the EnteroBase platform for web-based pathogen genome analysis. EnteroBase provides manually curated databases of genome sequence data and associated metadata from currently >1.1 million bacterial isolates, more rece...
SARS-CoV-2, the virus responsible for COVID-19, has undergone significant genetic evolution since its emergence in 2019. This study examines the genomic diversity of SARS-CoV-2 in Brazil after the worst phase of the pandemic, the wider adoption of routine vaccination, and the abolishment of other no...
Due to the limited treatment options, the widespread of carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a serious clinical challenge. The emergence of Klebsiella pneumoniae carbapenemase (KPC) and New Delhi metallo-β-lactamase (NDM) coproducing CRKP (KPC-NDM-CRKP) further aggravates thi...
In clinical practice, the emergence of ST11-K64 carbapenem-resistant Klebsiella pneumoniae (ST11-K64 CRKP) has become increasingly alarming. Despite this trend, limited research has been conducted to elucidate the clinical and molecular characteristics of these strains. This study aimed to comprehen...
Patients with severe COVID-19 may require intensive care unit (ICU) admission to manage life-threatening complications. However, ICU admission is associated with an increased risk of acquiring nosocomial infections caused by multidrug-resistant (MDR) bacteria, particularly carbapenem-resistant Enter...
Ciprofloxacin is important for treatment of severe or invasive infections in humans. As laboratories transition from phenotypic to genomics-based methods for determining ciprofloxacin non-susceptibility, it is important to define the correlation between genetic determinants of resistance and phenot...
The NRCS-A strain has emerged as a global cause of late-onset sepsis associated with outbreaks in neonatal intensive care units (NICUs) whose transmission is incompletely understood. Demographic and clinical data for 45 neonates with and 90 with other coagulase-negative staphylococci (CoNS) isolat...
Infections by carbapenemase-producing (CP-Pa) are concerning due to limited treatment options. The emergence of multidrug-resistant (MDR) high-risk clones is an essential driver in the global rise of CP-Pa. Insights into the molecular epidemiology of CP-Pa are crucial to understanding its clinical...
Background infection (CDI) is a severe infection that needs to be monitored. This infection predominantly occurs in hospitalised patients after antimicrobial treatment, with high mortality in elderly patients.AimWe aimed at estimating the incidence of CDI in Italian hospitals over 4 months in 2022.M...
The São Paulo state citrus belt in Brazil is a major citrus production region. Since at least 1957, citrus plantations in this region have been affected by citrus canker, an economically damaging disease caused by subsp. (). For about 50 years, until 2017, a citrus canker eradication programme was...
No abstract available
Bacterial meningitis and septicemia caused by is a serious infection that requires immediate medical attention and prompt treatment. In the United States, cases of serogroup Y increased sharply in 2023, leading to a CDC health advisory issued in March 2024, alerting public health agencies and heal...
Hypervirulent (hvKp) has emerged as a significant public health threat owing to its ability to cause invasive infections. This study aimed to investigate the clinical characteristics and epidemiological associations of hypervirulent Klebsiella pneumoniae (hvKp) and classical (cKp) among patients t...
To elucidate the molecular epidemiology, virulence repertoire and resistance gene characteristics of carbapenem-resistant complex (CRECC) in bloodstream infections (BSI), thereby providing evidence for precision therapy and infection control. We retrospectively collected 13 non-replicate CRECC-BSI...
The treatment of carbapenem-resistant (CRAB) infection faces great challenges. The purpose of this study was to investigate a suspected outbreak of CRAB infections in a cardiovascular surgical ICU to provide reference for clinical prevention and control. Patients infected with CRAB from 4 August to...
The manipulation of the gut microbiota of disease vectors has emerged as a new approach to use in the integrated control of vector-borne diseases. For this purpose, a deep knowledge of their gut microbial communities is essential. To our knowledge, to date, no study has documented the gut microbiome...
This study aimed to perform laboratory testing and traceability analysis of suspicious samples from a foodborne disease outbreak caused by () in a hospital in Ma'anshan City, Anhui Province, and to evaluate the application of whole-genome sequencing technology in the tracing of foodborne disease ou...
Candidemia, a life-threatening infection with rising incidence and substantial mortality, necessitates improved management strategies. This study aimed to investigate the clinical features, species distribution, risk factors, antifungal susceptibility, and molecular epidemiology of isolates from ca...
Carbapenem-resistant hypervirulent (CR-hvKP) represents a critical public health threat in China, characterized by the convergence of multidrug resistance and hypervirulence. The emergence of ceftazidime/avibactam (CZA) resistance further complicates clinical management. This study aimed to elucida...
During the COVID-19 pandemic, the emergence and detection of SARS-CoV-2 variants of concern highlighted the pivotal role of genomic epidemiology in public health decision and policy making. The pandemic also revealed a need for genomic epidemiologists to effectively engage with a broader audience, i...
Multidrug-resistant (MDR-AB) poses a critical threat in neonatal intensive care units (NICUs), however few studies have reported the molecular characterization of isolates from the NICU in China. This study aims to describe the molecular, biofilm and motility characteristics related to carbapenem...
Foodborne enteric infections are a major public health and economical burden, yet their surveillance often relies on latent indicators that delay containment efforts by several days and weeks. Conversely, whole metagenome shotgun sequencing of communal wastewater allows continuous monitoring of ente...
The European Antimicrobial Resistance Genes Surveillance Network (EURGen-Net) was established in 2017 to support the European survey of carbapenem- and/or colistin-resistant Enterobacterales in 37 countries. In parallel to large-scale international structured surveys with a central whole genome sequ...
Active screening for fecal colonization by carbapenem-resistant (CRE-FC) and interventions in intensive care unit (ICU) wards have become important measures to prevent carbapenem-resistant (CRE) infection. However, limited data are available on the molecular epidemiology and homology analysis of C...
Classical swine fever (CSF) is a highly contagious disease affecting domestic pigs and wild boars, posing a serious threat to the global swine industry. In Japan, CSF re-emerged on a pig farm in Gifu Prefecture in 2018, just 3 years after the country was declared CSF-free. The CSF virus (CSFV) was s...
After coronavirus disease 2019 pandemic restrictions, () re-surged widely across the world. This study aimed to determine the genomic epidemiological characteristics of resurging , which has dominated the respiratory infection outbreak in Beijing, China, since mid-September 2023. samples were coll...
The rapid dissemination of carbapenem-resistant (CRE) poses a severe global health threat due to limited treatment options. Polymyxin is currently considered a last-resort therapy for human infections caused by CRE. The increasing clinical use of polymyxin has resulted in alarming resistance rates....
Carbapenem-resistant (CRKP) infection has become a global public health problem in recent years. However, ceftazidime-avibactam-resistant (CAZ/AVI-R) () has emerged during treatment for CRKP infection. Therefore, understanding the molecular epidemiological characteristics and resistance-related mu...
Aedes aegypti and Aedes albopictus are the most competent vectors of multiple human arboviral diseases, posing a global public health concern, particularly in Bangladesh. While there are numerous genomic resources available worldwide, the genomic resources from Southeast Asian countries are scarce....
Group B (GBS) is a major cause of pregnancy complication and neonatal morbidity and mortality worldwide, particularly in developing regions. Despite its clinical importance, data on the molecular epidemiology, antibiotic resistance, and virulence factors of GBS in tropical regions are scarce. This...
The 2024 chikungunya virus (CHIKV) outbreak in Mansehra, Khyber Pakhtunkhwa, Pakistan, marked a significant public health event, providing a unique opportunity to investigate the genomic diversity and evolutionary dynamics of circulating strains. Using metagenomic next-generation sequencing (mNGS),...
The 2022 multi-country outbreak of monkeypox virus (MPXV) sparked global health concerns, as cases emerged increasingly outside traditionally endemic regions. This outbreak, spanning 2022-2023, was primarily driven by the clade IIb strain. Subsequently, a surge of MPXV cases caused by clades Ia and...
Highly pathogenic avian influenza (HPAI) virus A (H5N1) was first detected in North America in 2021. Ongoing spillover events from wild to domestic birds and subsequent transmission between domestic birds resulted in Canada's largest recorded epidemic of HPAI. Between December 2021 and April 2024, 4...
Pathogen genomics is rapidly becoming a cornerstone in the surveillance and response to infectious diseases. However, there is little evidence on how it shapes strategies for effective public health response and decision-making. This paper presents the evaluation protocol for the Australian Pathogen...
The molecular epidemiological methods are important in the study of transmission dynamics and population structure of Mycobacterium tuberculosis strains circulating in a geographical region. A total of 104 patients were selected who were diagnosed for the first time with pulmonary tuberculosis and w...
Carbapenem-resistant (CRPA) poses a significant global health risk, particularly for immunocompromised individuals. This study documents an outbreak of CRPA strains co-harboring and on IncP-2 plasmids in a Chinese tertiary hospital, resulting in poor outcomes for transplant patients. 17 ST313 V...
Aedes aegypti is the main vector of several arboviruses including chikungunya, dengue, yellow fever and Zika. Beyond arboviruses, Aedes aegypti harbours insect-specific viruses (ISVs), which can modulate mosquito's ability to transmit diseases by interfering with viral processes and triggering immun...
The COVID-19 pandemic started in Wuhan China and rapidly transmitted worldwide, the illness is characterised by respiratory manifestations like coughing, breathing difficulties and pneumonia that could lead to death. Real-time whole genome sequencing of severe acute respiratory syndrome corona virus...
Carbapenem-resistant hypervirulent (CR-hvKP) poses a significant public health challenge. This study investigated the molecular epidemiology, antimicrobial resistance patterns, clinical characteristics, and risk factors of CR-hvKP infection in Huaian, China. We retrospectively studied patients infe...
Highly pathogenic avian influenza (HPAI) viruses with H5 hemagglutinin (HA) genes (clade 2.3.4.4b) are causing an ongoing panzootic in wild birds. Circulation of these viruses is associated with spillover infections in multiple species of mammals, including a large, unprecedented outbreak in America...
Arboviruses (i.e., Arthropod-borne viruses) pose a threat to human health worldwide. This taxonomically-diverse group includes numerous viruses that recurrently spread into new regions. Therefore, periodic surveys of the arboviral diversity in a given region can help optimize the diagnosis of arbovi...
To analyse the impact of the COVID-19 pandemic on the epidemiological situation of invasive meningococcal disease (IMD) and molecular characteristics of Neisseria meningitidis isolates causing IMD in the Czech Republic. The study was based on IMD surveillance data for 2018-2024 (as of 27 May 2024),...
Rarely does occur in bloodstream infections (BSI), although it's typically found in cystic fibrosis. This study aims to decipher the genetic map and obtain insights of clinical symptoms into Pandoraea from BSI patients. 30 suspected BSI patients' diagnostic records and medical histories were record...
Here we report on a process evaluation conducted as part of a large multisite non-randomised trial of the effectiveness of a novel whole genome sequence report form (SRF) to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours during the COVID -19 pandemic....
Escherichia coli is a commensal organism but may become pathogenic by the acquisition of virulence factors involved with intestinal (IPEC) or extraintestinal (ExPEC) infections. Some strains, known as hybrids, may harbour virulence determinants of both IPEC and ExPEC pathotypes, increasing their vir...
Salmonellosis, caused by non-typhoidal , is a common foodborne gastrointestinal infection. Third-generation cephalosporins are recommended as the first-line treatment for infections. Our study aimed to investigate the molecular epidemiology, antimicrobial resistance, and the transmission of extende...
Monophasic Typhimurium sequence type 34 (mSTM ST34) has emerged as a significant global health threat, but our understanding of its genomic epidemiology and potential public health implications in international and regional contexts remains limited. This study aims to fill this crucial gap by asses...
The emergence of multidrug resistance in is a serious global problem, and gonorrhea may soon become an incurable disease. The aim of the study was to characterize the population in Russia from 2015 to 2023 and predict the potential spread of the most concerning clones. A total of 996 N isolates we...
is primarily transmitted via contaminated food and can cause listeriosis, an infection often associated with sepsis and meningitis in at-risk individuals. Accurate outbreak detection relies on whole genome sequencing (WGS) and core genome multilocus sequence typing (cgMLST), which use allele thresho...
Carbapenem-resistant hypervirulent (CRhvKP) poses a significant global health threat due to its enhanced virulence and resistance. This study analyzed 5,036 publicly available genomes from China (2005-2023), identifying 1,538 CRhvKP genomes, accounting for 44.6% of carbapenem-resistant isolates an...
Dengue, an acute febrile disease caused by dengue virus (DENV) infection, is endemic to Indonesia. During early 2020, an outbreak of severe dengue occurred in Maumere, East Nusa Tenggara province, a region with low dengue endemicity with limited data on the characteristics of the circulating DENV. B...
The rapid detection and containment of healthcare-associated infections (HCAIs) is critical in preventing and controlling infectious disease outbreaks within healthcare settings. Whole genome sequencing (WGS) has emerged as a powerful tool for tracking the transmission dynamics of pathogens and when...
Methicillin-resistant (MRSA) exhibits diverse genotypes with varying virulence and resistance profiles, particularly in the context of bloodstream infections (BSI). This study investigates the prevalence of the , , and genes among MRSA isolates from bloodstream infections in southern China and ana...
The methicillin-resistant Staphylococcus aureus (MRSA) genome varies by geographical location. This study aims to determine the genomic characteristics of MRSA using whole-genome sequencing (WGS) data from medical centers in Mexico and to explore the associations between antimicrobial resistance gen...
Romania is currently facing a prolonged measles outbreak. The aim of the study was to analyse the circulating human measles virus (HMV) strains by combining whole genome sequencing (WGS) with phylogenetic analysis, with a focus on the haemagglutinin gene. We conducted an observational study in the f...
is a clinically important pathogen capable of causing serious nosocomial infections and acquiring resistance to antimicrobials, particularly carbapenems, making treatment difficult and prolonging hospital stays. In Latin America, high carbapenem-resistance rates have been described among isolates,...
poses a profound global health threat because of multidrug resistance and its association with nosocomial infections. However, standard clinical diagnostics often report it together with other species as complex (ABC), which unavoidably conceals the attribution of non- species. This study reported...
Advances in deforestation and climate change directly cause changes in habits and the distribution of Culicidae across the globe, especially mosquitoes of medical importance and the main vectors of arboviruses. The viral metagenomics technique can be an important tool in characterizing viral diversi...
Virus surveillance using metagenomic analysis of sequences from wastewater appears to be a promising epidemiological tool for monitoring the spread of viruses in large populations. Its use during the COVID-19 pandemic enabled the monitoring of SARS-CoV-2 circulation without requiring the collection...
Foodborne outbreaks affecting millions of people worldwide are a significant and growing global health threat, exacerbated by the emergence of new and increasingly virulent foodborne pathogens. Traditional methods of detecting these outbreaks, including culture-based techniques, serotyping and molec...
Antimicrobial resistance (AMR) is a growing threat in healthcare systems, particularly in the management of infections in critically ill patients. This study highlights how to identify clusters and putative sharing of mobile genetic elements, such as transposons, in the hospital setting using long-r...
Methicillin-resistant Staphylococcus aureus (MRSA) continues to be a significant cause of healthcare-associated infections (HAIs). In this study, we aimed to characterize the MRSA isolates obtained from HAIs. A total of 200 clinical and 13 nasal MRSA isolates were collected and tested. The samples w...
infects more than half of the world's population and is the main risk factor for gastric cancer, although only a small percentage of those infected develop the disease. This disparity suggests the influence of bacterial, environmental, and host susceptibility factors. In Colombia, the department of...
Accurate identification of serovars for source attribution in foodborne illness outbreaks. Traditional serotyping, which relies on antigenic properties, continues to serve as gold standard; however, advances in whole-genome sequencing (WGS) have enabled to the development of in-silico serotyping to...
Whole-genome sequencing (WGS) is transforming communicable disease surveillance globally. The National Institute for Communicable Diseases, South Africa, participates in national laboratory-based surveillance for human isolates of . This study was to investigate human isolates from South Africa, 20...
SARS-CoV-2 remains globally circulating, yet post-pandemic comprehensive molecular, serological, and population-level immunity data from low-resource settings such as Ethiopia are limited. This study employed genomic surveillance with seroepidemiological assessment to characterize the epidemiology o...
Whole genome sequencing (WGS) was performed on 10 extensively drug-resistant (XDR) ST235 isolates to investigate potential healthcare-associated transmission of XDR P. aeruginosa ST235 within a U.S. military treatment facility (MTF), assess its environmental persistence, and determine its genomic r...
(Group A , GAS) is a re-emerging human pathogen responsible for a wide spectrum of diseases, from mild pharyngitis to life-threatening invasive infections that have risen globally in recent years. We performed a retrospective genomic and epidemiological analysis of 61 invasive Group A (iGAS) isolat...
Antimicrobial resistance (AMR) is a significant global health challenge that threatens the effectiveness of antibiotics and other antimicrobial agents. Here, we examined the molecular mechanisms that contribute to bacterial resistance, including alterations at target sites, enzymatic inactivation, e...
Whole-genome sequencing (WGS) is increasingly used as the primary typing method for foodborne disease surveillance. It offers high-resolution cluster analysis, interoperability, and comprehensive pathogen characterization. However, implementing WGS-based foodborne surveillance also poses challenges....
The World Health Organisation recommends integrating viral genome sequences and sentinel surveillance data. We report progress in linking clinical, virology, and sequence data to enable genomic surveillance of influenza, respiratory syncytial virus (RSV), and severe-acute-respiratory-syndrome corona...
The spike (S) gene of SARS-CoV-2 is pivotal to the processes of cell entry, immune evasion, and the adaptation of the host. This study aimed to comprehensively characterize the SARS-CoV-2 spike gene variants circulating in Iraq and assess the functional consequences of their mutations on ACE2 recept...
To investigate the geospatial epidemiology, clinical features, treatment patterns, and antimicrobial resistance (AMR) trends of bloodstream infections (BSIs) in Indian intensive care units (ICUs) participating in a standardized healthcare-associated infection (HAI) surveillance program from 2017 to...
The rise of antimicrobial resistance (AMR) in serovar Typhi poses a serious threat to global enteric fever control. In particular, the emergence of resistance to third-generation cephalosporins and azithromycin critically undermines available treatment options. Sustained genomic surveillance of hig...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing threat to global health. Wastewater-based surveillance (WBS) has proven to be an important tool for tracking the dissemination of SARS-CoV-2 variants of concern (VOCs) in the community. In Canada, metagenomic analysis of airc...
Understanding the genetic and genomic underpinnings of infectious disease outbreaks has emerged as a frontier of epidemiology. Here, we argue that epistasis-where the phenotypic effects of mutations or gene variants are dictated by the presence of other mutations or genes-should become a focus of ge...
The rise of antibiotic-resistant poses a significant global health threat. Plasmids, as mobile genetic elements, play a critical role in bacterial adaptation by facilitating the spread of resistance genes. To analyze plasmid-mediated antibiotic and heavy metal resistance in clinical strains, 33 s...
Typhimurium (STm) is a globally distributed foodborne pathogen showing increasing antimicrobial resistance (AMR), particularly to fluoroquinolones and third-generation cephalosporins. Multiple countries have implemented ongoing genomic surveillance programs for , but comprehensive global analyses in...
The New Variant Assessment Platform (NVAP) was a global genomic surveillance programme established by the UK Health Security Agency (UKHSA) in April 2021. The NVAP offered sequencing and biological assessment capabilities, technical assistance, and training to support the detection and assessment of...
Respiratory syncytial virus (RSV), a major cause of acute respiratory infections (ARIs) globally, poses a significant threat, especially to vulnerable populations. However, the spatial transmission dynamics of RSV strains, including the influence of environmental and socioeconomic factors, remain in...
Whole genome sequencing (WGS) is the gold standard for identifying emerging variants during epidemics but is resource intensive. Traditionally, a low RT-qPCR cycle threshold (Ct) is used to select samples with presumed high viral loads but whether better alternatives exist is unclear. This study int...
The multiple waves of intercontinental transmission of the highly pathogenic avian influenza (HPAI) H5Nx Gs/GD lineage since its identification in 1996 are testament to its resistance to control and prevention efforts. Knowledge of the predictors of HPAI international spread can help identify streng...
Whole genome sequencing (WGS) is increasingly supporting routine pathogen surveillance at local and national levels, providing comparable data that can inform on the emergence and spread of antimicrobial resistance (AMR) globally. However, the potential for shared WGS data to guide interventions aro...
Monkeypox virus (MPXV) is an emerging zoonotic pathogen with increasing human-to-human transmission. Since the first case in Shandong Province in June 2023, 61 cases were reported by the end of 2024, predominantly among young men who have sex with men. Genomic and phenotypic characterization of circ...
Bovine tuberculosis (TB), primarily caused by , is a chronic infectious disease of cattle with significant public health and economic implications due to its zoonotic potential and impact on livestock productivity. The control of the disease is hindered by complex epidemiological dynamics and the ch...
() is a major opportunistic pathogen associated with nosocomial infections, particularly in immunocompromised patients, including those with malignant cancer. The molecular epidemiology of isolated from distinct body sites from cancer patients remains poorly understood. This study aims to investiga...
Rabies virus (RABV) is a neglected tropical pathogen in Latin America predominantly transmitted to mammals by the common vampire bat (). Transmission of RABV among individuals and colonies is a function of individual dispersal between colonies, patterns of which can be inferred from population gene...
is a highly diverse group of organisms with over 2,500 serovars described to date. However, not all serovars are pathogenic to humans and animals. Many serovars typically cause self-limiting gastrointestinal infections, but certain host-adapted serovars, as well as those expressing specialized virul...
In January 2024, the Kenya Ministry of Health issued an outbreak alert following a surge in acute hemorrhagic conjunctivitis (AHC) cases along the Kenyan coast. Our investigations identified coxsackievirus A24 variant (CV-A24v) as the causative agent. In this study, we developed a novel whole genome...
This study reports a rare case of dual-strain Klebsiella pneumoniae infection involving genetically distinct isolates from the lung and eye of a previously immunocompetent patient. A rapid nanopore sequencing workflow on the Gseq-500 platform was used for whole-genome and plasmid sequencing. Compara...
To comprehend the time of emergence and extent of cryptic circulation for Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in Thailand, plasma specimens collected from patients at Siriraj Hospital, Bangkok, Thailand presenting with acute undifferentiated febrile illness (AUFI) were characte...
Carbapenem-resistant (CRSM) poses a significant threat in hospital settings due to its potential for persistence and transmission. This study aims to elucidate the virulence landscape of carbapenem-resistant (CRSM) during a hospital outbreak and to identify high-risk clones with enhanced persisten...
Domestic cats, among the most popular pets globally, may harbor antimicrobial resistance genes (ARGs) and zoonotic pathogens that impact human health. This study aims to investigate the resistome and bacteriome composition in the upper respiratory tract of domestic cats with respiratory signs in Chi...
is an opportunistic pathogen increasingly associated with urogenital infections and multidrug resistance. While polysaccharide capsules are known virulence factors in , their role in remains poorly understood. This study aimed to characterize a new capsular operon identified in and analyze the ant...
Evaluating travel restriction effectiveness in mitigating infectious disease burden, exemplified by COVID-19, is critical for informing pandemic response policy, yet methodologies and results evaluating their effectiveness vary considerably. We hypothesized Canadian COVID-19 travel restrictions, inc...
Varicella-zoster virus (VZV), a highly contagious α-herpesvirus, causes chickenpox and shingles. Although vaccines have been widely deployed, breakthrough infections still occur occasionally. Therefore, genomic surveillance of VZV remains essential. This study collected samples from 28 VZV-infected...
Listeria monocytogenes (Lm) is a major foodborne pathogen that can persist in food-processing environments and is responsible for listeriosis outbreaks. In this study, a total of 445 samples were collected from the beef supply chain, including 205 samples from cattle farms and 240 from retail market...
Mpox, caused by the monkeypox virus (MPXV), is a zoonotic disease that has gained global relevance after the 2022-2024 outbreak. MPXV exists in two distinct clades: clade I, associated with higher virulence and mortality, and clade II, which demonstrated increased human-to-human transmission and ada...
Foot-and-mouth disease (FMD), a highly contagious viral infection affecting cloven-hoofed animals, has significant implications for global livestock production and trade. In this study, we aimed to characterize and describe dispersal patterns and factors affecting pool 4 serotypes of FMD viruses (FM...
The coronavirus disease pandemic has underscored the importance of surveillance systems for timely response to public health threats. Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for tracking the emergence and dissemination of variants of the viru...
Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To u...
, a protozoan parasite of significant public health concern, is responsible for severe diarrhoeal disease, particularly in immunocompromised individuals and young children in resource-limited settings. Analysis of whole-genome next-generation sequencing (NGS) data is critical in improving our unders...
coagulase-negative staphylococci (CoNS) have emerged as significant pathogens in neonatal intensive care units (NICUs), especially as a leading cause of neonatal sepsis. In low-income countries, efforts to prevent sepsis-related mortality are hampered by a lack of comprehensive molecular data on bac...
Recent global pandemics have been caused by respiratory viruses in humans and animals with zoonotic spillover potential. Respiratory viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus (RSV), influenza A virus (IAV), and influenza B virus (IBV),...
The SARS-CoV-2 pandemic has caused a global crisis that has impacted not only health care systems, but also economies and societies. The constraints in clinical testing provide challenges in reliably assessing the prevalence of variations, particularly in regions with limited resources, testing, and...
The COVID-19 pandemic has led to substantial health, economic, and social impacts worldwide, and now, after more than 5 years since the start of the pandemic, it is possible to retrospectively evaluate patterns of SARS-CoV-2 spread and its consequences. Here we investigate the temporal dynamics of S...
is a commensal and opportunistic pathogen increasingly recognized for its antimicrobial resistance (AMR) and zoonotic potential. This study employs whole-genome sequencing (WGS) to characterize isolates from retail meat samples, focusing on antimicrobial resistance genes (ARGs), virulence determina...
spp., an opportunistic pathogen, has increasingly acquired resistance, particularly the emergence of carbapenemase-resistance. However, previous studies have focused on fragmented surveillance and have not conducted overall correlation. Here, 3769 non-duplicate genomes from sixty-five different cou...
Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne viral disease with a high mortality rate which is endemic in Iran. Laboratory diagnosis of CCHF is routinely conducted using PCR and IgM ELISA tests. However, nucleotide variations within CCHF virus (CCHFV) may lead to false-negative PCR results...
California's SARS-CoV-2 genomic surveillance program (California COVIDNet) developed whole genomic sequencing (WGS) capability from positive COVID-19 antigen tests to maintain genomic surveillance from public test sites. Over 4-months, COVIDNet sourced specimens from positive COVID-19 antigen tests...
The burden of infectious diseases and antimicrobial resistance (AMR) in Africa highlights the critical need for strengthened genomic surveillance capacities that are embedded within the national public health framework. In the East African Community (EAC), this challenge is compounded by limited inf...
In 2017 an outbreak of (), an infectious agent of cattle, was identified in Aotearoa New Zealand. This study characterizes the genomic population structure of the outbreak in New Zealand and compares it with the known global population structure using multilocus sequence typing (MLST) and genomic a...
This study aimed to comprehensively analyze the global landscape, trends, and research focus of nanopore sequencing technology in the field of pathogenic microorganism diagnosis using bibliometric analysis. Literature published between January 2014, and December 2024, was retrieved from the Web of S...
The distribution of arboviruses in endemic regions is experiencing a significant shift, along with the re-emergence of Oropouche virus (OROV) as a significant pathogen, characterized by dynamic vector-borne transmission. Despite growing public health relevance, OROV remains insufficiently characteri...
Contamination of food by antimicrobial-resistant pathogens poses significant risk to consumers and environment, potentially leading to foodborne illnesses, silent colonization, and dissemination of antibiotic-resistant bacteria across geographic borders. This study analyzed 32 retail meat samples (1...
, an opportunistic pathogen, is responsible for a wide range of healthcare-associated infections (HAIs), particularly in patients in intensive care units (ICUs). Carbapenem-resistant (CRAB) is of particular concern due to its extensive multidrug resistance (MDR) and limited treatment options. In Vi...
Cholera remains a public health challenge in Kenya. To better understand its dynamics, we analyzed genomes from clinical and environmental samples collected during the 2022-2023 outbreak. These strains were compared with historical genomes from Kenya, Uganda, Tanzania, and Haiti to inform strategie...
Influenza A virus (IAV) is a highly adaptable pathogen that poses a significant threat to human health. Genomic surveillance of IAVs is complex due to their broad host range, zoonotic potential, and rapid evolution. Strategies based on codon preference analysis have been successfully employed for th...
Nanopore-based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost-effective and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high- and low-resource settings. This scoping review (SR) aimed to (1) describe how na...
The evolution of HIV-1 virulence has significant implications for epidemic control. Recent phylogenomic analyses identified low-prevalence HIV-1 variants exhibiting significant differences in disease progression. We analysed 40 888 partial HIV-1 pol sequences from the UK HIV Drug Resistance Database...
Influenza A viruses (IAVs) in swine have zoonotic potential and pose a continuous threat of causing human pandemics, as demonstrated by the H1N1 pandemic in 2009. Despite increased genomic surveillance, we have limited knowledge of the IAV evolutionary dynamics leading to such zoonotic events and no...
Porcine brucellosis, caused by biovar 2, is currently the only type of brucellosis officially reported in farm animals in Germany, with outbreaks confirmed through direct pathogen detection. In most European countries, this bacterial pathogen is also found in wild animals, which are considered rese...
The evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has profoundly influenced the trajectory of the COVID-19 pandemic. In late 2020, the Alpha variant (Pango lineage B.1.1.7) emerged in South East England, characterized by enhanced transmissibility, increased mortality, and...
Dengue, caused by dengue virus (DENV) 1-4, remains a global public health concern, with Brazil experiencing some of the largest epidemics. The re-emergence of DENV-3 in Brazil between 2023 and 2024 has raised concerns about new outbreaks due to the absence of sustained circulation of this serotype i...
Continuous phylogeographic inference is a popular method to estimate parameters of the dispersal process and to reconstruct the spatial location of ancestors of extant populations from samples viral of genome sequences. However, these models typically ignore that replication and population growth ar...
The recombinant FY.4 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant was first reported in Kenya in March 2023 and was the dominant circulating variant between April and July 2023. The variant was characterized by two important mutations: Y451H in the receptor-binding domain of...
Since the emergence of the novel coronavirus SARS-CoV-2, public health measures have adapted as the virus evolve and acquired greater transmissibility and escape from the previous immune response. Genomic surveillance is a reliable and decisive tool for monitoring the evolutionary dynamics of the vi...
Getah virus (GETV) is a member of the of the . It is a single-stranded positive-RNA virus that is mainly transmitted by mosquitoes. In recent years, the spread of GETV has become increasingly serious, causing serious losses to the animal economy and posing a potential threat to public health. GETV...
Oropouche fever is a viral infectious disease caused by the Oropouche virus (OROV), primarily transmitted by the biting midge . Historically considered endemic to the Amazon region, particularly in Brazil, Peru, and Ecuador, Oropouche fever has resulted in an estimated 500,000 recorded infections. H...
High-throughput sequencing methods (e.g., whole-genome sequencing and metagenomics) are rapidly changing multiple fields of microbiology, including food safety and pathogen surveillance. Current foodborne pathogen surveillance relies heavily on resource-intensive, isolate-based approaches, limiting...
The fields of epidemiology and viral phylodynamics share the ultimate goal of disease control, but concepts, methodologies and data employed by each differ in ways that confer complementary strengths and different areas of weakness. We recently introduced EpiFusion, a model for joint inference of ou...
Methicillin-resistant (MRSA) stands as a pervasive and important pathogen in the co-infections during the COVID-19 pandemic given its high morbidity and mortality. This study aimed to characterize MRSA isolates obtained from COVID-19 pneumonia with MRSA co-infection patients during the COVID-19 pan...
To characterize a rare ST852 strain co-producing NDM-1 and KPC-2 isolated from a clinical patient. Minimum inhibitory concentrations (MICs) were measured using a VITEK 2 compact system and broth microdilution. Conjugation experiments were conducted using film matings. Whole genome sequencing (WGS)...
Multidrug-resistant poses a critical public health threat in Nigeria, where limited genomic surveillance hinders the understanding of virulence-resistance interplay. This cross-sectional study employed whole-genome sequencing to characterize 107 MDR-E isolates from a Nigerian tertiary hospital (201...
Carbapenem-resistant (CRKP) poses a significant threat to public health owing to its multidrug resistance and rapid dissemination. This study analyzed CRKP isolates collected from bloodstream infections in nine regions of South Korea using the Kor-GLASS surveillance system between 2017 and 2021. A...
Dengue virus (DENV) is a significant public health concern in Colombia, with increased transmission of DENV type 1 (DENV-1) in the departments of Risaralda and Valle del Cauca in the Central-West region of the country following a large outbreak in 2019. However, little is known about the source, gen...
Long-read sequencing (LRS) has revolutionized pathogen surveillance by enabling real-time, high-fidelity genomic analysis critical for outbreak response. This review synthesizes recent breakthroughs in LRS, evaluating its impact on genomic epidemiology, metagenomics, and public health decision-makin...
The global emergence of multidrug-resistant (MDR) , particularly carbapenem-resistant (CRKP), presents a severe public health threat, limiting available treatment options. Tigecycline and eravacycline, have been considered a last-resort therapeutic against MDR . However, strains were resistant to t...
Dengue is the most prevalent acute febrile disease with serious clinical consequences in the tropical and subtropical regions of Asia and America. In Peru, it represents a significant public health issue due to its hyperendemic nature, with serotype 2 (DENV-2) being the predominant serotype that lea...
stands out as one of the most devastating plant pathogens worldwide, rapidly expanding its range and impacting a wide range of host species. In this study, we investigated the virome of across 222 isolates from Africa, Asia, Europe, Oceania, and the Americas using stranded total RNA sequencing, rev...
In 2023, the dengue virus (DENV) outbreak infected over 0.3 million cases and 1500 deaths in Bangladesh. Our study conducted serotyping and genomic surveillance in four districts of Southwest Bangladesh between September and October 2023. The surveillance data from 2019 to 2023 extracted from the Di...
This study aimed to characterize the genomes of two rare ST592 isolates and to explore their evolution into carbapenem-resistant hypervirulent (CR-hvKp). The minimum inhibitory concentrations (MICs) were determined using a VITEK 2 compact system. Conjugation experiments were conducted using film m...
Hepatitis B virus (HBV) genotype B (HBV/B) is the predominant strain in Taiwan and several East Asian countries. The aim of this study is to use comprehensive phylogenetic analysis tools to monitor the long-term molecular evolution dynamic of HBV genotype B population in East Asia. In this study, fu...
The rapid evolution of respiratory viruses is characterized by the emergence of variants with concerning phenotypes that are efficient in antibody escape or show high transmissibility. This necessitates timely identification of such variants by surveillance networks to assist public health intervent...
Tuberculosis (TB), caused by members of the complex (MTBC), is a significant global health threat, with millions of cases diagnosed annually and an annual death toll exceeding 1.6 million. Zoonotic TB (zTB), transmitted between animals and humans, remains poorly understood and difficult to control....
Relative proportion of cases in a multi-strain pandemic like the COVID-19 pandemic provides insight on how fast a newly emergent variant dominates the infected population. However, the behavior of relative proportion of emerging variants is an understudied field. We investigated the emerging behavio...
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Over the past century, Influenza A virus (IAV) has caused four of the five reported pandemics, all of which originated from viruses possessing genome segments of avian origin. The recent spread of highly pathogenic avian influenza (HPAI) viruses, particularly the clade 2.3.4.4b A(H5N1) subtype, has...
The importance of genomic surveillance strategies for pathogens has been particularly evident during the coronavirus disease 2019 (COVID-19) pandemic, as genomic data from the causative agent, severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), have guided public health decisions worl...
As part of a multi-state viral genomic surveillance program, we conducted a case-only analysis to evaluate the effectiveness of XBB.1.5-adapated mRNA vaccines in preventing severe illness among individuals with medically attended SARS-CoV-2 infection. We compared prior receipt of an XBB.1.5-adapted...
Emerging viral pathogens, Indian citrus ringspot virus (ICRSV) and Citrus yellow vein clearing virus (CYVCV), pose significant threats to global citrus production, a cornerstone of agriculture and trade. The rapid transboundary spread of CYVCV underscores the urgent need for effective diagnostic too...
Immunodeficiency Virus (HIV) and Hepatitis C Virus (HCV) share the same routes of transmission, therefore, co-infection by both viruses represents a challenge to the goal of eliminating viral hepatitis as a public health threat. There are an estimated 2.3 million people living with HIV/HCV worldwide...
The COVID-19 pandemic highlighted the importance of genomic surveillance for monitoring pathogens evolution, mitigating the spread of infectious disorders, and informing decision-making by public health authorities. Since the need for the summarization and interpretation of large bodies of data, com...
Understanding the dispersal patterns of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) lineages is crucial to public health decision-making, especially in countries with limited access to viral genomic sequencing. This study provides a comprehensive epidemiological and phylodynamic per...
Immunosuppressive diseases, such as chicken infectious anemia virus (CIAV), pose a major threat to livestock farming due to reduced disease resistance, poor vaccine response, and overall poor productivity. CIAV, recognized globally for decades, shows a significant genetic diversity, but its implicat...
Despite the increasing burden of dengue in Kenya and Africa, the introduction and expansion of the virus in the region remain poorly understood. The objective of this study is to examine the genetic diversity and evolutionary histories of dengue virus (DENV) serotypes 1 and 3 in Kenya and contextual...
Viral hepatitis is a major public health challenge. Hepatitis C Virus (HCV) infection causes the progressive liver damage. A surprisingly high number of individuals tested positive for HCV infection during the Unnao Human Immunodeficiency Virus (HIV) outbreak investigation in 2017-2018 (more than 90...
In North America, raccoon rabies virus (RRV) is a public health concern due to its potential for rapid spread, maintenance in wildlife, and impact on human and domesticated animal health. RRV is an endemic zoonotic pathogen throughout the eastern USA. In 1991, an outbreak of RRV in Fairfield County,...
Influenza A and B viruses represent significant global health threats, contributing substantially to morbidity and mortality rates. However, a comprehensive understanding of the molecular epidemiology of these viruses in Brazil, a continental-size country and a crucial hub for the entry, circulation...
Mpox is a zoonotic viral disease caused by the (MPXV). Human cases have been mainly restricted to the African continent until the worldwide multi-country outbreak unfolded in 2022. We reconstructed epidemiological links of 53 MPXV infections using genomic epidemiology in Rio Grande do Sul State, so...
Poxviruses have exceptionally large genomes compared to most other viruses, which represent unique challenges to sequencing and assembly due to complex features such as repeat elements and low complexity sequences. The 2022 global mpox outbreak led to an unprecedented level of poxvirus sequencing as...
This document outlines the steps necessary to assemble and submit the standard data package required for contributing to the global genomic surveillance of enteric pathogens. Although targeted to GenomeTrakr laboratories and collaborators, these protocols are broadly applicable for enteric pathogens...
particularly the group, is a major cause of nosocomial infections, and carbapenem-resistant spp. are important human pathogens. We collected 492 spp. strains from two hospitals in Taiwan and classified them using MALDI-TOF MS and PCR; 94.5% were and 5.5% were non-. (NAB). We confirmed their id...
Deciphering precise sources and patterns of healthcare-associated Pseudomonas aeruginosa colonization/infection is crucial in defining strategies of prevention and control. To prospectively investigate the role of hospital environment in P. aeruginosa nosocomial bloodstream infections (Pa-BSIs) duri...
The IR Biotyper is a novel real-time typing tool, based on a Fourier-transform infrared (FTIR) spectroscopy system. It has emerged as a promising method for the strain typing of various microorganisms and for the detection of their clonal spread within hospitals. In this review, we aim to present th...
The investigation into risk factors, molecular epidemiology, and resistance mechanisms of carbapenem-resistant Pseudomonas aeruginosa (CRPA) in pediatric populations in China is currently inadequate. To assess epidemiology, molecular characteristics, and resistance mechanisms, virulence-associated g...
Escherichia coli has emerged as an important pathogen in urinary tract infections (UTIs) due to the rapid acquisition of antibiotic resistance genes. This enhances the ability of E. coli to colonize and creates therapeutic challenges within the healthcare system. This study aimed to identify the ext...
Rabies is a viral zoonosis that kills thousands of people annually in low- and middle-income countries across Africa and Asia where domestic dogs are the reservoir. 'Zero by 30', the global strategy to end dog-mediated human rabies, promotes a One Health approach underpinned by mass dog vaccination,...
In December 2021, influenza A viruses (IAV) were detected in a population of farmed mink in British Columbia, Canada. Circulation of IAVs in farmed mink populations has raised public health concerns due to similarities between mustelid and human respiratory physiology, potentially facilitating spill...
Hospital-acquired infection (HAI) and antimicrobial resistance (AMR) represent major challenges in healthcare system. Despite numerous studies have assessed environmental and patient samples, very few studies have explored the microbiome and resistome profiles of medical staff including nursing work...
Shiga toxin-producing (STEC) is a group of bacteria that causes gastrointestinal illness and occasionally causes large foodborne outbreaks. It represents a major public health concern due to its ability to cause severe illness which can sometimes be fatal. This study was undertaken as part of a rap...
The Covid-19 pandemic uncovered several lacunae in healthcare systems exposing global unpreparedness and triggering unprecedented challenges worldwide- necessitating a shift towards mitigation and robust surveillance strategies. Here, we report the use of Whole Genome Sequencing (WGS) to detect SARS...
Antibiograms have been used during outbreak investigations for decades as a surrogate for genetic relatedness of Methicillin-resistant (MRSA). In this study, we evaluate the accuracy of antibiograms in detecting transmission, using genomic epidemiology as the reference standard. We analysed epidemi...
Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic...
Molecular surveillance of FMD epidemiology is a fundamental tool for advancing our understanding of virus biology, monitoring virus evolution, and guiding vaccine design. The accessibility of genetic data will facilitate a more comprehensive delineation of FMDV phylogeny on a global scale. In this s...
Monkeypox (MPOX) is a zoonotic disease caused by Orthopoxvirus monkeypox (MPXV), belonging to the Orthopoxvirus genus, and exhibits symptoms similar to smallpox. In 2024, the monkeypox outbreak in the Democratic Republic of the Congo continued to develop, raising widespread global public health conc...
Analyses of mosquito-borne virus outbreaks have revealed the presence of similar virus strains over several years. However, it remains unclear how mosquito-borne viruses can persist over winter, when conditions are generally unfavorable for virus circulation. One potential route for virus persistenc...
We studied nosocomial transmission of multidrug-resistant bla-containing Klebsiella pneumoniae ST147 in a Dutch pediatric oncology center. Whole-genome multilocus sequence typing revealed two genetic clusters consisting of 2 and 5 K. pneumoniae isolates, both from Ukrainian medical evacuees and Dutc...
Whole genome sequencing (WGS) marks a turning point for outbreak investigations for microorganisms related to public health matters, like Legionella pneumophila (Lp). Here, we evaluated the available Lp WGS typing tools for isolates of previously documented Belgian outbreaks, as well as small groups...
The gene , encoding the mannitol transporter subunit IICBA of the phosphotransferase system, was the core gene with the greatest variability in and could be used as a new typing marker in . To expand its application, we performed an evolutionary analysis and found that the gene was present in nine...
Colonisation and infection with Carbapenem-resistant Enterobacterales (CRE) in healthcare settings poses significant risks, especially for vulnerable patients. Genomic analysis can be used to trace transmission routes, supporting antimicrobial stewardship and informing infection control strategies....
Clinical isolates of multi-drug resistant Acinetobacter baumannii are a major cause of nosocomial infections, often attributed to the highly adaptable genome that helps it to thrive under environmental selection pressure. Here, we aim to provide genotypic-based surveys and comparative whole genome s...
The dengue virus (DENV) is a mosquito-borne flavivirus endemic to many tropical and subtropical regions. Over the past few decades, the global incidence of dengue has risen dramatically, with the virus now present in over 100 countries, putting nearly half of the world's population at risk. This inc...
Ireland's COVID-19 response combined extensive SARS-CoV-2 testing to estimate incidence, with whole genome sequencing (WGS) for genome surveillance. As an island with two political jurisdictions-Northern Ireland (NI) and Republic of Ireland (RoI)-and access to detailed passenger travel data, Ireland...
Carbapenem-resistant Enterobacterales, particularly those producing carbapenemase (CPE), pose a major threat to human health, being listed among critical-priority resistant pathogens by the World Health Organization. To report on a large nosocomial spread of CPE of different species producing Verona...
The role of genomics in public health surveillance has been accentuated by its crucial contributions during the COVID-19 pandemic, demonstrating its potential in addressing global disease outbreaks. While Africa has made strides in expanding multi-pathogen genomic surveillance, the integration into...
Culex tritaeniorhynchus, a major vector of Japanese encephalitis virus (JEV), is found across a broad geographical range, including Africa, Asia, Australia and Europe. Understanding the population structure and genetic diversity of pathogen vectors is increasingly seen as important for effective dis...
Respiratory Syncytial Virus (RSV) infections are a cause of significant morbidity and mortality in children and the elderly. Despite the clinical burden of disease, very little is known about the inter- and intra-seasonal genomic variability of RSV. Furthermore, the recent approval of vaccines and m...
The ongoing outbreak of Marburg virus disease in Rwanda marks the third largest historically, although it has shown the lowest fatality rate. Genomic analysis of samples from 18 cases identified a lineage with limited internal diversity, closely related to a 2014 Ugandan case. Our findings suggest t...
poses a significant global health threat due to its multidrug-resistance and outbreak potential. In this study, we report its emergence in Minas Gerais, Brazil, supported by genomic surveillance that identified Clade-IV isolates, suggested a potential introduction from Colombia, and detected a misse...
This study investigated whole-cell oral cholera vaccine (kOCV) single-dose effectiveness and transmission dynamics of through 4 years of epidemiological and genomic surveillance in Democratic Republic of the Congo (DRC). Whole genome sequencing was performed on clinical and water strains from 200...
Nipah virus (NiV), a highly lethal virus in humans, circulates in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining viral genomes from bats means we have a poor understanding of NiV diversity. We develop phylogenetic approaches applied to the most comprehensive collection of...
In this review, we investigated the genetic diversity and evolutionary dynamics of the species that includes both Marburg virus (MARV) and Ravn virus (RAVV). Using sequence data from natural reservoir hosts and human cases reported during outbreaks, we conducted comprehensive analyses to explore th...
The emergence of antibiotic resistance has significantly elevated the threat posed by Acinetobacter baumannii as an opportunistic pathogen. A.baumannii, a notorious bacterium, poses a serious threat to health care, leading to severe nosocomial infections, particularly in immunocompromised individual...
The increasing detection rate of C. tropicalis and its azole resistance have made clinical treatment difficult. The presence of candiduria seems to correlate with invasive candida infection, especially for patients admitted to ICUs. However, the prevalence and antifungal resistance of C. tropicalis...
Pseudomonas aeruginosa ST111 is a global multidrug resistant (MDR) high-risk clone and comprehensive data about its molecular epidemiology is limited in Canada. Comprehensive data about the evolution of ST111 clades is limited. We characterized a Canadian collection of ST111 causing bloodstream infe...
Vancomycin-resistant (VREfm) is a major nosocomial pathogen, and molecular epidemiological tools are crucial for controlling its spread. Pulsed-field gel electrophoresis (PFGE) is still used in clinical laboratories despite the increased accessibility of whole-genome sequencing (WGS). As PFGE equip...
Oropouche virus is an arbovirus endemic to the Americas. Periodic outbreaks have occurred since its description in 1955. In late 2023, an outbreak occurred in Peru, centered in and around Iquitos in the Eastern Peruvian Amazon. An existing acute febrile illness (AFI) surveillance program was able to...
Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 h...
During the COVID-19 pandemic, SARS-CoV-2 caused an alarming number of cases and deaths worldwide. Brazil was severely affected from late 2020 onward, especially after the emergence of variants of concern (VOCs) and variants of interest (VOIs). Although much is known about the dynamics and evolution...
Brazil is considered an epicenter for emerging and re-emerging arboviruses that significantly impact public health. The mid-sized city of São José do Rio Preto (SJdRP) in northwestern São Paulo state is considered hyperendemic for arboviral diseases, with case numbers climbing each year. Only 45 cas...
The integration of genomic and geospatial data into infectious disease transmission analyses typically includes residential locations and excludes other activity spaces where transmission may occur ( work, school, or social venues). The objective of this analysis was to explore residential as well a...
Pathogen genomic surveillance in healthcare has the potential to enhance patient safety by detecting outbreaks earlier, thereby reducing morbidity and mortality. Despite benefits, there are barriers to adoption, including cost, expertise, and lack of standardized methodologies and incentives. This c...
Morganella morganii has been recognized as an important opportunistic pathogen that is becoming increasingly prevalent worldwide. However, the current global evolutionary dynamics and emergence of ARGs remain obscure. The present study determined the global distribution, genomic classification, phyl...
Between February and April 2018, within a unique 5-single nucleotide polymorphism (SNP) address was isolated from 28 cases with links to a small rural area of Northeast England, with five cases prospectively identified by whole genome sequencing (WGS). Infections had a severe clinical picture with...
This study provides an update on the status of the COVID-19 pandemic in Canada, building upon our initial analysis conducted in 2020 by incorporating an additional 2 years of data. This study aims to (1) summarize the status of the pandemic in Canada when the World Health Organization (WHO) declared...
, a significant cause of gastroenteritis and a growing public health concern, has become increasingly prevalent owing to the rise in ocean temperatures driven by climate change. This study aimed to characterize the genetic diversity, pathogenic potential, and antimicrobial resistance (AMR) profiles...
Bloodstream infections (BSIs) caused by antibiotic-resistant bacteria (ARB) represent a significant disease burden worldwide. However, a comprehensive analysis of the mortality rates and global epidemiology across different ARB species associated with BSIs is currently lacking. We conducted a system...
The spread of CRE has been rapid on a global scale and represents a significant challenge in nosocomial infections worldwide. The aim is to evaluate the risk factors for CRE colonization and to describe the molecular and clinical characteristics of CRE colonization in pediatric inpatients in Shenzhe...
Staphylococcus haemolyticus is a clinically relevant coagulase-negative staphylococcus frequently responsible for hospital-acquired infections, especially in premature newborns. To describe an outbreak of multidrug-resistant S. haemolyticus in a neonatal department. The outbreak was investigated usi...
In 2022, the U.S. Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and state partners conducted a sample-initiated investigation of a multistate outbreak of Senftenberg illnesses linked to peanut butter. Twenty-one illnesses and four hospitalizations were re...
Multidrug-resistant bacteria, including carbapenem-resistant Acinetobacter baumannii (CRAB), are considered a major public health threat, particularly those which are responsible for nosocomial infections. This study aimed to investigate the molecular mechanism of carbapenem resistance and the clona...
The Enterobacter cloacae complex, known for causing infections in hospitalised patients, displays resistance to β-lactam antibiotics due to AmpC β-lactamase expression. This study emphasises the genome sequence of Enterobacter roggenkampii, which coexists with MIR-1 and NDM-1 genes, isolated from th...
West Nile virus (WNV) is a mosquito-borne pathogen that can infect humans, equids, and many bird species, posing a threat to their health. It consists of eight lineages, with Lineage 1 (L1) and Lineage 2 (L2) being the most prevalent and pathogenic. Italy is one of the hardest-hit European nations,...
Rubella is listed as a disease that needs to be eliminated worldwide by the World Health Organization. This study aimed to investigate rubella epidemiology and genetic characteristics based on data from 12 years of laboratory-based surveillance (2009-2020) in Tianjin and to provide baseline genotype...
This study aims to inform the prevention and treatment of infections in China by analyzing the molecular epidemiology and distribution patterns of the pathogen. A cross-sectional study was conducted involving a retrospective analysis of 64 clinical strains of isolated from January 2018 to April 20...
During the COVID-19 pandemic, genomic surveillance was crucial for monitoring virus spread and identifying variants. Effective surveillance helped understand transmission dynamics. Singapore had success in combating COVID-19 through its surveillance programmes. This paper outlines Singapore's strate...
Hepatitis C virus (HCV) is a pathogenic virus of global health concern. The phylodynamics of HCV genotypes/subtypes 1a, 1b, 2, and 3 are explored only for specific geographic regions. However, their genome based global origin and detailed spatiotemporal spread, have yet to be extensively studied. To...
Shiga toxin-producing (STEC) is a zoonotic pathogen associated with illness ranging from mild diarrhoea to haemolytic uremic syndrome (HUS) or even death. Cross-sectoral data sharing provides an opportunity to gain insight in reservoirs and sources of human infections and starting points for pro-ac...
Burkholderia cepacia complex (Bcc) is an opportunistic pathogen that causes severe infections in immunocompromised individuals. It is a common contaminant of medical drugs, solutions and devices used in healthcare setups. This scoping review aimed to assess Bcc outbreaks in Indian hospital settings...
Background & objectives The global impact of COVID-19, with over 45 million cases and 533,300 deaths in India alone, necessitates effective surveillance methods. Traditional approaches face challenges in detecting pre-symptomatic and asymptomatic cases, prompting the exploration of wastewater-based...
Zika virus (ZIKV) outbreaks have raised major global health concerns recently, yet reported outbreaks are rare in Africa, where ZIKV was first discovered. Recent studies on Aedes aegypti, the mosquito that transmits ZIKV, might explain this phenomenon. The Ae aegypti subspecies present in Africa sho...
The genomic analysis of SARS-CoV-2 has served as a crucial tool for generating invaluable data that fulfils both epidemiological and clinical necessities. Long-read sequencing technology (e.g., ONT) has been widely used, providing a real-time and faster response when necessitated. A novel nanopore-b...
Disinfectants, such as bleaching powder, are widely employed in marine aquaculture worldwide to control the bacterial pathogens and eliminate antibiotic resistance genes (ARGs). Nevertheless, the rapid recovery of prokaryotic community compositions (PCCs) after disinfection may significantly influen...
Urinary tract infections (UTIs) are among the most prevalent infectious diseases, yet there is still limited understanding of the epidemiology of Enterococcal strains isolated from UTI patients in Shanghai. This study aims to elucidate the antimicrobial resistance profiles, virulence gene carriage,...
The aim of this study is to describe the genomic epidemiology of invasive Group A Streptococcus (iGAS) in Argentina during 2023. A total of 476 invasive GAS isolates were subtyped and analyzed by whole-genome sequencing. A high prevalence of the 1-type strain was observed. Among the 1 strains, two h...
Recombination plays a crucial role in the evolution of SARS-CoV-2. The Omicron XBB* recombinant lineages are a noteworthy example, as they have been the dominant SARS-CoV-2 variant worldwide in the first half of 2023. Since November 2023, a new recombinant lineage between Omicron subvariants XBB and...
Long-term comprehensive studies on the genomic epidemiology of both methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates are limited in China. Here, we aimed to assess the genomic epidemiological characteristics and population dynamics of S. aureus...
Acinetobacter seifertii, a member of A baumannii-calcoaceticus complex, can be considered a pathogen of concern due to the presence of resistance genes. The aim of the study was to describe an outbreak of carbapenem-resistant A seifertii among neonates admitted to the neonatal intensive care unit (N...
The biting midges Latreille, 1809 (Diptera: Ceratopogonidae) is highly relevant to epidemiology and public health, as it includes species that are potential vectors of human and animal arboviruses. The aim of this study was to investigate the presence of RNA viruses in species of the genus collect...
During prolonged FDC therapy, the emergence of FDC non-susceptibility in CRAB has been reported. Here, we report a transmission cluster of FDC-non-susceptible CRAB in four patients, all naïve to FDC treatment, characterized by a premature stop codon and amino acid deletion in the PirA protein. CRAB...
bacteria is a component of normal intestinal microflora of humans and animals, but can also be found in hospital settings causing urinary tract infections and sepsis. The problem of treating such infections is complicated by multidrug-resistant isolates producing extended spectrum beta-lactamases (E...
Since the beginning of May 2022, cases of mpox have been reported in several European and American countries where the disease is nonendemic. We performed a retrospective genomic characterisation of the 2022 mpox outbreak in Belgium, and assessed the in vitro sensitivity of three antiviral compounds...
Mycobacterium tuberculosis complex (MTBC) species evolve slowly, so isolates from individuals linked in transmission often have identical or nearly identical genomes, making it difficult to reconstruct transmission chains. Finding additional sources of shared MTBC variation could help overcome this...
Clostridioides difficile infection is a serious healthcare-associated infection linked to antimicrobial use. The severity of the disease can be associated with hypervirulent ribotypes such as RT027. The study aimed to investigate the molecular epidemiology and genomic characteristics of C. difficile...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) increases the difficulty of clinical treatment of giant pandas. This study aimed to investigate the antibiotic susceptibility, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence genes, and molecular epidemiology of CRKP str...
Tracking the emergence, introduction and spread of SARS-CoV-2 variants of concern are essential for informing public health strategies. In 2021, Cambodia faced two major epidemic waves of SARS-CoV-2 triggered by the successive rise of the Alpha and Delta variants. Phylodynamic analysis of 1,163 comp...
Shigella sonnei is a major cause of diarrhoea globally and is increasing in prevalence relative to other Shigella because of multiple demographic and environmental influences. This single-serotype species has traditionally received less attention in comparison to Shigella flexneri and Shigella dysen...
Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposon...
This study investigated a strain of Klebsiella pneumoniae, identified as GRTHES, which exhibited extensive antibiotic resistance. The strain was resistant to all beta-lactams, including combinations with newer agents such as meropenem/vaborbactam and imipenem/relebactam, as well as to aminoglycoside...
The genetic analysis of the Dengue virus circulating in Ethiopia's Afar region, in 2023, identified three distinct introductions with spatiotemporal clustering linked to genomes from Asia and Italy. These findings are crucial for enhancing prevention and control strategies, reinforcing the necessity...
This review presents a comprehensive perspective on the genomic surveillance of SARS-CoV-2 in Taiwan, with a focus on next-generation sequencing and phylogenetic interpretation. This article aimed to explore how Taiwan has utilized genomic sequencing technologies and surveillance to monitor and miti...
Polymerase chain reaction--based open-reading frame typing (POT) is used to investigate nosocomial infections caused by methicillin-resistant Staphylococcus aureus (MRSA). We analyzed the relationship between POT types, nosocomial infections, and toxin-producing and antiseptic resistance genes of MR...
Multidrug-resistant (MDR) bacteria pose a significant challenge to the treatment of infectious diseases. Of particular concern are members of the Klebsiella pneumoniae species complex (KpSC), which are frequently associated with hospital-acquired infections and have the potential to spread outside h...
Influenza A has been named as a priority pathogen by the WHO due to the potential to cause pandemics. Genomic sequencing of influenza strains is important to understand the evolution of the influenza strains and also to select the appropriate influenza vaccines to be used in the different influenza...
is an emerging fungal pathogen capable of causing extensive recalcitrant dermatophytosis exacerbated by frequently retained terbinafine resistance. Cases of dermatophytosis due to have increased dramatically in India in recent years. Other countries have reported imported infection cases, causing p...
Vibrio parahaemolyticus is a critical foodborne pathogen causing gastroenteritis worldwide. The occurrence of transmission and outbreaks attributed to V. parahaemolyticus has exhibited a notable upward trend during the past two decades. However, comprehensive information on this pathogen in inland c...
Multidrug-resistant organisms (MDRO) pose a significant threat to public health worldwide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for surveillance and infection prevention of MDRO. Molecular charac...
Understanding transmission pathways of important opportunistic, drug-resistant pathogens, such as extended-spectrum beta-lactamase (ESBL)-producing , is essential to implementing targeted prevention strategies to interrupt transmission and reduce the number of infections. To link transmission of ESB...
The use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mos...
Sentinel surveillance networks are sophisticated health information systems that warn about outbreaks and spread of infectious diseases with epidemic or pandemic potential, the effectiveness of countermeasures and pressures on health systems. They are underpinned by their ability to turn data into i...
is a Gram-negative bacterium associated with a wide range of community- and hospital-acquired infections. The emergence of clonal hypervirulent strains resistant to last-resort antimicrobial agents has become a global concern. The Kingdom of Saudi Arabia (KSA), with its diverse population and high t...
We report 2 outbreaks comprising a cluster of 18 group A Streptococcal infections across 2 nursing facilities. Point prevalence surveillance testing identified 8 of 18 cases, and whole genome sequencing validated transmission pathways. Infection prevention interventions at the facility level compris...
Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isola...
Our study aimed to conduct genomic characterization of strains carrying the gene in the intestinal tract of healthy individuals. The objectives were to underscore the importance of genomic surveillance for drug resistance in both commensal and pathogenic bacteria among healthy populations, and to...
Salmonella enterica serovar Panama, a causative agent of non-typhoidal salmonellosis (NTS), is one of several serovars that causes invasive NTS disease (iNTS) in humans. S. Panama is an understudied pathogen, with its pathobiology poorly understood. It is a predominant iNTS serovar in Australia, a h...
Crimean-Congo hemorrhagic fever virus (CCHFV) is a significant tick-borne virus causing severe hemorrhagic disease with high fatality rate. This report presents the genomic characterization of CCHFV strain from North Macedonia's first outbreak in over 50 years, emphasizing the importance of genomic...
Fiji is a Pacific Island nation grappling with the increasing threat of antimicrobial resistance (AMR). While genomic technologies are increasingly utilised to understand the emergence and spread of AMR globally, its application to inform outbreak responses in low- and middle-income settings has not...
The pandemic caused by SARS-CoV-2 has not only affected humans but also raised concerns about its transmission to wild animals, potentially creating natural reservoirs. Understanding these dynamics is critical for preventing future pandemics and developing control strategies. This study aims to inve...
Enterovirus D68 (EV-D68) is associated with severe respiratory disease and acute flaccid myelitis (AFM). The 2022 outbreaks showed increased viral circulation and hospital admissions, but the expected rise in AFM cases did not occur. We analyzed EV-D68 genomes and infection outcomes from 2022 (a yea...
In the last 6 years, Italy accounted for 36 % of the total autochthonous European West Nile virus (WNV) cases reported to ECDC. Since 2001, the country put in place a multi-species national surveillance plan. The plan was enhanced in 2020 by adopting a fully integrated "One Health" approach, includi...
Lymphogranuloma venereum (LGV) is a sexually transmitted infection caused by genotypes L1-L3. A combination of techniques with high discriminatory capacity such as multilocus sequence typing (MLST) and the analysis of the gene may be useful to determine the greater penetration of certain strains i...
Wesselsbron is a neglected, mosquito-borne zoonotic disease transmitted by several species of virus-infected Aedes mosquitoes endemic to tropical regions in Africa. It affects primarily domestic livestock species with teratogenic effects, but can jump to humans. Herein, we investigated the molecular...
Fluconazole-resistant Candida parapsilosis has emerged as a significant health-care-associated pathogen with a propensity to spread patient to patient and cause nosocomial outbreaks, similar to Candida auris. This study investigates a long-lasting outbreak of fluconazole-resistant C parapsilosis tha...
Oropouche virus (OROV) is an arbovirus endemic in the Amazon region that closely resembles other arboviruses in terms of human disease, leading to potential misdiagnoses. The virus ecology has mostly restricted its occurrence to the Amazon biome; however, after a large 2023-24 OROV epidemic in the B...
This study analyzed antibiotic resistance mechanisms and molecular epidemiology of multidrug-resistant Pseudomonas aeruginosa (MDR-PA), aiming at providing clues for prevention and control of MDR-PA infections. The carbapenemase resistance genes (VIM, IMP, NDM, KPC, GES, OXA-40) of MDR-PA strains we...
Within a multistate viral genomic surveillance program, we evaluated whether proportions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections attributed to the JN.1 variant and to XBB-lineage variants (including HV.1 and EG.5) differed between inpatient and outpatient care sett...
Release of Aedes aegypti mosquitoes infected with Wolbachia pipientis (wMel strain) is a biocontrol approach against Ae. aegypti-transmitted arboviruses. The Applying Wolbachia to Eliminate Dengue (AWED) cluster-randomised trial was conducted in Yogyakarta, Indonesia in 2018-2020 and provided pivota...
Melioidosis is a neglected tropical disease caused by Burkholderia pseudomallei, endemic to Southeast Asia and Northern Australia. Despite its increasing global public health and clinical significance, the molecular epidemiology of melioidosis and genetic diversity of B. pseudomallei in Cambodia rem...
Genomic epidemiology has helped reconstruct the global and regional movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is still a lack of understanding of SARS-CoV-2 spread in some of the world's least developed countries (LDCs). To begin to address this dispari...
Surveillance is essential in the fight against antimicrobial resistance (AMR), to monitor the extent of resistance, inform prevention, control measures, and evaluate intervention progress. Traditional surveillance methods based on phenotypic antimicrobial susceptibility data offer important but limi...
Limited genomic surveillance data is available for SARS-CoV-2 in Thailand during the second and third wave outbreaks, including both patient and environmental samples. This study investigated the presence of SARS-CoV-2 RNA in patient samples, on frequently touched surfaces, and in environmental swab...
Staphylococcus aureus bacteremia (SAB), especially when caused by methicillin-resistant S. aureus (MRSA), is of considerable clinical importance. In recent years, the proportion of MRSA among S. aureus has decreased, and a relative increase in the proportion of methicillin-susceptible S. aureus (MSS...
Recently, colistin and carbapenem-resistant hypervirulent Klebsiella pneumoniae (CCR-hvKP) has been observed sporadically. The aim of this study was to report a nosocomial outbreak due to CCR-hvKP, so as to control the transmission of CCR-hvKP and prevent future outbreaks. The clinical characteristi...
Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was eliminated from New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of SARS-CoV-2. However, in 2021, following a brief quarantine-free travel agreement with Aust...
Accurately estimating the effective reproduction number (Rt) of a circulating pathogen is a fundamental challenge in the study of infectious disease. The fields of epidemiology and pathogen phylodynamics both share this goal, but to date, methodologies and data employed by each remain largely distin...
Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Repres...
SARS-CoV-2 is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease. Genomic characterization of SARS-CoV-2 is important for monitoring and assessing its evolution. A total of 1.346 nasopharyngeal swab samples were collected but only 879 SARS-CoV-2 high-quality ge...
Infection control measures may be disrupted by inter- or intra-hospital transfers after major disasters. We report the possible outbreak and prevention of vancomycin-resistant Enterococcus spp. (VRE) strains carried by infants transferred to our neonatal intensive care unit from another unit after t...
The duration and magnitude of SARS-CoV-2 air dispersal during nosocomial outbreaks remain uncertain. This study evaluates the impact of mobile modular high-efficiency particulate air filter units (MMHUs) on SARS-CoV-2 air dispersal. We investigated a nosocomial COVID-19 outbreak in an infirmary unit...
Healthcare-associated infections (HAIs) are a significant burden to health systems, with antimicrobial resistance (AMR) further compounding the issue. The hospital environment plays a significant role in the development of HAIs, with microbial surveillance providing the foundation for interventions....
Zika virus (ZIKV), a Flaviviridae family member, has been linked to severe neurological disorders. Despite detailed studies on recent outbreaks, the early evolutionary history of ZIKV remains partially unclear. This study elucidates ZIKV origin and evolutionary dynamics, focusing on recombination ev...
Highly pathogenic avian influenza viruses continue to pose global risks to One Health, including agriculture, public, and animal health. Rapid and accurate genomic surveillance is critical for monitoring viral mutations, tracing transmission, and guiding interventions in near real-time. Oxford Nanop...
This study investigated the etiological characteristics and whole genome sequencing of (CP) from a food poisoning outbreak. Multiplex real-time PCR was employed to screen pathogens in collected samples. Based on the preliminary screening results, the isolation, cultivation, and identification of su...
Rabies is a viral zoonosis that causes an estimated 60,000 human deaths each year, mainly in Africa and Asia. The etiological agent of rabies, the Rabies Lyssavirus or Rabies Virus (RABV) has been characterized in dog populations in Cameroon, in previous studies. However, the dynamics of RABV mainte...
is widely recognised as one of the most common causes of healthcare-associated infections due to the ability of spores to survive for prolonged periods in the hospital environment. This study aimed to evaluate the efficacy of UV-C 254 nm light in the inactivation of the spores of different ribotyp...
Emerging and evolving Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages, adapted to changing epidemiological conditions, present unprecedented challenges to global public health systems. Here, we introduce an adapted analytical approach that complements genomic sequencing, applyi...
Candida auris, a multidrug-resistant yeast, poses significant challenges in healthcare settings due to its ability to form biofilms and resistance to common disinfectants. Understanding its susceptibility to biocides used in hospital disinfection practices is crucial for infection control. We invest...
To investigate the characteristics and clonal dynamics of tigecycline-resistant Acinetobacter baumannii (TRAB) isolates from a Chinese hospital from 2016 to 2021. A total of 64 TRAB isolates were screened and WGS was performed. Phylogenetic analysis and non-polymorphic mutation analysis were used to...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence of viral lineages which arrive by many routes of transmission including via transportation hubs. In the Canadian province of Ontario, nu...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a persistent nosocomial pathogen that poses a significant threat to global public health, particularly in intensive care units (ICUs). Here we report a three-month longitudinal genomic surveillance study conducted in a Hangzhou ICU in 2021. This...
The rising bacterial infections threaten world aquaculture and wild fish populations, making it imperative to increase the understanding of the mechanisms of pathogenic virulence and resistance. This study applies comparative genomic analysis to 21 bacterial fish pathogens, using whole-genome sequen...
BackgroundThe National Surveillance for Invasive Meningococcal Disease (IMD) initiative started in Japan in April 2013. Multiple international mass gathering events have since been held in Japan, and the COVID-19 pandemic has occurred.AimWe summarised 10 years of national surveillance data for IMD i...
We recently expanded the viral genomic surveillance program in Minnesota, USA, to include human respiratory syncytial virus. We performed whole-genome sequencing of 575 specimens collected at Minnesota healthcare facilities during July 2023-February 2024. Subgroups A and B differed in their genomic...
BackgroundNew Delhi metallo-beta-lactamase (NDM)-producing has been reported from European Union/European Economic Area (EU/EEA) countries with increasing frequency. During 2018 to 2022, 355 cases of NDM-producing were detected in seven hospitals reporting on NDM-production in Enterobacterales in...
Vulnerable patients in an intensive care unit (ICU) setting are at high risk of infection from bacteria including gut-colonising and species. Complex ICU procedures often depend on successful antimicrobial treatment, underscoring the importance of understanding the extent of patient colonisation b...
The Global Initiative on Sharing All Influenza Data, a public-access database for sharing severe acute respiratory syndrome coronavirus 2 genomic sequencing data, has received significantly less data from African countries compared to the global total. Furthermore, the contribution of these data was...
Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including the application of deep learning to overcome computational limitations, significant challenges persist due to data inadequacies and stati...
Congregate homeless shelters are disproportionately affected by infectious disease outbreaks. We describe enterovirus epidemiology across 23 adult and family shelters in King County, Washington, USA, during October 2019-May 2021, by using repeated cross-sectional respiratory illness and environmenta...
In 2008-2010, Malaysia experienced a nationwide chikungunya virus (CHIKV) outbreak caused by the Indian Ocean lineage E1-226V (valine) variant, adapted to Aedes albopictus. In 2017-2022, transition to an E1-226A (alanine) variant occurred. Ae. albopictus prevails in rural areas, where most cases occ...
In 2022-2024, three outbreaks of sheeppox (SPP) were reported in the European Union. These occurred in Spain, Bulgaria, and Greece and had serious economic consequences due to animal losses and trade restrictions. Five sheeppox virus (SPPV) whole-genome sequences (WGSs) were determined from samples...
In March 2024, the Pan American Health Organization (PAHO) issued an alert in response to a rapid increase in Oropouche fever cases across South America. Brazil has been particularly affected, reporting a novel reassortant lineage of the Oropouche virus (OROV) and expansion to previously non-endemic...
Microbial data sharing underlies evidence-based microbial research, as well as pathogen surveillance and analysis essential to public health. While the need for data sharing was highlighted during the SARS-CoV-2 pandemic, some concerns regarding secondary data use have also surfaced. Although genera...
The aim of this study was to explore the mechanisms and molecular epidemiology of carbapenem resistance in the carbapenem-resistant complex (CRECC) over a decade in a tertiary hospital in Zhejiang, China. From January 2011 to December 2021, we collected a total of 931 complex (ECC) isolates from a...
The hospital wastewater system has been reported as a source of nosocomial acquisition of carbapenemase producing Enterobacteriaceae (CPE) in various settings. Cleaning and disinfection protocols or replacement of contaminated equipment often fail to eradicate these environmental reservoirs, which c...
Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this...
The presence of erm(T) gene conferring resistance to macrolides, lincosamides and streptogramin B (MLS), was screened in 296 enterococci collected from clinical samples in a central Italy hospital and seven Enterococcus faecium isolates resulted positive to erm(T) by PCR. All isolates were resistant...
The Brazilian Amazon region is a highly endemic area for hepatitis Delta and has areas that are difficult to access. Understanding the dynamics of HDV transmission in these remote locations is important for elucidating the routes of infection. To investigate this, a molecular analysis of HDV was con...
Despite the general classification of L. monocytogenes strains as equally virulent by global safety authorities, molecular epidemiology reveals diverse subtypes in food, processing environments, and clinical cases. This study focuses on a highly virulent strain associated with a listeriosis outbreak...
Rabies remains a major public health problem in low- and middle-income countries. However, human rabies deaths are rarely laboratory-confirmed or sequenced, especially in Africa. Five human rabies deaths from Tanzania and Kenya were investigated and the causative rabies viruses sequenced, with the a...
The emergence of the SARS-CoV-2 virus led to a global pandemic, prompting extensive research efforts to understand its molecular biology, transmission dynamics, and pathogenesis. Recombination events have been increasingly recognized as significant contributor to the virus's diversity and evolution,...
Human mobility is strongly associated with the spread of SARS-CoV-2 via air travel on an international scale and with population mixing and the number of people moving between locations on a local scale. However, these conclusions are drawn mostly from observations in the context of the global north...
Clostridioides difficile infection (CDI) is one of the most significant causes of diarrhea in hospitalized patients. The aim of this study was to investigate the incidence and epidemiology of CDI after the COVID-19 pandemic in hospitalized patients in a rehabilitation center in Thessaloniki, Greece....
In 2019, became the first fungal pathogen included in the list of the urgent antimicrobial threats by the Centers for Disease Control (CDC). Short tandem repeat (STR) analysis and whole-genome sequencing (WGS) are considered the gold standard, and can be complemented by other molecular methods, for...
Retrospective and descriptive molecular epidemiology studies have shown that Mycobacterium tuberculosis whole genome sequencing can identify outbreaks and disease transmission events with higher resolution than conventional epidemiological investigations. Those studies have strengthened our understa...
The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV...
Chikungunya cases was reported to be on the rise in Malaysia from 2019 to 2021. Although potential endemicity was described previously, genotype shift during 2008 outbreak originating from the 2004 Indian Ocean Islands outbreak presents the probability of current CHIKV spread from neighboring countr...
Plasmid-mediated tigecycline resistance genes, notably the tet(X) and tmexCD-toprJ genes, have garnered considerable attention due to their transferability. This study aims to investigate the prevalence and resistance mechanisms associated with tet(X) and tmexCD-toprJ in flies, which are important r...
The integration of viral genomic data into public health surveillance has revolutionized our ability to track and forecast infectious disease dynamics. This review addresses two critical aspects of infectious disease forecasting and monitoring: the methodological workflow for epidemic forecasting an...
Monkeypox virus (MPXV) is endemic in western and Central Africa, and in May 2022, a clade IIb lineage (B.1) caused a global outbreak outside Africa, resulting in its detection in 116 countries and territories. To understand the global phylogenetics of MPXV, we analyzed all available MPXV sequences,...
Avian influenza (AI) is an extremely contagious viral disease of domestic and wild birds that can spread rapidly among bird populations, inducing serious economic losses in the poultry industry. During the winter season 2021-2022, we isolated seventeen highly pathogenic avian influenza (HPAI) H5N8 v...
This study updates the initial COVID-19 pandemic surveillance in sub-Saharan Africa (SSA) from 2020 by providing 2 additional years of data for the region. First, we aimed to measure whether there was an expansion or contraction in the pandemic in SSA when the World Health Organization (WHO) declare...
The Burkholderia cepacia complex comprises a group of bacteria with a growing threat as a contaminant of nonsterile solutions. We describe an outbreak of a Burkholderia cepacia complex involving patients at intensive care unit related to a no-rinse bathing solution (NRBS). We carried out patients, e...
Serratia marcescens is an aerobic Gram-negative Enterobacterales bacillus that has emerged as a cause of hospital-associated infections. To report the epidemiological, diagnostic, and genetic investigation of an outbreak involving five neonatal patients infected or colonized with S. marcescens inclu...
The COVID-19 pandemic has been the most significant health challenge of the last century. Multiple and successive waves of COVID-19 cases, driven particularly by the emergence of new SARS-CoV-2 variants, have kept the world in a constant state of alert. We present an observational, descriptive, cros...
Klebsiella pneumoniae is a common pathogen capable of causing a wide range of infections. Antibiotic resistance complicates treatment of these infections significantly. We are comparing resistance levels and genotypes among two collections of K. pneumoniae clinical isolates from Alexandria Main Univ...
is a group of emerging antimicrobial-resistant nontuberculous mycobacteria that causes severe lung disease in infected patients globally. Recently, molecular epidemiology studies have indicated that horizontal gene transfer (HGT) events in the gene are prevalent between subspecies. To determine th...
Non-typhoidal (NTS) is a common zoonotic foodborne pathogen, whose rising antimicrobial resistance has been an urgent threat to global public health. Here, we reported two carbapenem-resistant (CRSE) strains (NBFE-049 and NBFE-164) carrying the genes, which were recovered from two Chinese childr...
The 21st century has witnessed several clinical outcomes regarding AMR. One health concept has been foreseen as a standard global public health initiative in ensuring human, animal and environmental health. The present study explores critical Gram-negative ESKAPE pathogens encompassing Acinetobacter...
Elucidating disease spread between subpopulations is crucial in guiding effective disease control efforts. Genomic epidemiology and phylodynamics have emerged as key principles to estimate such spread from pathogen phylogenies derived from molecular data. Two well-established structured phylodynamic...
Influenza A has been named as a priority pathogen by the WHO due to the potential to cause pandemics. Genomic sequencing of influenza strains is important to understand the evolution of the influenza strains and also to select the appropriate influenza vaccines to be used in the different influenza...
The challenges in culturing Treponema pallidum have hindered molecular-biological analysis. This study aims to establish a molecular epidemiological analysis of syphilis among Japanese men who have sex with men (MSM) and to investigate the relationship between bacteremia and associated pathophysiolo...
Non-typhoidal Salmonella (NTS) is one of the top causes of diarrhea worldwide. Ceftriaxone is commonly recommended as the initial treatment option for Salmonella infections due to its antibacterial effectiveness. The objective of this study was to investigate the molecular epidemiological characteri...
Klebsiella pneumoniae is among the most important Gram-negative pathogens that can cause serious nosocomial infections. The emergence and prevalence of hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP) pose a significant challenge to public health. In this study, we characterized thirty car...
Molecular surveillance of methicillin-resistant Staphylococcus aureus (MRSA) isolated from Hospital Canselor Tuanku Muhriz (HCTM), a Malaysian teaching hospital revealed clonal replacement events of SCCmec type III-SCCmercury to SCCmec type IV strains before the year 2017; however, the reasons behin...
This study examines a case involving a 7-year-old child who developed dengue symptoms following Qdenga vaccination. Despite initial negative diagnostic results, molecular analysis confirmed an infection with DENV4. Next-generation sequencing detected viral RNA from both DENV2 and DENV4 serotypes, wh...
The dissemination of Klebsiella spp. producing multiple carbapenemases has been increasingly recognized. Between July 2019 and August 2021, ten patients were found to carry Klebsiella spp. co-harboring bla and bla across multiple wards at a Korean hospital, and one isolate was recovered from a hand-...
In 2023, a second wave of the global mpox epidemic, which is mainly affecting men who have sex with men (MSM), was observed in some countries. Herein, we benefited from a large viral sequence sampling (76/121; 63%) and vast epidemiological data to characterise the re-emergence and circulation of the...
The first era of genomics started with the publication of Watson and Crick's notable work on the description of the DNA double helix in 1953. This era lasted 50 years, until the publication of the human genome in April 2003. The second era is associated with the period between the completion of the...
The emergence of multidrug-resistant poses a significant threat to public health. isolates were collected from clinical patients in a Chinese hospital during 2020-2022. An unusual strain, GMU8049, was not susceptible to any of the antibiotics tested, including the novel β-lactam/β-lactamase inhibi...
On 27 May 2024, the Cuban Ministry of Health reported the first outbreak of Oropouche fever on the island. The etiologic agent, Oropouche virus (OROV), is a poorly understood arbovirus that has been known since the 1960s and represents a public health burden in Latin America. We report the whole-gen...
Pediatric patients are vulnerable to the threat of carbapenem-resistant Klebsiella pneumoniae (CRKP) due to their limited immunity and few available antibiotics. Especially when these pathogens exhibit hypervirulent phenotypes, they are often associated with poor clinical outcomes. In this study, we...
The global threat of Carbapenem-resistant Acinetobacter baumannii (CRAB) has intensified as resistance to carbapenems continues to rise in recent decades. We aimed to explore risk factors, molecular epidemiology, and antimicrobial therapy of CRAB infection. The clinical data of 110 patients infected...
Dengue fever is the most important arbovirosis for public health, with more than 5 million cases worldwide in 2023. Mosnodenvir is the first anti-dengue compound with very high preclinical pan-serotype activity, currently undergoing phase 2 clinical evaluation. Here, by analyzing dengue virus (DENV)...
Italy was significantly affected by the COVID-19 pandemic, experiencing multiple waves of infection following the sequential emergence of new variants. Understanding the transmission patterns and evolution of SARS-CoV-2 is vital for future preparedness. We conducted an analysis of viral genome seque...
The patterns of spread of influenza A viruses in local populations in tropical and sub-tropical regions are unclear due to sparsity of representative spatiotemporal sequence data. We sequenced and analyzed 58 influenza A(H3N2) virus genomes sampled between December 2015 and December 2016 from nine h...
Foodborne infections such as listeriosis caused by the bacterium Listeria monocytogenes represent a significant public health concern, particularly when outbreaks affect many individuals over prolonged time. Systematic collection of pathogen isolates from infected patients, whole genome sequencing (...
Genomic surveillance enables the early detection of pathogen transmission in healthcare facilities and contributes to the reduction of substantial patient harm. Fast turnaround times, flexible multiplexing, and low capital requirements make Nanopore sequencing well suited for genomic surveillance pu...
Households are a major setting for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, but there remains a lack of knowledge regarding the dynamics of viral transmission, particularly in the setting of preexisting SARS-CoV-2 immunity and evolving variants. We conducted a prospec...
The epidemiology of dengue has been demonstrating significant changes in recent years, with rising incidence of infection in countries with known endemicity and occurrence of fresh outbreaks in previously unaffected territories. India, which has been a traditional hotspot dengue virus (DENV) transmi...
Malassezia is a commensal that sometimes becomes pathogenic under the influence of diverse factors. Several species of Malassezia are difficult to culture, making traditional methods of identification challenging. The problem with molecular typing of Malassezia in association with seborrheic dermati...
Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chr...
Carbapenemase-producing (CP-Kp) isolates are a public health concern as they can cause severe hospital-acquired infections that are difficult to treat. It has recently been shown that CP-Kp can take up virulence factors from hypervirulent lineages. In this study, 109 clinical CP-Kp isolates from t...
Rotavirus group C is an important cause of sporadic cases and outbreaks of gastroenteritis worldwide. Whole-Genome sequences of human rotavirus C (RVC) in public databases are limited. We performed genome sequencing to analyze a RVC outbreak of acute gastroenteritis in China. Samples from 22 patient...
Norovirus is the leading cause of acute gastroenteritis (AGE) worldwide. Norovirus outbreaks at military facilities can cause loss of training and working days and increased healthcare utilization, affecting force readiness. During 2013-2023, we enrolled 2,304 US military recruits from 4 basic train...
Surveillance of antimicrobial resistance in Kenya, Uganda, and Jordan identified multidrug-resistant high-risk bacterial clones: Escherichia coli sequence types 131, 1193, 69, 167, 10, 648, 410, 405 and Klebsiella pneumoniae sequence types 14, 147, 307, 258. Clones emerging in those countries exhibi...
Genomic surveillance programs benefit greatly from a network of committed, well-supported laboratories that conduct ongoing surveillance activities for pathogens of public health importance. The experiences of the Global Emerging Infections Surveillance program provide insights for building and main...
is a common cause of multidrug-resistant (MDR) nosocomial infections worldwide, including Vietnam. Analysis of crucial genetic factors may link to epidemiological characteristics and antibiotic resistance of clinical strains in Vietnamese hospitals. Fifty-one . clinical strains from six different...
The Orthobunyavirus oropoucheense species encompasses a group of arthropod-borne zoonotic viruses transmitted by biting midges to animals including humans. Several large-scale human outbreaks caused by the prototype member of this species, Oropouche virus (OROV) have been documented since the 1970s...
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform the public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (Ca...
Influenza circulation was significantly affected in 2020-21 by the COVID-19 pandemic. During this time, few influenza cases were recorded. However, in the summer of 2021-22, an increase in atypical influenza cases was observed, leading to the resurgence of influenza in the southernmost state of Braz...
The seventh cholera pandemic started in 1961 in Indonesia and spread across the world in three waves in the decades that followed. Here, we utilised genomic evidence to detail the first wave of the seventh pandemic. Genomes of 22 seventh pandemic Vibrio cholerae isolates from 1961 to 1979 were compl...
is a globally distributed opportunistic pathogen in human health settings, including in intensive care units (ICUs). We investigated the contamination of a French small animal ICU with . We discovered repeated animal contamination by , and phylogenetic analysis traced contamination back to a potenti...
In September 2021, eight campylobacteriosis cases were identified in a town in Nebraska, USA. We assessed potential exposures for a case-control analysis. We conducted whole-genome sequencing on Campylobacter isolates from patients' stool specimens. We collected large-volume dead-end ultrafiltration...
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has mutated at a high rate since the beginning of the pandemic, leading to the formation of different variants. Alpha, Beta, Gamma, Delta and Omicron have emerged as concerning variants identified by the World Health Organization...
Antimicrobial resistance (AMR) poses a significant threat to global public health, with the potential to cause millions of deaths annually by 2050. Effective surveillance of AMR pathogens is crucial for monitoring and predicting their behaviour in response to antibiotics. However, many public health...
West Nile virus (WNV) is the most common cause of human arboviral disease in the contiguous United States, where only lineage 1 (L1) WNV had been found. In 2023, an immunocompetent patient was hospitalized in Nebraska with West Nile neuroinvasive disease and multisystem organ failure. Testing at the...
The frequent occurrence of Acinetobacter baumannii in hospital settings and the elevated rate of antimicrobial resistance in this pathogen represent a serious clinical and public health threat worldwide, and particularly in Lebanon where outbreak surveillance and control are still insufficient. Whol...
In December 2018, an outbreak of Enteritidis infections was identified in Canada by whole-genome sequencing (WGS). An investigation was initiated to identify the source of the illnesses, which proved challenging and complex. Microbiological hypothesis generation methods included comparisons of iso...
An investigation into an outbreak of Newport infections in Canada was initiated in July 2020. Cases were identified across several provinces through whole-genome sequencing (WGS). Exposure data were gathered through case interviews. Traceback investigations were conducted using receipts, invoices,...
In epidemiological investigations, pathogen genomics can provide insights and test epidemiological hypotheses that would not have been possible through traditional epidemiology. Tools to synthesize genomic analysis with other types of data are a key requirement of genomic epidemiology. We propose a...
The malaria parasites Plasmodium falciparum and Plasmodium vivax differ in key biological processes and associated clinical effects, but consequences on population-level transmission dynamics are difficult to predict. This co-endemic malaria study from Guyana details important epidemiological contra...
H5 subtype high-pathogenicity avian influenza (HPAI) viruses continue to devastate the poultry industry and threaten food security and public health. The first outbreak of H5 HPAI in the Philippines was reported in 2017. Since then, H5 HPAI outbreaks have been reported in 2020, 2022, and 2023. Here,...
This study explored the molecular epidemiology and resistance mechanisms of 271 non-duplicate Salmonella enterica (S. enterica) strains, isolated mainly from adults (209/271) in a tertiary hospital in Hangzhou between 2020 and 2021. Through whole-genome sequencing and bioinformatics, the bacterial s...
Monkeypox virus (MPXV) is the zoonotic agent responsible for mpox, an often-self-limiting pox-like disease. Since May 2022, an outbreak characterized by increased human-to-human transmission was detected outside the endemic regions. Whole genome sequencing (WGS) has been successfully used to keep tr...
Streptococcus suis is a major swine pathogen and zoonotic agent, causing important economic losses to the porcine industry. Here, we used genomics approaches to characterize 251 S. suis isolates recovered from diseased pigs across Belgium, France, Germany, Hungary, the Netherlands, Spain, and the Un...
Invasive pneumococcal disease (IPD) due to non-vaccine serotypes after the introduction of pneumococcal conjugate vaccines (PCV) remains a global concern. This study used pathogen genomics to evaluate changes in invasive pneumococcal lineages before, during and after vaccine introduction in South Af...
Dengue is a widespread viral infection transmitted from mosquitoes to humans, mainly in tropical and subtropical climates. In Benin, only dengue virus (DENV) serotype 2 infection has been previously described in humans. This study aimed to investigate DENV infection and serotypes in suspected patien...
In November 2023, the National Reference Laboratory for Enteroviruses (Budapest, Hungary) received stool, pharyngeal swab and cerebrospinal fluid samples from five newborns suspected of having human parechovirus (PEV-A) infection. The neonates were born in the same hospital and presented with fever...
The coronavirus disease of 2019 (COVID-19) pandemic is characterized by sequential emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, lineages, and sublineages, outcompeting previously circulating ones because of, among other factors, increased transmissibility and i...
Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phyl...
Since the outbreak of the coronavirus disease (COVID-19) pandemic in 2019, the Korea Disease Control and Prevention Agency (KDCA) has been conducting genomic surveillance using whole-genome sequencing to monitor SARS-CoV-2 variants in the Republic of Korea (ROK). Since the JN.1 lineage, derived from...
The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. pv. is one of the major pathogens causing bacterial spot disease of tomatoes. After its first report in the 1950s, there were no formal reports on this pathogen until the 1990s, despi...
We traced back a nationwide outbreak of human listeriosis in Switzerland to a persisting production line contamination of a factory producing baker's yeast with Listeria monocytogenes serotype 1/2a sequence type 3141. We used whole-genome sequencing to match clinical isolates to isolates from produc...
Asia remains vulnerable to new and emerging infectious diseases. Understanding how to improve next generation sequencing (NGS) use in pathogen surveillance is an urgent priority for regional health security. Here we developed a pathogen genomic surveillance assessment framework to assess capacity in...
The COVID-19 pandemic is marked by the successive emergence of new SARS-CoV-2 variants, lineages, and sublineages that outcompete earlier strains, largely due to factors like increased transmissibility and immune escape. We propose DeepAutoCoV, an unsupervised deep learning anomaly detection system,...
Current methods are insufficient alone for outbreak detection in hospitals. Real-time genomic surveillance using offers the potential to detect otherwise unidentified outbreaks. We initiated and evaluated the Enhanced Detection System for Healthcare-associated Transmission (EDS-HAT), a real-time gen...
Surveillance data from wildlife and poultry was used to describe the spread of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in British Columbia (B.C.) and the Yukon, Canada from September 2022 - June 2023 compared to the first "wave" of the outbreak in this region, which occurred Apr...
The emergence of infectious diseases, particularly those caused by respiratory pathogens like COVID-19 and influenza viruses, poses a significant threat to public health, especially in the context of climate change. Vulnerable variants and major pathogenicities are appearing, leading to a wide range...
Gram-negative Salmonella bacilli are one of the most common bacterial causes of gastrointestinal infections. Well-selected and targeted microbiological diagnostics enable the detection and identification of the etiological agent of infection, however, standardized, routine and recommended methods do...
Rapid expansion of pathogen sequencing capacity in Africa has led to a paradigm shift from relying on others to locally generating genomic data and sharing it with the global community. However, several barriers remain to be unlocked for timely processing, analysis, dissemination, and effective use...
remains a significant foodborne pathogen globally with . Typhimurium presenting as a frequently occurring serovar. This study aimed to characterize 67 . Typhimurium isolates from humans, food, farms, and slaughterhouses collected in Singapore from 2016 to 2017. Using whole-genome sequencing analysis...
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrat...
Non-typhoidal is a common cause of gastroenteritis worldwide, but current non-typhoidal surveillance is suboptimal. Here, we evaluated the utility of wastewater monitoring to enhance traditional surveillance for this foodborne pathogen. In June 2022, we tested raw sewage collected twice a week fro...
Genomic epidemiology (GE) is an integration of genomics and epidemiology. The field has evolved significantly in the past decade, enhancing our understanding of genetic susceptibility, drug resistance, disease transmission patterns, outbreak surveillance, and vaccine development. It employs an arsen...
The Brazilian western Amazon is experiencing its largest laboratory-confirmed Oropouche virus (OROV) outbreak, with more than 6,300 reported cases between 2022 and 2024. In this study, we sequenced and analyzed 382 OROV genomes from human samples collected in Amazonas, Acre, Rondônia and Roraima sta...
has emerged as a significant human pathogen, acquiring multiple antibiotic resistance genes, including carbapenemases. This study focuses on characterizing the plasmids harboring the and (Y) genes in two carbapenem-resistant isolates (UCO-553 and UCO-554) obtained in Chile during the COVID-19 pand...
Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The coronavirus disease 2019 (COVID-19) pandemic and resulting non-pharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South...
Transmission of plant viruses by insect vectors is facilitated by unequivocal tri-partite interactions among host plants, viruses, and associated vectors. The advent of next-generation sequencing including whole genome sequencing, RNA/small RNA sequencing, proteomics, and metabolomics aided in eluci...
Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the exis...
Streptococcus pneumoniae, a medically important opportunistic bacterial pathogen of the upper respiratory tract, is a major public health concern, causing a wide range of pneumococcal illnesses, both invasive and noninvasive. It is associated with significant global morbidity and mortality, includin...
The aim of this work was to provide a theoretical and scientific basis for the treatment, prevention, and control of clinical drug-resistant bacterial infections by studying the molecular epidemiology and horizontal transfer mechanism of -carrying linezolid-resistant strains (LREfs) that were clini...
Similarly to wild poliovirus, vaccine-derived poliovirus (VDPV) strains can cause acute flaccid paralysis, posing a considerable challenge to public health and the eradication of poliovirus. VDPV outbreaks, particularly VDPV type 2 (VDPV2), are increasing worldwide, including in high-income countrie...
Ventilator-associated pneumonia (VAP) is the main healthcare-associated infection in intensive care units with Staphylococcus aureus as the first pathogen in early VAP. To compare, using whole-genome sequencing (WGS), consecutive S. aureus isolates from lower respiratory samples of mechanically vent...
We aimed to determine the prevalence of genes associated with high-level mupirocin and biocide resistance in methicillin-resistant Staphylococcus aureus (MRSA) isolates among hospitalized patients and to characterize their genomic and epidemiologic features. Study conducted on an integrated health s...
To determine the prevalence, trends, and potential nosocomial transmission events of the hidden reservoir of rectal carriage of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). From 2013 to 2022, yearly point prevalence surveys were conducted in a large Dutch teaching hospital....
The expansion of sequencing technologies as a result of the response to the COVID-19 pandemic enabled pathogen (meta)genomics to be deployed as a routine component of surveillance in many countries. Scaling genomic surveillance, however, comes with associated costs in both equipment and sequencing r...
Between 2018 and 2024, we conducted systematic whole-genome sequencing and phylogenomic analysis on 263 O1 isolates from cholera patients across four provinces in the Democratic Republic of Congo (North-Kivu, South-Kivu, Tanganyika, and Kasai Oriental). These isolates were classified into the AFR10...
During the COVID-19 pandemic, there has been an increasing trend in healthcare-associated infections (HAIs) caused by carbapenem-resistant Acinetobacter baumannii (CRAB), posting a global public health concern. The heightened sensitivity of whole-genome sequencing (WGS) renders it an optimal and pot...
1. Gallinarum strains isolated from a southern Brazil fowl typhoid outbreak were subjected to phenotypic and genotypic analyses to identify genetic elements that could improve prevention and control strategies.2. Whole-genome sequencing revealed the presence of the gene, conferring aminoglycoside...
From 1 January 2022 to 31 May 2024, the World Health Organization (WHO) reported 97,745 laboratory-confirmed Mpox cases, including 203 deaths, across 116 countries. Despite a 2.3% decrease in new cases in May 2024 compared to April 2024, significant regional variations persist. The African Region re...
Wheat yellow mosaic virus (WYMV) is one of the most serious viral pathogens causing reductions in wheat yield in East Asia. We investigated the phylodynamics of WYMV by analysing the CP, VPg and P1 genes to understand the origin and dispersal of the virus. A Bayesian phylogenetic analysis revealed t...
Characteristics of non-clinical strains of methicillin-resistant Staphylococcus aureus (MRSA) especially from fishery environment are poorly understood. This research, in addition to comprehensive characterisation, sought to delineate the genetic relatedness between the MRSA strains originating from...
High pathogenicity avian influenza (HPAI) virus H5N1 first emerged in Bangladesh in 2007. Despite the use of vaccines in chickens since 2012 to control HPAI, HPAI H5Nx viruses have continued to infect poultry, and wild birds, resulting in notable mass mortalities in house crows (). The first HPAI H5...
Helicobacter pylori infects the stomach and/or small intestines in more than half of the human population. Infection with H. pylori is the most common cause of chronic gastritis, which can lead to more severe gastroduodenal pathologies such as peptic ulcer, mucosa-associated lymphoid tissue lymphoma...
Despite the increasing burden of dengue, the regional emergence of the virus in Kenya has not been examined. This study investigates the genetic structure and regional spread of dengue virus-2 in Kenya. Viral RNA from acutely ill patients in Kenya was enriched and sequenced. Six new dengue-2 genomes...
Salmonella as a foodborne pathogen, has a very important impact on human health. This study characterized the serotype, plasmid replicon, MLST typing, resistance phenotype and resistance gene of 282 strains of Salmonella isolated from the environment, animals, foods, and patients in China. These str...
Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via cont...
Carbapenem-resistant Acinetobacter baumannii (CRAB) frequently causes both healthcare-associated infections and nosocomial outbreaks in burn medicine/plastic surgery and beyond. Owing to the high antibiotic resistance, infections are difficult to treat, and patient outcomes are often compromised. Th...
Computer-aided analysis of proteins or nucleic acids seems like a matter of course nowadays; however, the history of Bioinformatics and Computational Biology is quite recent. The advent of high-throughput sequencing has led to the production of "big data", which has also affected the field of virolo...
African swine fever virus (ASFV) has been responsible for the globally devastating epidemics in wild and domesticated pigs. Of the 24 identified ASFV genotypes, genotype II is the primary cause for the pandemic occurring in Europe and Asia since its emergence in Georgia in 2007. The current study ai...
Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To u...
Genomic surveillance of pathogen evolution is essential for public health response, treatment strategies, and vaccine development. In the context of SARS-COV-2, multiple models have been developed including Multinomial Logistic Regression (MLR) describing variant frequency growth as well as Fixed Gr...
Surveillance systems that monitor pathogen genome sequences are critical for rapidly detecting the introduction and emergence of pathogen variants. To evaluate how interactions between surveillance capacity, variant properties, and the epidemiological context influence the timeliness of pathogen var...
The emergence of tmexCD-toprJ, a novel plasmid-mediated resistance-nodulation-division (RND) type efflux pump gene cluster, poses a significant threat to public health by diminishing bacterial susceptibility to the last-resort antibiotics, including tigecycline. Between 2020 and 2022, 18 Klebsiella...
Biofilm formation and toxin production are some of the virulence factors of Clostridioides difficile (C. difficile), which causes hospital-acquired C. difficile infection (HA-CDI). This work investigated the prevalence and distribution of different strains recovered from HA-CDI patients hospitalized...
Brucellosis infects humans and animals worldwide but is particularly prevalent in Asia. In many Asian countries, molecular diagnostic tools for accurate molecular diagnostics and molecular epidemiology are lacking. Nonetheless, some countries have conducted in-depth molecular epidemiological studies...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major nosocomial infectious pathogen with rapidly increasing prevalence. The genomic epidemiological characteristics of CRKP nationwide, especially the evolving trends within the predominant clones, should be evaluated clearly. We collected 3415...
Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae...
The occurrence of carbapenemases encoding genes in is a critical public health concern since this species has intrinsic resistance to several antimicrobials, including polymyxins. The identification of this multidrug-resistant (MDR) pathogen outside the hospital setting has become increasingly freq...
Sapovirus (SaV) infection is increasing worldwide. Herein, we provided evidence of a significant increase in SaV infection in Japan during 2010-2022, primarily due to the considerable (p = 0.0003) rise of the GI.1 genotype. Furthermore, we found that all major and minor SaV outbreaks in Japan, inclu...
Shiga-toxin producing (STEC) O157 is a food-borne pathogen which causes gastrointestinal illness in humans. Ruminants are considered the main reservoir of infection, and STEC exceedance has been associated with heavy rainfall. In September 2022, a large outbreak of STEC O157:H7 was identified in th...
Plague is a deadly zoonosis that still poses a threat in many regions of the world. We combined epidemiologic, host, and vector surveillance data collected during 1961-1980 from the Araripe Plateau focus in northeastern Brazil with ecologic, geoclimatic, and Yersinia pestis genomic information to el...
This study retrospectively analyzed the genetic characteristics of influenza A H3N2 (A/H3N2) viruses circulating in New South Wales (NSW), the Australian state with the highest number of influenza cases in 2022, and explored the phylodynamics of A/H3N2 transmission within Australia during this perio...
While conducting genomic surveillance of carbapenemase-producing (CPE) from patient colonisation and clinical infections at Birmingham's Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes, including the carbapenemase gene . T...
Verona integron-encoded metallo-β-lactamase-producing Pseudomonas aeruginosa (VIM-PA) outbreaks are frequently linked to contaminated sink-drains in the intensive care unit (ICU). This study aims to investigate a VIM-PA outbreak occurring at 4 ICUs in a Belgian university center. Between 01/01/2019...
This study characterised type O foot-and-mouth disease (FMD) viruses recovered from outbreaks that were reported between 2010 and 2019 in the Republic of Korea. We used 96 newly generated whole-genome sequences (WGS) along with 131 already published WGSs from samples collected from countries in East...
This study aims to investigate the drug resistance, regulation mechanism of quorum sensing system, expression of related virulence genes, and epidemiological characteristics of carbapenem-resistant Pseudomonas aeruginosa (CRPA).In this study, Polymerase chain reaction amplification was performed to...
HIV-1 infections remain a global public health concern. Scaled-up antiretroviral treatment (ART) is crucial for reducing morbidity and mortality related to HIV/AIDS. The emergence of drug-resistance mutations (DRMs) compromises viral suppression and contributes to the continued HIV-1 transmission. S...
Since 2022, many countries have reported an upsurge in invasive group A streptococcal (iGAS) infections. We explored whether changes in carriage rates or emergence of strains with potentially altered virulence, such as 1 variants M1 and M1, contributed to the 2022/2023 surge in the Netherlands. We...
The global epidemic of Mpox virus (MPXV) continues, and a local outbreak has occurred in Shenzhen city since June 2023. Herein, the evolutionary trajectory and characteristics of MPXV in 2023 were analyzed using 92 MPXV sequences from the Shenzhen outbreak and the available genomes from GISAID and G...
This study updates the COVID-19 pandemic surveillance in Central Asia we conducted during the first year of the pandemic by providing 2 additional years of data for the region. The historical context provided through additional data can inform regional preparedness and early responses to infectious...
No abstract available
Commonly used approaches for genomic investigation of bacterial outbreaks, including SNP and gene-by-gene approaches, are limited by the requirement for background genomes and curated allele schemes, respectively. As a result, they only work on a select subset of known organisms, and fail on novel o...
This study updates our findings from the COVID-19 pandemic surveillance we first conducted in South Asia in 2020 with 2 additional years of data for the region. We assess whether COVID-19 had transitioned from pandemic to endemic at the point the World Health Organization (WHO) ended the public heal...
Early detection of disseminating vancomycin-resistant (VREfm) in ICU wards is crucial for outbreak identification and the implementation of prompt infection control measures. Genotypic methods like pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) are costly and time-consumi...
Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain fe...
Brazil is one of the countries most affected by COVID-19, with the highest number of deaths recorded. Brazilian Health Institutions have reported four main peaks of positive COVID-19 cases. The last two waves were characterized by the emergence of the VOC Omicron and its sublineages. This study aime...
is an opportunistic pathogen and a leading cause of bloodstream infections, with its capacity to acquire antibiotic resistance genes posing significant treatment challenges. This pilot study characterizes the genomic profiles of isolates from patients with bloodstream infections in KwaZulu-Natal, S...
Influenza A has been named as a priority pathogen by the WHO due to the potential to cause pandemics. Genomic sequencing of influenza strains is important to understand the evolution of the influenza strains and also to select the appropriate influenza vaccines to be used in the different influenza...
Mycobacterium caprae is linked to regular outbreaks of tuberculosis (TB) in geographically distinct caprine populations across Europe, namely Iberia where this ecovar may represent up to 8% of total animal TB cases, circulating in multi-host communities encompassing domestic ruminants and wildlife,...
The increase in syphilis rates worldwide necessitates development of a vaccine with global efficacy. We aimed to explore Treponema pallidum subspecies pallidum (TPA) molecular epidemiology essential for vaccine research by analysing clinical data and specimens from early syphilis patients using whol...
Submitted genomic data for respiratory viruses reflect the emergence and spread of new variants. Although delays in submission limit the utility of these data for prospective surveillance, they may be useful for evaluating other surveillance sources. However, few studies have investigated the use of...
Melioidosis, a severe bacterial illness caused by Burkholderia pseudomallei, is prevalent in most parts of Thailand, including its southern region situated within the Malay Peninsula. Despite a lower reported incidence rate of melioidosis in the South compared to the Northeast, the mortality rate re...
We determined the dengue virus (DENV) serotypes and genotypes in archived serum samples that were collected during the 2014-2016 and 2021 dengue outbreaks in Dire Dawa City and the Somali region in Ethiopia. DENV serotype 1 (DENV-1) was predominant followed by DENV serotype 2 (DENV-2). Thirteen of t...
In spring 2022, an increase in metallo-β-lactamase-producing (MBL-Pa) infections was detected in a hospital in Upper Austria. To identify the source of infection and to stop further transmissions, an epidemiological outbreak investigation including whole-genome sequencing (WGS)-based typing was con...
In early 2021, the 10-valent Pneumococcal conjugate vaccine (PCV10) was replaced with 13-valent (PCV13) by the federal directorate of immunization (FDI), Pakistan. We assessed the impact of a higher valent vaccine, PCV13, on the serotype distribution of nasopharyngeal carriage in rural Pakistan. Chi...
Respiratory disease, attributed to influenza, respiratory syncytial virus (RSV), and SARS-CoV-2, was reported nationally during the 2023/2024 respiratory viral season. The emergence of novel SARS-CoV-2 variants was considered a significant factor contributing to the rise in COVID-19 cases. Data from...
Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application...
The COVID-19 pandemic caused by the SARS-CoV-2 virus infected more than 775,686,716 humans and was responsible for the death of more than 7,054,093 individuals. COVID-19 has taught us that the development of vaccines, repurposing of drugs, and understanding the mechanism of a disease can be done wit...
The One Health approach, recognizing the interconnectedness of human, animal, and environmental health, has gained significance amid emerging zoonotic diseases and antibiotic resistance concerns. This paper aims to demonstrate the utility of a collaborative tool, the SIEGA, for monitoring infectious...
The 2022 global outbreak of monkeypox virus (MPXV), previously confined to Central and West Africa, necessitates an enhanced understanding of its spread. Comprehensive genomic surveillance to understand the virus's evolution and spread is needed, particularly in Asia. Genomic data from 169 MPXV geno...
The COVID-19 pandemic underscored the significance of omics technology and Wastewater-Based Epidemiology for epidemic preparedness. This study investigates the virosphere in wastewater samples from Natal (Brazil), aiming to understand its structure, relationships, and potential. Metaviromic analysis...
Enforcing strict protocols that prevent transmission of airborne infections in prisons is challenging. We examine a large severe acute respiratory syndrome coronavirus 2 outbreak in a Catalan penitentiary center in February-April 2021, prior to vaccination deployment. The aim was to describe the evo...
The role of sub-Saharan Africa in the global spread of influenza viruses remains unclear due to insufficient spatiotemporal sequence data. Here, we analyzed 222 codon-complete sequences of influenza A viruses (IAVs) sampled between 2011 and 2013 from five countries across sub-Saharan Africa (Kenya,...
Clostridioides difficile is an important human pathogen, for which there are very limited treatment options, primarily the glycopeptide antibiotic vancomycin. In recent years, vancomycin resistance has emerged as a serious problem in several gram-positive pathogens, but high-level resistance has yet...
French Guiana experienced an unprecedented dengue epidemic during 2023-2024. Prior to the 2023-2024 outbreak in French Guiana, DENV-3 had not circulated in an epidemic manner since 2005. We therefore studied retrospectively the strains circulating in the French Territories of the Americas (FTA)-Fren...
The transition from MIRU-VNTR-based epidemiology studies in tuberculosis (TB) to genomic epidemiology has transformed how we track transmission. However, short-read sequencing is poor at analyzing repetitive regions such as the MIRU-VNTR loci. This causes a gap between the new genomic data and the l...
Cholera is a life-threatening gastrointestinal infection caused by a toxigenic bacterium, Vibrio cholerae. After a lull of almost 30 years, a first case of cholera was detected in Lebanon in October 2022. The outbreak lasted three months, with 8007 suspected cases (671 laboratory-confirmed) and 23 d...
species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid . However, its epidem...
Despite the provision of a mumps vaccination program in Canada for over three decades, mumps has not reached elimination. Instead, a re-emergence has been observed in vaccinated populations, particularly in young adults. These outbreaks have been almost exclusively due to genotype G infections, a tr...
Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to...
In July 2017, a family of three members, a 46-year-old male, a 45-year-old female and their 8-year-old daughter, returned to South Africa from Thailand. They presented symptoms consistent with mosquito-borne diseases, including fever, headache, severe body aches and nausea. Mosquito bites in all fam...
Coxsackievirus A24 (CV-A24) is a human enterovirus that causes acute flaccid paralysis. However, a Coxsackievirus A24 variant (CV-A24v) is the most common cause of eye infections. The causes of these variable pathogenicity and tissue tropism remain unclear. To elucidate the phylodynamics of CV-A24 a...
and are responsible for transmitting major human arboviruses such as Dengue, Zika, and Chikungunya, posing a global threat to public health. The lack of etiological treatments and efficient vaccines makes vector control strategies essential for reducing vector population density and interrupting th...
Wastewater-based genomic surveillance can improve community prevalence estimates and identify emerging variants of pathogens. Wastewater influents and treated effluents from six wastewater treatment plants (WWTPs) in Tunisia were analyzed between December 2021 and July 2022. Wastewater samples were...
Between 2017 and 2019, pulsed-field gel electrophoresis was replaced by whole genome sequencing (WGS) for identifying enteric disease clusters in Canada. The number and characteristics of all clusters of , , Shiga toxin-producing (STEC), and spp. between 2015 and 2021 were analyzed. Following the...
Pseudomonas aeruginosa AUST-03 (ST242) has been reported to cause epidemics in people with CF (pwCF) from Australia and has been associated with multidrug resistance and increased morbidity and mortality. Here, we report an epidemic P. aeruginosa (AUST-03) strain in South African pwCF detected at a...
The first case of COVID-19 was detected in Bangladesh on 8 March 2020. Since then, the Government of Bangladesh (GoB) has implemented various measures to limit the transmission of COVID-19, including widespread testing facilities across the nation through a laboratory network for COVID-19 molecular...
The Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is a very prevalent viral pathogen that can induce reproductive failure in infected sows. PRRSV infection can result in smaller litters, foetal death, late-term abortions and retarded growth of infected piglets. Not all sows respond equ...
The rising frequency of multidrug-resistant (MDR) Acinetobacter baumannii infections represents a significant public health challenge in Bangladesh. Genomic analysis of bacterial pathogens enhances surveillance and control efforts by providing insights into genetic diversity, antimicrobial resistanc...
The COVID-19 pandemic led to the institution of public health measures in many countries which reduced respiratory infections. We aimed to identify and characterize changes in pediatric (<18 years) invasive pneumococcal disease (pIPD) in Portugal in 2018-2023. pIPD cases were identified by culture a...
Mycoplasma pneumoniae (M. pneumoniae) continues to pose a significant disease burden on global public health as a respiratory pathogen. The antimicrobial resistance among M. pneumoniae strains has complicated the outbreak control efforts, emphasizing the need for robust surveillance systems and effe...
Klebsiella spp. are leading causes of nosocomial infections. Their ability to harbour antimicrobial resistance genes makes them an important public health threat. This study aimed to report the genomic background of carbapenemase-producing Klebsiella quasipneumoniae (HV55B) and Klebsiella michiganen...
is considered by many to be the deadliest microbe, with the estimated annual cases numbering more than 10 million. The bacteria, including , are classified into nine major lineages and hundreds of sublineages, each with different geographical distributions and levels of virulence. The phylogeographi...
Melioidosis is a zoonotic disease, with its outbreaks being rare and indicative of an unusual concurrence of extreme climate and natural environmental factors. An outbreak of melioidosis cases emerged in Hainan following Typhoon "Dianmu" from October to December 2021, presenting an opportunity to id...
, both commensal and pathogenic, can colonize plants and persist in various environments. It indicates fecal contamination in water and food and serves as a marker of antimicrobial resistance. In this context, 61 extended-spectrum β-lactamase (ESBL)-producing from irrigation water and fresh produce...
Tuberculosis (TB) remains an important infectious disease and different genotypes have been reported. This study aimed to investigate the genetic diversity and molecular epidemiology of TB in the lower northern region of Thailand, where genotyping data are limited. A total of 159 Mycobacterium tuber...
Vancomycin-resistant (VREfm) is a prevalent healthcare-acquired pathogen. Gastrointestinal colonization can lead to difficult-to-treat bloodstream infections with high mortality rates. Prior studies have investigated VREfm population structure within healthcare centers. However, little is known abo...
Cryptococcosis is an important fungal infection for both humans and cats, but molecular epidemiological studies on strains isolated from cats are limited. We conducted multi-locus sequence typing analysis and antifungal susceptibility testing of 14 Cryptococcus spp. strains from domestic cats in Jap...
Seasonal H3N2 influenza virus, known for its rapid evolution, poses a serious threat to human health. This study focuses on analyzing the influenza virus trends in Jining City (2018-2023) and understanding the evolving nature of H3N2 strains. Data on influenza-like cases were gathered from Jining Ci...
The investigation of Candida auris outbreaks is needed to provide insights into its population structure and transmission dynamics. We genotypically and phenotypically characterised a C. auris nosocomial outbreak occurred in Consorcio Hospital General Universitario de Valencia (CHGUV), Spain. Data a...
The East African Community (EAC) is experiencing an unprecedented, emerging mpox outbreak since July 2024 in five of eight partner states. We highlight rapid regional response measures, initiated August 2024 coordinated by EAC: field deployment of six mobile laboratories in Burundi, Rwanda, Uganda,...
Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enh...
The global mpox epidemic in 2022 was likely caused by transmission of mpox virus (MPXV) through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing a phylogeographic and epidemiological analysis of MPXV, we identify at lea...
Stenotrophomonas maltophilia is a carbapenem-resistant Gram-negative pathogen increasingly responsible for difficult-to-treat nosocomial infections. To describe the contemporary clinical characteristics and genome epidemiology of patients colonized or infected by S. maltophilia in a multicentre, pro...
Necrotizing enterocolitis is the most severe life-threatening acquired gastrointestinal disorder among preterm neonates. We describe here an outbreak of Clostridium butyricum-related necrotizing enterocolitis in preterm neonates that occurred in three different neonatal centres, in southeast France....
Extended-spectrum β-lactamases (ESBLs)-producing E. coli have been proposed as an indicator bacterium for antimicrobial resistance (AMR) surveillance within a OneHealth framework. However, it is important to understand the effects and potential biases ESBL-selection has on E. coli populations. Utili...
Hand, foot, and mouth disease (HFMD) is a global public health concern, notably within the Asia-Pacific region. Recently, the primary pathogen causing HFMD outbreaks across numerous countries, including China, is coxsackievirus (CV) A6, one of the most prevalent enteroviruses in the world. It is a n...
The mosquito, Aedes aegypti, is the principal vector for several arboviruses. The mosquito midgut is the initial tissue that gets infected with an arbovirus acquired along with a blood meal from a vertebrate host. Blood meal ingestion leads to midgut tissue distention thereby increasing the pore siz...
Group B Streptococcus (GBS) causes invasive infections in newborns and elderly individuals, but is a noninvasive commensal bacterium in most immunocompetent people. Recently, the incidence of invasive GBS infections has increased worldwide, and there is growing interest in the molecular genetic char...
Malawi experienced its deadliest Vibrio cholerae (Vc) outbreak following devastating cyclones, with >58,000 cases and >1700 deaths reported between March 2022 and May 2023. Here, we use population genomics to investigate the attributes and origin of the Malawi 2022-2023 Vc outbreak isolates. Our res...
Acinetobacter baumannii (A. baumannii) is a common opportunistic pathogen in hospitals that causes nosocomial infection. In order to understand the phenotypic and genotypic characteristics of A. baumannii isolates, we sequenced and analyzed 62 A. baumannii isolates from a hospital in Gansu province....
Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evo...
Influenza, a human disease caused by viruses in the Orthomyxoviridae family, is estimated to infect 5% -10 % of adults and 20% -30 % of children annually. Influenza A (IAV) and Influenza B (IBV) viruses accumulate amino acid substitutions (AAS) in the hemagglutinin (HA) and neuraminidase (NA) protei...
Canine distemper virus (CDV) is a highly infectious virus that represents a threat for domestic dogs and several wild species. Despite recognized in several African countries, current knowledge of its molecular epidemiology is scarce and poorly updated. Twenty-two hemagglutinin sequences, obtained f...
The SARS-CoV-2 pandemic resulted in a scale-up of viral genomic surveillance globally. However, the wet lab constraints (economic, infrastructural, and personnel) of translating novel virus variant sequence information to meaningful immunological and structural insights that are valuable for the dev...
Usutu virus (USUV), an arbovirus from the Flaviviridae family, genus Flavivirus, has recently gained increasing attention because of its potential for emergence. After his discovery in South Africa, USUV spread to other African countries, then emerged in Europe where it was responsible for epizootic...
The Chikungunya virus (CHIKV) poses a significant global public health concern, especially in Africa. Since its first isolation in Tanzania in 1953, CHIKV has caused recurrent outbreaks, challenging healthcare systems in low-resource settings. Recent outbreaks in Africa highlight the dynamic nature...
Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Rec...
The COVID-19 pandemic has been marked by novel viral variants, posing challenges to global public health. Recombination, a viral evolution mechanism, is implicated in SARS-CoV-2's ongoing evolution. The XBB recombinant lineage, known for evading antibody-mediated immunity, exhibits higher transmissi...
Meningococcal () serogroup B (MenB) strain antigens are diverse and a limited number of strains can be evaluated using the human serum bactericidal antibody (hSBA) assay. The genetic Meningococcal Antigen Typing System (gMATS) was developed to predict the likelihood of coverage for large numbers of...
Chikungunya virus has caused millions of cases worldwide over the past 20 years, with recent outbreaks in Kedougou region in the southeastern Senegal, West Africa. Genomic characterization highlights that an ongoing epidemic in Kedougou in 2023 is not due to an introduction event but caused by the r...
In Cameroon, mosquitoes transmit various arboviruses, posing significant health risks. We aimed to characterize the virome in southwestern Cameroon and identify potential core viruses which might be associated with vector competence. A total of 398 mosquitoes were collected from four locations (B...
The presence of soil-borne disease obstacles and antibiotic resistance genes (ARGs) in soil leads to serious economic losses and health risks to humans. One area in need of attention is the evolution of ARGs as pathogenic soil gradually develops, which introduces uncertainty to the dynamic ability o...
Biting midges () are vectors of many pathogens of medical and veterinary importance, but their viromes are poorly characterized compared to certain other hematophagous arthropods, e.g., mosquitoes and ticks. The goal of this study was to use metagenomics to identify viruses in from Mexico. A total...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) have been around for more than 3 years now. However, due to constant viral evolution, novel variants are emerging, leaving old treatment protocols redundant. As treatment options dwindle, infecti...
Emergence of drug-induced antimicrobial resistance (AMR) forms a crippling health and economic crisis worldwide, causing high mortality from otherwise treatable diseases and infections. Next Generation Sequencing (NGS) has significantly augmented detection of culture independent microbes, potential...
Rift Valley fever (RVF), a mosquito-borne transboundary zoonosis, was first confirmed in Rwanda's livestock in 2012 and since then sporadic cases have been reported almost every year. In 2018, the country experienced its first large outbreak, which was followed by a second one in 2022. To determine...
is ubiquitous and sporadically infects humans causing Legionnaire's disease (LD). Globally, reported cases of LD have risen fourfold from 2000 to 2014. In 2016, Sydney, Australia was the epicenter of an outbreak caused by serogroup 1 (Lpsg1). Whole-genome sequencing was instrumental in identifying...
This study examines the epidemiological and genomic characteristics, along with the transmission dynamics, of SARS-CoV-2 within prison units I and II in Campo Grande, Mato Grosso do Sul, Brazil. Conducted between May and October 2022, it reveals how the virus spreads in the confined settings of pris...
Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantin...
In Ecuador, data on molecular epidemiology, as well as circulating clones, are limited. Therefore, this study aims to know the population structure of Pseudomonas aeruginosa by identifying clones in clinical samples in Quito-Ecuador. A significant set (45) clinical P. aeruginosa isolates were select...
Whole genome sequencing (WGS) of respiratory viruses from rapid antigen tests (RAT-WGS) is a novel approach to expanding genomic surveillance of respiratory infections. To date however, there are limited data on the genomic stability of these viruses on RATs. In this study, we investigated the effec...
Multi-type birth-death processes underlie approaches for inferring evolutionary dynamics from phylogenetic trees across biological scales, ranging from deep-time species macroevolution to rapid viral evolution and somatic cellular proliferation. A limitation of current phylogenetic birth-death model...
, the causative agent of melioidosis, is highly genetically recombinant, resulting in significant genomic diversity. Multiple virulence factors have been associated with specific disease presentations. To date, there are limited data relating to genomic diversity and virulence factors associated wit...
Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a...
Nosocomial outbreaks caused by carbapenem-resistant Acinetobacter baumannii (CRAB) strains are rapidly emerging worldwide and are cause for concern. Herein, we aimed to describe the genomic characteristics of CRAB strains isolated from two hospitals in China in 2023. The A. baumannii isolates were m...
Shigellosis is a gastrointestinal infection caused by species of . A large outbreak of serotype 2a occurred in Albuquerque, New Mexico (NM) between May 2021 and November 2023 that involved humans and nonhuman primates (NHP) from a local zoo. We analyzed the genomes of 202 New Mexico isolates as wel...
We conducted an integrative analysis to elucidate the spatial epidemiological patterns of the Vesicular Stomatitis New Jersey virus (VSNJV) during the 2014-15 epizootic cycle in the United States (US). Using georeferenced VSNJV genomics data, confirmed vesicular stomatitis (VS) disease cases from su...
Swine acute diarrhoea syndrome coronavirus (SADS-CoV; Coronaviridae, ) was detected in 2017 in Guangdong Province (China), where it caused high mortality rates in piglets. According to previous studies, SADS-CoV evolved from horseshoe bat reservoirs. Here, we report the first five genomes sequenced...
() is the most frequent etiological agent of yersiniosis and has been responsible for several national outbreaks in Norway and elsewhere. A standardized high-resolution method, such as core genome Multilocus Sequence Typing (cgMLST), is needed for pathogen traceability at the national and internatio...
The aim of this study was to investigate to what extent fragments of the HEV genome could be used for accurate diagnostics and inference of viral population-scale processes. For this, we selected all the published whole genome sequences from the NCBI GenBank and trimmed them to various fragment leng...
The prevalence of vancomycin-resistant Enterococcus faecium (VREfm) has increased significantly in Taiwan. We investigated the molecular epidemiology of clinical VREfm isolates to increase our understanding on their spread and changes in population structure over a 14-year span. A total of 1113 E. f...
Bangladesh experienced the largest and deadliest dengue outbreak in 2023, after the virus had reappeared in the country 2 decades earlier. A total of 1,705 people died in Bangladesh, representing the highest case fatality rate (0.5%) due to dengue in the world for that year. The severity of dengue i...
The Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) has been undergoing evolutionary changes to improve its ability to thrive within human hosts, leading to the emergence of specific variants associated with subsequent waves of the coronavirus diseases 2019 (COVID-19) pandemic. In...
We describe the demographics, clinical and molecular epidemiology of extended-spectrum β-lactamase (ESBL) Escherichia coli bloodstream infections (BSI) in Central Australia. All ESBL-producing E. coli bloodstream isolates from January 2018 to December 2020 were retrospectively identified. Demographi...
Hospitals are subject to strict microbial control. Stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity, but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital mic...
Enteric fever is a serious public health concern. The causative agents, Salmonella enterica serovars Typhi and Paratyphi A, frequently have antimicrobial resistance (AMR), leading to limited treatment options and poorer clinical outcomes. We investigated the genomic epidemiology, resistance mechanis...
Brucella canis is a zoonotic pathogen and the main causative agent of canine brucellosis. In the Netherlands, B. canis had previously only been detected in individual cases of imported dogs. However, an outbreak of B. canis occurred for the first time in a cohort of autochthonous dogs in a breeding...
Nontuberculous mycobacteria (NTM) has been reported to be transmitted between people with cystic fibrosis (CF) attending CF centres. A suspected outbreak was investigated at the University of Texas Southwestern (UTSW) Adult CF Program using a combination of pathogen genomic sequencing and epidemiol...
To examine the molecular epidemiology of carbapenem-resistant (CRKP) and investigate the horizontal transmission of and genes for the prevention and treatment of CRKP. A total of 49 clinically isolated CRKP strains were retrospectively analyzed from January to December 2022 at The First Hospital...
Influenza A viruses (IAV) impose significant respiratory disease burdens in both swine and humans worldwide, with frequent human-to-swine transmission driving viral evolution in pigs and highlighting the risk at the animal-human interface. Therefore, a comprehensive One Health approach (interconnect...
Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The Coronavirus disease 2019 (COVID-19) pandemic and resulting nonpharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South...
A clonal shift from staphylococcal cassette chromosome mec (SCCmec) type II/ST5 methicillin-resistant Staphylococcus aureus (MRSA) to SCCmec type IV/clonal complex (CC)1 MRSA has occurred rapidly in Japan. Our previous research in a geriatric hospital found SCCmec type IV/CC1 MRSA prevalence in long...
Genomic surveillance based on sequencing the entire genetic code of SARS-CoV-2 involves monitoring and studying genetic changes and variations in disease-causing organisms such as viruses and bacteria. By tracing the virus, it is possible to prevent epidemic spread in the community, ensuring a 'prec...
Brucellosis is among the key zoonotic infectious diseases in China, and The Ningxia Hui Autonomous Region represents a major endemic area, and it is one of the main causes of poverty in the region due to illness. In Ningxia, there is substantial research on Brucella melitensis, studies on the molecu...
During the coronavirus disease 2019 (COVID-19) pandemic, the number and types of dashboards produced increased to convey complex information using digestible visualizations. The pandemic saw a notable increase in genomic surveillance data, which genomic epidemiology dashboards presented in an easily...
Genomic surveillance of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) is crucial for virulence, drug-resistance monitoring, and outbreak containment. Genomic analysis on 87 KPC-Kp strains isolated from 3 Northern Italy hospitals in 2019-2021 was performed by whole geno...
We have recently introduced MAPLE (MAximum Parsimonious Likelihood Estimation), a new pandemic-scale phylogenetic inference method exclusively designed for genomic epidemiology. In response to the need for enhancing MAPLE's performance and scalability, here we present two key components: (i) CMAPLE...
Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolution...
Infectious disease dynamics are driven by the complex interplay of epidemiological, ecological, and evolutionary processes. Accurately modeling these interactions is crucial for understanding pathogen spread and informing public health strategies. However, existing simulators often fail to capture t...
Community-associated methicillin-resistant (CA-MRSA) infections are now a public health concern in both community and healthcare settings worldwide. We previously identified a suspected case of a maternity clinic-centred outbreak of CA-MRSA skin infection in a regional community in Japan by PFGE-ba...
The reliable and timely recognition of outbreaks is a key component of public health surveillance for foodborne diseases. Whole genome sequencing (WGS) offers high resolution typing of foodborne bacterial pathogens and facilitates the accurate detection of outbreaks. This detection relies on groupin...
Using phylogenomic analysis, we provide genomic epidemiology analysis of a large blastomycosis outbreak in Ontario, Canada, caused by Blastomyces gilchristii. The outbreak occurred in a locale where blastomycosis is rarely diagnosed, signaling a possible shift in geographically associated incidence...
Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana are scarce. This study investigated the genomic diversity, antimicrobial resistance patterns, and clonal relationships of 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern...
Hepatitis E virus (HEV) infection is prevalent among domestic pigs and wild boar in Europe. This study focused on the genetic diversity of HEV subtypes 3c, 3e and 3f among swine and wild boar in Europe as well as their circulation. Phylogenetic analysis and Bayesian phylogenetic inference were appli...
The dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission are influenced by a variety of factors, including social restrictions and the emergence of distinct variants. In this study, we delve into the origins and dissemination of the Alpha, Delta, and Omicron-BA.1 var...
In Senegal, molecular diagnosis was widely used for the detection and management of COVID-19 patients. However, genomic surveillance was very limited in the public sector. This study aimed to share the experience of a Senegalese public sector laboratory in response to the COVID-19 pandemic, and to d...
MPT64 is a key protein used for (MTB) complex strain identification. We describe protracted transmission of an MPT64 negative MTB strain in Queensland, Australia, and explore genomic factors related to its successful spread. All MPT64 negative strains identified between 2002 and 2022 by the Queensl...
Over almost three decades, average nucleotide identity (ANI) analysis has been instrumental in operationally defining species in bacteria. However, barely any attention has been paid to soundly defining intra-species units employing ANI analyses until recently. Notably, some very recent publications...
This study examined the diversity and persistence of in the surface waters of agricultural regions of Brazil, Chile, and Mexico. Research groups (three in 2019-2020 and five in 2021-2022) conducted a long-term survey of surface water across 5-8 months annually ( = 30 monthly). On-site, each team fi...
A diagnostic investigation into an outbreak of fatal respiratory disease among young goats in Iowa, USA revealed bronchitis lesions of unknown etiology and secondary bacterial bronchopneumonia. Hypothesis-free metagenomics identified a previously unreported picornavirus (USA/IA26017/2023), and furth...
The aim was to highlight the incidence and epidemiology of infections (CDI) in a tertiary Greek hospital during the COVID-19 pandemic. A single-center prospective observational cohort study was conducted (October 2021 until April 2022). 125 isolates were cultured from hospitalized patients stool s...
We report a group A streptococcal outbreak in a geriatric mental health inpatient unit. Communication with cognitively impaired patients, limitations in adherence to hygiene practices, and communal dining may have facilitated transmission. Settle plates aided in identifying a colonized patient. Rapi...
SARS-CoV-2 molecular testing coupled with whole-genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOCs) as well as discovery of novel variants. Since the beginning of the pandemic, millions of SARS...
To describe the in vivo emergence of ceftazidime-avibactam resistance in GES-type carbapenemases and to characterize an unusual outbreak of GES-6-producing Serratia marcescens during the COVID-19 pandemic in Spain. Retrospective study to describe a GES-CPSM outbreak based on whole genome sequencing...
The COVID-19 pandemic has profoundly affected all aspects of our lives. Through real-time monitoring and rapid vaccine implementation, we succeeded in suppressing the spread of the disease and mitigating its consequences. Finally, conclusions can be summarized and drawn. Here, we use the example of...
Human Immunodeficiency virus type 1 (HIV-1) remains a significant global health threat partly due to its ability to develop resistance to anti-retroviral therapies. HIV-1 genotype and drug resistance analysis of the polymerase (pol) sequence is a mainstay of its clinical and public health management...
In this study, we built upon our initial research published in 2020 by incorporating an additional 2 years of data for Europe. We assessed whether COVID-19 had shifted from the pandemic to endemic phase in the region when the World Health Organization (WHO) declared the end of the public health emer...
Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of paramount importance to guide vaccine strategies. The aim of this study was to explore the molecular epidemiology of influenza A v...
The emergence of new SARS-CoV-2 variants in Palestine highlights the need for continuous genetic surveillance and accurate screening strategies. This case series study aimed to investigate the geographic distribution and genetic variation of the SARS-CoV-2 Delta Variant in Palestine in August 2021....
The first nationwide outbreak of COVID-19 in Vietnam started in late April 2021 and was caused almost exclusively by a single Delta lineage, AY.57. In early 2022, multiple Omicron variants co-circulated with Delta variants and quickly became dominant. The co-circulation of Delta and Omicron happened...
FIM-1 metallo-β-lactamase was previously detected in sporadic clinical isolates. Here, we report on FIM-1-positive from two patients who had shared the same ward in a long-term acute care rehabilitation hospital. Whole-genome sequencing analysis revealed close relatedness of these isolates, which...
Respiratory syncytial virus (RSV) infection imposes substantial health burden and disproportionally affects young infants, elderly, and immunocompromised hosts. RSV harbors key surface glycoproteins F and G, both crucial for viral infection and evolution. In this study, we examined the genetic chara...
A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole...
Five years before the 2022-2023 global mpox outbreak Nigeria reported its first cases in nearly 40 years, with the ongoing epidemic since driven by sustained human-to-human transmission. However, limited genomic data has left questions about the timing and origin of the mpox virus' (MPXV) emergence....
Salmonella Paratyphi A, one of the major etiologic agents of enteric fever, has increased in prevalence in recent decades in certain endemic regions in comparison to S. Typhi, the most prevalent cause of enteric fever. Despite this increase, data on the prevalence and molecular epidemiology of S. Pa...
Community-acquired (CA), community-onset methicillin-resistant Staphylococcus aureus (CO-MRSA) infection presents a significant public health challenge, even where MRSA rates are historically lower. Despite successes in reducing hospital-onset MRSA, CO-MRSA rates are increasing globally, with a need...
The aim of the study was to identify and monitor the circulating strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the samples received at our center and update the existing national and international genomic surveillance data. SARS-CoV-2 is no exception to the basic nature...
To prevent nosocomial infection, it is important to screen for potential vancomycin-resistant Enterococcus (VRE) among patients. In this study, we analyzed enterococcal isolates from inpatients in one hospital without any apparent outbreak of VRE. Enterococcal isolates were collected from inpatients...
The Escherichia coli species is comprised of several 'ecotypes' inhabiting a wide range of host and natural environmental niches. Recent studies have suggested that novel naturalized ecotypes have emerged across wastewater treatment plants and meat processing facilities. Phylogenetic and multilocus...
This study updates the COVID-19 pandemic surveillance in the Middle East and North Africa (MENA) we first conducted in 2020 with 2 additional years of data for the region. The objective of this study is to determine whether the MENA region meets the criteria for moving from a pandemic to endemic. In...
() is widely distributed in the intestinal tract of humans, animals, and in the environment. It is the most common cause of diarrhea associated with the use of antimicrobials in humans and among the most common healthcare-associated infections worldwide. Its pathogenesis is mainly due to the product...
Disease surveillance is an essential component of public health and a core function of National Public Health Institutes (NPHIs), including to better prepare and respond to infectious diseases outbreaks. Strengthening NPHIs in their efforts to establish and maintain efficient surveillance systems is...
The strong invasiveness and rapid expansion of dengue virus (DENV) pose a great challenge to global public health. However, dengue epidemic patterns and mechanisms at a genetic scale, particularly in term of cross-border transmissions, remain poorly understood. Importation is considered as the prima...
SUMMARY subsp. (SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co...
Salmonella enterica and Escherichia coli are major food-borne human pathogens, and their genomes are routinely sequenced for clinical surveillance. Computational pipelines designed for analyzing pathogen genomes should both utilize the most current information from annotation databases and increase...
Chikungunya virus (CHIKV) has emerged as a significant public health concern due to its rapid spread and potential for causing debilitating epidemics. In Argentina, the virus has garnered attention since its introduction to the Americas in 2013, due to its growing incidence and impact in neighbourin...
Chikungunya virus (CHIKV) is transmitted by mosquito bites and causes chikungunya fever (CHIKF). CHIKV has a single-stranded RNA genome and belongs to a single serotype with three genotypes. The Asian lineage has recently emerged in the Western Hemisphere, likely due to travel-associated introductio...
The co-production of KPC and NDM carbapenemases in carbapenem-resistant Klebsiella pneumoniae (CRKP) complicates clinical treatment and increases mortality rates. The emergence of KPC-NDM CRKP is believed to result from the acquisition of an NDM plasmid by KPC CRKP, especially under the selective pr...
Next-generation sequencing (NGS) has proven clinical utility on disease management and serves as an important tool for genomic surveillance. Currently, hurdles surrounding its implementation, namely the complex and demanding analytical workflows, have impeded its widespread use in many laboratories....
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a serious threat to public health. Globally, carbapenemases-producing CRPA isolates mainly belong to 'high-risk' clones; however, the molecular epidemiology of CRPA isolates circulating in Chile are scarce, where this pathogen is the main aetiolo...
The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing ba...
Phylogeographic analyses are able to exploit the location data associated with sampled molecular sequences to reconstruct the spatio-temporal dispersal history of a pathogen. Visualisation software is commonly used to facilitate the interpretation of the accompanying estimation results, as these are...
Surveillance systems revealed that the prevalence of vancomycin-resistant (VREfm) has increased. We aim to investigate the epidemiological and genomic characteristics of VREfm in China. We collected 20,747 non-redundant isolates from inpatients across 19 hospitals in six provinces between January...
The global circulation of SARS-CoV-2 has been extensively documented, yet the dynamics within Central America, particularly Nicaragua, remain underexplored. This study characterizes the genomic diversity of SARS-CoV-2 in Nicaragua from March 2020 through December 2022, utilizing 1064 genomes obtaine...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA genome-containing virus which has infected millions of people all over the world. The virus has been mutating rapidly enough, resulting in the emergence of new variants and sub-variants which have r...
The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV...
, a Gram-positive conditional pathogen of group species, is capable of causing foodborne and waterborne illnesses, leading to intestinal diseases in humans characterized by diarrhoea and vomiting. However, documented cases of infection outbreaks are rare in the world, and the genomic background of...
In 2022, an outbreak with severe bloodstream infections caused by occurred in an adult intensive care unit (ICU) in Hungary. Eight cases, five of whom died, were detected. Initial control measures could not stop the outbreak. We conducted a matched case-control study. In univariable analysis, the c...
Dengue, a mosquito-borne viral disease, poses a significant public health challenge in Pakistan, with a significant outbreak in 2023, prompting our investigation into the serotype and genomic diversity of the dengue virus (DENV). NS-1 positive blood samples from 153 patients were referred to the Nat...
BackgroundThe COVID-19 pandemic was largely driven by genetic mutations of SARS-CoV-2, leading in some instances to enhanced infectiousness of the virus or its capacity to evade the host immune system. To closely monitor SARS-CoV-2 evolution and resulting variants at genomic-level, an innovative pip...
Historically, the Wa-like strains of human group A rotavirus (RVA) have been major causes of gastroenteritis. However, since the 2010s, the circulation of non-Wa-like strains has been increasingly reported, indicating a shift in the molecular epidemiology of RVA. Although understanding RVA evolution...
Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant , but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 ( )-type carbapenemases are increasing in abundance in Canada and elsewhere; these ge...
Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, in December 2019, it has spread rapidly, and many coronavirus disease (COVID-19) cases have occurred in Gwangju, South Korea. Viral mutations following the COVID-19 epidemic have increased interest...
As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achieving these goals for algorithms, pipelines and instruments oft...
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) persistence in COVID-19 patients could play a key role in the emergence of variants of concern. The rapid intra-host evolution of SARS-CoV-2 may result in an increased transmissibility, immune and therapeutic escape which could be a direct...
Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to gener...
Prevention of toilet-to-patient transmission of multidrug-resistant Pseudomonas aeruginosa (MDR PA) poses management-related challenges at many bone marrow transplant units (BMTUs). To conduct a longitudinal retrospective analysis of the toilet-to-patient transmission rate for MDR PA under existing...
Clusters of nosocomial coronavirus disease 2019 (COVID-19) have been reported globally during the recent pandemic. Unfortunately, these clusters negatively affect inpatient morbidity, mortality, and hospital functioning. Using epidemiological data and whole-genome sequencing (WGS) of SARS-CoV-2, thi...
Despite its popularity for water activities, such as swimming, surfing, fishing, and rafting, inland and coastal bathing areas occasionally experience outbreaks of highly pathogenic avian influenza virus (HPAI), including A(H5N1) clade 2.3.4.4b. Asymptomatic infections and symptomatic outbreaks ofte...
Respiratory diseases, including influenza and coronaviruses, pose recurrent global threats. This study delves into the respiratory surveillance systems, focusing on the effectiveness of SARI sentinel surveillance for total and severe cases incidence estimation. Leveraging data from the COVID-19 pand...
Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA's genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the U...
During the SARS-CoV-2 pandemic, next-generation sequencing (NGS) technologies like the Ion Torrent S5 and Illumina MiSeq, alongside advanced software, improved genomic surveillance in South Africa. This study analysed anonymized samples from the Eastern Cape using Genome Detective and NextClade, sho...
Serratia marcescens is an opportunistic pathogen found ubiquitously in the environment and associated with a wide range of nosocomial infections. This multidrug-resistant bacterium has been a cause of concern for hospitals and healthcare facilities due to its ability to spread rapidly and cause outb...
Hand, Foot and Mouth Disease (HFMD) is a highly contagious viral illness primarily affecting children globally. A significant epidemiological transition has been noted in mainland China, characterized by a substantial increase in HFMD cases caused by non-Enterovirus A71 (EV-A71) and non-Coxsackievir...
Wastewater surveillance is an effective tool for monitoring community spread of COVID-19 and other diseases. Quantitative PCR (qPCR) analysis for wastewater surveillance is more susceptible to mutations in target genome regions than binary PCR analysis for clinical surveillance. The SARS-CoV-2 conce...
Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected fro...
Genomic surveillance of pathogen evolution is essential for public health response, treatment strategies, and vaccine development. In the context of SARS-COV-2, multiple models have been developed including Multinomial Logistic Regression (MLR) describing variant frequency growth as well as Fixed Gr...
Bacterial genotyping through whole-genome sequencing plays a crucial role in disease surveillance and outbreak investigations in public health laboratories. This study assessed the effectiveness of Oxford Nanopore Technologies (ONT) sequencing in the genotyping of and serovar Enteritidis. Our resu...
Avian encephalomyelitis (AE) is an important infectious poultry disease worldwide that is caused by avian encephalomyelitis virus (AEV). The causative virus can be transmitted both horizontally and vertically. In the present study, an AEV suspected outbreak with typical neurological signs occurred i...
The drug-resistant genes carried by carbapenem-resistant (CRKP) limit clinical treatment options, and its virulence genes severely affect patient prognosis. This study aims to investigate the distribution of virulence genes, capsular serotypes, and molecular epidemiological characteristics of CRKP...
Pseudomonas aeruginosa is an opportunistic pathogen responsible for complicated UTIs and exhibits high antibiotic resistance, leading to increased mortality rates, especially in cases of multidrug-resistant strains. This study aimed to investigate the antibiotic susceptibility patterns and genomic c...
In recent decades, growing attention has been directed worldwide toward antimicrobial-resistant (AMR) bacterial pathogens causing infections in clinical, environmental, and food chain production settings [...].
Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and re...
The social restriction measures implemented due to the COVID-19 pandemic have impacted the pattern of occurrences of respiratory viruses. According to surveillance results in the Gwangju region of South Korea, respiratory syncytial virus (RSV) did not occur during the 2020/2021 season. However, ther...
An emergence of multidrug-resistant (MDR) has been observed in the neonatal intensive care unit (NICU) of Nîmes University Hospital in southern France. A case-control analysis was conducted on 96 neonates, to identify risk factors associated with infection, focusing on clinical outcomes. Forty-eig...
Wolbachia bacteria are common endosymbionts of insects and have recently been applied for controlling arboviral vectors, especially Aedes aegypti mosquito populations. However, several medically important mosquito species in Sri Lanka were present with limited information for the Wolbachia infection...
ViralFlow v1.0 is a computational workflow developed for viral genomic surveillance. Several key changes turned ViralFlow into a general-purpose reference-based genome assembler for all viruses with an available reference genome. New virus-agnostic modules were implemented to further study nucleotid...
Plasmids encoding bla genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 bla -encoding plasmids, from...
The coronavirus disease 2019 (COVID-19) is a viral infection characterized by respiratory and gastrointestinal symptoms. The causative agent of this infection is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic study helps in understanding the pathogenesis, epidemiology,...
Few studies have examined the genetic population structure of vector-borne microparasites in wildlife, making it unclear how much these systems can reveal about the movement of their associated hosts. This study examined the complex host–vector–microbe interactions in a system of bats, wingless ecto...
On 20 September 2022, Uganda declared its fifth Sudan virus disease (SVD) outbreak, culminating in 142 confirmed and 22 probable cases. The reproductive rate (R) of this outbreak was 1.25. We described persons who were exposed to the virus, became infected, and they led to the infection of an unusua...
Lumpy Skin Disease (LSD), a poxvirus disease affecting cattle, emerged in India in 2019 and intensified in 2022, resulting in significant economic losses for dairy farmers. There was unusual shift in mortality and morbidity patterns during the second wave. A comprehensive genetic study conducted, an...
To investigate genetic relatedness and antibiotic resistance of Klebsiella pneumoniae from retail meat samples, clinical source samples, and hospital environmental samples in Wuhan, China. Hypermucoviscosity and biofilm formation of K. pneumoniae were assessed by string test and crystal violet stain...
In Taiwan, sequence type (ST) 239 and ST59 were two major clones among meticillin-resistant Staphylococcus aureus (MRSA) clinical isolates in the past two decades. USA300 (ST8) prevailed in the Americas but not in outside areas. Recently USA300 (ST8) emerged and was increasingly identified in Taiwan...
Serratia marcescens is known to cause outbreaks in neonatal intensive care units (NICUs). Traditionally epidemiological data, antimicrobial resistance patterns and epidemiological typing have been used to guide infection prevention methods. Whole-genome sequencing (WGS) applications such as core-gen...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.17...
Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the exis...
In May 2020, the World Health Organization (WHO) declared Latin America and the Caribbean (LAC) the epicenter of the COVID-19 pandemic, with over 40% of worldwide COVID-19-related deaths at the time. This high disease burden was a result of the unique circumstances in LAC. This study aimed to (1) me...
The emergence of new virulent genotypes and the continued genetic drift of Newcastle disease virus (NDV) implies that distinct genotypes of NDV are simultaneously evolving in different geographic locations across the globe, including throughout Africa, where NDV is an important veterinary pathogen....
Carbapenemase-producing spp. , , spp., and (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate...
It is so far unclear how the COVID-19 winter waves started and what should be done to prevent possible future waves. In this study, we deciphered the dynamic course of a winter wave in 2021 in Saxony, a state in Eastern Germany neighbouring the Czech Republic and Poland. The study was carried out th...
Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in pr...
Amid the global challenges posed by the COVID-19 pandemic, unraveling the genomic intricacies of SARS-CoV-2 became crucial. This study explores viral evolution using an innovative high-throughput next-generation sequencing (NGS) approach. By taking advantage of nasal swab and mouthwash samples from...
To estimate the prevalence of carbapenemase-producing Enterobacterales (CPE) carriage among pets using faecal specimens submitted to veterinary diagnostic laboratories throughout the US. A secondary aim was to employ whole-genome sequencing (WGS) to characterize isolates of CPE from companion animal...
In arthropod-associated microbial communities, insect-specific viruses (ISVs) are prevalent yet understudied due to limited infectivity outside their natural hosts. However, ISVs might play a crucial role in regulating mosquito populations and influencing arthropod-borne virus transmission. Some stu...
We aimed to characterize the genomes of monkeypox virus isolates from the Far East, providing insights into viral transmission and evolution. Genomic analysis was conducted on 8 isolates obtained from patients with monkeypox virus disease in the Republic of Korea between May 2022 and early 2023. The...
In 2020, an outbreak of Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Hadar strain caused an outbreak that was linked to ground turkey consumption....
Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) cases are more prone to Influenza and SARS-CoV-2 infection. Accordingly, we genetically characterized Influenza and SARS-CoV-2 in 633 ILI and SARI cases by rRT-PCR and WGS. ILI and SARI cases showed H1N1pdm09 prevalence of 20...
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOG...
In the mountainous, rural regions of eastern China, tuberculosis (TB) remains a formidable challenge; however, the long-term molecular epidemiological surveillance in these regions is limited. This study aimed to investigate molecular and spatial epidemiology of TB in two mountainous, rural counties...
To investigate cases of five Campylobacter jejuni outbreaks and describe laboratory characteristics of these infections. Whole-genome sequencing and conventional methods were combined to thoroughly investigate the outbreaks, and data of contemporaneous sporadic cases was included for comparison. Sev...
Wastewater surveillance can reveal population-level infectious disease burden and emergent public health threats can be reliably assessed through wastewater surveillance. While molecular methods for wastewater monitoring of microorganisms have traditionally relied on PCR-based approaches, next-gener...
Understanding the transmission dynamics of carbapenem-resistant Enterobacterales (CRE) is critical to addressing the escalating global threat of antimicrobial resistance (AMR). Although hospital transmission of CRE has been extensively studied, information on community transmission is lacking. To id...
To describe an outbreak of sequence type (ST)2 infection (CDI) detected by a recently implemented multilocus sequence type (MLST)-based prospective genomic surveillance system using Oxford Nanopore Technologies (ONT) sequencing. Hemato-oncology ward of a public tertiary referral centre. From Februa...
Infections caused by multidrug-resistant gram-negative bacteria present a severe threat to global public health. The WHO defines drug-resistant Klebsiella pneumoniae as a priority pathogen for which alternative treatments are needed given the limited treatment options and the rapid acquisition of no...
We conducted a molecular epidemiological study of using whole-genome sequence data and clinical data of isolates from nasal swabs of patients admitted to the intensive care unit (ICU) of Hiroshima University hospital. The relationship between isolate genotypes and virulence factors, particularly fo...
Haemophilus influenzae, a causative agent of severe invasive infections such as meningitis, sepsis and pneumonia, is classified into encapsulated or typeable (represented by serotypes A to F) and non-typeable varieties (NTHi) by the presence or absence of the polysaccharide capsule. Invasive disease...
Infections caused by linezolid-resistant enterococci (LRE) are clinically difficult to treat and threaten patient health. However, there is a lack of studies on long time-span LRE strains in China. For this reason, our study comprehensively revealed the resistance mechanisms of LRE strains collected...
Listeriosis is a notifiable disease in Switzerland. In summer 2022, the Swiss Federal Office of Public Health noticed an increase in reports of listeriosis cases, indicating a possible ongoing outbreak. Here we present the approaches applied for rapidly confirming the outbreak, detecting the underly...
Foodborne diseases are a growing public health concern with a notable disease burden in China. Two children with diarrhea visited a healthcare facility within 24 hours on August 1 and 2, 2023. Grumpensis was detected in their stool samples by the public health laboratory. Whole genome sequencing (W...
To assess the residual risk of waterborne contamination by Pseudomonas aeruginosa from a water network colonized by a single genotype [sequence type (ST) 299] despite the presence of antimicrobial filters in a medical intensive care unit (ICU). During the first 19-month period since the ICU opened,...
Surveillance of avian influenza virus (AIV) was conducted in the 2021-2022 winter season at a wintering site of migratory in Japan. An H5N8 subtype high pathogenicity AIV (HPAIV) with a unique gene constellation and four low pathogenicity AIVs (LPAIVs) were isolated from environmental samples. The...
Regular quality-assured WGS with antimicrobial resistance (AMR) and epidemiological data of patients is imperative to elucidate the shifting gonorrhoea epidemiology, nationally and internationally. We describe the dynamics of the gonococcal population in 11 cities in Brazil between 2017 and 2020 and...
In Australia, invasive meningococcal disease (IMD) incidence rapidly increased between 2014 and 2017 due to rising serogroup W (MenW) and MenY infections. We aimed to better understand the genetic diversity of IMD during 2017 and 2018 using whole genome sequencing data. Whole genome sequencing data...
In February 2023, sequence type (ST) 38 producing oxacillinase 244 (OXA-244-Ec ST38) was detected from three patients in a hospital in western Poland. Overall, OXA-244-Ec ST38 was detected from 38 colonised patients in 13 wards between February and June 2023. The outbreak was investigated on site b...
In June 2023, UKHSA surveillance systems detected an outbreak of severe gastrointestinal symptoms caused by a rare serotype of Shiga toxin-producing , STEC O183:H18. There were 26 cases aged 6 months to 74 years (42 % cases were aged 0-9 years), distributed across the UK with onset dates range betwe...
The aim of this study was to go through the molecular methods used for typing of carbapenem-resistant (CRAB) isolates for investigating the molecular epidemiology all over the world. Multiple typing techniques are required to understand the source and nature of outbreaks caused by () and acquired...
Human immunodeficiency virus (HIV)-1 subtype C is the most prevalent globally and is thought to have originated in non-human primates in the Democratic Republic of Congo. Although the global dominance of HIV-1 subtype C is well established, a thorough understanding of its evolutionary history and tr...
We investigated molecular evolution and spatiotemporal dynamics of atypical Legionella pneumophila serogroup 1 sequence type 1905 and determined its long-term persistence and linkage to human disease in dispersed locations, far beyond the large 2014 outbreak epicenter in Portugal. Our finding highli...
In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (...
We sought to capture the evolutionary itinerary of the Mycobacterium tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, where it caused a major multidrug-resistant (MDR) tuberculosis outbreak in a context strictly negative for HIV infection. We combined whole genome sequencing and Bayesia...
Human Mpox (formerly monkeypox) infection is an emerging zoonotic disease caused by the Mpox virus (MPXV). We describe the complete genome annotation, phylogeny, and mutational profile of a novel, sustained Clade I Mpox outbreak in the city of Kamituga in Eastern Democratic Republic of the Congo (DR...
Escherichia coli (E. coli) is the major cause of extraintestinal infections in the urinary tracts and bloodstream in humans in the community and health care institutions. Several studies on the genetic characterization of E. coli among clinical and environmental isolates were performed and revealed...
, a non-fermentative, ubiquitous, gram-negative aerobic bacterium, is associated with high mortality rates, particularly in immunocompromised or debilitated patients. The prevalence rate of ICU-acquired pneumonia episodes caused by this microorganism has been found to be 2%. has been identified as...
Sepsis and drug resistance represent a complex of the most common global causes of mortality in intensive care units (ICUs) especially among patients with comorbidities. Extraintestinal pathogenic (ExPEC) strains are highly implicated in systemic infections, with multidrug resistance exacerbating t...
Broiler chickens are frequently colonized with Extended-Spectrum Beta-Lactamase- (ESBL-) and plasmid mediated AmpC Beta-Lactamase- (pAmpC-) producing Enterobacterales, and we are confronted with the potential spread of these resistant bacteria in the food chain, in the environment, and to humans. Re...
Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity an...
Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generatio...
The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clin...
Enteric yersiniosis, the third most common food-borne zoonosis in Europe, is mainly caused by the pathogen . In France the yersiniosis microbiological surveillance is conducted at the National Reference Laboratory (YNRL). Since 2017, isolates have been characterized by whole genome sequencing (WGS)...
SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving a large death toll. As of January 2023, Brazil is among the countries with the highest number of registered deaths. Nonpharmacological and pharmacological interventions have been heterogeneously implemented in th...
In this study, conducted at the National Institute of Health, Islamabad, during an outbreak of human respiratory syncytial virus (hRSV) from December 2022 to January 2023, the first whole-genome sequences of hRSV isolates from Islamabad, Pakistan, were determined. Out of 10 positive samples, five we...
This study was to clarify the molecular epidemiology and clinical infection characteristics of Ralstonia pickettii and establish sequence typing system. 48 nonrepetitive Ralstonia pickettii strains were collected from January 2008 to December 2013 at the Chinese People's Liberation Army General Hosp...
Limited data are available on Mpox breakthrough infections. The purpose of this study is to investigate a Mpox breakthrough outbreak in 3 vaccinated individuals. Study participants provided informed consent. Serology testing was performed in one involved individual (ID-1) using an in-house assay det...
Information regarding haboring carbapenemase in Japan is limited. A comprehensive nationwide survey was conducted from September 2014 to December 2022, and 67 non-duplicate strains of carbapenem-resistant were isolated from 57 healthcare facilities in Japan. Through genetic testing and whole-genom...
No abstract available
In this study, the genetic differences and clinical impact of the carbapenemase-encoding genes among the community and healthcare-acquired infections were assessed. This retrospective, multicenter cohort study was conducted in Colombia and included patients infected with carbapenem-resistant Gram-ne...
This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequen...
The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest and of clinical relevance. The impact of SARS-CoV-2, the etiological agent of the Coronavirus Disease 2019 (CO...
Foot-and-mouth disease is a highly contagious disease affecting cloven-hoofed animals, resulting in considerable economic losses. Its causal agent is foot-and-mouth disease virus (FMDV), a picornavirus. Due to its error-prone replication and rapid evolution, the transmission and evolutionary dynamic...
An epizootic of highly pathogenic avian influenza A (H5N1) has spread worldwide since 2022. Even though this virus has been extensively studied for many decades, little is known about its evolution in South America. Here, we describe the sequencing and characterization of 13 H5N1 genomes collected f...
Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent local transmission dynamics and eco-epidemiologica...
Genomic surveillance of SARS-CoV-2 has given insight into the evolution and epidemiology of the virus and its variant lineages during the COVID-19 pandemic. Expanding this approach to include a range of respiratory pathogens can better inform public health preparedness for potential outbreaks and ep...
is an opportunistic human and animal pathogen severely understudied. Here, we conducted the largest genomic epidemiological study on this pathogen to date. Our data show that this bacterium has spread globally. Also, we found that some human and non-human isolates are not well differentiated from on...
Sequencing of SARS-CoV-2 from rapid diagnostic tests (RDTs) can bolster viral genomic surveillance efforts; however, approaches to maximise and standardise pathogen genome recovery from RDTs remain underdeveloped. We aimed to systematically optimise the elution of genetic material from RDT component...
Candidemia is the most common healthcare associated invasive fungal infection. Over the last few decades, candidemia caused by Candida species other than Candida albicans, particularly the Candida parapsilosis complex, has emerged worldwide. The aims of this study were: to analyze the genotypic and...
In 2023, Nepal faced its second largest dengue outbreak ever, following a record-breaking number of dengue cases in 2022, characterized by the expansion of infections into areas of higher altitudes. However, the characteristics of the 2023 circulating dengue virus (DENV) and the vector density remai...
In the first half of 2023, a global shift was observed towards the predominance of XBB variants. China faced a significant epidemic between late 2022 and early 2023 due to Omicron subvariants BA.5.2 and BF.7. This study aims to depict the evolving variant distribution among provincial-level administ...
Global warming has seriously disturbed the Earth's ecosystems, and in this context, Asian honeybee (Apis cerana) has experienced a dramatic decline in recent decades. Here, we examined both direct and indirect effects of climate change on A. cerana through ecological niche modeling of A. cerana, and...
This study describes an outbreak caused by multispecies carbapenemase-producing Enterobacterales (CPE) occurring in a pediatric ward at an academic medical center in Tokyo. The index case involved a 1-year-old boy with Klebsiella variicola (CPE) detected in anal swabs in June 2016. The second case w...
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children and the second leading cause of infant death worldwide. While global circulation has been extensively studied for respiratory viruses such as seasonal influenza, and more recently also i...
In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in optimizing interventions, particularly when resources...
Experimental evidence suggests that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) remains viable within aerosols with a half-life of approximately 3 hours; however, it remains unclear how long airborne SARS-CoV-2 can transmit infection. Whole genome sequencing during an outbreak sugge...
No abstract available
The presence of different mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can be related to changes in coronavirus disease (COVID-19) infection. Besides, these viral alterations associated with factors such as massive number of positive cases, vaccination and rei...
Lumpy skin disease virus (LSDV) is a member of the capripoxvirus (CPPV) genus of the family. LSDV is a rapidly emerging, high-consequence pathogen of cattle, recently spreading from Africa and the Middle East into Europe and Asia. We have sequenced the whole genome of historical LSDV isolates from...
Klebsiella pneumoniae species complex (KpSC) bloodstream infections (BSIs) are associated with considerable morbidity and mortality, particularly in elderly and multimorbid patients. Multidrug-resistant (MDR) strains have been associated with poorer outcome. However, the clinical impact of KpSC phyl...
To investigate the source and transmission dynamics of an endoscope-associated New Delhi metallo-β-lactamase-producing (NDM-KP) outbreak. Epidemiological and genomic investigation. Academic acute care hospital in New Jersey. Five patients with active NDM-KP infection identified on clinical isolates...
The emergence of viral variants with altered phenotypes is a public health challenge underscoring the need for advanced evolutionary forecasting methods. Given extensive epistatic interactions within viral genomes and known viral evolutionary history, efficient genomic surveillance necessitates earl...
No abstract available
The SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center. We analyzed 61,397 SARS-CoV-2 genom...
The aim of the study was to evaluate the relationship between carbapenem-resistant Acinetobacter baumannii isolates carrying oxacillinase-type carbapenemase genes with "international high-risk clones" (IC I, II, and III) by different molecular epidemiological methods and to statistically compare the...
In 2023, an increase of OXA-48-producing was noticed by the Lithuanian National Public Health Surveillance Laboratory. Whole genome sequencing (WGS) of 106 OXA-48-producing isolates revealed three distinct clusters of carbapenemase-producing high-risk clones, including sequence type (ST) 45 (n =...
(Enterobacterales: Erwiniaceae) are a group of cosmopolitan bacteria best known as the causative agents of various plant diseases. However, other species in this genus have been found to play important roles as insect endosymbionts supplementing the diet of their hosts. Here, I describe Erwinia imp...
We used pathogen genomics to test orangutan specimens from a museum in Bonn, Germany, to identify the origin of the animals and the circumstances of their death. We found monkeypox virus genomes in the samples and determined that they represent cases from a 1965 outbreak at Rotterdam Zoo in Rotterda...
Genomic epidemiology enhances the ability to detect and refute methicillin-resistant (MRSA) outbreaks in healthcare settings, but its routine introduction requires further evidence of benefits for patients and resource utilization. We performed a 12 month prospective study at Cambridge University H...
Phytophthora pseudosyringae is a self-fertile pathogen of woody plants, particularly associated with tree species from the genera Fagus, Notholithocarpus, Nothofagus and Quercus, which is found across Europe and in parts of North America and Chile. It can behave as a soil pathogen infecting roots an...
Carbapenem-resistant Escherichia coli has been categorized as a pathogen of critical priority by the World Health Organization as it is highly infectious with high mortality and morbidity rates and widespread transmission potential. Carbapenem resistance is primarily mediated by carbapenemase-encodi...
In 2020, a sylvatic dengue virus serotype 2 infection outbreak resulted in 59 confirmed dengue cases in Kedougou, Senegal, suggesting those strains might not require adaptation to reemerge into urban transmission cycles. Large-scale genomic surveillance and updated molecular diagnostic tools are nee...
Salmonella enterica serovar Abortusovis is a ovine-adapted pathogen that causes spontaneous abortion. Salmonella Abortusovis was reported in poultry in 2009 and has since been reported in human infections in New South Wales, Australia. Phylogenomic analysis revealed a clade of 51 closely related iso...
The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phy...
Aim of the study was the molecular characterization of 21 ceftazidime/avibactam resistant (CZA-R) Klebsiella pneumoniae strains, collected in the period October 2021-March 2022 from an Intensive Care COVID Unit in a Northern Italian Hospital. After growth on selective/chromogenic culture media and s...
Reading the viral genome through whole genome sequencing (WGS) enables the detection of changes in the viral genome. The rapid changes in the SARS-CoV-2 viral genome may cause immune escape leading to an increase in the pathogenicity or infectivity. Monitoring mutations through genomic surveillance...
Newborns admitted to neonatal intensive care units (NICU) are at increased risk of health care-associated infections. Serratia marcescens represent the third most common pathogen in NICU outbreaks. Here we present an outbreak investigation performed using Whole Genome Sequencing (WGS) analyses and t...
The COVID-19 pandemic was initiated by the rapid spread of a SARS-CoV-2 strain. Though mainly classified as a respiratory disease, SARS-CoV-2 infects multiple tissues throughout the human body, leading to a wide range of symptoms in patients. To better understand how SARS-CoV-2 affects the proteome...
Contact between humans and wildlife presents a risk for both zoonotic and anthropozoonotic disease transmission. In this study we report the detection of human strains of Mycobacterium tuberculosis in sun bears and an Asiatic black bear in a wildlife rescue centre in Cambodia, confirming for the fir...
Pseudomonas aeruginosa (PA) is a common cause of healthcare-associated infection (PA-HAI) in the intensive care unit (ICU). To describe the epidemiology of PA-HAI in ICUs in Ontario, Canada, and to identify episodes of sink-to-patient PA transmission. This was a prospective cohort study of patients...
Avian influenza virus subtype H9N2 is endemic in commercial poultry in Tunisia. This subtype affects poultry and wild birds in Tunisia and poses a potential zoonotic risk. Tunisian H9N2 strains carry, in their hemagglutinins, the human-like marker 226 L that is most influential in avian-to-human vir...
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has prompted global concern due to its profound impact on public health and the economy. Effective treatment of COVID-19 patients in the acute phase or of those with long COVID is a major challenge. Using data-independent acquisition (DIA) technolog...
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and...
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chai...
Avian metapneumovirus (aMPV), classified within the family, wreaks havoc on poultry health. It typically causes upper respiratory tract and reproductive tract infections, mainly in turkeys, chickens, and ducks. Four subtypes of AMPV (A, B, C, D) and two unclassified subtypes have been identified, o...
The evolutionary dynamics of viruses, particularly exemplified by SARS-CoV-2 during the ongoing COVID-19 pandemic, underscore the intricate interplay between genetics, host adaptation, and viral spread. This paper delves into the genetic evolution of SARS-CoV-2, emphasizing the implications of viral...
In response to Mpox endemic and public health emergency, DCHHS aimed to develop NGS based techniques to streamline Mpox viral clade and lineage analysis. The Mpox sequencing workflow started with DNA extraction and adapted Illumina's COVIDSeq assay using hMpox primer pools from Yale School of Public...
SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility da...
Several historic, scientific events have occurred in the decade 2013-2023, in particular the COVID-19 pandemic. This massive pathogenic threat, which has affected the world's population, has had a devastating effect on scientific production worldwide. [...].
The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolat...
Streptococcus equi. subsp. zooepidemicus (S. zooepidemicus) associated diseases in dogs have emerged as a significant concern over recent decades. S. zooepidemicus occurs sporadically in dog populations globally, with increased prevalence in shelters/kennels. This study used multilocus sequence typi...
Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. , r...
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover s...
Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81...
Data on the molecular epidemiology of methicillin-resistant Staphylococcus aureus isolates from patients with bacteraemia in Slovenia are lacking. The aim of this study was to phenotypically and genotypically investigate 82 MRSA strains isolated from patients with bloodstream infections in central S...
Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses in the swine industry. Frequent mutations and recombinations account for PRRSV immune evasion and the emergence of novel strains. In this study, we isolated and characterized two novel PRRSV-2 strains from...
Until the May 2022 Monkeypox (MPXV) outbreak, which spread rapidly to many non-endemic countries, the virus was considered a viral zoonosis limited to some African countries. The Andalusian circuit of genomic surveillance was rapidly applied to characterize the MPXV outbreak in the South of Spain. W...
The unprecedented precision and resolution of whole genome sequencing (WGS) can provide definitive identification of infectious agents for epidemiological outbreak tracking. WGS approaches, however, are frequently impeded by low pathogen DNA recovery from available primary specimens or unculturable...
Cholera continues to be a global health threat. Understanding how cholera spreads between locations is fundamental to the rational, evidence-based design of intervention and control efforts. Traditionally, cholera transmission models have used cholera case-count data. More recently, whole-genome seq...
To investigate the clinical characteristics and molecular epidemiology of carbapenem-resistant (CRKP) isolated from patients with bloodstream infections in a large tertiary-care general hospital in Southwest China. A total of 131 strains of non-repeating CRKP were collected from the blood cultures...
The global challenge posed by the prolonged COVID-19 pandemic underscores the critical need for ongoing genomic surveillance to identify emerging variants and formulate effective public health strategies. This retrospective observational study, conducted in a reference hospital in Northeast Brazil a...
The high-risk clone ST307, associated with various carbapenem resistance genes, exhibits a global distribution and prevalence. However, in China, it has remained sporadic and has rarely been detected. In this study, we reported an outbreak caused by nine ST307 CRKP isolates harboring in Shanghai,...
From 1993 to 1994, 64 free-ranging elephants () succumbed to encephalomyocarditis in the Kruger National Park, South Africa, of which 83% were adult bulls. rodents were implicated as the reservoir host of the (EMCV) based on serology and RT-PCR. However, in the absence of sequence-confirmation of...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) exhibit high mortality rates in pediatric patients and usually belong to international high-risk clones. This study aimed to investigate the molecular epidemiology and carbapenem resistance mechanisms of K. pneumoniae isolates recovered from pediatri...
This study aimed to construct geographically, temporally, and epidemiologically representative data sets for SARS-CoV-2 in North Africa, focusing on Variants of Concern (VOCs), Variants of Interest (VOIs), and Variants Under Monitoring (VUMs). SARS-CoV-2 genomic sequences and metadata from the EpiCo...
During the SARS-CoV-2 pandemic, many countries directed substantial resources toward genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. We aimed to inves...
The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study...
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-sc...
Lassa fever is a hemorrhagic disease caused by Lassa virus (LASV), which has been classified by the World Health Organization as one of the top infectious diseases requiring prioritized research. Previous studies have provided insights into the classification and geographic characteristics of LASV l...
spp. are the most concerning foodborne pathogen in infant formula milk powder. Currently, there are many reports on the prevalence of spp. in infant formula milk and its processing environment, but there are few studies on the prevalence of spp. on dairy farms. We have, therefore, undertaken this...
The spread of infectious diseases is shaped by spatial and temporal aspects, such as host population structure or changes in the transmission rate or number of infected individuals over time. These spatiotemporal dynamics are imprinted in the genome of pathogens and can be recovered from those genom...
Among the most problematic bacteria with clinical relevance are the carbapenem-resistant Enterobacterales (CRE), as there are very limited options for their treatment. Treated wastewater can be a route for the release of these bacteria into the environment and the population. The aim of this study w...
Marek's disease virus (MDV) has become an increasingly virulent pathogen in the poultry industry despite vaccination efforts to control it. Brazil has experienced a significant rise of Marek's disease (MD) outbreaks in recent years. Our study aimed to analyze the complete gene sequences to understa...
Multidrug-resistant (MDR) Infantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases of Infantis infections have...
The aim of this study was to compare Illumina and Oxford Nanopore Technology (ONT) sequencing data to quantify genetic variation to assess within-outbreak strain relatedness and characterise microevolutionary events in the accessory genomes of a cluster of 23 genetically and epidemiologically linked...
is a bacterial gram-positive pathogen that causes invasive infections in swine and is also a zoonotic disease agent. Traditional molecular typing techniques such as ribotyping, multilocus sequence typing, pulse-field gel electrophoresis, or randomly amplified polymorphic DNA have been used to invest...
Rotavirus A (RVA) is a major cause of acute gastroenteritis globally that is classically genotyped by its two immunodominant outer capsid proteins, VP7 (G-) and VP4 (P-). Recent evidence suggests that the reassortant equine-like G3P[8] strain played a substantial role in RVA transmission in Brazil s...
There has been an unprecedented effort to sequence the SARS-CoV-2 virus and examine its molecular evolution. This has been facilitated by the availability of publicly accessible databases, the Global Initiative on Sharing All Influenza Data (GISAID) and GenBank, which collectively hold millions of S...
Healthcare-associated infections caused by vancomycin-resistant (VREFM) pose a significant threat to healthcare. Confirming the relatedness of the bacterial isolates from different patients is challenging. We aimed to assess the efficacy of IR-Biotyper, multilocus sequencing typing (MLST), and core...
The classical lineage of is the most prevalent clonal group associated with Buruli ulcer in humans. Its reservoir is strongly associated with the environment. We analyzed together 1,045 isolates collected from 13 countries on two continents to define the evolutionary history and population dynamics...
The type VI secretion system (T6SS) serves as a crucial molecular weapon in interbacterial competition and significantly influences the adaptability of bacteria in their ecological niche. However, the distribution and function of T6SS in clinical , a common opportunistic nosocomial pathogen, have no...
The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of ot...
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has severely impacted public health. In 2022, the Omicron variant of SARS-CoV-2 rapidly became the dominant circulating variant in the local COVID-19 outbreaks in Tianjin Municipal...
Streptococcus suis, a zoonotic bacterial pathogen circulated through swine, can cause severe infections in humans. Because human S. suis infections are not notifiable in most countries, incidence is underestimated. We aimed to increase insight into the molecular epidemiology of human S. suis infecti...
<b>Background and Objective:</b> The global SARS-CoV-2 pandemic highlights the importance of tracking virus evolution through genomic surveillance, especially concerning mutations in the SARS-CoV-2 spike protein, crucial for vaccine development. Despite global concern over variants, regi...
The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is e...
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patie...
Following the worldwide surge in mpox (monkeypox) in 2022, cases have persisted in Asia, including South Korea, and sexual contact is presumed as the predominant mode of transmission, with a discernible surge in prevalence among immunocompromised patients. Drugs such as tecovirimat can result in dru...
Monkeypox virus (MPXV), originally endemic in West Africa (Clade II) and Central Africa (Clade I), has recently emerged worldwide and has reinforced the need for rapid and accurate MPXV diagnostics. This review presents and critically discusses the range of virological methods for laboratory diagnos...
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five glo...
Zoonotic sporotrichosis is a neglected fungal disease, whereby outbreaks are primarily driven by Sporothrix brasiliensis and linked to cat-to-human transmission. To understand the emergence and spread of sporotrichosis in Brazil, the epicentre of the current epidemic in South America, we aimed to co...
Escherichia coli is a Gram-negative bacterium that causes a variety of clinical infections in humans, including diarrhea, sepsis, and urinary tract infection. This bacterium is a common multidrug-resistant threat in community and hospital settings worldwide. This study examined the antimicrobial sus...
Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed (Pv) and (Pf) transmission dynamics, resistance markers, and Pf deletions in Nueva Jerusalén (NJ), a remote, indigenous community in th...
Malaria elimination requires closely co-ordinated action between neighbouring countries. In Southern Africa several countries have reduced malaria to low levels, but the goal of elimination has eluded them thus far. The Southern Africa Development Community (SADC) Malaria Elimination Eight (E8) init...
Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV...
Methicillin-resistant (MRSA) is one of the major human pathogens. It could carry numerous resistance genes and virulence factors in its genome, some of which are related to the severity of the infection. An observational, descriptive, cross-sectional study was designed to molecularly analyze MRSA i...
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections causing significant morbidity and mortality among children and the elderly; two RSV vaccines and a monoclonal antibody have recently been approved. Thus, there is an increasing need for a detailed and co...
The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS...
Globally, the isolation of community-associated methicillin-resistant Staphylococcus aureus (MRSA) harbouring both the Panton-Valentine leucocidin (PVL) and toxic shock syndrome toxin 1 (TSST-1) genes is rare. However, we encountered an outbreak of the ST22-PT clone exhibiting this phenotype in Japa...
While there is a high burden of methicillin-resistant Staphylococcus aureus (MRSA) infections among pediatric patients, studies on the molecular epidemiology of MRSA infections in Korean children since the 2010s are lacking. This study aimed to investigate the molecular genotypes and clinical charac...
Lumpy skin disease virus (LSDV) belongs to the genus Capripoxvirus and family Poxviridae. LSDV was endemic in most of Africa, the Middle East and Turkey, but since 2015, several outbreaks have been reported in other countries. In this study, we used whole genome sequencing approach to investigate th...
Huanglongbing (HLB) is a fatal citrus disease that is currently threatening citrus varieties worldwide. One putative causative agent, Liberibacter asiaticus (Las), is vectored by , known as the Asian citrus psyllid (ACP). Understanding the details of Las infection in HLB disease has been hindered b...
New Delhi metallo-β-lactamase (NDM) is an emergent mechanism of carbapenem resistance associated with high mortality and limited treatment options. Because the bla resistance gene is often carried on plasmids, traditional infection prevention and control (IP&C) surveillance methods and reactive whol...
Colistin and carbapenem-resistant Klebsiella pneumoniae (Col-CRKP) represent a significant and constantly growing threat to global public health. We report here an outbreak of Col-CRKP infections during the fifth wave of COVID-19 pandemic. The outbreak occurred in an intensive care unit with 22 beds...
is a major cause of bovine mastitis. Intermittent shedding of the organism for many months is a feature of cows with intramammary infection. A dairy farm in Japan experienced a mastitis outbreak caused by in 2016, as well as 2 additional outbreaks and 1 case in 2020-2021. The causative strains in t...
Dried blood spots (DBS) have emerged as a promising alternative to traditional venous blood for hepatitis C virus (HCV) testing. However, their capacity to accurately reflect the genetic diversity of HCV remains poorly understood. We employed deep sequencing and advanced phylogenetic analyses on pai...
Staphylococcus aureus is a common clinical pathogen that causes various human infections. The aim of this study was to investigate the antibiotic susceptibility pattern, molecular epidemiological characteristics, and biofilm formation ability of S. aureus isolates from clinical specimens in Xiangyan...
Infections caused by carbapenem-resistant are a global threat causing a high number of fatal infections. This microorganism can also easily acquire antibiotic resistance determinants, making the treatment of infections a big challenge, and has the ability to persist in the hospital environment unde...
As the COVID-19 pandemic reached its peak, many countries implemented genomic surveillance systems to track the evolution and transmission of SARS-CoV-2. Transition from the pandemic to the endemic phase prioritized alternative testing strategies to maintain effective epidemic surveillance at the po...
No abstract available
In most of Europe and especially in Germany, there is currently a concerning rise in the number of hospital-acquired infections due to vancomycin-resistant Enterococcus faecium (VREfm). Therefore, there is a need to improve our understanding of the way VREfm spreads in hospitals. In this study, we i...
We describe 2 cases of extensively drug-resistant Pseudomonas aeruginosa infection caused by a strain of public health concern, as it was recently associated with a nationwide outbreak of contaminated artificial tears. Both cases were detected through database review of genomes in the Enhanced Detec...
To carry out a whole genome sequencing (WGS)-based investigation on the emergence and spread of the largest multidrug-resistant tuberculosis (MDR TB) outbreak that has been thriving among HIV-negative patients, Tunisia, since the early 2000s. We performed phylogeographic analyses and molecular datin...
To characterize Coronavirus Disease 2019 (COVID-19) transmission dynamics in each of the metropolitan statistical areas (MSAs) surrounding Dallas, Houston, New York City, and Phoenix in 2020 and 2021, we extended a previously reported compartmental model accounting for effects of multiple distinct p...
Fourier-transform infrared (FTIR) spectroscopy has the potential to be used for bacterial typing and outbreak characterization. We evaluated FTIR for the characterization of an outbreak caused by Elizabethkingia miricola. During the 2020-2021 period, 26 isolates (23 clinical and 3 environmental) wer...
In China, is one of the most frequent causes of bacterial gastroenteritis, and food handlers in restaurants as an important contaminated source were rarely reported. In May 2023, an outbreak of serovar Enteritidis infection in a restaurant in Jiangxi Province, China, was investigated. Cases were i...
Highly pathogenic avian Influenza virus (HPAIV) has spread in an unprecedented extent globally in recent years. Despite the large reports of cases in Asia, Europe, and North America, little is known about its circulation in South America. Here, we describe the isolation, and whole genome characteriz...
Omicron has become the dominant variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since first reported in November 2021. From the initially detected Wuhan lineage, sublineages BA.2, BA.4, BA.5, BQ, XAG, and XBB have emerged over time and are dominant in many countries. Therefor...
is a critical foodborne pathogen that causes severe invasive and noninvasive diseases and is associated with high mortality. Information on the prevalence of infections in Taiwan is very limited. This study aimed to analyze the molecular epidemiological surveillance and virulence gene distribution...
New Delhi metallo-β-lactamases (NDMs) are major contributors to the spread of carbapenem resistance globally. In Australia, NDMs were previously associated with international travel, but from 2019 we noted increasing incidence of NDM-positive clinical isolates. We investigated the clinical and genom...
There has been high uptake of rapid antigen test device use for point-of-care COVID-19 diagnosis. Individuals who are symptomatic but test negative on COVID-19 rapid antigen test devices might have a different respiratory viral infection. We aimed to detect and sequence non-SARS-CoV-2 respiratory vi...
Enterocytozoon bieneusi is a zoonotic pathogen widely distributed in animals and humans. It can cause diarrhea and even death in immunocompromised hosts. Approximately 800 internal transcribed spacer (ITS) genotypes have been identified in E. bieneusi. Farmed foxes and raccoon dogs are closely assoc...
Control measures are being introduced globally to reduce the prevalence of antibiotic resistance (ABR) in bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in bacterial species with the potential to be key opportunistic human pathogens, such as on...
Shiga-toxin-producing (STEC) is associated with diarrhea and hemolytic uremic syndrome (HUS). STEC infections in Costa Rica are rarely reported in children. We gathered all the records of STEC infections in children documented at the National Children's Hospital, a tertiary referral hospital, from...
infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and the genomic determinants of disease outcomes. Across two wards over 6 months, we...
Ecuador is a tropical country reporting Dengue virus (DENV) outbreaks with areas of hyperendemic viral transmission. Entomo-virological surveillance and monitoring effort conducted in the Northwestern border province of Esmeraldas in April 2022, five pools of female mosquitoes from a rural communit...
Oropouche virus (OROV) is characterized as a re-emerging arbovirus of great concern for public health, being responsible for several outbreaks of acute fever identified in Latin American countries, registering more than half a million reported cases. The incidence of reports of this virus is intrins...
Cutaneous burn trauma, compromise of dermal layers and immune defense system is a physical and fiscal burden on healthcare systems. Burn-wound infections are a serious complication of thermal injury and contribute significantly to care burden. After burn-induced trauma, sepsis by Pseudomonas aerugin...
Households are a major setting for SARS-CoV-2 infections, but there remains a lack of knowledge regarding the dynamics of viral transmission, particularly in the setting of widespread pre-existing SARS-CoV-2 immunity and evolving variants. We conducted a prospective, case-ascertained household trans...
Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection is...
Introduction Since its emergence, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive genomic evolution, impacting public health policies, diagnosis, medication, and vaccine development. This study leverages advanced bioinformatics to assess the virus's temporal and...
The Eastern Mediterranean Region (EMR) faces ongoing challenges in its public health system due to limited resources, logistical issues, and political disruptions. The COVID-19 pandemic accelerated the need for stronger laboratory capacities to handle the increased demand for testing. In a phased re...
The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands of distinct cases detected outside the endemic areas of Africa as of December 2023. In this article, we analyze the sequences of full genomes of Mpox virus from Europe and compare th...
Shiga toxin-producing E. coli (STEC), including the subgroup of enterohemorrhagic E. coli (EHEC), are important bacterial pathogens which cause diarrhea and the severe clinical manifestation hemolytic uremic syndrome (HUS). Genomic surveillance of STEC/EHEC is a state-of-the-art tool to identify inf...
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure,...
Pneumonic plague (PP) is characterized by high infection rate, person-to-person transmission, and rapid progression to severe disease. In 2017, a PP epidemic occurred in 2 Madagascar urban areas, Antananarivo and Toamasina. We used epidemiologic data and Yersinia pestis genomic characterization to d...
Efficient infection control during carbapenem-resistant Enterobacterales outbreaks demands rapid and simple techniques for outbreak investigations. WGS, the current gold standard for outbreak identification, is expensive, time-consuming and requires a high level of expertise. Fourier-transform infra...
The species complex (KpSC) is a major source of nosocomial infections globally with high rates of resistance to antimicrobials. Consequently, there is growing interest in understanding virulence factors and their association with cellular metabolic processes for developing novel anti-KpSC therapeut...
The human immunodeficiency virus type 1 (HIV-1) A6 sub-subtype is highly prevalent in Eastern Europe. Over the past decade, the dissemination of the A6 lineage has been expanding in Poland. The recent Russian invasion of Ukraine may further escalate the spread of this sub-subtype. While evolutionary...
Mutations associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resistance to antiprotease nirmatrelvir were reported. We aimed to detect them in SARS-CoV-2 genomes and quasispecies retrieved in our institute before drug availability in January 2022 and to analyze the impact o...
Existing tools for phylogeographic and epidemiological visualisation primarily provide a macro-geographic view of epidemic and pandemic transmission events but offer little support for detailed investigation of outbreaks in healthcare settings. Here, we present HAIviz, an interactive web-based appli...
the main agent of bovine tuberculosis (bTB), presents as a series of spatially-localised micro-epidemics across landscapes. Classical molecular typing methods applied to these micro-epidemics, based on genotyping a few variable loci, have significantly improved our understanding of potential epidemi...
Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education...
A state-wide prospective longitudinal investigation of the genomic surveillance of the omicron B.1.1.529 SARS-CoV-2 variant and its sublineages in Tamil Nadu, India, was conducted between December 2021 and March 2023. The study aimed to elucidate their mutational patterns and their genetic interrela...
While ceftriaxone resistance remains scarce in Switzerland, global (NG) antimicrobial resistance poses an urgent threat. This study describes clinical characteristics in MSM (men who have sex with men) diagnosed with NG infection and analyses NG resistance by phenotypic and genotypic means. Data of...
Fundamental to effective Legionnaires' disease outbreak control is the ability to rapidly identify the environmental source(s) of the causative agent, . Genomics has revolutionized pathogen surveillance, but has a complex ecology and population structure that can limit source inference based on sta...
causes infections in humans and livestock. Bacterial isolates are challenging to obtain, and very little is known about the genomic epidemiology of this species in Africa. Here, we report the complete genome sequence of a isolate cultured from a febrile human in northern Tanzania.
Acinetobacter baumannii has emerged as a main nosocomial pathogen exhibiting high rates of resistance to clinically relevant antibiotics. Six pandrug-resistant A. baumannii (PDR-A. baumannii) were recovered from three patients in a Tunisian Intensive Care Unit (ICU) between 10th and 16th of May 2018...
Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, providing higher resolution compared to standard Sanger sequencing. To more fully utilize these rich data and account for the uncertainties in outcomes from phylogenetic analyses, we propose a spa...
Dengue virus is becoming a major public health threat worldwide, principally in Africa. From 2016 to 2020, 23 outbreaks were reported in Africa, principally in West Africa. In Senegal, dengue outbreaks have been reported yearly since 2017. Data about the circulating serotypes and their spatial and t...
The recent worldwide spread of New Delhi metallo-beta-lactamase-producing Klebsiella pneumoniae (NDM-KP) in health-care settings remains a concern. The aim of the study was to describe an outbreak of extensively drug-resistant ST147 NDM-1-KP in the Apulia region of Southern Italy that occurred betwe...
Quickly understanding the genomic changes that lead to pathogen emergence is necessary to launch mitigation efforts and reduce harm. In this study, we tracked in real time a 2022 bacterial plant disease outbreak in U.S. geraniums ( × ) caused by Xhp2022, a novel lineage of . Genomes from 31 Xhp2022...
Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important...
The clinical and microbial factors associated with Klebsiella pneumoniae bloodstream infections (BSIs) are not well characterized. Prior studies have focused on highly resistant or hypervirulent isolates, limiting our understanding of K. pneumoniae strains that commonly cause BSI. We performed a rec...
In 2019-2020, dengue virus (DENV) type 4 emerged to cause the largest DENV outbreak in Paraguay's history. This study sought to characterize dengue relative to other acute illness cases and use phylogenetic analysis to understand the outbreak's origin. Individuals with an acute illness (≤7 days) wer...
Nipah virus (NiV), a biosafety level 4 agent, was first identified in human clinical cases during an outbreak in 1998 in Malaysia and Singapore. While flying foxes are the primary host and viral vector, the infection is associated with a severe clinical presentation in humans, resulting in a high mo...
The Democratic Republic of the Congo has had 15 Ebola virus disease (EVD) outbreaks, from 1976 to 2023. On June 1, 2020, the Democratic Republic of the Congo declared an outbreak of EVD in the western Équateur Province (11th outbreak), proximal to the 2018 Tumba and Bikoro outbreak and concurrent wi...
Infection by carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a serious clinical problem worldwide. However, the molecular epidemiology of the clinical isolates varies depending on the region. This study was conducted to analyse the resistance phenotype and clarify the genetic and epidemiologic...
Carbapenemase-producing Citrobacter freundii has been reported as a leading cause of healthcare-associated infections. Particularly, C. freundii belonging to the sequence type (ST) 18 is considered to be an emerging nosocomial clone. To report the genomic background and phylogenomic analysis of a mu...
Vibrio cholerae, as a natural inhabitant of the marine environment is among the world-leading causes of diarrheal diseases. The present study aimed to investigate the genetic relatedness of Iran 2012-2016 V. cholerae outbreaks with 7th pandemic cholera and to further characterize the non-ST69/non-ST...
Increasing evidence suggests that microbial species have a strong within species genetic heterogeneity. This can be problematic for the analysis of prokaryote genomes, which commonly relies on a reference genome to guide the assembly process. Differences between reference and sample genomes will the...
Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to...
Understanding the genetic dynamics of circulating Human Adenovirus (HAdV) types is pivotal for effectively managing outbreaks and devising targeted interventions. During the West Bengal outbreak of 2022-2023, an investigation into the genetic characteristics and outbreak potential of circulating HAd...
Advances in the molecular epidemiological studies of the Human Immunodeficiency Virus (HIV) at the Robert Koch Institute (RKI) by laboratory and bioinformatic automation should allow the processing of larger numbers of samples and more comprehensive and faster data analysis in order to provide a hig...
(BoAHV-1) infection is common in cattle worldwide. However, information on the spread of BoAHV-1-circulating strains in Italy remains limited. In this study, we investigated an outbreak characterized by severe respiratory symptoms in a cattle herd ( = 30) located in Central Italy. BoAHV-1 was isolat...
SARS-CoV-2 genomic analysis has been key to the provision of valuable data to meet both epidemiological and clinical demands. High-throughput sequencing, generally Illumina-based, has been necessary to ensure the widest coverage in global variant tracking. However, a speedier response is needed for...
SARS-CoV-2 has expressively changed its sequences during the COVID-19 pandemic situation by encompassing persistent evolutionary mutational changes resulting in the emergence of many clades and lineages. Evolution of these SARS-CoV-2 variants have significantly imparted fitness advantage to the viru...
The entire world is facing the stiff challenge of COVID-19 pandemic. To overcome the spread of this highly infectious disease, several short-sighted strategies were adopted such as the use of broad-spectrum antibiotics and antifungals. However, the misuse and/or overuse of antibiotics have accentuat...
Infectious diseases are the leading cause of morbidity and mortality worldwide. Causative pathogenic microbes readily mutate their genome and lead to outbreaks, challenging the healthcare and the medical support. Understanding how certain symptoms manifest clinically is integral for therapeutic deci...
The transmission of antimicrobial resistant bacteria in the urban environment is poorly understood. We utilized genomic sequencing and phylogenetics to characterize the transmission dynamics of antimicrobial resistant Escherichia coli (AMR-Ec) cultured from putative canine (canine) and human feces p...
Sever Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is still a threat to human health globally despite the World Health Organization (WHO) announcing the end of the COVID-19 pandemic. Continued surveillance of SARS-CoV-2 at national borders would be helpful in understanding the epidemics of...
The United Kingdom (UK) and Europe have seen successive outbreaks of H5N1 clade 2.3.4.4b high-pathogenicity avian influenza virus (HPAIV) since 2020 peaking in the autumn/winter periods. During the 2021/22 season, a mass die-off event of Svalbard Barnacle Geese () was observed on the Solway Firth, a...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility and immune escape have emerged periodically throughout the coronavirus disease 2019 (COVID-19) pandemic, but the impact of these variants on disease severity has remained unclear. In this single-cent...
Mycoplasma (M.) hyosynoviae is a commensal of the upper respiratory tract in swine, which has the potential to spread systemically, usually resulting in arthritis in fattening pigs and gilts. To date, very little is known about the epidemiology of M. hyosynoviae, mainly due to a lack of suitable typ...
Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns during 2020-2022, in a setting of changing policy. We descr...
During October 2022-March 2023, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus caused outbreaks in South Korea, including 174 cases in wild birds. To understand the origin and role of wild birds in the evolution and spread of HPAI viruses, we sequenced 113 HPAI isolates from w...
Patients in burns centres are at high risk of acquiring multi-drug-resistant organisms (MDROs) due to the reduced skin barrier and long hospital stay. This study reports the investigation and control of an outbreak of MDR Acinetobacter baumannii in a burns centre. The 27 patients hospitalized in the...
is a major opportunistic pathogen causing hospital-acquired infections, and it is imperative to comprehend its evolutionary and epidemiological dynamics in hospitals to prevent and control nosocomial transmission. Here, we present a comprehensive genomic epidemiological study involving the genomic s...
The pathogenic characteristics of V. parahaemolyticus isolated from a gastroenteritis outbreak event in Deqing County of Huzhou City in 2022 were analyzed. Pathogen detection was performed on 30 anal swabs (26 patients, 1 chef and 3 waiters). The isolates of V. parahaemolyticus were analyzed by seru...
To characterize Coronavirus Disease 2019 (COVID-19) transmission dynamics in each of the metropolitan statistical areas (MSAs) surrounding Dallas, Houston, New York City, and Phoenix in 2020 and 2021, we extended a previously reported compartmental model accounting for effects of multiple distinct p...
Epidemic waves of coronavirus disease 2019 (COVID-19) infections have often been associated with the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Rapid detection of growing genomic variants can therefore serve as a predictor of future waves, enabling time...
We analyzed an outbreak of Bacillus cereus group (Bcg) at a single-center neonatal intensive care unit level IV by conducting comprehensive sampling of both patients and the environment. Between 06/2020 and 10/2021, all Bcg isolates identified by both regular colonization screening and additional sa...
Clusters of group B Streptococcus (GBS) infections in neonatal intensive care units (NICU) are poorly documented. We aimed to assess GBS cross-transmission during an outbreak of GBS sepsis. The study was carried out between October and November 2021 in a French University Hospital. Neonatal intensiv...
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). The ENA is one of the three members of the International Nucleotide Sequence Database Collaboration (INSDC). It serves the bioin...
We estimate the basic reproductive number and case counts for 15 distinct Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, distributed across 11 populations (10 countries and one cruise ship), based solely on phylodynamic analyses of genomic data. Our results indicate that, pr...
In recent months, Paraguay has been grappled with a notable monkeypox outbreak, straining its healthcare infrastructure. The sudden spike in cases underlines the imperative need for a comprehensive understanding of the virus's dynamics, enabling the formulation of robust containment measures. To add...
The interruption of bacteriological surveillance due to the COVID-19 pandemic brought serious consequences, such as the collapse of health systems and the possible increase in antimicrobial resistance. Therefore, it is necessary to know the rate of resistance and its associated mechanisms in bacteri...
In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However, transmission analysis cannot rely solely on a phylogeny of t...
The genomic surveillance of viral pathogens such as SARS-CoV-2 and HIV-1 has been critical to modern epidemiology and public health, but the use of sequence analysis pipelines requires computational expertise, and web-based platforms require sending potentially sensitive raw sequence data to remote...
Timely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public Health Laboratory in Chicago developed and employed a genomic survei...
We determined that the dengue outbreak in São Tomé and Príncipe during 2022 was caused by dengue virus serotype 3 genotype III. Phylogenomic analyses showed that the outbreak strain was closely related to the newly identified GIII-American-II lineage and that the virus probably was introduced from t...
Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), multi-antigen sequence typing (NG-MAST) and sequence typing for antimicrobial resista...
Mpox is an emerging zoonotic disease which has now spread to over 113 countries as of August 2023, with over 89,500 confirmed human cases. The Netherlands had one of the highest incidence rates in Europe during the peak of the outbreak. In this study, we generated 158 near-complete mpox virus (MPXV)...
Although neonates are commonly exposed to vaginal herpes simplex virus (HSV)-2, neonatal herpes is rare. Therefore, we analyzed paired infant and maternal HSV-2 isolates from two cases of mother-to-infant transmission to identify viral factors contributing to vertical transmission. Sixteen infant is...
is a Gram-negative rod which may cause invasive infections when they contaminate liquid medical products. After was detected in blood cultures and a stem cell product from three patients in a tertiary care hospital in Germany, whole genome sequencing of these three isolates and two water isolates f...
The emergence and spread of antibiotic-resistant bacterial pathogens are a critical public health concern across the globe. Mobile genetic elements (MGEs) play an important role in the horizontal acquisition of antimicrobial resistance genes (ARGs) in bacteria. In this study, we have decoded the who...
To study the genomic epidemiology of Streptococcus pyogenes causing bloodstream infections (GAS-BSI) in a Spanish tertiary hospital during the United Kingdom invasive S. pyogenes outbreak alert. Retrospective epidemiological analysis of GAS-BSI during the January-May 2017-2023 period. WGS was perfor...
is a food-borne pathogen, typically affecting the elderly, immunocompromised patients and pregnant women. The aim of this study was to determine the population structure of clonal complex 1 (CC1) in the UK and describe the genomic epidemiology of this clinically significant CC. We interrogated a wo...
is a Gram-negative, opportunistic pathogen that is often associated with nosocomial infections. Here, the genomic characteristics and antimicrobial resistance (AMR) of clinical isolates between 2016 and 2023 were determined. A total of 218 clinical isolates were mainly identified from urinary tract...
Carbapenem-resistant (CRKP) is a critical pathogen in healthcare settings, associated with high mortality due to its extensive antibiotic resistance. In this study, we report an outbreak of CRKP in a neonatal intensive care unit (NICU) within a 200-bed tertiary hospital. The main goal of this study...
Mosquito-borne diseases have a significant public health threat worldwide, with arboviruses accounting for a high proportion of infectious diseases and mortality annually. Brazil, in particular, has been suffering outbreaks of diseases transmitted by mosquito viruses, notably those of the genus, su...
has emerged as a critical global health threat due to its exceptional survival skills in adverse environment and its ability to acquire antibiotic resistance, presenting significant challenges for infection treatment and control. The World Health Organization has classified carbapenem-resistant as...
is a transmitted respiratory pathogen that causes high morbidity and mortality in children, especially those under 5 years of age. During the implementation of population control measures for COVID-19 in mainland China, the detection rate in pediatric patients decreased. However, with the second wa...
Since the rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a global COVID-19 pandemic affecting millions of people globally, it has become one of the most urgent research topics worldwide to better understand the pathogenesis of COVID-19 and the impact of the harmfu...
Pathogen genomics, where whole genome sequencing technologies are used to produce complete genomic sequences of pathogens, is being increasingly used for infectious disease surveillance and outbreak response. Although proof-of-concept studies have highlighted the viability of using pathogen genomics...
The increasing incidence and high mortality rate of infection in ICU patients is an important issue. Therefore, it is imperative to investigate the antifungal susceptibility profiles and epidemiological characteristics in local regions. Herein, antifungal susceptibility testing was conducted to det...
This article describes the origin of a S. marcescens outbreak in a neonatal intensive care unit (NICU). A retrospective case-control study including 12 S. marcescens-positive and 22 S. marcescens-negative neonates in the NICU was performed to identify the source of the outbreak. S. marcescens isolat...
This study used whole-genome sequencing (WGS) to explore the genetic diversity, virulence factors, and antimicrobial resistance determinants of string test-positive (KP) over a 4-year surveillance period in Huzhou, China. In total, 632 clinical isolates were collected via hospital surveillance from...
is a Gram-negative, rod-shaped bacterium belonging to the family of , a common pathogen in aquaculture animals, However, studies on its impact on (mud crabs) are limited. In this study, we isolated SWS from dead mud crab during a disease outbreak in a Hong Kong aquaculture farm, which caused up to...
Monkeypox (Mpox) is a zoonotic disease caused by the monkeypox virus (MPXV). MPXV can be transmitted by close contact with lesions, body fluids, respiratory droplets, and contaminated materials. A new pattern of spread among sexual networks has been recently described. The present work aimed to repo...
An outbreak of Salmonella Stanley in the United States associated with dried wood ear mushrooms imported from China prompted us to conduct serotyping of Salmonella isolated from dried wood ear mushrooms in voluntary testing, and quantitative test for Salmonella along with enumeration of hygienic ind...
Viral outbreaks are a constant threat to aquaculture, limiting production for better global food security. A lack of diagnostic testing and monitoring in resource-limited areas hinders the capacity to respond rapidly to disease outbreaks and to prevent viral pathogens becoming endemic in fisheries p...
The "Investigating and translating genomic evidence for public health response to SARS-CoV-2 (INSIDE SARS-CoV-2)" project is part of the initiative "Joint science and technology cooperation call for joint project proposals for the years 2021-2023" promoted by the Italian Ministry of Foreign Affairs...
Nosocomial outbreaks of Burkholderia cepacia complex, transmitted through contaminated medical surfaces or equipment have been reported. Pulsed-field Gel Electrophoresis (PFGE) is recognized as the "gold standard" for molecular subtyping, yet studies on clonal relationships in India are limited. PFG...
To investigate mycobacterial cases of farmed yellowtail fish in coastal areas of western Japan (Kagoshima, Kyushu), where aquaculture fisheries are active, Mycobacterium pseudoshottsii, the causative agent, was isolated from six neighboring fishing ports in 2012 and 2013. A phylogenetic ana-lysis re...
Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of a...
Türkiye confirmed its first case of SARS-CoV-2 on March 11, 2020, coinciding with the declaration of the global COVID-19 pandemic. Subsequently, Türkiye swiftly increased testing capacity and implemented genomic sequencing in 2020. This paper describes Türkiye's journey of establishing genomic surve...
C. difficile has been increasingly reported as a cause of gastrointestinal disease in children, ranging from mild self-limiting diarrhea to severe conditions such as pseudomembranous colitis and toxic megacolon. Only two pediatric research groups reported the presence of C. difficile infection in Br...
The increasing incidence of Klebsiella pneumoniae and carbapenem-resistant Klebsiella pneumoniae (CRKP) has posed great challenges for the clinical anti-infective treatment. Here, we describe the molecular epidemiology and antimicrobial resistance profiles of K. pneumoniae and CRKP isolates from hos...
The world has seen unprecedented gains in the global genomic surveillance capacities for pathogens with pandemic and epidemic potential within the last 4 years. To strengthen and sustain the gains made, WHO is working with countries and partners to implement the Global Genomic Surveillance Strategy...
The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome's impact on its host's health and fitness is well known. However, most studies on mosquito microbiomes have been...
Mpox virus (MPXV) has recently spread outside of sub-Saharan Africa. This large multicentre study was conducted in Lombardy, the most densely populated Italian region accounting for more than 40% of Italian cases. The present study aims to: i) evaluate the presence and the shedding duration of MPXV...
Norway has a low prevalence of methicillin-resistant Staphylococcus aureus (MRSA) and reporting of all MRSA cases has been mandatory, including infections and carriage, since 1995 and 2005 accordingly. This provides a unique window to study the spread of MRSA in Norway over time. The aim of this stu...
SARS-CoV-2 has claimed several million lives since its emergence in late 2019. The ongoing evolution of the virus has resulted in the periodic emergence of new viral variants with distinct fitness advantages, including enhanced transmission and immune escape. While several SARS-CoV-2 variants of con...
This study describes the detection and tracking of emergency neurosurgical cross-transmission infections with carbapenem-resistant (CRKO). We conducted an epidemiological investigation and a rapid screening of 66 surveillance samples using the chromogenic selective medium. Two CRKO isolates from in...
The extent to which sinks are contaminated by carbapenem-resistant (CRAB) in intensive care units (ICUs) and the association between these contaminated sinks and hospital-acquired CRAB infections during the non-cluster period remains largely unknown. Here, we performed a prospective multicenter stu...
There are multiple ongoing outbreaks of carbapenem resistant (CR) infection in Fiji's hospitals. CR is able to colonize and persist on various hospital surfaces for extended periods. We conducted a study to understand the extent of hospital environmental contamination and phylogenetic links with cl...
Carbapenemase-producing strains (CP-Kps) have recently been observed to spread rapidly worldwide. New Delhi metallo-β-lactamase (NDM) producing clones of cause a significant healthcare burden, particularly in Indian sub-continent, where this clone is circulating widely. However, in Italy, data on...
, a difficult-to-manage nosocomial pathogen, poses a serious threat to clinical outcomes in intensive care (ICU) patients due to its high antimicrobial resistance (AMR). To promote effective management, it is essential to investigate the genomic and phenotypic differences in AMR expression of the is...
Outbreaks are a risk to public health particularly when pathogenic, hypervirulent, and/or multidrug-resistant organisms (MDROs) are involved. In a hospital setting, vulnerable populations such as the immunosuppressed, intensive care patients, and neonates are most at risk. Rapid and accurate outbrea...
Monkeypox virus (MPXV) is the etiological agent of monkeypox (mpox), a zoonotic disease. MPXV is endemic in the forested regions of West and Central Africa, but the virus has recently spread globally, causing outbreaks in multiple non-endemic countries. In this paper, we review the characteristics o...
One of the primary public health functions of a tuberculosis (TB) program is to arrest the spread of infection. Traditionally, TB programs have relied on epidemiological information, gathered through contact tracing, to infer that transmission has occurred between people. The ability of drawing such...
Whole genome sequencing (WGS) plays an important role in the advanced characterization of pathogen transmission and is widely used in studies of major bacterial and viral diseases. Although protozoan parasites cause serious diseases in humans and animals, WGS data on them are relatively scarce due t...
The COVID-19 pandemic highlighted the critical role of viral genomic surveillance, prompting numerous countries to enhance their monitoring systems for acute respiratory infections (ARIs), especially influenza-like illnesses (ILIs). Given the significance of asymptomatic cases in severe acute respir...
Bedaquiline, an antimicrobial used to treat drug-resistant tuberculosis (DR-TB), was introduced in Brazil in October 2021. Monitoring the emergence and transmission of DR-TB is crucial for implementing public health to control the spread of DR strains of . To measure its impact on the multi-drug tre...
Next-generation sequencing (NGS) is crucial for monitoring and investigating infectious disease outbreaks, providing essential data for public health decisions. The COVID-19 pandemic has significantly expanded pathogen sequencing and bioinformatics capacities worldwide, creating an opportunity to le...
Arbovirus surveillance of wild-caught mosquitoes is an affordable and sensitive means of monitoring virus transmission dynamics at various spatial-temporal scales, and emergence and re-emergence during epidemic and interepidemic periods. A variety of molecular diagnostics for arbovirus screening of...
West Nile Virus, an emerging zoonotic pathogen, has been circulating in Serbia for over a decade, with its first detection in mosquitoes in 2010. Since then, the virus has led to increasing cases in both animals and humans, peaking in 2018 with 415 human cases and 36 fatalities. This study aimed to...
The Bronx, New York, exhibited unique peaks in the number of coronavirus disease 2019 (COVID-19) cases and hospitalizations compared to national trends. To determine which features of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus might underpin this local disease epidemiolog...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a high transmissibility profile which favors the accumulation of mutations along its genome, providing the emergence of new variants. In this context, haplotype studies have allowed mapping specific regions and combining approaches and...
Pathogen sequencing during the COVID-19 pandemic has generated more whole genome sequencing data than for any other epidemic, allowing epidemiologists to monitor the transmission and evolution of SARS-CoV-2. However, large parts of the world are heavily underrepresented in sequencing efforts, includ...
Health authorities were notified of a suspected outbreak of foodborne disease in a hospital in South Africa, where staff and patients reported acute onset of abdominal cramps, diarrhoea, fever and rigours after eating a chicken pasta meal. The aim of this report is to discuss the use of whole genome...
Porcine circovirus 2 (PCV2) emerged more than three decades ago as one of the most impactful pathogens in the swine industry. Despite being a DNA virus, one of the hallmarks of PCV2 is its high evolutionary rate, which has led to the emergence of different genotypes, each exhibiting varying degrees...
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed extraordinary challenges to global health systems and economies. The virus's rapid evolution has resulted in several variants of concern (VOCs), including the highly tr...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the coronavirus disease 2019 (COVID-19) pandemic, which is still a global public health concern. During March 2022, a rapid and confined single-source outbreak of SARS-CoV-2 was identified in a community in Nanjing municipal cit...
The routine genomic surveillance of pathogens in diverse geographical settings and equitable data sharing are critical to inform effective infection control and therapeutic development. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of routine genomic surveillance of sev...
is an emerging marine zoonotic pathogen. In this study, we first reported the infections in patients and animals in Hainan Province, China. Currently, there is still relatively little known about the whole-genome characteristics of in most tropical regions, including in southern China. Here, we se...
During the 3 years following the emergence of the COVID-19 pandemic, the African continent, like other regions of the world, was substantially impacted by COVID-19. In Morocco, the COVID-19 pandemic has been marked by the emergence and spread of several SARS-CoV-2 variants, leading to a substantial...
is a globally emerged fungal pathogen causing nosocomial invasive infections. Here, we use cutting-edge genomic approaches to elucidate the temporal and geographic epidemiology of drug-resistant within the UK. We analysed a representative sample of over 200 isolates from multiple UK hospitals to as...
In recent years, coxsackievirus (CV) A10 has been associated with increasing sporadic hand, foot, and mouth disease (HFMD) cases and outbreaks globally. In addition to mild symptoms such as pharyngitis and herpangina, CVA10-related complications or even fatality can occur. Currently, systematic phyl...
Epitopes are specific structures in antigens that are recognized by the immune system. They are widely used in the context of immunology-related applications, such as vaccine development, drug design, and diagnosis / treatment / prevention of disease. The SARS-CoV-2 virus has represented the main po...
Determining the appropriate computational requirements and software performance is essential for efficient genomic surveillance. The lack of standardized benchmarking complicates software selection, especially with limited resources. We developed a containerized benchmarking pipeline to evaluate sev...
The recombinant SARS-CoV-2 Omicron XBB.1.5 variant was first detected in New York City (NYC) and rapidly became the predominant variant in the area by early 2023. The increased occurrence of circulating variants within the SARS-CoV-2 XBB-sublineage prompted the modification of COVID-19 mRNA vaccines...
has emerged as a human pathogen in the past decade. Here, we present findings related to a strain carrying the gene, which was isolated from a urinary tract infection in China. Global transmission dynamics and genomic epidemiology of -carrying were further investigated. The complete genome sequen...
A characteristic of the COVID-19 pandemic has been the sequential emergence and global dissemination of SARS-CoV-2 variants, noted for their enhanced transmission efficiency. These variants with mutations in the Spike glycoprotein (S-glycoprotein), which interacts with ACE2 receptors in human cells...
As of December 2022, Cameroon had observed a slight resurgence of COVID-19, raising concerns on genomic surveillance of related-SARS-CoV-2 variants under circulation. Following a laboratory-based survey, positive SARS-CoV-2 samples detected from December-2022 through March-2023 were processed for ta...
Urinary tract infection (UTI) associated with poses a serious threat for inpatients. This study aimed to describe the genomic characteristics of causing UTI in a tertiary-care hospital in Beijing, China. A total of 20 strains collected from 2020 to 2021 were performed whole-genome sequencing. The...
An outbreak of multidrug-resistant infections in a neonatal ward within a tertiary hospital in South Africa resulted in the mortality of 10 patients within six months. In this work, the genomic epidemiology of and the molecular factors mediating this outbreak were investigated. Bacterial cultures o...
Clade 2.3.4.4b highly pathogenic avian influenza A (HPAI) viruses have been detected in wild birds worldwide, causing recurrent outbreaks since 2016. During the winter of 2021-2022, we detected one H5N8 and forty-three H5N1 clade 2.3.4.4b HPAI viruses from wild birds in South Korea. Phylogenetic ana...
Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence nearly all of the ~30,000 nucleotide SARS-CoV-2 genome, using a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA...
Avian influenza viruses (AIVs) of the H9N2 subtype have become widespread in Western Africa since their first detection in 2017 in Burkina Faso. However, the genetic characteristics and diffusion patterns of the H9N2 virus remain poorly understood in Western Africa, mainly due to limited surveillanc...
Highly pathogenic avian influenza (HPAI) is a viral disease that causes significant rates of morbidity and mortality in domestic poultry and wild birds, with occasional spillover into mammals, including humans. Beginning in November 2021, Canada experienced its longest and largest outbreak of HPAI i...
Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the...
Porcine reproductive and respiratory syndrome virus (PRRSV) poses a serious threat to the pig industry in China. Our previous study demonstrated that PRRSV persists with local circulations and overseas imports in China and has formed a relatively stable epidemic pattern. However, the sudden African...
Wild migratory birds are considered the central reservoirs of avian influenza viruses. H12 viruses are one of the 16 hemagglutinin (HA) subtypes of avian influenza viruses and are rarely reported because they are infrequently detected in birds. Consequently, the ecological and genetic profiles of H1...
Tuberculosis (TB), particularly drug-resistant TB (DR-TB), remains a significant public health concern in Ningbo, China. Understanding its molecular epidemiology and spatial distribution is paramount for effective control. From December 24, 2020, to March 12, 2023, we collected clinical (MTB) strai...
is a species within the complex sensu lato, associated with lizards as reservoirs and as its main vector. is predominantly distributed in Central and Southeast Europe, and in countries of the Mediterranean basin, such as Portugal, Morocco, Tunisia, and Italy where this spirochete appears to infec...
No abstract available
African swine fever (ASF), a contagious viral disease, poses a significant threat to the global swine industry. In South Korea, ASF outbreaks have occurred since 2019, highlighting the need for a comprehensive understanding of the epidemiology and genetic characterization of the circulating African...
Multi-type birth-death (MTBD) models are phylodynamic analogies of compartmental models in classical epidemiology. They serve to infer such epidemiological parameters as the average number of secondary infections Re and the infectious time from a phylogenetic tree (a genealogy of pathogen sequences)...
Birth-death (BD) models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model...
Although the impact of the SARS-CoV-2 pandemic on major metropolitan areas is broadly reported and readily available, regions with lower populations and more remote areas in the United States are understudied. The objective of this study is to determine the progression of SARS-CoV-2 sequence variant...
is a Gram negative facultative anaerobic bacterium involved in various community-acquired pneumonia, nosocomial and lungs associated infections. Frequent usage of several antibiotics and acquired resistance mechanisms has made this bacterium multi-drug resistance (MDR), complicating the treatment of...
This paper aims to describe the investigation and control of an outbreak of USA300 ST8 Panton-Valentine leucocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA), confirmed by whole genome sequencing (WGS), within a maternity and neonatal setting in the UK. The identification of tw...
The recent COVID-19 pandemic shows the critical need for novel broad spectrum antiviral agents. Scorpion venoms are known to contain highly bioactive peptides, several of which have demonstrated strong antiviral activity against a range of viruses. We have generated the first annotated reference tra...
Listeria monocytogenes is a ubiquitous foodborne pathogen causing human and animal listeriosis with high mortality. Neurological and maternal-neonatal listeriosis outbreaks in Europe and the United States were frequently associated with clonal complexes CC1, CC2 and CC6 harboring Listeria Pathogenic...
To evaluate the utility of selective reactive whole-genome sequencing (WGS) in aiding healthcare-associated cluster investigations. Mixed-methods quality-improvement study. Thes study was conducted across 8 acute-care facilities in an integrated health system. We analyzed healthcare-associated coron...
In the coronavirus disease 2019 (COVID-19) pandemic, correctional facilities are potential hotspots for transmission. We examined the genomic epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the pandemic in one of the country's largest urban jails. Existing SARS-...
Various water-based heater-cooler devices (HCDs) have been implicated in nontuberculous mycobacteria outbreaks. Ongoing rigorous surveillance for healthcare-associated (HA-Mab) put in place following a prior institutional outbreak of alerted investigators to a cluster of 3 extrapulmonary infectio...
Carbapenemase-producing Enterobacterales (CPE) is an increasing problem in healthcare settings. This study aimed to identify the source of a CPE outbreak that occurred in 2022, in a tertiary hospital in the North of Portugal, to identify exposed patients, and to assess the risk of becoming CPE-posit...
In-depth phenotypic and genomic analyses on a carbapenem-resistant Escherichia coli isolate, recovered from the faeces of a farm dog in Lebanon, focusing on its antimicrobial resistance (AMR) patterns and the underlying resistome. E. coli strain EC-106 was identified using MALDI-TOF-MS. Analyses usi...
Spacer oligonucleotide typing (spoligotyping), the first-line genotyping assay for (MTB), plays a fundamental role in the investigation of its epidemiology and evolution. In this study, we established a single-tube spoligotyping assay using MeltArray, a highly multiplex polymerase chain reaction (P...
Cerebral granulomas are associated with nervous signs in Pullorum outbreak.Bone marrow is also a recommended tissue for isolation of Pullorum.Rapid plate agglutination test detects Pullorum antibodies in a vaccinated flock.Phylogenetic analysis showed clonality of isolates within the outbreak.
Emergence of carbapenem-resistant A. baumannii (CRAB) is a global, ongoing healthcare concern. CRAB is among the topmost priority pathogens, with various studies focusing on its global population structure and resistant allelic profiles. However, carbapenem-susceptible A. baumannii (CSAB) isolates a...
Environmental testing of high-touch objects is a potential noninvasive approach for monitoring population-level trends of SARS-CoV-2 and other respiratory viruses within a defined setting. We aimed to determine the association between SARS-CoV-2 contamination on high-touch environmental surfaces, co...
We present a novel framework enhancing the prediction of whether novel lineage poses the threat of eventually dominating the viral population. The framework is based purely on genomic sequence data, without requiring prior established biological analysis. Its building blocks are sets of coevolving s...
Despite a clear appreciation of the impact of human pathogens on community health, efforts to understand pathogen dynamics within populations often follow a narrow-targeted approach and rely on the deployment of specific molecular probes for quantitative detection or rely on clinical detection and r...
Our study emphasizes the efficacy of whole-genome sequencing (WGS) in addressing outbreaks of vancomycin-resistant enterococci. WGS enables the identification and tracking of resistant bacterial strains, early detection and management of novel infectious disease outbreaks, and the appropriate select...
Multidrug-resistant Acinetobacter baumannii is still a major contributor to outbreaks and infections health care-associated infections. This study aimed to investigate an outbreak of wound infection due to A baumannii in trauma patients injured in the Kahramanmaraş earthquake. This retrospective cas...
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory sy...
Fowl adenoviruses (FAdVs, species FAdV-A/-E) are responsible for several clinical syndromes reported with increasing frequency in poultry farms in the last decades. In the present study, a phylodynamic analysis was performed on a group of FAdV-D Hexon sequences with adequate available metadata. The...
Dirofilaria repens is a paradigmatic example of an emerging vector-borne pathogen (VBP) in both human and veterinary fields. The spatial expansion and the increasing zoonotic impact of this VBP can be related to several drivers including the genetic structure of parasite populations. Italy is one of...
Streptococcus ruminantium is the causative agent of several bovine and ovine diseases, however reports are uncommon and application of whole genome sequencing to identify is rare. We report for the first time, a severe ovine mastitis outbreak caused by S. ruminantium in Italy, 2022. S. ruminantium w...
Although the World Health Organization and many governments have recategorized COVID-19 as a generally mild to moderately severe disease, consecutive pandemic waves driven by immune escape variants have underscored the need for timely and accurate prediction of the next outbreak. Nevertheless, littl...
No abstract available
Canine parvovirus is a highly contagious pathogen affecting domestic dogs and other carnivores globally. Monitoring CPV through continuous genomic surveillance is crucial for mapping variability and developing effective control measures. Here, we developed a method using multiplex-PCR-next-generatio...
While the SARS-CoV-2 dynamic has been described globally, there is a lack of data from Sub-Saharan Africa. We herein report the dynamics of SARS-CoV-2 lineages from March 2020 to March 2022 in Cameroon. Of the 760 whole-genome sequences successfully generated by the national genomic surveillance net...
Bacillus atrophaeus and Bacillus pumilus spores are widely used as biological indicators to assess the effectiveness of decontamination procedures. Spores are intricate, multi-layered cellular structures primarily composed of proteins, which significantly contribute to their extreme resistance. Ther...
Mutations in the SARS-CoV-2 genome can alter the virus' fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the i...
The COVID-19 pandemic has transformed laboratory management, with a surge in demand for diagnostic tests prompting the adoption of new diagnostic assays and the spread of variant surveillance tools. Rapid antigen tests (RATs) were initially used only for screening and later as suitable infection ass...
HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participan...
We present a protocol to efficiently sequence genomes of the MPXV-causing mpox. This enables researchers and public health agencies to acquire high-quality genomic data using a rapid and cost-effective approach. Genomic data can be used to conduct surveillance and investigate mpox outbreaks. We pres...
Nosocomial Stenotrophomonas maltophilia-related cases are rising and pose a threat to immunocompromised patients. Twelve patients from our pediatric intensive care unit (PICU) presented with S maltophilia-associated bloodstream infection. This outbreak investigation includes 12 patients from PICU be...
The highly transmissible severe acute respiratory syndrome-Coronavirus-2 was responsible for the 2020 COVID-19 pandemic. COVID-19 mostly affects the respiratory system; however, this infection also affects several other organs. In addition, the sequelae of this disease affect patients for several mo...
Global and even national genome surveillance approaches do not provide the resolution necessary for rapid and accurate direct response by local public health authorities. Hence, a regional network of microbiological laboratories in collaboration with the health departments of all districts of the Ge...
From June 7th to 11th, 2023, eight cases of Mpox were identified in Guangzhou, China. This is the first report of multiple local sporadic cases after the imported case in Chongqing, China. Epidemiological investigation revealed that these cases had no history of international travel and no connectio...
Thailand experienced five waves of coronavirus disease 2019 (COVID-19) between 2020 and 2022, with the Bangkok Metropolitan Region (BMR) being at the centre of all outbreaks. The molecular evolution of the causative agent of the disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),...
To advance our understanding of respiratory syncytial virus (RSV) impact through genomic surveillance, we describe two PCR-based sequencing systems, (i) RSVAB-WGS for generic whole-genome sequencing and (ii) RSVAB-GF, which targets major viral antigens, G and F, and is used as a complement for chall...
causes pertussis (or whooping cough), a severe respiratory infectious disease in infants, although it can be prevented by whole cell and acellular vaccines. The recent pertussis resurgence in industrialised countries is partly attributed to pathogen adaptation to vaccines, while emergence of antimic...
Following the global emergence of the SARS-CoV-2 Alpha variant of concern (VOC) in 2020, the Delta variant triggered another wave in 2021. The AY.69 lineage, a Delta VOC, was particularly prevalent in Republic of Korea (South Korea) from May 2021 to January 2022, despite the synchronized implementat...
Monkeypox (MPOX) is a zoonotic disease endemic to regions of Central/Western Africa. The geographic endemicity of MPV has expanded, broadening the human-monkeypox virus interface and its potential for spillover. Since May 2022, a large multi-country MPV outbreak with no proven links to endemic count...
This proof-of-concept study introduces a hybrid capture oligo panel for whole-genome sequencing of all six human pathogenic hepatitis A virus (HAV) subgenotypes, exhibiting a higher sensitivity than some conventional genotyping assays. The ability of hybrid capture to enrich multiple targets allows...
Listeria monocytogenes is a Gram positive foodborne pathogen that regularly causes outbreaks of systemic infectious diseases. The bacterium maintains a facultative intracellular lifestyle; it thrives under a variety of environmental conditions and is able to infect human host cells. L. monocytogenes...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are a fatal pathogen resulting in substantial morbidity and mortality, and posing a great threat to human health with epidemics and pandemics. Next-generation sequencing (NGS) was performed to investigate the SARS-CoV-2 genomic ch...
Stenotrophomonas maltophilia is an opportunistic human pathogen associated with nosocomial and community-acquired infections. We have conducted a microbiological and genomic surveillance study of broad-spectrum cephalosporin- and carbapenem-resistant Gram-negative bacteria colonizing wild birds inha...
Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African co...
The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS w...
Multidrug-resistant (MDR) bacteria in farm environments can be transferred to humans through the food chain and occupational exposure. Enterococcus infections caused by linezolid resistant enterococci (LRE) are becoming more challenging to treat as their resistance to antibiotics intensifies. Theref...
Dengue fever is expanding as a global public health threat including countries within Africa. For the past few decades, Cameroon has experienced sporadic cases of arboviral infections including dengue fever. Here, we conducted genomic analyses to investigate the origin and phylogenetic profile of Ca...
The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extractio...
Disease surveillance systems provide early warnings of disease outbreaks before they become public health emergencies. However, pandemics containment would be challenging due to the complex immunity landscape created by multiple variants. Genomic surveillance is critical for detecting novel variants...
The disease caused by methicillin-resistant Staphylococcus aureus (MRSA) is a global public health challenge that threatens society and patients seriously. Therefore, the molecular epidemiology and change trend of MRSA is essential for the control and treatment of diseases caused by the pathogen in...
Tilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and co...
This study aimed to map MDRO carriage and potential transmission within and between three Flemish tertiary care hospitals and their neighbouring nursing homes. A cross-sectional MDRO prevalence survey was organized between October 2017 and February 2019. Perianal swabs were cultured for detection of...
In 2022, a global outbreak of monkeypox occurred with a significant shift in its epidemiological characteristics. The monkeypox virus (MPXV) belongs to the B.1 lineage, and its genomic variations that were linked to the outbreak were investigated in this study. Previous studies have suggested that v...
The circulation and the genomic evolution of influenza A(H3N2) viruses during the 2021/2022 and 2022/2023 seasons were studied and associated with infection outcomes. Remnant influenza A-positive samples following standard-of-care testing from patients across the Johns Hopkins Health System (JHHS) w...
This study provides a laboratory framework to ensure ongoing relevance and performance of amplification-based whole genome sequencing to strengthen public health surveillance during extended outbreaks or pandemics. The framework integrates regular reviews of the performance of a genomic surveillance...
The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pa...
The intersection of human, animal, and ecosystem health at One Health interfaces is recognised as being of key importance in the evolution and spread of antimicrobial resistance (AMR) and represents an important, and yet rarely realised opportunity to undertake vital AMR surveillance. A working grou...
Ventilator-associated pneumonia (VAP) and pyogenic liver abscess (PLA) due to Klebsiella pneumoniae infection can trigger life-threatening malignant consequences, however, there are few studies on the strain-associated clinical pathogenic mechanisms between VAP and PLA. A total of 266 patients consi...
Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is gradually becoming the dominant nosocomial pathogens in the healthcare setting. A retrospective study was conducted on patients with CR-KP from July 2021 to May 2022 in a teaching hospital. We identified bacterial isolates, collec...
Reovirus infections in turkeys are associated with arthritis and lameness. Viral genome sequence data are scarce, which makes an accurate description of the viral evolution and epidemiology difficult. In this study, we isolated and characterized turkey reoviruses from Hungary. The isolates were iden...
We describe the genotypic characteristics and antimicrobial resistance (AMR) determinants of Salmonella enterica serovar Isangi (Salmonella Isangi) clinical isolates in South Africa from 2020 through 2021. During the years 2020 to 2021, the Centre for Enteric Diseases of the National Institute for C...
HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participan...
Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity an...
Afghanistan experienced various outbreaks before and during the Covid-19 pandemic, including dengue, Crimean Congo hemorrhagic fever (CCHF), measles, and acute watery diarrhea (AWD). Diagnostic and surveillance support was limited, with only the Central Public Health Laboratory equipped to handle ou...
Malaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium parasites has provided insights into the genomic epidemiology of malaria. Genome sequencing is rapidly gaining traction as a diagnostic and surveillance tool for clinical settin...
The continued emergence of Salmonella enterica serovar Typhi, with ever increasing antimicrobial resistance, necessitates the use of vaccines in endemic countries. A typhoid fever outbreak in Harare, Zimbabwe, in 2018 from a multidrug resistant S Typhi with additional resistance to ciprofloxacin was...
The aim of this work was to analyze the metadata of the SARS-CoV-2 sequences obtained from samples collected in Mexico from 2020 to 2022. Metadata of SARS-CoV-2 sequences from samples collected in Mexico up to 31 December 2022 was retrieved from GISAID and manually cured for interpretation. As of De...
Haemophilus influenzae is one of the main bacteria responsible for otitis media (OM) among children worldwide. We aimed to estimate the distribution of encapsulated and non-capsulated variants (NTHi), biotypes, antibiotic susceptibility, and molecular epidemiology of H. influenzae isolates recovered...
as an opportunistic pathogen can cause serious infection, and moreover the emergence of multi-drug-resistant strains poses a potentially life-threatening risk to public health. However, a comprehensive genomic study to reveal the population structure and dissemination of is still lacking. In this...
Bacterial whole-genome sequencing (WGS) and determination of genetic relatedness is an important tool for investigation of epidemiologically suspected outbreaks. This prospective cohort study evaluated a comprehensive, prospective bacterial WGS-based surveillance programme for early detection of tra...
There is growing interest in the molecular surveillance of the Respiratory Syncytial Virus and the monitorization of emerging mutations that could impair the efficacy of antiviral prophylaxis and treatments. A simple, scalable protocol for viral nucleic acid enrichment could improve the surveillance...
Klebsiella pneumoniae is an important opportunistic Gram-negative pathogen. This study describes an outbreak due to colistin-resistant and carbapenem-resistant Klebsiella pneumoniae (ColR-CRKP) in a tertiary hospital related to six patients successively admitted to the department of medical intensiv...
We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy in order to classify viral isolates in a potential hotspot for virus spread. Positive samples were subjected to Next-Generation Sequencing (NGS) o...
Bat-borne viruses have attracted considerable research, especially in relation to the Covid-19 pandemic. Although bats can carry multiple zoonotic viruses that are lethal to many mammalian species, they appear to be asymptomatic to viral infection despite the high viral loads contained in their bodi...
The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis and quantification of infectious pathogens withi...
Hantaviruses zoonotically infect humans worldwide with pathogenic consequences and are mainly spread by rodents that shed aerosolized virus particles in urine and feces. Bioinformatics methods for hantavirus diagnostics, genomic surveillance and epidemiology are currently lacking a comprehensive app...
The COVID-19 pandemic has necessitated the rapid development and implementation of whole-genome sequencing (WGS) and bioinformatic methods for managing the pandemic. However, variability in methods and capabilities between laboratories has posed challenges in ensuring data accuracy. A national worki...
A surge in chikungunya was observed during 2020-21 in Pune district of Maharashtra, India. Whole genome sequencing and phylogenetic analysis of 21 samples/sequences revealed them as Indian ocean lineage of East Central South African genotype. Two distinct sequence clusters were found to circulate du...
Next-generation sequencing technology has revolutionised pathogen surveillance over the last two decades. However, the benefits are not equitably distributed, with developing countries lagging far behind in acquiring the required technology and analytical capacity. Recent declines in the cost associ...
Since its outbreak in late 2021, the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely reported to be able to evade neutralizing antibodies, becoming more transmissible while causing milder symptoms than previous SARS-CoV-2 strains. Understanding the und...
Since 2022, European countries have been facing an outbreak of mainly cutaneous diphtheria caused by toxigenic among asylum seekers. In Belgium, between 1 March and 31 December 2022, 25 cases of toxigenic infection were confirmed among asylum seekers, mostly among young males from Afghanistan. Mul...
Rapid pathogen identification is a critical first step in patient isolation, treatment, and controlling an outbreak. Real-time PCR is a highly sensitive and specific approach commonly used for infectious disease diagnostics. However, mismatches in the primer or probe sequence and the target organism...
This study aimed to investigate the prevalence, molecular types, and virulence genes of methicillin-resistant Staphylococcus aureus (MRSA) causing skin and soft tissue infections (SSTIs) in the Shaoxing region. MRSA strains were collected from patients with SSTIs in Shaoxing People's Hospital from J...
Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable. We introduce here pyMLST, a new complete, stand-alone, free and open source pipeline for cgMLST analysis. pyMLST can create or import a core genome...
Melioidosis, caused by the environmental gram-negative bacterium Burkholderia pseudomallei, usually develops in adults with predisposing conditions and in Australia more commonly occurs during the monsoonal wet season. We report an outbreak of 7 cases of melioidosis in immunocompetent children in Au...
The National Tuberculosis Programme (NTBP) monitors the occurrence and spread of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) in Singapore. Since 2020, whole-genome sequencing (WGS) of isolates has been performed at the National Public Health Laboratory (NPHL) for genomic surveillance, rep...
The ongoing coronavirus disease 2019 (COVID-19) pandemic, driven by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the critical role of genomic surveillance in tracking rapidly spreading viruses and their evolving lineages. The emergence of the SARS-CoV-2 tiling array,...
Since the beginning of the pandemic, SARS-CoV-2 has shown a great genomic variability, resulting in the continuous emergence of new variants that has made their global monitoring and study a priority. This work aimed to study the genomic heterogeneity, the temporal origin, the rate of viral evolutio...
is a major public health concern, for which many genomic epidemiology studies have been conducted in the last decade. However, the vast majority of these are local studies focusing on hospitals from one or a few countries. Proper global genomic epidemiology studies are needed if we are to understand...
Our results indicate that most severe acute respiratory syndrome coronavirus 2 genomes sampled from patients had a mutation rate ≤1.07 ‰ and genome-tail proteins (including S protein) were the main sources of genetic polymorphism. The analysis of the virus-host interaction network of genome-tail pro...
Zoonotic viral infections continue to pose significant threats to global public health, as highlighted by the COVID-19 pandemic caused by the SARS-CoV-2 virus. The emergence of SARS-CoV-2 served as a stark reminder of the potential for zoonotic transmission of viruses from animals to humans. Underst...
No abstract available
Since the beginning of the COVID-19 pandemic, large-scale genomic sequencing has immediately pointed out that SARS-CoV-2 has rapidly mutated during the course of the pandemic, resulting in the emergence of variants with a public health impact. In this context, strictly monitoring the circulating str...
Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts in which infection was transmitted from one to the other - is using the variation of the pathogen within each single host (within-host variation). How...
Lumpy skin disease virus (LSDV) has a complex epidemiology involving multiple strains, recombination, and vaccination. Its DNA genome provides limited genetic variation to trace outbreaks in space and time. Sequencing of LSDV whole genomes has also been patchy at global and regional scales. Here, we...
The proportion of VREfm among all isolated from blood cultures in German hospitals has increased in the period 2015-2020 from 11.9% to 22.3% with a country-wide spread of the clonal lineage ST117/CT71 . In this study, we provided useful information about the genetic diversity of invasive strains of...
No abstract available
Staphylococcus haemolyticus belongs to the Coagulase-Negative Staphylococci (CoNS), exhibiting the highest levels of antibiotic resistance within this group of bacteria. This species has been increasingly implicated in nosocomial and animal infections worldwide, with a prevalence of methicillin-resi...
Effective management of emerging diseases relies on timely pathogen identification and monitoring. The emergence of COVID-19 in December 2019, rapidly evolved into a global pandemic, with millions of cases and deaths reported worldwide. The accumulation of SARS-CoV-2 genomes provided unprecedented o...
This study aimed to evaluate antibiotic resistance genes and virulence genes and the clonal relationship of the carbapenem-nonsusceptible Klebsiella pneumoniae strains by molecular methods which are isolated from various clinical specimens from patients treated in tertiary care hospital in Turkey. I...
Infectious diseases are not only a threat to humans and animals but also to an entire ecosystem if the three axis of One Health are considered. Elizabethkingia miricola is a water-borne and opportunistic pathogen frequently evolving to high morbidity and mortality outcomes. More recently, reports on...
Early detection of emerging SARS-CoV-2 variants is critical to guiding rapid risk assessments, providing clear and timely communication messages, and coordinating public health action. CDC identifies and monitors novel SARS-CoV-2 variants through diverse surveillance approaches, including genomic, w...
The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative d...
We analyzed over 22,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes of patient samples tested at Mayo Clinic Laboratories during a 2-year period in the COVID-19 pandemic, which included Alpha, Delta, and Omicron variants of concern to examine the roles and relationships of M...
SNP addresses are a pathogen typing method based on whole-genome sequences (WGSs), assigning groups at seven different levels of genetic similarity. Public health surveillance uses it for several gastro-intestinal infections; this work trialled its use in veterinary surveillance for salmonella outbr...
Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology in individuals. These techniques require prior knowledge of the target viral genome and are l...
Infectious bronchitis virus (IBV) is prevalent in Pakistan causing enormous economic losses. To date no clear data are available on circulating genotypes and phylogeographic spread of the virus. Hence current study assessed these parameters for all available IBV Pakistani isolates, based on the 9 ne...
In Brazil, the state of Tocantins, located in north-central Brazil, has experienced a significant number of cases of arboviral disease, particularly Dengue virus (DENV). This study aimed to deepen the knowledge on DENV circulation within that state by conducting full genome sequencing of viral genom...
Since its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequencing assisted in the characterization and classification of SARS-CoV-2, an...
The public health emergency caused by the Covid-19 outbreak in March 2020 encouraged worldwide initiatives to monitor the genetic diversity and features of the SARS-CoV-2 circulating variants, mainly based on the genomic surveillance. However, due to the impossibility to carry out extensive sequenci...
This study highlights a subspecies () strain isolated from an outbreak in Indiana, which resulted in mortality events among a swine herd in 2021. The Indiana outbreak strain was found to be genetically and phylogenetically distant to a strain isolated from the 2019 outbreaks in Ohio and Tennessee,...
To investigate the clinical characteristics and molecular epidemiology of CRKP infection in neonatal patients in a children's hospital in China from 2017 to 2021. Species identification and antibiotic susceptibilities were tested with matrix-assisted laser desorption/ionization time-of-flight mass s...
Tuberculosis (TB) is a preventable, treatable, and curable disease. However, in 2020, 9∙9 million people were estimated to have developed tuberculosis, and 1.5 million people were estimated to have died from it. Whereas in India, 2.6 million were diagnosed with TB and 436,000 succumbed to TB in 2019...
Pathogenic bacteria, viruses, fungi, and protozoa can cause food and waterborne diseases. Surveillance methods must therefore screen for these pathogens at various stages of water distribution and of food from production to consumption. Detection using nucleic acid amplification methods offer rapid...
The COVID-19 pandemic highlighted the critical role of pathogen sequencing in making informed public health decisions. Initially, the Eastern Mediterranean Region faced limitations in sequencing capacity. However, with robust WHO and stakeholder support, the situation significantly improved. By 2022...
Respiratory syncytial virus (HRSV) is the leading cause of respiratory tract infections in infants and young children. we investigated the prevalence and characteristics of HRSV in Morocco and explored trends in circulating genotypes through partial G gene analysis of HRSV strains prevalent from 201...
vanB-carrying vancomycin-resistant Enterococcus faecium (VREfm) of the sequence types 80 (ST80) and ST117 have dominated Germany in the past. In 2020, our hospital witnessed a sharp increase in the proportion of vanA-positive VREfm. To attempt to understand these dynamics through whole-genome sequen...
With the rapidly growing amount of biological data, powerful but also flexible data management and visualization systems are of increasingly crucial importance. The COVID-19 pandemic has more than highlighted this need and the challenges scientists are facing. Here, we provide an example and a step-...
Emerging infectious diseases require continuous pathogen monitoring. Rapid clinical diagnosis by nucleic acid amplification is limited to a small number of targets and may miss target detection due to new mutations in clinical isolates. Whole-genome sequencing (WGS) identifies genome-wide variations...
The number of known virus species has increased dramatically through metagenomic studies, which search genetic material sampled from a host for non-host genes. Here, we focus on an important viral family that includes influenza viruses, the , with over 100 recently discovered viruses infecting hosts...
The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across...
It is unclear whether West Nile virus (WNV) circulates between Africa and Europe, despite numerous studies supporting an African origin and high transmission in Europe. We integrated genomic data with geographic observations and phylogenetic and phylogeographic inferences to uncover the spatial and...
To support the COVID-19 pandemic response, many countries, including Belgium, implemented baseline genomic surveillance (BGS) programs aiming to early detect and characterize new SARS-CoV-2 variants. In parallel, Belgium maintained a sentinel network of six hospitals that samples patients with sever...
is a leading cause of infectious diarrhea in humans and production animals and can be found in a variety of environmental sources. The prevalence and diversity of multi-locus sequence type clade 5 strains of in Australian production animals suggest Australia might be the ancestral home of this line...
It is well recognized that only O1 causes cholera pandemics. However, not all O1 strains cause pandemic-level disease. In this study, we analyzed non-pandemic O1 isolates from the 1960s to the 1990s from China and found that they fell into three lineages, one of which shared the most recent common...
The recently observed increase in invasive infections causes concern in Europe. However, conventional molecular typing methods lack discriminatory power to aid investigations of outbreaks caused by . Therefore, there is an urgent need for high-resolution molecular typing methods to assess genetic r...
is an emerging infectious agent associated with life-threatening infections in immunocompromised individuals. However, there are limited data available on the genomic features of . This study aims to characterize the geographical distribution, phylogenetic evolution, pathogenesis, and transmission o...
There has been a decrease in healthcare-associated infection in Australia, but an increase in the genetic diversity of infecting strains, and an increase in community-associated cases. Here, we studied the genetic relatedness of isolated from patients at a major hospital in Melbourne, Australia. D...
SARS-CoV-2, a novel coronavirus within the Coronaviridae family, is the causative agent behind the respiratory ailment referred to as COVID-19. Operating on a global scale, COVID-19 has led to a substantial number of fatalities, exerting profound effects on both public health and the global economy....
To identify the antibiotic resistance, virulence genes, and sequence types of () strains isolated from blood. From November 2014 to December 2021, a total of 94 nonrepetitive isolates were obtained from blood samples of patients at the First Affiliated Hospital of Shandong First Medical Universit...
Wolbachia are endosymbiotic bacteria found within many arthropods, including insects. A variety of benefits are provided by these bacteria to human and insect hosts, including protection from viruses and parasites and the ability to kill males. In this study, Wolbachia was identified in Aedes aegypt...
Genomic characterization of the dengue virus (DENV) is useful for understanding its molecular evolution, transmission, pathogenicity and infectivity. The DENV genomic RNA encodes three structural proteins, capsid (C) envelope (E) and membrane (M) proteins mediating viral entry and assembly during ho...
Endogenous retroviruses (ERVs) are evolutionary remnants of retroviral infections in which the viral genome became embedded as a dormant regulatory element within the host germline. When ERVs become activated, they comprehensively rewire genomic regulatory networks of the host and facilitate critica...
Nipah virus (NiV), a highly lethal virus in humans, circulates silently in bats throughout South and Southeast Asia. Difficulty in obtaining genomes from bats means we have a poor understanding of NiV diversity, including how many lineages circulate within a roost and the spread of NiV over increas...
Outbreaks of the immunosuppressive infectious bursal disease (IBD) are frequently reported worldwide, despite the vaccination regimes. A 2009 Californian IBD outbreak caused by rA and rB isolates was described as very virulent (vv) IBD virus (IBDV); however, molecular factors beyond this virulence w...
This study aimed to investigate the clinical infection characteristics and analyze the resistance gene carrying status of carbapenem-resistant Providencia rettgeri via whole genome sequencing (WGS). Carbapenem-resistant P. rettgeri were collected from clinical patients between January 2020 and Decem...
Military operations involve the global movement of personnel and equipment, increasing the risk of spreading infectious pathogens such as SARS-CoV-2. Given the continuous engagement of the Polish Armed Forces in overseas operations, an active surveillance program targeting Variants of Concern (VOC)...
Potato virus Y, an important viral pathogen of potato, has several genetic variants and geographic distributions which could be affected by environmental factors, aphid vectors, and reservoir plants. PVY is transmitted to virus-free potato plants by aphids and passed on to the next vegetative genera...
Understanding the factors driving the spread and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the local, regional, national, and international levels is important in protecting against future pandemics. By exploring their viral genomes, we attempted to analyse the spr...
No abstract available
is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40, 000 bloodstream infections (BSI) in the United Kingdom (UK) annually. The number of BSI has increased over the last decade in the UK, and emerging antimicrobial resistance (AMR) profiles threate...
New Delhi metallo-beta-lactamase (NDM)-producing () ST147 caused a large multi-hospital outbreak in Italy from 2018 to 2021. We describe a new ST6668 NDM-producing clone, belonging to CC147, which rapidly spread across hospitals in the Pavia province (Northern Italy) from February to August 2023....
The rapid spread and remarkable mutations of SARS-CoV-2 variants, particularly Omicron, necessitate an understanding of their evolutionary characteristics. In this study, we analyzed representative high-quality whole-genome sequences of 2008 SARS-CoV-2 variants to explore long-term dynamic changes i...
() is one of the most important foodborne pathogens, and can cause foodborne poisoning by producing enterotoxins. Pork is a preferable reservoir and its contamination often occurs during the slaughter process. Our findings revealed significant differences in the prevalence, antimicrobial resistance,...
Next-generation sequencing (NGS) of genomic data has established its fundamental value in public health surveillance, research and development, and precision medicine. In Africa, severe shortages of competent experts in genomics and bioinformatics, few opportunities for research, and inadequate geno...
Dengue is a mosquito-borne viral disease posing a significant threat to public health. Dengue virus (DENV) evolution is often characterized by lineage turnover, which, along with ecological and immunological factors, has been linked to changes in dengue phenotype affecting epidemic dynamics. Utilizi...
Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chik...
Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eight...
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged, some leading to large increases in infections, hospitalizations and deaths globally. The virus's impact on public health depends on ma...
Nine surgical site infections caused by Serratia marcescens were diagnosed in neurosurgical patients in a 3500-bed hospital between 2 February and 6 April 2022. To trace the source of infections caused by S. marcescens to expedite termination of the outbreak and prevent future epidemics. A review of...
Antimicrobial resistance remains an utmost concern in human and veterinary medicine, impacting humans, animals, and the environment while significantly influencing the principles of One Health. While Riemerella anatipestifer (R. anatipestifer) is recognized as a waterfowl pathogen with multidrug-res...
Acinetobacter baumannii, a Gram-negative and oxidase-negative bacterium, is a major cause of nosocomial infections, leading to high mortality rates in hospitalized patients. The use of 2 prominent molecular typing methods (i.e., enterobacterial repetitive intergenic consensus-polymerase chain reacti...
To contain infectious diseases, it is crucial to determine the origin and transmission routes of the pathogen, as well as how the virus evolves. With the development of genome sequencing technology, genome epidemiology has emerged as a powerful approach for investigating the source and transmission...
In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression...
Even though Brazil is a country where the dengue virus (DENV) is endemic, until recently, Southern states did not have significant viral circulation, such as Rio Grande do Sul (RS), and some municipalities were even considered dengue-free. During 2022, these places have shown a sharp increase in the...
The COVID-19 pandemic has been met with an unprecedented response from the scientific community, leading to the development, investigation, and authorization of vaccines and antivirals, ultimately reducing the impact of SARS-CoV-2 on global public health. However, SARS-CoV-2 is far from being eradic...
SARS-CoV-2 caused a life-threatening COVID-19 pandemic outbreak worldwide. The Southeastern Region of Wisconsin, USA (SERW) includes large urban Milwaukee and six suburban counties, namely Kenosha, Ozaukee, Racine, Walworth, Washington and Waukesha. Due to the lack of detailed SARS-CoV-2 genomic sur...
Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that...
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has brought about significant challenges worldwide. In this study, we present a comprehensive analysis of the genomic epidemiology and lineage dynamics of SARS-CoV-2 in Bulgaria over a three-year period. Thr...
Aminoglycoside antimicrobials remain valuable therapeutic options, but their effectiveness has been threatened by the production of bacterial 16S ribosomal RNA methyltransferases (16S-RMTases). In this study, we evaluated the genomic epidemiology of 16S-RMTase genes among Gram-negative bacteria circ...
Syphilis is a sexually transmitted bacterial infection caused by Treponema pallidum subspecies pallidum. Since 2012, syphilis rates have risen dramatically in many high-income countries, including England. Although this increase in syphilis prevalence is known to be associated with high-risk sexual...
is an opportunistic pathogen responsible for healthcare-associated infections (HAIs) and outbreaks. Antimicrobial resistance mechanisms and virulence factors allow it to survive and spread in the hospital environment. However, the molecular mechanisms of these traits and their association with inter...
In the ongoing antimicrobial resistance crisis, carbapenem-resistant strains of are critical threats to public health. Besides globally disseminated clones, the burden of local problem clones remains substantial. Although genomic analysis is a powerful tool for improving pathogen and antimicrobial...
We report a newly emerged SARS-CoV-2 Omicron subvariant FY.4 that has mutations Y451H in spike and P42L in open reading frame 3a proteins. FY.4 emergence coincided with increased SARS-CoV-2 cases in coastal Kenya during April-May 2023. Continued SARS-CoV-2 genomic surveillance is needed to identify...
The number of COVID-19 cases in Indonesia reflects the disease severity and rapid dissemination. In response to the mounting threat, SARS-CoV-2 genomic surveillance and the investigation of naso-oropharyngeal bacterial communities in West Java were conducted, as dysbiosis of the upper respiratory tr...
Acute otitis media (AOM) is the most common childhood bacterial infectious disease requiring antimicrobial therapy. Most cases of AOM are caused by translocation of Streptococcus pneumoniae or Haemophilus influenzae from the nasopharynx to the middle ear during an upper respiratory tract infection (...
The fitness of indels in pathogen genome evolution has rarely been studied. We developed a computational methodology to investigate the severe acute respiratory coronavirus 2 genomes and analyze over 33 million records of indels systematically, ultimately proposing the concept of featured indels tha...
can cause severe foodborne illness, including miscarriage during pregnancy or death in newborn infants. When outbreaks of illness occur, it may be possible to determine the food source of the outbreak. However, most reported illnesses do not occur as part of a recognized outbreak and most of the t...
Monkeypox, a viral zoonotic disease, has emerged as a significant global threat in recent years. This review focuses on the importance of global monitoring and rapid response to monkeypox outbreaks. The unpredictable nature of monkeypox transmissions, its potential for human-to-human spread, and its...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial infection-causing pathogen. The clonal shift from staphylococcal cassette chromosome mec (SCCmec) type II MRSA to SCCmec type IV MRSA has occurred rapidly in acute-care hospitals. However, the epidemiology and clinical impacts...
Pathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dy...
Pseudomonas aeruginosa, a versatile bacterium, has dual significance because of its beneficial roles in environmental soil processes and its detrimental effects as a nosocomial pathogen that causes clinical infections. Understanding adaptability to environmental stress is essential. This investigati...
Southeast Asia is a uniquely complex region of malaria transmission that maintains an astounding level of species diversity among potential malaria vectors and also generates drug-resistant and quickly diverging populations of malaria parasites. All five human malaria species circulate in Southeast...
Extraintestinal pathogenic (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 is...
Staphylococcal food poisoning results from the consumption of food contaminated by staphylococcal enterotoxins. In July 2022, the Turin local health board was notified of a suspected foodborne outbreak involving six children who had consumed döner kebab purchased from a takeaway restaurant. The symp...
Fowl adenovirus 1 (FAdV-1) is the main cause of gizzard erosion in chickens. Whole genome sequencing and sequence analyses of 32 FAdV-1 strains from a global collection provided evidence that multiple recombination events have occurred along the entire genome. In gene-wise phylogenies, only the aden...
is an environmental bacterium and clinical pathogen that can cause an array of infections. We describe an environmental sampling and comparative genomics approach used to investigate a multi-year outbreak of at a correctional facility. Whole genome sequencing analysis revealed a predominant cluster...
Bacterial Healthcare-Associated Infections (HAIs) are a major threat worldwide, which can be counteracted by establishing effective infection control measures, guided by constant surveillance and timely epidemiological investigations. Genomics is crucial in modern epidemiology but lacks standard met...
In this study the antibiotic susceptibility pattern and bla genes were characterized in Klebsiella pneumoniae clinical isolates that fingerprinted by rep-PCR and PFGE methods at Kurdistan Province, Iran. A total of 70 K. pneumoniae were isolated from clinical samples to detect the antimicrobial susc...
China experienced a severe influenza season that began at the end of February 2023. The aim of this post hoc analysis was to investigate the clinical, epidemiological, and genomic features of this outbreak in Beijing. The number of cases increased rapidly from the end of February and reached its pea...
The circulation of carbapenemase-producing Escherichia coli (CPEC) in our society is a serious concern for vulnerable patients in nosocomial environments. However, the genomic epidemiology of the circulation of CPEC bacteria among companion animals remains largely unknown. In this study, epidemiolog...
Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phylogenetic and epidemiological models, we reconstructed the recent transmission histor...
Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively associated with increased arsenic tolerance. This strain is a re...
Respiratory diphtheria is a serious infection caused by toxigenic , and disease transmission mainly occurs through respiratory droplets. Between 2017 and 2019, a large diphtheria outbreak among forcibly displaced Myanmar nationals densely settled in Bangladesh was investigated. Here we utilized whol...
The XBB.1.16 SARS-CoV-2 variant, also known as , is a recent descendant lineage of the recombinant XBB (nicknamed ). Compared to its direct progenitor, XBB.1, XBB.1.16 carries additional spike mutations in key antigenic sites, potentially conferring an ability to evade the immune response compared t...
During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only...
The severe acute respiratory syndrome coronavirus 2 EG.5 lineage is the latest variant under monitoring, and it is generating significant concern due to its recent upward trend in prevalence. Our aim was to gain insights into this emerging lineage and offer insights into its actual level of threat....
Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure and movement rates has been hindered by difficu...
Group B Streptococci (GBS) are common vaginal bacteria found in 20-30% of pregnant women and a significant cause of invasive infections in newborns. Recently, attention has been focused on the efficacy of probiotics during the perinatal period. However, the effect of probiotic intake on the mother-t...
Many vaccine candidate proteins in the malaria parasite Plasmodium falciparum are under strong immunological pressure and confer antigenic diversity. We present a sequencing and data analysis platform for the genomic surveillance of the insertion or deletion (indel)-rich antigens merozoite surface p...
Aleutian disease (AD) is a multi-systemic infectious disease in American mink (Neogale vison) caused by the Aleutian mink disease virus (AMDV). Commonly referred to as mink plasmacytosis, AD is an economically significant disease in mink-breeding countries. Aleutian disease mainly induces weight los...
Colistin is one of the last resort therapeutic options for treating carbapenemase-producing Enterobacterales, which are resistant to a broad range of beta-lactam antibiotics. However, the increased use of colistin in clinical and livestock farming settings in Thailand and China, has led to the inevi...
The Korea Disease Control and Prevention Agency (KDCA) has been conducting national genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). To monitor and characterize circulating SARS-CoV-2 variants in South Korea, 102,873 oropharyngeal/nasopharyngeal swab samples coll...
Klebsiella pneumoniae causing nosocomial infections is increasingly multi-drug-resistant. Rapid and efficient typing tools are required for monitoring. To assess a simple, rapid (<5 h) multiplex polymerase chain reaction method based on multi-locus variable number tandem repeat analysis (MLVA) as a...
Since its discovery in early 1916, dengue fever, a common vector-borne illness in Brazil, has resulted in extensive urban outbreaks and poses a serious threat to the public's health. Understanding the dynamics of Dengue Virus (DENV) serotypes circulating in different regions of Brazil is essential f...
Acinetobacter baumannii international clone II (IC2) is a widespread pandemic clone, however, it is rarely described in South America. The present study reported an outbreak caused by XDR IC2 strains in a clinical setting in Rio de Janeiro in 2022. Molecular epidemiology analysis was conducted with...
Globally invasive Aedes aegypti disseminate numerous arboviruses that impact human health. One promising method to control Ae. aegypti populations is transinfection with Wolbachia pipientis, which naturally infects ~40-52% of insects but not Ae. aegypti. Transinfection of Ae. aegypti with the wMel W...
Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent local transmission dynamics and eco-epidemiologica...
is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of is...
Plague, caused by Yersinia pestis, is a zoonotic disease that can reemerge and cause outbreaks following decades of latency in natural plague foci. However, the genetic diversity and spread pattern of Y. pestis during these epidemic-silent cycles remain unclear. In this study, we analyze 356 Y. pest...
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID -19, is constantly evolving, requiring continuous genomic surveillance. In this study, we used whole-genome sequencing to investigate the genetic epidemiology of SARS-CoV-2 in Bangladesh, with particular empha...
Genomic surveillance of pets for severe acute respiratory syndrome coronavirus 2 is important to monitor the emergence of new variants of the virus associated with these animals. Pets can serve as a potential reservoir for the virus, and their close contact with humans increases the risk of transmis...
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could...
Nosocomial infections (NIs) appear in patients under medical care in the hospital. The surveillance of the bacterial communities employing high-resolution 16S rRNA profiling, known as metabarcoding, represents a reliable method to establish factors that may influence the composition of the bacterial...
The COVID-19 pandemic has not only strained healthcare systems in Africa but has also intensified the impact of emerging and re-emerging diseases. Specifically in Equatorial Guinea, mirroring the situation in other African countries, unique zoonotic outbreaks have occurred during this challenging pe...
Serial intervals - the time between symptom onset in infector and infectee - are a fundamental quantity in infectious disease control. However, their estimation requires knowledge of individuals' exposures, typically obtained through resource-intensive contact tracing efforts. We introduce an altern...
To contain intra-hospital transmission of third-generation cephalosporin-resistant Enterobacterales (3GCR-E), contact isolation precautions are recommended. To quantify transmissions of 3GCR Escherichia coli and 3GCR Klebsiella pneumoniae within a hospital. An automated outbreak detection system (AO...
Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses. To systematically appraise available literature, published between January 1, 2020 and June 30, 2022, describing t...
The SARS-CoV-2 virus, a novel member of the Coronaviridae family, is responsible for the viral infection known as Coronavirus Disease 2019 (COVID-19). In response to the urgent and critical need for rapid detection, diagnosis, analysis, interpretation, and treatment of COVID-19, a wide variety of bi...
DENV-2 was the main responsible for a 70% increase in dengue incidence in Brazil during 2019. That year, our metagenomic study by Illumina NextSeq on serum samples from acute febrile patients (n = 92) with suspected arbovirus infection, sampled in 22 cities of the state of Mato Grosso (MT), in the m...
In epidemiology, endemicity characterizes sustained pathogen circulation in a geographical area, which involves a circulation that is not being maintained by external introductions. Because it could potentially shape the design of public health interventions, there is an interest in fully uncovering...
To clarify whether there were clandestine intra-hospital spreads of vancomycin-resistant Enterococcus faecium (VRE-fm) isolates that led to specific strain of VRE lingering in the hospital and/or developing outbreaks that rendered a progressively increasing trend of healthcare-associated infections...
The difficulties in the identification of C. auris and the delays in the implementation of infection control precautions contribute to outbreaks. This study analyzed 10 patients with COVID-19 and C. auris candidemia, their characteristic and clinical features and phylogenetic features, and the antif...
Nontyphoidal Salmonella (NTS) is a major foodborne pathogen causing from acute gastroenteritis to bacteraemia, particularly in paediatric and elderly patients. Antimicrobial resistance of NTS, especially resistance to extended-spectrum cephalosporins, has emerged over the past decades. Thirteen NTS...
Globalization has made agricultural commodities more accessible, available, and affordable. However, their global movement increases the potential for invasion by pathogens and necessitates development and implementation of sensitive, rapid, and scalable surveillance methods. Here, we used 35 strain...
There are many studies that require researchers to extract specific information from the published literature, such as details about sequence records or about a randomized control trial. While manual extraction is cost efficient for small studies, larger studies such as systematic reviews are much m...
No abstract available
The impact and frequency of infectious disease outbreaks demonstrate the need for timely genomic surveillance to inform public health responses. In the largest known outbreak of mpox, genomic surveillance efforts have primarily focused on high-incidence nations in Europe and the Americas, with a pau...
BackgroundEpidemics of keratoconjunctivitis may involve various aetiological agents. Microsporidia are an uncommon difficult-to-diagnose cause of such outbreaks.AimDuring the third quarter of 2022, a keratoconjunctivitis outbreak was reported across Israel, related to common water exposure to the Se...
Bacterial healthcare-associated infections (HAIs) are a substantial source of global morbidity and mortality. The estimated cost associated with HAIs ranges from $35 to $45 billion in the USA alone. The costs and accessibility of whole genome sequencing (WGS) of bacteria and the lack of sufficiently...
Inferring the spatiotemporal spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via Bayesian phylogeography has been complicated by the overwhelming sampling bias present in the global genomic dataset. Previous work has demonstrated the utility of metadata in addressing this bias...
Genomic surveillance is vital for detecting outbreaks and understanding the epidemiology and transmission of bacterial strains, yet it is not integrated into many national antimicrobial resistance (AMR) surveillance programmes. Key factors are that few scientists in the public health sector are trai...
No abstract available
No abstract available
This comprehensive review focuses on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its impact as the cause of the COVID-19 pandemic. Its objective is to provide a cohesive overview of the epidemic history and evolutionary aspects of the virus, with a particular emphasis on its...
Clustering pathogen sequence data is a common practice in epidemiology to gain insights into the genetic diversity and evolutionary relationships among pathogens. We can find groups of cases with a shared transmission history and common origin, as well as identifying transmission hotspots. Motivated...
(1) Background: The HIV subtype D is generally associated with a faster decline in CD4 T cell counts, a higher viral load, and a faster progression to AIDS. However, it is still poorly characterized in Brazil. In this study, we used genomics and epidemiological data to investigate the transmission d...
Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For...
Serratia marcescens is an opportunistic nosocomial pathogen, and recent reports have highlighted the rapid increase in multidrug resistance in this organism. There is a paucity in genomic data for carbapenem-resistant (CRSM). A retrospective cohort study describing laboratory-confirmed CRSM from a...
SARS-CoV-2 recombinants involving the divergent Delta and Omicron lineages have been described, and one of them, "Kraken" (XBB.1.5), has recently been a matter of concern. Recombination requires the coexistence of two SARS-CoV-2 strains in the same individual. Only a limited number of studies have f...
Genomic surveillance has emerged as a crucial tool in monitoring and understanding the dynamics of viral variants during the COVID-19 pandemic. In the Midwest region of Brazil, Mato Grosso do Sul has faced a significant burden from the SARS-CoV-2 epidemic, with a total of 613,000 confirmed cases as...
We have developed a machine learning (ML) approach using Gaussian process (GP)-based spatial covariance (SCV) to track the impact of spatial-temporal mutational events driving host-pathogen balance in biology. We show how SCV can be applied to understanding the response of evolving covariant relatio...
Raw milk may contain some infectious bacteria and usually requires pasteurization before drinking. In this study, we report rare outbreaks of campylobacteriosis associated with raw milk in Japan, and the application of whole genome sequencing (WGS) to studies on foodborne diseases. In August 2018, t...
This work aimed to study the role of different SARS-CoV-2 lineages in the epidemiology of multiple waves of the COVID-19 pandemic in Ribeirão Preto (São Paulo state), with comparison within Brazil and globally. Viral genomic sequencing was combined with clinical and sociodemographic information of 2...
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomona...
Even in the era of the COVID-19 pandemic, trauma remains the global leading cause of mortality under the age of 49. Trauma-induced coagulopathy is a leading driver of early mortality in critically ill patients, and transfusion of platelet products is a life-saving intervention to restore hemostasis...
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans has been monitored at an unprecedented level due to the public health crisis, yet the stochastic dynamics underlying such a process is dubious. Here, considering the number of acquired mutations as the displaceme...
Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transm...
Staphylococcus aureus is an opportunistic pathogen and a leading cause of morbidity and mortality worldwide. Genomic-based surveillance has greatly improved our ability to track the emergence and spread of high-risk clones, but the full potential of genomic data is only reached when used in conjunct...
Genomic epidemiology has proven to be a useful tool for investigating pandemic outbreaks and tracking pathogen spread and evolution. This study describes the circulation of SARS-CoV-2 strains in N. Macedonia during a period of one year, encompassing three waves of the COVID-19 pandemic. A certain pe...
Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding of sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the colonization patterns of multidrug-resistant organisms (MDROs) in intensive...
The Illumina iSeq low-capacity sequencing platform was evaluated for use in foodborne disease surveillance and outbreak detection. The platform produced high quality sequence data comparable to that of the Illumina MiSeq and was cost-effective with fast turn-around time in low sample volume environm...
Vancomycin-resistant Enterococcus faecium (VRE) is a leading cause of nosocomial infection, driven by its ability to spread between patients and persist in the hospital environment. To investigate the impact of a long-established cardiothoracic hospital moving to new premises with close to 100% sing...
Viral genomic surveillance has been integral in the global response to the SARS-CoV-2 pandemic. Surveillance efforts rely on the availability of representative clinical specimens from ongoing testing activities. However, testing practices have recently shifted due to the widespread availability and...
Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence the ~30,000 nucleotide SARS-CoV-2 genome that use a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight p...
Enterococcus faecium has been classified as a "high priority" pathogen by the World Health Organization. Enterococcus faecium has rapidly evolved as a global nosocomial pathogen with adaptation to the nosocomial environment and the accumulation of resistance to multiple antibiotics. Phage therapy is...
We isolated a highly colistin-resistant Escherichia coli, strain 58, from fresh chicken wings in Lebanon. Here, we performed in-depth phenotypic and genomic analyses to identify the resistome of the isolate, focusing on the determinants that encoded colistin resistance. The minimum inhibitory concen...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) pose an emerging clinical threat. We investigated its introduction and transmission in a new hospital, evaluating the effect of whole-genome sequencing (WGS) as an infection control measure. Based on WGS of identified K. pneumoniae (Kpn) strains, a p...
Dried blood spots (DBS) have emerged as a promising alternative to traditional venous blood for HCV testing. However, their capacity to accurately reflect the genetic diversity of HCV remains poorly understood. We employed deep sequencing and advanced phylogenetic analyses on paired plasma and DBS s...
Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and genomic surveillance. In particular, single-molecule nucleotide sequence data originating from Oxford Nanopore Technologies (ONT) sequencing p...
Among the high-risk clones of Acinetobacter baumannii, called international clones (ICs), IC2 represents the main lineage causing outbreaks worldwide. Despite the successful global spread of IC2, the occurrence of IC2 is rarely reported in Latin America. Here, we aimed to evaluate the susceptibility...
With the progression of the COVID-19 pandemic, large datasets of SARS-CoV-2 genome sequences were collected to closely monitor the evolution of the virus and identify the novel variants/strains. By analyzing genome sequencing data, health authorities can 'hunt' novel emerging variants of SARS-CoV-2...
() is a highly problematic pathogen with an enormous capacity to acquire or upregulate antibiotic drug resistance determinants. The genomic epidemiology and resistome structure of 46 clinical isolates were studied using whole-genome sequencing. The isolates were chosen based on reduced susceptibili...
To effectively mitigate the spread of communicable diseases, it is necessary to understand the interactions that enable disease transmission among individuals in a population; we refer to the set of these interactions as a contact network. The structure of the contact network can have profound effec...
African swine fever (ASF) is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally. After the first Nigerian outbreak in 1997, there have been frequent reports of ASF in pig-producing regions in the country. To facilitate control, it is im...
Salmonellosis is a significant public health problem globally. In Australia, serovar Enteritidis is one of the main causes of salmonellosis. This study reports how the implementation of routine genetic surveillance of isolates from human . Enteritidis cases enabled identification of the likely sour...
When a monkeypox virus outbreak began in several parts of the world in May 2022, timely and accurate diagnosis became mandatory. In our laboratory, a real-time quantitative PCR was designed and evaluated in several patient samples and compared with isolation results. Genomic viral load was related t...
The emergence of vancomycin-resistant (VREfm) has left the vancomycin-sensitive (VSEfm) strains almost unnoticed. Molecular characteristics, hospital transmission patterns and clinical impact of VSEfm have changed, and VSEfm is a predictor of VREfm introduction. We wanted to do a molecular charact...
is one the most worrisome nosocomial pathogens, which has long been considered almost mainly as a hospital-associated bacterium. There have been some studies about animal and environmental isolates over the last decade. However, little effort has been made to determine if this pathogen dwells in the...
Human astrovirus (HAstV) is a single-stranded, positive-sense RNA virus and is the leading cause of viral gastroenteritis. However, despite its prevalence, astroviruses still remain one of the least studied enteroviruses. In this study, we sequenced 11 classical astrovirus strains from clinical samp...
Huge datasets containing whole-genome sequences of bacterial strains are now commonplace and represent a rich and important resource for modern genomic epidemiology and metagenomics. In order to efficiently make use of these datasets, efficient indexing data structures-that are both scalable and pro...
Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of dis...
Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped....
is a poxvirus from the genus that mainly affects bovines and it causes severe economic losses to livestock holders. The is currently dispersing in Asia, but little is known about detailed phylogenetic relations between the strains and genome evolution. We reconstructed a whole-genome-sequence (WGS...
The increasing incidence of non-O1/non-O139 Vibrio cholerae (NOVC) has been observed worldwide. However, septicemia caused by NOVC remains a rare condition that has received limited attention. Currently, there are no established treatment guidelines for bloodstream infections caused by NOVC, and the...
No abstract available
Ongoing diarrheal disease surveillance throughout Bangladesh over the last decade has revealed seasonal localised cholera outbreaks in Cox's Bazar, where both Bangladeshi Nationals and Forcibly Displaced Myanmar Nationals (FDMNs) reside in densely populated settlements. FDMNs were recently targeted...
. The Mycobacterium tuberculosis Beijing genotype is globally spread lineage with important medical properties that however vary among its subtypes. M. tuberculosis Beijing 14717-15-cluster was recently discovered as both multidrug-resistant, hypervirulent, and highly-lethal strain circulating in th...
We evaluated the performance of an early-warning algorithm, based on ward-specific incidence cutoffs for detecting transmission in hospitals. We also sought to determine the frequency of intrahospital transmission in our setting. Diagnostic performance of the algorithm was tested with confirmed tr...
All four serotypes of the dengue virus (DENV1-4) cause a phenotypically similar illness, but serial infections from different serotypes increase the risk of severe disease. Thus, genomic surveillance of circulating viruses is important to detect serotype switches that precede community outbreaks of...
The rise of antimicrobial resistance is a global challenge that requires a coordinated effort to address. In this study, we examined the genetic similarity of carbapenem-resistant (CRKP) in countries belonging to the Gulf Cooperation Council (GCC) to gain a better understanding of how these bacteri...
is a Gram-negative bacterium presenting intrinsic resistance to polymyxins that has emerged as an important human pathogen. Although previous studies reported the occurrence of multidrug-resistance (MDR) isolates in the nosocomial settings, herein, we described isolates of this extensively drug-res...
Novel transmission routes can allow infectious diseases to spread, often with devastating consequences. Ectoparasitic varroa mites vector a diversity of RNA viruses, having switched hosts from the eastern to western honey bees ( to ). They provide an opportunity to explore how novel transmission rou...
is a major pathogen implicated in healthcare-associated infections. Extended-spectrum β-lactamase (ESBL) and carbapenemase-producing isolates are a public health concern. This study investigated the existence of some ESBL and carbapenemase genes among clinical isolates of in Southwest Nigeria and...
Barley yellow dwarf virus (BYDV) has caused considerable losses in the global production of grain crops such as wheat, barley and maize. We investigated the phylodynamics of the virus by analysing 379 and 485 nucleotide sequences of the genes encoding the coat protein and movement protein, respectiv...
Infectious diseases are a major threat for biodiversity conservation and can exert strong influence on wildlife population dynamics. Understanding the mechanisms driving infection rates and epidemic outcomes requires empirical data on the evolutionary trajectory of pathogens and host selective proce...
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly spread worldwide in the population since it was first detected in late 2019. The transcription and replication of coronaviruses, although not fully understood, is characterised by the production of genomic length RNA and shorte...
Antimicrobial resistance is a pressing issue in Ukraine, with healthcare-associated infections caused by multidrug-resistant organisms being a major concern. A recent prospective multicenter study revealed a staggering rate of 48.4% antimicrobial resistance to carbapenems among Enterobacterales caus...
Pseudomonas aeruginosa and other Gram-negative bacteria have the ability to persist in moist environments in healthcare settings, but their spread from these areas can result in outbreaks of healthcare-associated infections. This study reports the investigation and containment of a multi-drug-resist...
Ocular bacterial infections are important causes of morbidity and vision loss. Early antimicrobial therapy is necessary to save vision, but their efficacy is increasingly compromised by antimicrobial resistance (AMR). We assessed the etiology of ocular bacterial infections seen at Massachusetts Eye...
The next-generation sequencing (NGS) technology facilitates in-depth study of host-pathogen metatranscriptome. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know/understand the dengue virus (DENV) origin and host response with dengue fever. In this st...
The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein...
Mathematical modelling studies have shown that repetitive screening can be used to mitigate SARS-CoV-2 transmission in primary schools while keeping schools open. However, not much is known about how transmission progresses within schools and whether there is a risk of importation to households. Dur...
The massive scale of the global SARS-CoV-2 sequencing effort created new opportunities and challenges for understanding SARS-CoV-2 evolution. Rapid detection and assessment of new variants has become one of the principal objectives of genomic surveillance of SARS-CoV-2. Because of the pace and scale...
CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including the Omicron variant. This report summarizes U.S. trends in variant proportions from national genomic surveillance during January 2022-May 2023....
Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotempora...
Genomic technologies have become routine in the surveillance and monitoring of the coronavirus disease 2019 (COVID-19) pandemic, as evidenced by the millions of SARS-CoV-2 sequences uploaded to international databases. Yet the ways in which these technologies have been applied to manage the pandemic...
Increasing levels of antibiotic resistance in many bacterial pathogen populations are a major threat to public health. Resistance to an antibiotic provides a fitness benefit when the bacteria are exposed to this antibiotic, but resistance also often comes at a cost to the resistant pathogen relative...
The SARS-CoV-2 virus has evolved throughout the pandemic and is likely to continue evolving into new variants. Some of these variants may affect functional properties, including infectivity, interactions with host immunity, and disease severity. And compromised vaccine efficacy is an emerging concer...
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox inf...
The continuously emerging new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made the global coronavirus disease 2019 (COVID-19) pandemic unpredictable. Since the beginning of the pandemic, densely populated South and Southeast Asia have suffered great losses due to mu...
The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country...
Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level...
Eastern equine encephalitis virus (EEEV) causes a rare but severe disease in horses and humans and is maintained in an enzootic transmission cycle between songbirds and Culiseta melanura mosquitoes. In 2019, the largest EEEV outbreak in the United States for more than 50 years occurred, centered in...
A Canadian outbreak investigation was initiated in January 2022 after a cluster of cases of Shiga-toxin-producing (STEC) O157 was identified through whole genome sequencing (WGS). Exposure information was collected through case interviews. Traceback investigations were conducted, and samples from c...
Mpox is caused by a zoonotic orthopoxvirus capable of infecting several animal species, including humans. The analysis of cases in the current outbreak showed that, differently from what happens in the classical disease, mpox has mostly affected men who have sex with men (MSM) and bisexuals, includi...
A sentinel plot case study was carried out to identify and map the distribution of begomovirus-betasatellite complexes in sentinel plots and commercial cotton fields over a four-year period using molecular and high-throughput DNA 'discovery' sequencing approaches. Samples were collected from 15 stud...
Experimental data show that drug-resistance-conferring mutations are often associated with a decrease in the replicative fitness of bacteria in vitro, and that this fitness cost can be mitigated by compensatory mutations; however, the role of compensatory evolution in clinical settings is less clear...
Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the mpox outbreak in 2022 have demonstrated the value of genomic sequencing data for tracking the origin and spread of pathogens. Laboratories around the globe generated new sequences at unprecedented speed and volume and bioinformatician...
Multiomics approaches to studying systems biology are very powerful techniques that can elucidate changes in the genomic, transcriptomic, proteomic, and metabolomic levels within a cell type in response to an infection. These approaches are valuable for understanding the mechanisms behind disease pa...
Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis...
serovar Paratyphi A, the causative agent of paratyphoid fever, is a neglected tropical disease with a high burden and mortality in low- and middle-income countries. Limited information is available regarding its genomic diversity, especially from South Asian countries that are collectively responsib...
In May 2022, several countries reported mpox cases from patients without history of traveling to endemic areas. France was one of the most affected European countries by this outbreak. In this study, the clinical characteristics of mpox cases in France were described, and the genetic diversity of th...
In 2022, Austria experienced a severe respiratory syncytial virus (RSV) epidemic with an earlier-than-usual start (Weeks 35/2021-45/2022) and increased numbers of pediatric patients in emergency departments. This surge came 2 years after a season with no cases detected as a result of coronavirus dis...
The role of canines in transmitting antibiotic resistant bacteria to humans in the urban environment is poorly understood. To elucidate this role, we utilized genomic sequencing and phylogenetics to characterize the burden and transmission dynamics of antibiotic resistant (ABR-Ec) cultured from can...
Although infections caused by have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this st...
The National Institute for Communicable Diseases in South Africa participates in national laboratory-based surveillance for human isolates of species. Laboratory analysis includes whole-genome sequencing (WGS) of isolates. We report on WGS-based surveillance of serovar Typhi ( Typhi) in South Afri...
is one of the most prevalent Gram-negative species associated with drug resistant infections. Strains that produce extended-spectrum beta-lactamases (ESBLs) or carbapenemases are both particularly problematic and disproportionately impact resource limited healthcare settings where last-line antimicr...
H5Nx highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4 have caused outbreaks in Europe among wild and domestic birds since 2016 and were introduced to North America via wild migratory birds in December 2021. We examined the spatiotemporal extent of HPAI viruses across continents and...
The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many public health laboratories did not have the infrastructure in place to handle the vast amount of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequenc...
Despite its increasing role in the understanding of infectious disease transmission at the applied and theoretical levels, phylodynamics lacks a well-defined notion of ideal data and optimal sampling. We introduce a method to visualize and quantify the relative impact of pathogen genome sequence and...
From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level. Filling th...
The increasing prevalence of antibiotic-resistant bacteria is an emerging threat to global health. The analysis of antibiotic-resistant enterobacteria in wastewater can indicate the prevalence and spread of certain clonal groups of multiresistant bacteria. In a previous study of Escherichia coli tha...
Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMR...
Dengue virus (DENV) has been a major public health concern in Paraguay, with frequent outbreaks occurring since early 1988. Although control measures have been implemented, dengue remains a significant health threat in the country, and continued efforts are required for prevention and control. In re...
This review summarises the current knowledge of whole genome sequencing (WGS) which has become the standard method for genetic characterisation of bacteria in surveillance and outbreak investigation. Although the method offers many advantages, its use in outbreak investigations is hampered by the re...
, the most widespread species within the genus , is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide analysis of 40 strains from Lithuania to determine the genetic relationship, pangenome structure, putative virulence, and potential...
Recent technological advances and substantial cost reductions have made the genomic surveillance of pathogens during pandemics feasible. Our paper focuses on full genome sequencing as a tool that can serve two goals: the estimation of variant prevalences, and the identification of new variants. Assu...
Dog-mediated rabies is endemic across Africa causing thousands of human deaths annually. A One Health approach to rabies is advocated, comprising emergency post-exposure vaccination of bite victims and mass dog vaccination to break the transmission cycle. However, the impacts and cost-effectiveness...
The Americas, particularly Brazil, were greatly impacted by the widespread Zika virus (ZIKV) outbreak in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on...
This study aimed to characterise carbapenemase-producing Acinetobacter baumannii (A. baumannii) isolates from Danish patients using whole genome sequencing (WGS). It also compared typing and epidemiological data for further investigation of the spread and origin of the carbapenemase-producing A. bau...
In early February 2023, the Omicron subvariant XBB.1.5, also known as "Kraken", accounted for more than 44% of new COVID-19 cases worldwide, whereas a relatively new Omicron subvariant named CH.1.1, deemed "Orthrus", accounted for less than 6% of new COVID-19 cases during the subsequent weeks. This...
The human immunodeficiency virus (HIV) type 1 A6 variant is dominating in high-prevalence Eastern European countries, with increasing prevalence over the remaining regions of Europe. The recent war in Ukraine may contribute to further introductions of this A6 lineage. Our aim was to model the transm...
SARS-CoV-2 continues to pose a threat to public health. Main protease (M) is one of the most lucrative drug targets for developing specific antivirals against SARS-CoV-2 infection. By targeting M, peptidomimetic nirmatrelvir is able to inhibit viral replication of SARS-CoV-2 and reduce the risk for...
Toxigenic diphtheria is rare in Australia with generally fewer than 10 cases reported annually; however, since 2020, there has been an increase in toxin gene-bearing isolates of cases in North Queensland, with an approximately 300% escalation in cases in 2022. Genomic analysis on both toxin gene-be...
The repeated emergence of new genetic variants of PRRSV-2, the virus that causes porcine reproductive and respiratory syndrome (PRRS), reflects its rapid evolution and the failure of previous control efforts. Understanding spatiotemporal heterogeneity in variant emergence and spread is critical for...
Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration. GraphSNP is an interactive visualisation tool...
The COVID-19 pandemic has ushered in high-throughput sequencing technology as an essential public health tool. Scaling up and operationalizing genomics in Africa is crucial as enhanced capacity for genome sequencing could address key health problems relevant to African populations. High-quality geno...
Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal ro...
Understanding transmission dynamics of SARS-CoV-2 in institutions of higher education (IHEs) is important because these settings have potential for rapid viral spread. Here, we used genomic surveillance to retrospectively investigate transmission dynamics throughout the 2020-2021 academic year for t...
To investigate an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) sequence type 78 (ST78) in a large tertiary Australian hospital. A collection of 63 VREfm ST78 isolates, identified during a routine genomic surveillance program, were subjected to genomic epidemiological analysis based...
The aim of this study was to investigate the genomic features of a carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) isolate (K-2157) collected in Chile. Antibiotic susceptibility was determined using the disk diffusion and broth microdilution methods. Whole-genome sequencing (WGS)...
The first 18 months of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Colombia were characterized by three epidemic waves. During the third wave, from March through August 2021, intervariant competition resulted in Mu replacing Alpha and Gamma. We employed Bayesian phylod...
Based Epidemiology (WBE) consists of quantifying biomarkers in sewerage systems to derive real-time information on the health and/or lifestyle of the contributing population. WBE usefulness was vastly demonstrated in the context of the COVID-19 pandemic. Many methods for SARS-CoV-2 RNA determination...
A massive outbreak of dengue-like illness was reported from Pune district of Maharashtra, India during May-June 2022. Isolation and characterization of the etiological agent at genomic level for possible mutations that led to higher transmissibility is the topic of the study. Entomological investig...
The genetic diversity of the dengue virus is characterized by four circulating serotypes, several genotypes, and an increasing number of existing lineages that may have differences in the potential to cause epidemics and disease severity. Accurate identification of the genetic variability of the vir...
To summarize and analyze the strains' molecular epidemiology and clinical characteristics of 6 strains of post-influenza community-associated methicillin-resistant (CA-MRSA) pneumonia. Six cases of CA-MRSA pneumonia after influenza from 2014 to 2022 were retrospectively collected and CA-MRSA strai...
The increase of multidrug-resistant Enterobacteriaceae bacteria has led to the reintroduction of colistin for clinical treatments, and colistin has become a last resort for infections caused by multidrug-resistant bacteria. Enterobacteriaceae bacteria carrying the mcr-1 gene are majorly related to c...
Healthcare facilities have been challenged by the risk of SARS-CoV-2 transmission between healthcare workers (HCW) and patients. During the first wave of the COVID-19 pandemic, infections among HCW were observed, questioning infection prevention and control (IPC) measures implemented at that time. T...
Millions of SARS-CoV-2 whole genome sequences have been generated to date. However, good quality data and adequate surveillance systems are required to contribute to meaningful surveillance in public health. In this context, the network of Spanish laboratories for coronavirus (RELECOV) was created w...
On August 2019 a staphylococcal food poisoning outbreak occurred in an elderly home in Piedmont, Italy. The epidemiological investigation performed among the persons that consumed the meal identified chicken salad as the most likely source of the outbreak. Staphylococcus aureus was isolated from a t...
subspecies is one of the most important foodborne pathogens and the causative agent of salmonellosis, which affects both humans and animals producing numerous infections every year. The study and understanding of its epidemiology are key to monitoring and controlling these bacteria. With the develo...
Carbapenem-resistant (CRAB) is a major public health concern globally. Often studied in the context of hospital outbreaks, little is known about the persistence and evolutionary dynamics of endemic CRAB populations. A three-month cross-sectional observational study was conducted in a 28-bed intensi...
As part of efforts to rapidly identify and care for individuals with COVID-19, trace and quarantine contacts, and monitor disease trends over time, most African countries implemented interventions to strengthen their existing disease surveillance systems. This research describes the strengths, weakn...
Colonization and subsequent health care-associated infection (HCAI) with Acinetobacter baumannii are a concern for vulnerable patient groups within the hospital setting. Outbreaks involving multidrug-resistant strains are associated with increased patient morbidity and mortality and poorer overall o...
Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection, and provide an early warning of COVID-19 community spread. Here, we investigated the spread of SARS-CoV-2 infections across Utah by characterizing lineages and mutations det...
The advent of next generation sequencing technologies (NGS) has greatly accelerated our understanding of critical aspects of organismal biology from non-model organisms. Bats form a particularly interesting group in this regard, as genomic data have helped unearth a vast spectrum of idiosyncrasies i...
Insufficient tracking of virus introduction, spread, and new lineage emergence for the human monkeypox (mpox) virus 1 (hMPXV1) outbreak of 2022 hindered epidemiological studies and public health response. hMPXV1 mutations accumulated unexpectedly faster than predicted. Thus, new variants with altere...
High blood pressure (BP) and type-2 diabetes (T2DM) are forerunners of chronic kidney disease and left ventricular dysfunction. Home BP telemonitoring (HTM) and urinary peptidomic profiling (UPP) are technologies enabling risk stratification and personalized prevention. UPRIGHT-HTM (NCT04299529) is...
Professional soccer athletes are at risk of acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). United States Major League Soccer (MLS) uses protocol-based SARS-CoV-2 testing for identification of individuals with coronavirus disease 2019. Per MLS protocol, fully vaccinated playe...
To describe IMP-type carbapenemase-producing outbreaks at Galdakao University Hospital between March 2021 to December 2021. Outbreak report. Galdakao University Hospital is a tertiary-care hospital in the Basque Country (northern Spain). All patients with a positive IMP-type carbapenemase producing...
An outbreak involving an extensively antibiotic-resistant Acinetobacter baumannii strain in three military treatment facilities was identified. Fifty-nine isolates recovered from 30 patients over a 4-year period were found among a large collection of isolates using core genome multilocus sequence ty...
Investigation of risk factors for the presence of vancomycin-resistant enterococci (VRE) in inpatients on surgical wards and associated intensive care units of a German tertiary care hospital. A single-centre retrospective matched case-control study was performed with surgical inpatients admitted be...
The SARS-CoV-2 pandemic has highlighted the importance of viable infection surveillance and the relevant infrastructure. From a German perspective, an integral part of this infrastructure, genomic pathogen sequencing, was at best fragmentary and stretched to its limits due to the lack or inefficient...
is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Pulsed-field gene electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST) have been historically used to differentiate sporadic from outbreak isolates. Whole genome sequencing (WGS) has been shown to provide...
International airports can have a key role in screening, detecting, and mitigating cross-border transmission of SARS-CoV-2 and potentially other infectious diseases. With aircraft passengers representing a subpopulation of a country or region, aircraft-based wastewater surveillance can be a promisin...
Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importanc...
Rising rates of multidrug-resistant infections necessitate a comprehensive understanding of the major strains and plasmids driving spread of resistance elements. Here, we analysed 540 clinical, screen and environmental isolates recovered from across Wales between 2007 and 2020 using combined short...
Eggplant is one of the important vegetable crops grown across the world, and its production is threatened by both biotic and abiotic stresses. Diseases caused by viruses are becoming major limiting factors for its successful cultivation. A survey for begomovirus-like symptoms in 72 eggplant fields l...
Dengue fever is among the most significant public health concerns in Brazil. To date, the highest number of Dengue notifications in the Americas has been reported in Brazil, with cases accounting for a total number of 3,418,796 reported cases as of mid-December 2022. Furthermore, the northeastern re...
Lodderomyces elongisporus is a recently emerging yeast pathogen predominantly reported in adult patients who had immunosuppression and/or intravenous access devices. Here, we report a fungemia outbreak caused by in a neonatal intensive care unit (NICU) in Delhi, India, from September 2021 to Februa...
OXA-232 carbapenemase is becoming a threat in China due to its high prevalence, mortality, and limited treatment options. However, little information is available on the impact of OXA-232-producing Klebsiella pneumoniae in China. This study aims to characterize the clonal relationships, the genetic...
To characterise the clinical features of Acinetobacter baumannii infections and investigate the phylogenetic structure and transmission dynamics of A. baumannii in Vietnam. Between 2019 and 2020, a surveillance of A. baumannii (AB) infections was conducted at a tertiary hospital in Ho Chi Minh City,...
Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehens...
The pandemic caused by COVID-19 and the emergence of new variants of SARS-CoV-2 have generated clinical and epidemiological impacts on a global scale. The use of strategies for monitoring viral circulation and identifying mutations in genomic regions involved in host interaction are important measur...
Although France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) movement within France, but also involving France in Europe and in the world, remain only partially characterized in this tim...
SARS-CoV-2 has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread, and to inform policy decisions. We sequenced viral genomes from over 22,000 patient samples tested at Mayo Clinic Laborator...
Wolbachia pipientis is an endosymbiont bacterium that induces cytoplasmic incompatibility and inhibits arboviral replication in mosquitoes. This study aimed to assess Wolbachia prevalence and genetic diversity in different mosquito species from Cape Verde. Mosquitoes were collected on six islands of...
Drug appropriateness is a pillar of modern evidence-based medicine, but the turnaround times of genomic sequencing are not compatible with the urgent need to deliver treatments against microorganisms. Massive worldwide genomic surveillance has created an unprecedented landscape for exploiting viral...
Genomic epidemiology can facilitate an understanding of evolutionary history and transmission dynamics of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak. We used next-generation sequencing techniques to study SARS-CoV-2 genomes isolated from patients and health care workers...
The aim of this study was to perform a genomic investigation of a multiple fluoroquinolone-resistant Leclercia adecarboxylata strain isolated from a synanthropic pigeon in São Paulo, Brazil. Whole-genome sequencing was performed using an Illumina platform, and in silico deep analyses of the resistom...
The origin and spread of dengue virus (DENV) circulating in Africa remain poorly characterized, with African sequences representing <1% of global sequence data. Whole genome sequencing was performed on serum samples (n = 29) from an undifferentiated fever study in 2016 in the Democratic Republic of...
Accurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their spread. Here we introduce HaploCoV, a novel software framework that enables the exploration...
In the wake of the SARS-CoV-2 pandemic, scientists have scrambled to collect and analyze SARS-CoV-2 genomic data to inform public health responses to COVID-19 in real time. Open source phylogenetic and data visualization platforms for monitoring SARS-CoV-2 genomic epidemiology have rapidly gained po...
A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in . In this work, we propose a publicly available cgMLST scheme for using chewBBACA. In total 72 complete genomes, representing the diversity of this species, were used to set up a...
Mycobacterium tuberculosis (MTB) is a global public health issue. Although Oman reduced the burden of tuberculosis (TB) by 85% in under 25 years, the annual incidence rate remains stagnant. Whole genome sequencing (WGS) is used to investigate the transmission dynamics of MTB complex. This study aime...
Phylogenetic analysis of 34 monkeypox virus genome sequences isolated from patients in Minas Gerais, Brazil, revealed initial importation events in early June 2022, then community transmission within the state. All generated genomes belonged to the B.1 lineage responsible for a global mpox outbreak....
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is emerging as a worldwide public health concern; however, molecular epidemiological surveillance of clinical CRKP bloodstream infection (BSI) in China is limited. We conducted a retrospective observational study to assess risk factors and the molecu...
SARS-CoV-2 genomic surveillance is necessary for the detection, monitoring, and evaluation of virus variants, which can have increased transmissibility, disease severity, or other adverse effects. We sequenced 330 SARS-CoV-2 genomes during the sixth wave of the COVID pandemic in Iran and compared th...
Whole genome sequencing (WGS) has greatly improved the detection of methicillin-resistant Staphylococcus aureus (MRSA) transmission between people. We describe the transmission of two unique MRSA clones among homeless people in Copenhagen using WGS and core genome MLST (cgMLST). In 2014, an accumula...
Brucella canis is the main causative agent of canine brucellosis, which affects domestic and wild canids and leads to clinical signs and symptoms of the reproductive and locomotor systems. Owing to the scarce information on this pathogen, here we addressed the genetic diversity of the circulating st...
Tilapia farming is one of the most important sectors in aquaculture worldwide and of major importance to global food security. Infectious spleen and kidney necrosis virus (ISKNV) has been identified as an agent of high morbidity and mortality, threatening tilapia aquaculture. ISKNV was detected in L...
We aimed to describe the genomic epidemiology of the foodborne gastrointestinal pathogen, Shiga toxin-producing Escherichia coli (STEC) serotype O26:H11 belonging to clonal complex 29 (CC29) in England. Between 01 January 2014 and 31 December 2021, 834 human isolates belonging to CC29 were sequenced...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from sampl...
Japanese encephalitis virus (JEV; Flaviridae: Flavivirus) causes Japanese encephalitis (JE), which is the most important arboviral disease in Asia and the western Pacific. Among the five JEV genotypes (GI-V), GI has dominated traditional epidemic regions in the past 20 years. We investigated the tra...
serovar Enteritidis is one of the most frequent causes of Salmonellosis globally and is commonly transmitted from animals to humans by the consumption of contaminated foodstuffs. In the UK and many other countries in the Global North, a significant proportion of cases are caused by the consumption o...
A new study in PLOS Biology highlights the alarming potential of a pandemic clone of wheat blast disease to evolve fungicide-insensitive variants and argues the urgent need for genomic surveillance and preemptive breeding of resistant wheat.
Virus evolution shapes the epidemiological patterns of infectious disease, particularly via evasion of population immunity. At the individual level, host immunity itself may drive viral evolution towards antigenic escape. Using compartmental SIR-style models with imperfect vaccination, we allow the...
Wheat, one of the most important food crops, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory...
Whole-genome sequencing (WGS) has revolutionized surveillance of infectious diseases. Disease outbreaks can now be detected with high precision, and correct attribution of infection sources has been improved. Listeriosis, caused by the bacterium Listeria monocytogenes, is a foodborne disease with a...
Monkeypox Virus (MPXV) is a growing public health threat with increasing cases and fatalities globally. To date, no specific vaccine or small molecule therapeutic choices are available for the treatment of MPXV disease. In this work, we employed proteomics and structural vaccinology approaches to de...
Chikungunya is an arboviral infection caused by the Chikungunya virus (CHIKV) transmitted to humans by mosquitoes of Aedes spp. CHIKV has been confined to African countries and South-East Asia up to 2004, but since then, the pathogen has become more global, and its high morbidity rate has become mor...
Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently...
Methicillin-resistant Staphylococcus aureus (MRSA) infections cause substantive morbidity and mortality in neonates. Using publicly available resources from the National Center of Biotechnology Information (NCBI) and Food and Drug Administration's (FDA) GalaxyTrakr pipeline, we illustrate the dynami...
Klebsiella pneumoniae is a common cause of hospital- and community-acquired infections globally, yet its population structure remains unknown for many regions, particularly in low- and middle-income countries (LMICs). Here, we report for the first-time whole-genome sequencing (WGS) of a multidrug-re...
The blacklegged tick (Ixodes scapularis (Journal of the Academy of Natural Sciences of Philadelphia, 1821, 2, 59)) is a vector of Borrelia burgdorferi sensu stricto (s.s.) (International Journal of Systematic Bacteriology, 1984, 34, 496), the causative bacterial agent of Lyme disease, part of a slow...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly...
serotype b has been the main cause of invasive infections in children, during the prevaccination period. More than 20 years after the introduction of the conjugate vaccine against Hib, HiNT has emerged as the cause of localized infections in children and adults. The main objective of this work is to...
Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this...
During the COVID-19 pandemic, the death rate was reportedly 5-8 fold lower in India which is densely populated as compared to less populated western countries. The aim of this study was to investigate whether dietary habits were associated with the variations in COVID-19 severity and deaths between...
The SARS-CoV‑2 pandemic has shown a deficit of essential epidemiological infrastructure, especially with regard to genomic pathogen surveillance in Germany. In order to prepare for future pandemics, the authors consider it urgently necessary to remedy this existing deficit by establishing an efficie...
Brucellosis is a worldwide zoonosis with important public health, animal health and economic implications. , commonly associated with small ruminants, is an emerging bovine pathogen in dairy farms. We analysed all outbreaks affecting dairy farms in Israel since 2006, combining traditional and genom...
Recombination, the process whereby a segment of genetic material from one genome is inserted into another, producing a new chimeric genome, is an important evolutionary mechanism frequently observed in coronaviruses. The risks posed by recombination include the shuffling of advantageous mutations th...
A difficult-to-control outbreak of is ongoing in a large tertiary care hospital in Liguria, Italy, where it first emerged in 2019. In a retrospective analysis, 503 cases of carriage or infection were observed between July 2019 and December 2022. Genomic surveillance identified putative cases that...
Since the beginning of the pandemic, the generation of new variants periodically recurs. The XBB.1.5 SARS-CoV-2 variant is one of the most recent. This research was aimed at verifying the potential hazard of this new subvariant. To achieve this objective, we performed a genome-based integrative appr...
During the COVID-19 pandemic caused by SARS-CoV-2, new waves have been associated with new variants and have the potential to escape vaccinations. Therefore, it is useful to conduct retrospective genomic surveillance research. Herein, we present a detailed analysis of 88 SARS-CoV-2 genomes belonging...
With the recent ongoing autumn/winter 2022 COVID-19 wave and the adjustment of public health control measures, there have been widespread SARS-CoV-2 infections in Chinese mainland. Here we have analyzed 369 viral genomes from recently diagnosed COVID-19 patients in Shanghai, identifying a large numb...
Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA...
Epidemiological surveillance relies on microbial strain typing, which defines genomic relatedness among isolates to identify case clusters and their potential sources. Although predefined thresholds are often applied, known outbreak-specific features such as pathogen mutation rate and duration of so...
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued, with the persistent emergence of variants of concern (VOCs). Therefore, this study aimed to track the genomic evolution of SARS-CoV-2 strains by sequencing the spike protein for 29 months, which ac...
COVID-19 has significantly affected hospital infection prevention and control (IPC) practices, especially in intensive care units (ICUs). This frequently caused dissemination of multidrug-resistant organisms (MDROs), including carbapenem-resistant (CRAB). Here, we report the management of a CRAB ou...
Variants of concern (VOCs) of SARS-CoV-2 are viral strains that have mutations associated with increased transmissibility and/or increased virulence, and their main mutations are in the receptor binding domain (RBD) region of the viral spike. This study aimed to characterize SARS-CoV-2 VOCs via Sang...
Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified as pathotypes of diarrhoeagenic Escherichia coli or Shigella species and is generally only detected during genomic surveillance of other Enterobacteriaceae. The in...
Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and f...
Mechanisms contributing to COVID-19 severity in people with HIV (PWH) are poorly understood. We evaluated temporal changes in plasma proteins following SARS-CoV-2 infection and identified pre-infection proteomic markers associated with future COVID-19. We leveraged data from the global Randomized Tr...
, a notorious pathogen for opportunistic health care-associated infections, represents increasing multidrug resistance, particularly to carbapenems. OXA-232 carbapenemase, as a variant of OXA-48, has been increasingly reported worldwide. ST231, an epidemic, multidrug resistant (MDR) clone in south...
In 2015, an outbreak caused by OXA-48-producing Enterobacteriaceae affected a neonatal intensive care unit at a Swedish University Hospital. The aim was to explore the transmission of OXA-48-producing strains between infants and the transfer of resistance plasmids between strains during the outbreak...
Recurrent cases of Clostridioides difficile infection (rCDI) remain one of the most common and serious challenges faced in the management of CDI. The accurate distinction between a relapse (caused by infection with the same strain) and reinfection (caused by a new strain) has implications for infect...
Vancomycin-resistant E. faecium (VREfm) is a significant public health concern because of limited treatment options. Genomic surveillance can be used to monitor VREfm transmission and evolution. Genomic analysis of VREfm has not been reported for the Dallas/Fort Worth/Arlington, TX, area, which is c...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility, virulence and immune escape abilities have heavily altered the COVID-19 pandemic's course. Deciphering local and global transmission patterns of those variants is thus key in building a profound un...
In recent decades, waves of yellow fever virus (YFV) from the Amazon Rainforest have spread and caused outbreaks in other regions of Brazil, including the Cerrado, a savannah-like biome through which YFV usually moves before arriving at the Atlantic Forest. To identify the vectors involved in the ma...
At the time when the COVID-19 pandemic was responsible for more than six million deaths worldwide, the antiquity of coronaviruses remains undefined. We investigated individuals buried during the 16th century in France for the direct and paleoserological diagnosis of the coronavirus. The 2011-2012 ex...
Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the int...
Epidemiology has been transformed by the advent of Bayesian phylodynamic models that allow researchers to infer the geographic history of pathogen dispersal over a set of discrete geographic areas [1, 2]. These models provide powerful tools for understanding the spatial dynamics of disease outbreaks...
The coronavirus disease 2019 (COVID-19) pandemic has been spreading quickly, threatening the public health system. Consequently, positive COVID-19 cases must be rapidly detected and treated. Automatic detection systems are essential for controlling the COVID-19 pandemic. Molecular techniques and med...
Bartonella quintana is an important cause of culture-negative endocarditis. Although humans have been considered as its only reservoir, recent studies showed that macaque species are also reservoirs of B. quintana. Based on multi-locus sequence typing (MLST) B. quintana strains have been classified...
The pandemic has led to the production and accumulation of various types of data related to coronavirus disease 2019 (COVID-19). To understand the features and characteristics of COVID-19 data, we summarized representative databases and determined the data types, purpose, and utilization details of...
To characterize the prevalence and genomic epidemiology of from acute diarrheal patients in Shenzhen City from 2013 to 2021. Based on the Shenzhen Infectious Diarrhea Surveillance System, acute diarrheal patients were actively monitored in sentinel hospitals from 2013 to 2021. Whole-genome sequenc...
Reports of infection in patients without epidemiologic links to prior outbreaks are scarce. We describe the genomic epidemiology of such a case in Western New York. Before emergence, the patient received >60 days of excess antibiotics. was recovered on near-patient surfaces after enhanced terminal...
We sequenced 54 respiratory syncytial virus (RSV) genomes collected during 2021-22 and 2022-23 outbreaks in Washington, USA, to determine the origin of increased RSV cases. Detected RSV strains have been spreading for >10 years, suggesting a role for diminished population immunity from low RSV expos...
Klebsiella pneumoniae is an important cause of nosocomial infections and displays increasing resistance to fluoroquinolones (FQ). This study surveyed the mechanisms of FQ resistance and molecular typing of K. pneumoniae isolates from intensive care units patients in Tehran, Iran. A total of 48 cipro...
No abstract available
In Australia, gonococcal isolates are monitored for antimicrobial susceptibilities. In Western Australia (WA), gonorrhoea notification rates increased by 63 % between 2013 and 2016, with the steepest increase occurring between 2015 and 2016, before stabilizing at this higher baseline between 2017 an...
No abstract available
In 2022, one of its worst cholera outbreaks began in Bangladesh and the icddr,b Dhaka hospital treated more than 1300 patients and ca. 42,000 diarrheal cases from March-1 to April-10, 2022. Here, we present genomic attributes of V. cholerae O1 responsible for the 2022 Dhaka outbreak and 960 7th pand...
Different variants of severe acute respiratory syndrome coronavirus 2 have been discovered globally. At present, the Omicron variant has been extensively circulated worldwide. There have been several outbreaks of the Omicron variant in China. Here, we investigated the epidemiologic, genetic characte...
Eliminating carbapenem-resistant Acinetobacter baumannii (CRAb) disease requires comprehensive knowledge of how this noncommensal organism propagates among at-risk hosts. We molecularly characterized an ongoing surge of CRAb cases among patients in a Midwest US healthcare system, which coincided wit...
Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education...
In the management of infectious disease outbreaks, grouping cases into clusters and understanding their underlying epidemiology are fundamental tasks. In genomic epidemiology, clusters are typically identified either using pathogen sequences alone or with sequences in combination with epidemiologica...
BackgroundLateral flow antigen-detection rapid diagnostic tests (Ag-RDTs) for viral infections constitute a fast, cheap and reliable alternative to nucleic acid amplification tests (NAATs). Whereas leftover material from NAATs can be employed for genomic analysis of positive samples, there is a pauc...
COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The...
We aimed to describe the epidemiological situation during the Omicron variant circulation in light of genomic surveillance data in Martinique, a territory with low vaccination rates. We exploited COVID-19 national databases of virological tests, for the collection of hospital data and for the sequen...
The first case of coronavirus disease 2019 (COVID-19) within the White Mountain Apache Tribe (WMAT) in Arizona was diagnosed almost 1 month after community transmission was recognized in the state. Aggressive contact tracing allowed for robust genomic epidemiology of severe acute respiratory syndrom...
The aetiological bacterial agent of gonorrhoea, Neisseria gonorrhoeae, has become resistant to each of the first-line antibiotics used to treat it, including ciprofloxacin. One diagnostic approach to identify ciprofloxacin-susceptible isolates is to determine codon 91 in the gene encoding the A subu...
Large, open-source DNA sequence databases have been generated, in part, through the collection of microbial pathogens by swabbing surfaces in built environments. Analyzing these data in aggregate through public health surveillance requires digitization of the complex, domain-specific metadata that a...
The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit SARS-CoV-2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white-tailed deer. Among farmed animals, American mink...
The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data. A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE. Despite having a uniquely long history of plague (∼5,...
Beginning December 6, 2021, all international air passengers boarding flights to the United States were required to show either a negative result from a SARS-CoV-2 viral test taken ≤1 day before departure or proof of recovery from COVID-19 within the preceding 90 days (1). As of June 12, 2022, prede...
Due to the frequent international and intercontinental transmission of multidrug-resistant bacteria, it is imperative to understand the epidemiology, phylogeography, and population structure of carbapenem-resistant Salmonella enterica (CRSE) across the globe. During the period of 2015-2022, two bla-...
Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phytophthora × cambivora is an invasive, destructive pathogen of forest and fruit trees causing severe damage worldwide to chestnuts (Castanea), apricots, peaches, plums, almonds and cherries (Prunus), apples...
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution...
H10 subtype avian influenza viruses (AIVs) have been isolated from wild and domestic avian species worldwide and have occasionally crossed the species barrier to mammalian hosts. Fatal human cases of H10N8 infections and the recent detection of human H10N3 infections have drawn widespread public att...
Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism...
Brazil is one of the nations most affected by Coronavirus disease 2019 (COVID-19). The introduction and establishment of new virus variants can be related to an increase in cases and fatalities. The emergence of Omicron, the most modified SARS-CoV-2 variant, caused alarm for the public health of Bra...
Mpox (Monkeypox) is a zoonotic disease caused by mpox virus (MPXV). A multi-country MPXV outbreak in non-endemic demographics was identified in May 2022. A systematic evaluation of MPXV evolutionary trajectory and genetic diversity could be a timely addition to the MPXV diagnostics and prophylaxis....
Exposure of blood to malaria parasites can lead to infection even in the absence of the mosquito vector. During a stay in a healthcare facility, accidental inoculation of the skin with blood from a malaria patient might occur, referred to as nosocomial malaria. Between 2007 and 2021, we identified 6...
Following the emergence of COVID-19 in December 2019, caused by the coronavirus SARS-CoV-2, the disease spread dramatically worldwide. The use of genomics to trace the dissemination of the virus and the identification of novel variants was essential in defining measures for containing the disease. W...
Technological advancements in phylodynamic modeling coupled with the accessibility of real-time pathogen genetic data are increasingly important for understanding the infectious disease transmission dynamics. In this study, we compare the transmission potentials of North American influenza A(H1N1)pd...
Lumpy skin disease (LSD) is an economically important poxviral disease endemic to Asia, Europe, and Africa. Recently, LSD has spread to naïve countries, including India, China, Bangladesh, Pakistan, Myanmar, Vietnam, and Thailand. Here, we describe the complete genomic characterization of LSDV from...
Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly...
Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of speci...
The COVID-19 pandemic has presented a unique opportunity to understand how real-time pathogen genomics can be used for large-scale outbreak investigations. On 12 August 2021, the Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta (B.1.617.2) variant. Prior to this date,...
remains a dangerous pathogen and poses a great threat to public health worldwide. The prevalence of the clonotype is temporally and geographically variable. The genomic and phenotypic characteristics of isolates in Tianjin, which is among the four big municipalities in China, are unclear. In the p...
Outbreak strains of are promising candidates as targets in the search for intrinsic determinants of transmissibility, as they are responsible for many cases with sustained transmission; however, the use of low-resolution typing methods and restricted geographical investigations represent flaws in a...
is an environmental bacterium and clinical pathogen that causes many life-threating outbreaks of an atypical pneumonia called Legionnaires' disease (LD). Studies of this pathogen have focused mainly on Europe and the United States. A shortage in data is clearly observed for developing countries. To...
Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is c...
is one of the most common bacterial pathogens of a wide range of community-acquired infections. It has been more and more recognized that this bacterium could also play a role as a cause of nosocomial infections. In this study, by retrospective analysis of the phenotypic resistance characteristics a...
No abstract available
Prospective whole-genome sequencing (WGS)-based surveillance may be the optimal approach to rapidly identify transmission of multi-drug resistant (MDR) bacteria in the healthcare setting. We prospectively collected methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci...
The ongoing coronavirus disease 2019 pandemic significantly burdens hospitals and other healthcare facilities. Therefore, understanding the entry and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for effective prevention and preparedness measures. We perfor...
RNA viruses have short generation times and high mutation rates, allowing them to undergo rapid molecular evolution during epidemics. However, the extent of RNA virus phenotypic evolution within epidemics and the resulting effects on fitness and virulence remain mostly unknown. Here, we screened the...
No abstract available
In Brazil, a yellow fever (YF) outbreak was reported in areas considered YF-free for decades. The low vaccination coverage and the increasing forest fragmentation, with the wide distribution of vector mosquitoes, have been related to yellow fever virus (YFV) transmission beyond endemic areas since 2...
An emerging serotype O10:K4 of Vibrio parahaemolyticus has been predominantly isolated from outbreaks and sporadic cases in China. Herein, we report the first case of infection due to V. parahaemolyticus O10:K4 isolated from a hospitalized patient with acute diarrhea in Thailand. We sequenced the wh...
We conducted a genomic analysis of monkeypox virus sequences collected early in the 2022 outbreak, during July-August , in Washington, USA. Using 109 viral genomes, we found low overall genetic diversity, multiple introductions into the state, ongoing community transmission, and potential for co-inf...
Serotype 3 has persisted to be an important cause of invasive pneumococcal disease in adults in the post-vaccine era. We aimed to investigate clinical and microbiological characteristics of Streptococcus pneumoniae serotype 3 infection in Taiwan and identify the risk factors associated with severe c...
Paratyphi B infections in England are the least common imported typhoidal infection but can still cause invasive disease. Sentinel surveillance at the reference laboratory detected an outbreak from Iraq due to reported travel history, enabling enhanced PCR testing for a quick diagnosis.
Pathogen sequencing guided understanding of SARS-CoV-2 evolution during the COVID-19 pandemic. Many health systems developed pathogen genomics services to monitor SARS-CoV-2. There are no agreed guidelines about how pathogen genomic information should be used in public health practice. We undertook...
The global prevalence of vancomycin-resistant Enterococcus faecium (VREfm) highlights the need for new anti-enterococcal agents. Here, we assessed the molecular epidemiology of clinical VREfm bacteraemic isolates from a medical centre in northern Taiwan in 2019-2020 and to evaluate their susceptibil...
The study of characteristics, prevalence and patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is significant to monitor and define the status of the pandemic, helping to design and evaluate control strategies. In this setting, the continuous emergence of new varian...
No abstract available
Whole-genome sequencing (WGS) has unparalleled ability to distinguish between bacteria, with many public health applications. The generation and analysis of WGS data require significant financial investment. We describe a systematic review summarizing economic analyses of genomic surveillance of bac...
Human adenoviruses (HAdV) are genetically diverse and can infect a number of tissues with severities varied from mild to fatal. HAdV types 3, 4, 7, 11, 14, 21, and 55 were associated with acute respiratory illnesses outbreaks in the United States and in other countries. The risk of outbreaks can be...
Oxford Nanopore Technologies (ONT) sequencing has rich potential for genomic epidemiology and public health investigations of bacterial pathogens, particularly in low-resource settings and at the point of care, due to its portability and affordability. However, low base-call accuracy has limited the...
ST372 are widely reported as the major sequence type in dogs globally. They are also a sporadic cause of extraintestinal infections in humans. Despite this, it is unknown whether ST372 strains from dogs and humans represent shared or distinct populations. Furthermore, little is known about genomic...
Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult...
The ongoing outbreak of monkeypox virus (hMPXV1) is the largest recorded in historically nonendemic countries. Genomic surveillance has emerged as a pivotal tool to track the spread and monitor the evolution of viral pathogens. Therefore, to assess the genetic diversity of circulating hMPXV1 in nort...
The aim of this study is to evaluate the effectiveness of a CRISPR-based human and bacterial ribosomal RNA (rRNA) depletion kit (JUMPCODE Genomics) on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shotgun metagenomic sequencing in weakly positive respiratory samples. Shotgun metagenom...
The coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review considers implications for now moving clinical metagenomics into routine service, with respiratory metage...
The objective of this study was to understand the molecular transmission characteristics of newly reported HIV infections in the city of Pengzhou, Sichuan Province, to analyze the risk factors of transmission network and spatial clustering and the transmission characteristics, and to provide a scien...
The COVID-19 pandemic continues to impose a major impact on global health and economy since its identification in early 2020, causing significant morbidity and mortality worldwide. Caused by the SARS-CoV-2 virus, along with a growing number of variants, COVID-19 has led to 651,918,402 confirmed case...
Shigella spp have been associated with community-wide outbreaks in urban settings. We analysed a sustained shigellosis outbreak in Seattle, WA, USA, to understand its origins and mechanisms of antimicrobial resistance, define ongoing transmission patterns, and optimise strategies for treatment and i...
is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomi...
Carbapenem resistant Enterobacteriaceae (CRE) colonization is a risk factor for CRE infection. CRE infection results in an increase in mortality in patients with cirrhosis. However, minimal data regarding the prevalence and the risk factors of CRE colonization in patients with liver disease yet with...
Bayesian space-time regression models are helpful tools to describe and predict the distribution of infectious disease outbreaks and to delineate high-risk areas for disease control. In these models, structured and unstructured spatial and temporal effects account for various forms of non-independen...
The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detectio...
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chroni...
Tixagevimab-cilgavimab is used for pre-exposure prophylaxis of COVID-19 in immunocompromised patients, though in vitro data has shown reduced neutralizing activity against SARS-CoV-2 Omicron subvariants. We performed genomic sequencing of SARS-CoV-2 isolated from patients diagnosed with COVID-19 fol...
Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections,...
An understanding of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission in schools is important. It is often difficult, using epidemiological information alone, to determine whether cases associated with schools represent multiple introductions from the community or transmissio...
Renibacterium salmoninarum (Rs) is the etiological agent of bacterial kidney disease (BKD), which significantly affects farmed and wild salmonids worldwide. Although the whole genome of Rs (~3.1 million nucleotides) is highly conserved, genomic epidemiology analyses have identified four sub-lineages...
Tracking the spread of infection amongst individuals within and between communities has been a major challenge during viral outbreaks. With the unprecedented scale of viral sequence data collection during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the possibility of u...
Mpox was diagnosed in 2 women returning to Vietnam from the United Arab Emirates. The monkeypox viruses belonged to an emerging sublineage, A.2.1, distinct from B.1, which is responsible for the ongoing multicountry outbreak. Women could contribute to mpox transmission, and enhanced genomic surveill...
Phylodynamics is a set of population genetics tools that aim at reconstructing demographic history of a population based on molecular sequences of individuals sampled from the population of interest. One important task in phylodynamics is to estimate changes in (effective) population size. When appl...
São Paulo is the financial center of Brazil, with a population of over 12 million, that receives travelers from all over the world for business and tourism. It was the first city in Brazil to report a case of COVID-19 that rapidly spread across the city despite the implementation of the restriction...
Salmonella enterica subsp. enterica serovar Enteritidis (SE) has become the prevalent serovar isolated from gastroenteritis cases in Brazil since the 1990s. To better understand the genomic diversity and phylogenetic relationship amongst SE epidemic isolates from Brazil, 30 SE isolates from a variet...
The emergence and spread of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals is a major global public health concern. The current study sought to characterize 25 MRSA clinical isolates collected in a Tunisian hospital from December 2015 to September 2016, with the genetic lineages, vi...
A. Baumannii is an opportunistic nosocomial pathogen which has severe antibiotic resistance. However, the epidemiology is less clearly understood in Jilin province and China. Thus, 89 A. baumannii isolates from a single hospital in Jilin province between 2013-2017 were performed by MLST. In order to...
COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate combined with high rates of transmission and fatality can cause a deadly worldwide pandemic in a matter of weeks (Plato et al., 2021). Apart from vaccines and post-infection treatment options, stra...
The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In t...
Environmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS-CoV-2 has complemented routine diagnostic surveillance by capturing near real-time virus circulation at a population level. In this longitudinal study con...
Emerging infectious diseases are one of the most important global health challenges because of their impact on human and animal health. The vector-borne West Nile virus (WNV) is transmitted between birds by mosquitos, but it can also infect humans and horses causing disease. The local circulation of...
Characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on analyzing the evolution and mutations of viruses is crucial for tracking viral infections, potential mutants, and other pathogens. The purpose was to study the complete sequences of SARS-CoV-2 to reveal genetic...
The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented. The time to fixation of BA.1, the diversity of Delta sublineages, the popul...
The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, t...
Leclercia adecarboxylata is a bacteria closely related to Escherichia coli according to its biochemical characteristics and is commonly considered non-pathogenic although a growing number of publications classify it as an emerging pathogen. Fosfomycin resistance is a common trait for L. adecarboxyla...
Porcine parvovirus 1 (PPV1) is recognized as a major cause of reproductive failure in pigs, leading to several clinical outcomes globally known as SMEDI. Despite being known since the late 1960s its circulation is still of relevance to swine producers. Additionally, the emergence of variants such as...
Pakistan, a dengue-endemic country, has encountered several outbreaks during the past decade. The current study aimed to explore the serotype and genomic diversity of dengue virus responsible for the 2022 outbreak in Pakistan. From August to October 2022, NS-1 positive blood samples (n = 343) were c...
The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases. However, our understanding of the diversity, prevalence, and transmission of honeybee viruses is largely obscu...
The Pseudomonas aeruginosa population has a nonclonal epidemic structure. It is generally composed of a limited number of widespread clones selected from a background of many rare and unrelated genotypes recombining at high frequency. Due to the increasing prevalence of nosocomial infections caused...
Salmonella enterica serovar Enteritidis is one of the leading causes of salmonellosis in Australia. In this study, a total of 568 Enteritidis isolates from two Australian states across two consecutive years were analyzed and compared to international strains, using the Enteritidis multilevel genom...
Invasive meningococcal disease (IMD) is a major health problem. Given the post-COVID-19 pandemic scenario with the loosening of the non-pharmacological measures to control the virus transmission and considering the observed global reduction of meningococcal vaccination coverage, an increase in IMD c...
Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and f...
The first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (mean = 27 tests per 100,000 people per day). We simulated...
The adaptive evolution of SARS-CoV-2 variants is driven by selection for increased viral fitness in transmissibility and immune evasion. Understanding the dynamics of how an emergent variant sweeps across populations can better inform public health response preparedness for future variants. Here, we...
The emergence of highly transmissible SARS-CoV-2 variants and vaccine breakthrough infections globally mandated the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed 2.13 million SARS-CoV-2 genomes from 188 countries/territories (up to June 2021) and per...
Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods,...
Typhi (. Typhi) and Paratyphi A (. Paratyphi A) are the causative agents of enteric fever, a systemic human disease with a burden of 300 000 cases per year in India. The majority of enteric fever cases are associated with . Typhi, resulting in a paucity of data regarding . Paratyphi A, specifically...
No abstract available
. is part of the family , and is naturally resistant to various antimicrobial drugs. In recent years, outbreaks of severe nosocomial infections caused by carbapenem-resistant (CR-PMI) have been frequently reported. Few studies exist on the whole-genome molecular characteristics of this bacterium i...
Globally, 390 million people are at risk of dengue infection and over the past 50 years, the virus incidence increased thirty-fold. In Senegal, an unprecedented occurrence of outbreaks and sporadic cases have been noticed since 2017. In October 2018, an outbreak of Dengue virus 2 (DENV-2) was report...
Since the end of 2022, when China adjusted its COVID-19 response measures, the SARS-CoV-2 epidemic has rapidly grown in the country. It is very necessary to monitor the evolutionary dynamic of epidemic variants. However, detailed reports presenting viral genome characteristics in China during this p...
Carbapenem-resistant (CRAB) has emerged as a predominant strain of healthcare-associated infections worldwide, particularly in intensive care units (ICUs). Therefore, it is imperative to study the molecular epidemiology of CRAB in the ICUs using multiple molecular typing methods to lay the foundati...
Tuberculosis (TB) is among the deadliest diseases worldwide, and its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, nonadherence to treatment and circulation of previously resistant isolates of Mycobacteri...
COVID-19 is an acute respiratory infectious disease caused by SARS-CoV-2. It was first reported in Wuhan, China in December 2019 and rapidly spread globally in early 2020, triggering a global pandemic. In December 2022, China adjusted the dynamic COVID-zero strategy that lasted for three years. The...
The COVID-19 pandemic had a major impact on indigenous populations. Understanding the viral dynamics within this population is essential to create targeted protection measures. A total of 204 SARS-CoV-2 positive samples collected between May 2020 and November 2021 from an indigenous area in Mato Gro...
Staphylococcus pseudintermedius is an important cause of clinical infections in small-animal-veterinary medicine. Evolutionary changes of strains using multilocus sequence typing (MLST) have been observed among S. pseudintermedius in European countries and the United States. However, there are limit...
Being the second most populous country in the world, India presents valuable lessons for the world about dealing with the SARS-CoV-2 pandemic. From this perspective, we attempted a retrospective evaluation of India's SARS-CoV-2 genomic surveillance strategy and also gave some recommendations for und...
Entomological surveillance for mosquito-borne viruses is vital for monitoring disease transmission and vector control programs. The vector control program is reliant not only on vector density but also on the timely detection of mosquito-borne infections. In the present study, we conducted an entomo...
The onset of the COVID-19 pandemic triggered a rapid scale-up in the use of genomic surveillance as a pandemic preparedness and response tool. As a result, the number of countries with in-country SARS-CoV-2 genomic sequencing capability increased by 40% from February 2021 to July 2022. The Global Ge...
is an aggressive invasive mosquito species widely distributed around the world, and it is also a known vector of arboviruses. Virus metagenomics and RNA interference (RNAi) are important in studying the biology and antiviral defense of . However, the virome and potential transmission of plant viruse...
The emergence of multidrug-resistant poses a global threat, but the distribution and resistance profiling are unclear, especially in young children. Infections due to are common, associated with high mortality, and increasingly β-lactam drug resistant. We studied the molecular epidemiology and ant...
Non-aureus (NAS) species are currently the most commonly identified microbial agents causing sub-clinical infections of the udder and are also deemed as opportunistic pathogens of clinical mastitis in dairy cattle. More than 10 NAS species have been identified and studied but little is known about...
The aim of this study was to investigate the effectiveness of infection control measures to prevent transmission of SARS-CoV-2 within a professional sports team using whole genome sequencing. Prospective cohort study. 74 players and staff members of a Dutch professional male football team were follo...
The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-lengt...
Although the yeast () has been rarely reported in human infections, nosocomial outbreaks caused by this organism have been documented. Here we report a pseudo-outbreak of in a urology department of a Chinese hospital over a two-week period. Three patients were admitted to the urology department of...
The study aims to isolate and understand cytopathogenesis, ultrastructure, genomic characteristics and phylogenetic analysis of SARS-CoV-2 virus of B.1.210 lineage, that circulated in India during first wave of the pandemic. Clinical specimen from an interstate traveller from Maharashtra to Karnatak...
Cholera is a severe diarrheal disease caused by the aquatic bacterium Vibrio cholerae. Interestingly, to date, only one major clade has emerged to cause pandemic disease in humans: the clade that encompasses the strains from the O1 and O139 serogroups. In this chapter, we provide a comprehensive per...
Boosted by the COVID-19 pandemic, as well as the tightened General Data Protection Regulation (GDPR) legislation within the European Union (EU), individuals have become increasingly concerned about privacy. This is also reflected in how willing individuals are to consent to sharing personal data, in...
Staphylococcus aureus is a human pathogen causing nosocomial infections and increased hospitalization and mortality among human communities. Methicillin-resistant S. aureus strains are considered a severe threat in nosocomial infections and cause complications in the remedy process of bacterial infe...
Fluoroquinolones (FQs) are not commonly prescribed in children, yet the increasing incidence of multidrug-resistant (MDR) Enterobacterales (Ent) infections in this population often reveals FQ resistance. We sought to define the role of FQ resistance in the epidemiology of MDR Ent in children, with a...
is a frequently isolated non- species and invasive infections in older patients are associated with high mortality rates. Opportunistic infections in critically ill patients may be either endogenous or nosocomial in origin and this distinction is critical for effective intervention strategies. Thi...
Vaccines are instrumental tools to fight against novel and re-emerging pathogens and curb pandemics. Vaccination has been an integral part of the multifaceted public health response to the COVID-19 pandemic. Diverse vaccine platforms have been designed and are currently at different stages of develo...
The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laborato...
An outbreak of monkeypox (encoded enveloped double stranded DNA), resurgence and expansion has emerged in early 2022, posing a new threat to global health. Even though, many reports are available on monkeypox, still a comprehensive updated review is needed. Present updated review is focused to fill...
() is an important cause of nosocomial infection, especially in intensive care units (ICUs). It has the propensity to tolerate various environments and multiple classes of antibiotics. Our study aimed to characterize the comparative genomes of from hospital environments and clinical isolates. Clini...
Accurate genome sequences form the basis for genomic surveillance programs, the added value of which was impressively demonstrated during the COVID-19 pandemic by tracing transmission chains, discovering new viral lineages and mutations, and assessing them for infectiousness and resistance to availa...
Since its appearance, COVID-19 has immensely impacted our society. Public health measures, from the initial lockdowns to vaccination campaigns, have mitigated the crisis. However, SARS-CoV-2's persistence and evolving variants continue to pose global threats, increasing the risk of reinfections. Des...
India had faced three waves throughout the Coronavirus disease 2019 (COVID-19) pandemic, which had already impacted economic lives and affected the healthcare setting and infrastructure. The widespread impacts have inspired researchers to look for clinical indicators of severe acute respiratory synd...
Recombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the viral evolution. This study introspects the phenomenon of...
is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased the knowledge on the epidemiology of this disease. However, due to the difficulties associated with the...
Bovine viral diarrhea virus (BVDV) is one of the most important cattle pathogens worldwide, causing major economic losses and animal welfare issues. Disease eradication programs have been implemented in several countries, including Germany where an obligatory nationwide control program is in force s...
is a foodborne pathogen that can produce serious, even fatal, infections. Among other foods, it can be found in unpasteurized dairy and ready-to-eat products. Surveillance of is of great interest since sources of infection are difficult to determine due to the long incubation period, and because th...
Wastewater-based genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provides a comprehensive approach to characterize evolutionary patterns and distribution of viral types in a population. This study documents the molecular epidemiology of SARS-CoV-2, in Northern So...
Methicillin resistant (MRSA) is a major contributor to the global burden of antimicrobial resistance (AMR). As MRSA continues to evolve, the need for continued surveillance to evaluate trends remains crucial. This study was carried out to assess MRSA trends in the United Arab Emirates (UAE) based o...
The Philippines has had a rapidly growing human immunodeficiency virus (HIV) epidemic with a shift in the prevalent subtype from B to CRF01_AE. However, the phylodynamic history of CRF01_AE in the Philippines has yet to be reconstructed. We conducted a descriptive retrospective study reconstructing...
Phylodynamic methods have lately played a key role in understanding the spread of infectious diseases. During the coronavirus disease (COVID-19) pandemic, large scale genomic surveillance has further increased the potential of dynamic inference from viral genomes. With the continual emergence of nov...
Lassa fever (LF) is a potentially lethal viral haemorrhagic infection of humans caused by Lassa mammarenavirus (LASV). It is an important endemic zoonotic disease in West Africa with growing evidence for increasing frequency and sizes of outbreaks. Phylogeographic and molecular epidemiology methods...
Although carbapenemases are frequently reported in resistant clinical isolates, other chromosomally mediated elements of resistance that are considered essential are frequently underestimated. Having a wide substrate range, multidrug efflux pumps frequently underlie antibiotic treatment failure. Re...
Viruses of the genus are classified into several genotypes (GT1 to GT7), of which only GT1 (classic rabies virus-RABV) has a cosmopolitan distribution and circulates in Brazil. GT1 is subdivided into several antigenic variants (AgV) maintained in independent cycles with a narrow host range and dist...
Genomics has significantly revolutionized pathogen surveillance, particularly in epidemiological studies, the detection of drug-resistant strains, and disease control. Despite its potential, the representation of Latin American countries in the genomic catalogues of Mycobacterium tuberculosis (Mtb),...
The present study was undertaken to address the recent spate of pasteurellosis outbreaks among sea-farmed Atlantic salmon () in Norway and Scotland, coinciding with sporadic disease episodes in lumpfish () used for delousing purposes in salmon farms. Genome assemblies from 86 bacterial isolates cult...
The purpose of this study was to highlight the clinical and molecular features of 13 strains isolated from clinical environments in Ecuador, and to perform comparative genomics with previously published genomes of spp. As is primarily found in environmental, clinical settings, we focused our work...
Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes...
Dengue has been endemic in Southeast Asian countries for decades. There are few reports tracing the dynamics of dengue in real time. In this study, we generated hundreds of pathogen genomes to understand the genomic epidemiology of an outbreak in a hyper-endemic area of dengue. We leveraged whole-ge...
subspecies (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized. We carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream infections obtained through national surveillance prog...
The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and raci...
To provide an insight into the Whole-genome sequencing (WGS) data of MRSA strains circulating in a teaching hospital in north India. An exploratory study was conducted in which fifty non-repetitive MRSA isolates obtained from pus samples of inpatients from July 2018 to February 2019 were subjected t...
The pv. () is a bacterial pathogen causing bacterial blight disease in rice, resulting in significant yield reductions of up to 50% in rice production. Despite its serious threat to food production globally, knowledge of its population structure and virulence evolution is relatively limited. In th...
The SARS-CoV-2 is still undergoing rapid evolution, resulting in the emergence of several variants of concern, especially the Omicron variants (B.1.1.529), which are surging worldwide. In this study, we tracked Omicron subvariant BA.5.1.3 as the causative agent in the Hainan Province wave in China,...
is an important pathogen causing approximately 20-30% of the cases-with antibiotic-associated diarrhea and 90% of those with . However, limited surveillance of infections (CDI) in China is done at present, especially in terms of multi-hospital epidemiological reports. Between June 2020 and November...
When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-...
COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemi...
The genomic data generated from next-generation sequencing (NGS) provides nucleotide-level resolution of bacterial genomes which is critical for disease surveillance and the implementation of prevention strategies to interrupt the spread of antimicrobial resistance (AMR) bacteria. Infection with AMR...
Canine distemper virus (CDV) is a lethal viral disease of carnivores which is considered to be a serious threat to domestic and wild species. Despite the widespread use of vaccines, CDV still occurs in vaccinated animals and current vaccines does not guarantee complete protection. In this study, a t...
Inference of effective population size from genomic data can provide unique information about demographic history and, when applied to pathogen genetic data, can also provide insights into epidemiological dynamics. The combination of nonparametric models for population dynamics with molecular clock...
Hepatitis B is a viral infection that has a high prevalence in Indonesia. The Ministry of Health of Indonesia has conducted a national vaccination program for hepatitis B. In order to evaluate the success of the hepatitis B vaccination in Indonesia, a community study based on basic health research (...
Rabbit haemorrhagic disease (RHD) is a significant and debilitating viral disease affecting lagomorphs. In September 2020, Singapore reported its first cases of RHD virus (RHDV) infection in domesticated rabbits. The initial findings reported that the outbreak strain belonged to genotype GI.2 (RHDV2...
Infectious bronchitis virus (IBV) is distributed worldwide and causes significant losses in the poultry industry. In recent decades, lineages GI-19 and GI-7 have become the most prevalent IBV strains in China. However, the molecular evolution and phylodynamics of the lineage GI-7 IBV strains remain...
Coronavirus disease 2019 (COVID-19) has caused an enormous loss of life worldwide. The spike protein of the severe acute respiratory syndrome coronavirus 2 is the cause of its virulence. Bamlanivimab, a recombinant monoclonal antibody, has been used alone or in combination with etesevimab to provide...
() is an important food-borne zoonotic pathogen that causes swine streptococcosis, which threatens human health and brings economic loss to the swine industry. Three-quarters of human infections are caused by serotype 2. A retrospective analysis of human cases in Shenzhen, a megacity in China, wit...
Listeriosis, caused by infection with (), is a relatively rare but severe disease with one of the highest mortality rates among bacterial foodborne illnesses. A better understanding on the degree of clustering, the temporal distribution of the clusters, and their association with the various food...
Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and transmission patterns of outbreaks and detect the emerg...
Usutu virus (USUV) is an emerging mosquito-borne Flavivirus, with birds as the main zoonotic reservoir. Humans are accidental hosts and mostly develop mild or even asymptomatic infections, although severe complications such as encephalitis can also arise. Detailed characterization of the pathogen's...
Prolonged infections of immunocompromised individuals have been proposed as a crucial source of new variants of SARS-CoV-2 during the COVID-19 pandemic. In principle, sustained within-host antigenic evolution in immunocompromised hosts could allow novel immune escape variants to emerge more rapidly,...
Understanding disease burden and transmission dynamics in resource-limited, low-income countries like Nepal are often challenging due to inadequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the...
Influenza A viruses (IAVs) of the H1N1 classical swine lineage became endemic in North American swine following the 1918 pandemic. Additional human-to-swine transmission events after 1918, and a spillover of H1 viruses from wild birds in Europe, potentiated a rapid increase in genomic diversity via...
is an important zoonotic pathogen that is frequently identified in dairy farming systems. An increase in antibiotic resistance has led to inadequate results of treatments, with impacts on animal and human health. Here, the phenotypic and genotypic susceptibility patterns of isolates from dairy catt...
Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome sequences sampled within Mozambique were phylogenetically analy...
The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome...
We evaluated the added value of infection control-guided, on demand, and locally performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic sequencing to support outbreak investigation and control in acute-care settings. This 18-month prospective molecular epidemiology study was con...
(ISKNV) is a species within the genus (family Iridoviridae), which causes high mortality disease in many freshwater and marine fish species. ISKNV was first reported in Asia and is an emerging threat to aquaculture with increasing global distribution, in part due to its presence in ornamental fish...
Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patte...
Globally, the human respiratory syncytial virus (RSV) is one of the major causes of lower respiratory tract infections (LRTIs) in children. The scarcity of complete genome data limits our understanding of RSV spatiotemporal distribution, evolution, and viral variant emergence. Nasopharyngeal samples...
Bayesian phylogeographic inference is a powerful tool in molecular epidemiological studies, which enables reconstruction of the origin and subsequent geographic spread of pathogens. Such inference is, however, potentially affected by geographic sampling bias. Here, we investigated the impact of samp...
Influenza A viruses are a major pathogen that causes significant clinical and economic harm to many animals. In Indonesia, the highly pathogenic avian influenza (HPAI) H5N1 virus has been endemic in poultry since 2003 and has caused sporadic deadly infections in humans. The genetic bases that determ...
subsp. (MAP) is the pathogen responsible for paratuberculosis or Johne's Disease (JD) in ruminants, which is responsible for substantial economic losses worldwide. MAP transmission primarily occurs through the fecal-oral route, and the introduction of an MAP infected animal into a herd is an import...
Precise public health and clinical interventions for the COVID-19 pandemic has spurred a global rush on SARS-CoV-2 variant tracking, but current approaches to variant tracking are challenged by the flood of viral genome sequences leading to a loss of timeliness, accuracy, and reliability. Here, we d...
The recent increase in monkeypox (MPX) cases has attracted attention of public health authorities due to its quick spread and transmission across non-endemic regions. This outbreak, unlike previous ones, displays different epidemiological features and transmission dynamics, which appear to be largel...
Coronaviruses have a broad host range and exhibit high zoonotic potential. In this chapter, we describe their genomic organization in terms of encoded proteins and provide an introduction to the peculiar discontinuous transcription mechanism. Further, we present evolutionary conserved genomic RNA se...
To better understand the factors underlying the continued incidence of clinical episodes of falciparum malaria in E-2025 countries targeting elimination, we characterized the molecular epidemiology of disease transmission after a clonal outbreak in Ecuador. Here we study disease transmission by doc...
Researchers studying the evolution of viral pathogens and other organisms increasingly encounter and use large and complex data sets from multiple different sources. Statistical research in Bayesian phylogenetics has risen to this challenge. Researchers use phylogenetics not only to reconstruct the...
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resultin...
Extra-intestinal pathogenic Escherichia coli (ExPEC) are a leading cause of bloodstream and urinary tract infections worldwide. Over the last two decades, increased rates of antibiotic resistance in E. coli have been reported, further complicating treatment. Worryingly, specific lineages expressing...
With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of...
Mansonella perstans is among the most neglected of the neglected tropical diseases and is believed to cause more human infections than any other filarial pathogen in Africa. Based largely upon assumptions of limited infection-associated morbidity, this pathogen remains understudied, and many basic q...
Coinfection with two SARS-CoV-2 viruses is still a very understudied phenomenon. Although next generation sequencing methods are very sensitive to detect heterogeneous viral populations in a sample, there is no standardized method for their characterization, so their clinical and epidemiological imp...
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic since 2019. Variants of concern (VOCs) declared by the World Health Organization require continuous monitoring because of their possible changes in transmissibility, virulence, and antigenicity....
Salmonella Paratyphi A, the primary etiology of paratyphoid, is estimated to cause 3.4 million infections annually, worldwide. With rising antimicrobial resistance and no licensed vaccines, genomic surveillance is key to track and monitor transmission, but there is currently no reliable genotyping f...
In recent years, whole genome sequencing (WGS) in combination with bioinformatic analyses has become state of the art in evaluating the pathogenicity/resistance potential and relatedness of bacteria. WGS analysis thus represents a central tool in the investigation of the resistance and virulence pot...
Whole-genome sequencing (WGS) is an approach for studying and analysing the entire genomic sequence of pathogens. It provides the most comprehensive characterization of an organism's genetic make-up. In January 2020, scientists used next-generation sequencing (NGS) as one of several sequencing techn...
Since their introduction in 1859, European rabbits () have had a devastating impact on agricultural production and biodiversity in Australia, with competition and land degradation by rabbits being one of the key threats to agricultural and biodiversity values in Australia. Biocontrol agents, with th...
Corynebacterium striatum has recently received increasing attention due to its multiple antimicrobial resistances and its role as an invasive infection/outbreak agent. Recently, whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) has been used in epidemiological studi...
The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 101 immunologically distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mu...
Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencin...
Mycobacterium tuberculosis whole-genome sequencing (WGS) has been widely used for genotypic drug susceptibility testing (DST) and outbreak investigation. For both applications, Illumina technology is used by most public health laboratories; however, Nanopore technology developed by Oxford Nanopore T...
Though detection of transmission clusters of methicillin-resistant Staphylococcus aureus (MRSA) infections is a priority for infection control personnel in hospitals, the transmission dynamics of MRSA among hospitalized patients with bloodstream infections (BSIs) has not been thoroughly studied. Who...
Human Coronaviruses (hCoVs) belongs to the enormous and dissimilar family of positive-sense, non-segmented, single-stranded RNA viruses. The RNA viruses are prone to high rates of mutational recombination resulting in emergence of evolutionary variant to alter various features including transmissibi...
Listeria monocytogenes has been implicated in numerous outbreaks and related deaths of listeriosis. In food production, L. monocytogenes occurs in raw food material and above all, through postprocessing contamination. The use of next-generation sequencing technologies such as whole-genome sequencing...
SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility da...
The Black Death, a notorious devastating pandemic caused by Yersinia pestis infection during the 14th century, posed a formidable challenge to human immune defenses. A new article by Klunk et al. reports that a variant in an antigen-processing gene may have favored survival during the plague and may...
Studying the genomic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may help determine outbreak clusters and virus transmission advantages to aid public health efforts during the pandemic. Thus, we tracked the evolution of SARS-CoV-2 by variant epidemiology, breakthrough i...
() is one of the most common community-associated pathogens responsible for pneumonia in children. This retrospective study aimed to investigate the molecular characteristics of isolated from children with community-acquired pneumonia (CAP) under 5 years in Chengdu, China. Molecular characteristics...
Monitoring the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is an important public health objective. We investigated how the Gamma variant was established in New York City (NYC) in early 2021 in the presence of travel restrictions that aimed to preven...
The global effort to sequence millions of SARS-CoV-2 genomes has provided an unprecedented view of viral evolution. Characterizing how selection acts on SARS-CoV-2 is critical to developing effective, long-lasting vaccines and other treatments, but the scale and complexity of genomic surveillance da...
Methicillin-resistant Staphylococcus aureus (MRSA) rates have remained relatively low in Finland. In Southwest Finland, however, annual MRSA incidence increased from 12 to 25/100,000 between 2007 and 2016 with spa t172 strain causing one fourth (237/983) of all cases. This provoked us to study the m...
Getah virus (GETV) mainly causes disease in livestock and may pose an epidemic risk due to its expanding host range and the potential of long-distance dispersal through animal trade. Here, we used metagenomic next-generation sequencing (mNGS) to identify GETV as the pathogen responsible for reemergi...
Whole genome sequencing (WGS) is a powerful tool to analyze bacterial genomes rapidly, and can be useful to study and detect AMR genes. We carried out WGS on a group of ( = 30), sampled from healthy animals and farm environment in four pigsties in northern Italy. Two × 250bp paired end sequencing s...
SARS-CoV-2 (SARS2) regularly mutates resulting to variants of concern (VOC) which have higher virulence and transmissibility rates while concurrently evading available therapeutic strategies. This highlights the importance of amino acid mutations occurring in the SARS2 spike protein structure since...
Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host adaptation, expansion, and dissemination are limited. is a major bacterial pathogen of humans and a leading cause...
The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on public health measures, architectural design, and urban resilien...
Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. We aimed to characterise the population and AMR mechanisms of Salmonella with whole genome sequencing (WGS) and compare it with laboratory surveillance methods. The serotype, multilocus sequence type, AMR g...
Klebsiella pneumoniae often causes life-threatening infections in patients globally. Despite its notability, little is known about potential nosocomial outbreak and spread of K. pneumoniae among pediatric patients in low- and middle-income countries. Ninety-eight K. pneumoniae strains isolated from...
Viral genomic surveillance has been a critical source of information during the COVID-19 pandemic, but publicly available data can be sparse, concentrated in wealthy countries, and often made public weeks or months after collection. We used publicly available viral genomic surveillance data submitte...
is an emerging species and has increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole-ge...
Whooping cough (pertussis) is a highly contagious respiratory disease caused by the bacterium Despite high vaccine coverage, pertussis has re-emerged in many countries including Australia and caused two large epidemics in Australia since 2007. Here, we undertook a genomic and phylogeographic study...
Invasive listeriosis, caused by , is a severe foodborne infection, especially for immunocompromised individuals. The aim of our investigation was the identification and analysis of listeriosis outbreaks in Germany with smoked and graved salmon products as the most likely source of infection using wh...
This study describes a large nosocomial outbreak of infections (CDI) dominated by ribotype (RT) 046 in a Swedish hospital. The present study aimed to examine the pathogenicity of this RT, explore epidemiological links by whole genome sequencing (WGS), and evaluate different interventions implemente...
After FC428 was first found in Japan, ceftriaxone-resistant strains disseminated globally, and the gonococcal resistance rate increased remarkably. Epidemiological investigations are greatly significant for the analysis of antimicrobial resistance (AMR) trends, molecular features and evolution. To...
carbapenemase (KPC)-producing are prevalent worldwide and pose an alarming threat to public health. The incidence and transmission of gene via horizontal gene transfer (e.g. transposition) have been well documented. However, the dynamics of transposon structure bearing and their exact effects on...
(basonym ) is a bacterial enteropathogen associated with cases of infection that can result in pseudomembranous colitis, rapid fluid loss, and death. For decades following its isolation, was thought to be a solely nosocomial pathogen, being isolated from individuals undergoing antimicrobial therap...
causes healthcare-associated infections worldwide. Capsular polysaccharide (CPS) is shown an important virulence factor of both and . Capsule locus 2 (KL2) for CPS is the most common KL type and is associated with carbapenem resistance. It is unclear whether KL2 is related to the clinical outcome...
bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasiveness. In Nigeria, the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole-geno...
Clinical isolates that produce extended-spectrum β-lactamases (ESBLs) have been increasingly reported at a global scale. However, comprehensive data on the molecular epidemiology of ESBL-producing strains are limited and few studies have been conducted in non-outbreak situations.We used whole-genom...
Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and...
Genomic surveillance is important for pandemic preparedness. By deep sequencing of wastewater samples, we monitored the genetic dynamics of circulating SARS-CoV-2 virus variants in Austria from December 2020 to February 2022. We show how wastewater-based epidemiology enables robust quantification of...
, an environmental yeast widely used in industry and agriculture, is also an opportunistic pathogen resistant to multi-antifungals. During the national surveillance in China, has been documented from various hospitals and regions. At present, the molecular epidemiology of invasive infections caused...
Newcastle disease caused by Newcastle disease virus (NDV) is one of the most serious threats to chickens and has two clinical forms, typical and atypical, caused by velogenic and lentogenic strains, respectively. To control the epidemic, many vaccines against velogenic class II NDVs have been introd...
Malaria outbreaks are important public health concerns that can cause resurgence in endemic regions approaching elimination. We investigated a Plasmodium falciparum outbreak in Attapeu Province, Laos, during the 2020-21 malaria season, using genomic epidemiology methods to elucidate parasite populat...
Coxsackievirus B5 (CVB5) is an important enterovirus B species (EV-Bs) type. We used the full-length genomic sequences of 53 viral sequences from the national hand, foot, and mouth disease surveillance network in the Chinese mainland (2001-2021). Among them, 69 entire coding region nucleotide seque...
The COVID-19 pandemic continues to affect several countries. One of the best ways to control its spread is the timely identification of infected patients for isolation and quarantine. While an episode of infection lasts an average of 8-10 days from the onset of symptoms, there is literature describi...
Limiting outbreaks in long-term care facilities (LTCFs) is a cornerstone strategy to avoid an excess of COVID-19-related morbidity and mortality and to reduce its burden on the health system. We studied a large outbreak that occurred at an LTCF, combining methods of classical and genomic epidemiolog...
Data from the past decade indicates that Clostridioides difficile infection (CDI) is not only a nosocomial infection but is also increasingly recognized as a disease in the community. We aimed to study community-onset (CO) CDI in the various age groups in south Serbia with its clinical characteristi...
Salmonella infections represent an important public health problem. In 2018, a multistate outbreak of S. enterica subsp. enterica serovar Thompson infection associated with contaminated chocolate cakes in schools was reported in South Korea. In this study, we sequenced the 37 S. Thompson strains iso...
In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon...
Clostridioides difficile infection (CDI) is an important cause of diarrhea in hospitals worldwide. The incidence of CDI in Latin America has not yet been standardized. To fill this gap, the present study performed a daily active surveillance, for three months, between April to July of 2021, at a qua...
, due to its long survival time in a hospital environment, is considered to be one of the most frequent factors in healthcare-associated infections. Patient care requires not only rapid and accurate diagnosis, but also knowledge of individual risk factors for infections, e.g., with , in various clin...
is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, infection can lead to fulm...
Genomic epidemiology has guided research and policy for various viral pathogens and there has been a parallel effort towards using genomic epidemiology to combat diseases that are caused by eukaryotic pathogens, such as the malaria parasite. However, the central concept of viral genomic epidemiology...
Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adapta...
Rice stripe virus (RSV) is one of the most important viral pathogens of rice in East Asia. The origin and dispersal of RSV remain poorly understood, but an emerging hypothesis suggests that: (i) RSV originates from Yunnan, a southwest province of China; and (ii) some places of eastern China have act...
The species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by strains recovered from animals and the environme...
Clostridioides difficile infection (CDI) in patients with inflammatory bowel disease (IBD) is of increasing concern. This study aimed to investigate the molecular epidemiology and antimicrobial susceptibilities of toxigenic C. difficile isolated from IBD patients and to evaluate the risk factors for...
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing inte...
Global SARS-CoV-2 genomic surveillance efforts have provided critical data on the ongoing evolution of the virus to inform best practices in clinical care and public health throughout the pandemic. Impactful genomic surveillance strategies generally follow a multi-disciplinary pipeline involving cli...
The strains associated with foodborne Thompson outbreaks in Korea have not been identified. Therefore, we characterized S. Thompson strains isolated from chocolate cakes linked to foodborne outbreaks in Korea. A total of 56 strains were isolated from preserved cake products, products in the supply...
Klebsiella pneumoniae is an opportunistic pathogen that causes serious infections in humans and animals. However, the availability of epidemiological information on clinical mastitis due to K. pneumoniae is limited. To acquire new information regarding K. pneumoniae mastitis, data were mined about K...
Multilevel genome typing (MGT) enables the genomic characterization of bacterial isolates and the relationships among them. The MGT system describes an isolate using multiple multilocus sequence typing (MLST) schemes, referred to as levels. Thus, for a new isolate, sequence types (STs) assigned at m...
Throughout the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, healthcare workers (HCWs) have faced risk of infection from within the workplace via patients and staff as well as from the outside community, complicating our ability to resolve transmission chains in order to inf...
Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynami...
Sequencing of the gene of methicillin-resistant Staphylococcus aureus (MRSA) is used for assigning types to e.g., detect transmission and control outbreaks. Traditionally, typing is performed by Sanger sequencing but has in recent years been replaced by whole-genome sequencing (WGS) in some labor...
To investigate the source in an outbreak of carbapenem-resistant (CRA) in a general hospital due to contamination of a laundry evaporative cooler and the laundry environment using multilocus sequence typing (MLST). For CRA culture, clinical samples were collected from infected patients and close co...
Clinical research studies have navigated many changes throughout the COVID-19 pandemic. We sought to describe the pandemic's impact on research operations in the context of a clinical genomics research consortium that aimed to enroll a majority of participants from underrepresented populations. We i...
New variants of SARS-CoV-2 continue to evolve. The novel SARS-CoV-2 variant of concern (VOC) B.1.1.529 (Omicron) was particularly menacing due to the presence of numerous consequential mutations. In this study, we reviewed about 12 million SARS-CoV-2 genomic and associated metadata using extensive b...
Staphylococcus epidermidis is an emerging pathogen causing infant pyelonephritis. There is a lack of genomic data on Staphylococcus epidermidis as the etiology of pyelonephritis and its resistant determinants. In this study, we have conducted a genomic and microbiologic investigation of an S. epider...
The main protease (M) of SARS-CoV-2 is essential for viral replication and has been the focus of many drug discovery efforts since the start of the COVID-19 pandemic. Nirmatrelvir (NTV) is an inhibitor of SARS-CoV-2 M that is used in the combination drug Paxlovid for the treatment of mild to moderat...
Mosquito-borne diseases such as malaria and dengue are global severe public health threats. Due to the lack of efficient control methods, alternative approaches to decreasing arboviral transmitted diseases are prioritized to reduce morbidity and mortality in every endemic region. Mosquito midgut bac...
Carbapenem-heteroresistant isolates can be misclassified as susceptible by in vitro susceptibility tests, leading to treatment failure. The underlying mechanisms of heteroresistance, where the bacterial isolate harbors both resistant and susceptible subpopulations, are poorly understood. The aim of...
This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program. COVID-19 samples that tested positive by reverse transcription polymerase chain reaction and with cycle thresho...
subsp. serovar Dublin (. Dublin) is a zoonotic pathogen causing infections in animals, especially in cattle. In this study, we report draft genome sequences of four . Dublin isolated between 1956 and 1957 from cattle and fox in Poland. Whole genome sequencing was performed on the Illumina platform...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, emanated from the Wuhan Province in China and rapidly spread across the globe causing extensive morbidity and mortality rate, and affecting the global economy and livelihoods. Contrary to early predictio...
The intracellular bacterium inhibits virus replication and is being harnessed around the world to fight mosquito-borne diseases through releases of mosquitoes carrying the symbiont. strains vary in their ability to invade mosquito populations and suppress viruses in part due to differences in thei...
serovar Typhimurium (. Typhimurium) comprises a group of closely related human and animal pathogens that account for a large proportion of all infections globally. The epidemiological record of . Typhimurium in Europe is characterized by successive waves of dominant clones, each prevailing for appr...
The soaring resistance of to fluoroquinolones in PR China has substantially limited the application of these antimicrobials, especially in those clinical settings that were threatened by persistent carbapenem-resistant (CRKP), necessitating strict implementation of antimicrobial stewardship and ac...
is a lactic acid bacterium that confers beneficial health effects in humans. However, lately, a number of strains have been linked to the spread of nosocomial infections in the hospital environment. Therefore, any potential commercial usage of isolates should be preceded by an assessment of infect...
Cholera caused by Vibrio cholerae O139 was first reported in Bangladesh and India in 1992. To determine the genomic epidemiology and origins of O139 in China, we sequenced 104 O139 isolates collected from Zhejiang Province, China, during 1994-2018 and compared them with 57 O139 genomes from other co...
Nontyphoidal salmonellosis is the leading reported foodborne illness in Florida. Although the diversity of serotypes circulating in Florida has been identified, the geographical characteristics of the major serotypes are poorly described. Here we examined the geospatial patterns of 803 whole-genome...
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for causing Coronavirus Disease-2019 (COVID-19), a heterogeneous clinical condition that manifests varying symptom severity according to the demographic profile of the studied population. While many studies have focused on t...
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been a continuing source of hospital-acquired infection and outbreaks. At Akershus University Hospital in Norway, traditional contact tracing has been combined with whole-genome sequencing (WGS) surveillance in real-time to investigate...
An unusual increase in Salmonella enterica serovar Paratyphi A infection rate in Japanese travelers returning from Myanmar was observed in 2015. We analyzed epidemiologic data of returned travelers with enteric fever from 2005-2019. We also analyzed 193 Salmonella Paratyphi A isolates, including 121...
Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in v...
Bovine viral diarrhea virus (BVDV) is a worldwide distributed pathogen of livestock classified into three species, BVDV-1 (Pestivirus A), BVDV-2 (Pestivirus B), and HoBi-like pestivirus (HoBiPeV; Pestivirus H). Despite being considered endemic in several regions of the Americas, the spatiotemporal d...
Influenza A viruses (IAV) circulate endemically among many wild aquatic bird populations that seasonally migrate between wintering grounds in southern latitudes to breeding ranges along the perimeter of the circumpolar arctic. Arctic and subarctic zones are hypothesized to serve as ecologic drivers...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/coronavirus disease 2019 (COVID-19) pandemic has highlighted an important role for efficient surveillance of microbial pathogens. High-throughput sequencing technologies provide valuable surveillance tools, offering opportunities to co...
Genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) could transform outbreak investigations, but its clinical introduction is hampered by the lack of automated data analysis tools to rapidly and accurately define transmission based on sequence relatedness. We aimed to evaluate...
Island communities are interesting study sites for microbial evolution during epidemics, as their insular nature reduces the complexity of the population's connectivity. This was particularly true on Reunion Island during the first half of 2021, when international travel was restricted in order to m...
Data sharing in research is fraught with controversy. Academic success is premised on competitive advantage, with research teams protecting their research findings until publication. Research funders, by contrast, often require data sharing. Beyond traditional research and funding requirements, surv...
Genomic Epidemiology (genEpi) is a branch of public health that uses many different data types including tabular, network, genomic, and geographic, to identify and contain outbreaks of deadly diseases. Due to the volume and variety of data, it is challenging for genEpi domain experts to conduct data...
No abstract available
We report SARS-CoV-2 genomic surveillance results between Belo Horizonte, Brazil's third and fourth case waves. Samples were obtained through a routine university monitoring COVID-19 program from the 9th to the 22nd epidemiological weeks (March and June 2022). We identified ten samples from the BA.1...
The chikungunya virus (CHIKV) is a mosquito-borne virus of the family Togaviridae transmitted to humans by spp. mosquitoes. In Brazil, imported cases have been reported since June 2014 through two independent introductions, one caused by Asian Lineage in Oiapoque, Amapá state, North Region, and ano...
Since the onset of the COVID-19 pandemic, no viral genome sequences of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been documented from the Republic of Moldova, a developing country geographically located in Eastern Europe between Romania and Ukraine. Here, we report the an...
An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemente...
The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and raci...
Genomic technologies have led to tremendous gains in understanding how pathogens function, evolve and interact. Pathogen diversity is now measurable at high precision and resolution, in part because over the past decade, sequencing technologies have increased in speed and capacity, at decreased cost...
Vancomycin-resistant enterococci (VRE) are one of the most important bacterial causes of healthcare-associated infections (HAIs). In China, the detection rate of VRE Enterococcus faecium (VREfm) is low, although VREfm had a high prevalence in our hospitals between 2013-2015. In this study, we used m...
The COVID-19 pandemic remains a global public health concern. Advances in sequencing technologies has allowed for high numbers of SARS-CoV-2 whole genome sequence (WGS) data and rapid sharing of sequences through global repositories to enable almost real-time genomic analysis of the pathogen. WGS da...
Genomic epidemiology is now widely used for viral outbreak investigations. Still, this methodology faces many challenges. First, few methods account for intra-host viral diversity. Second, maximum parsimony principle continues to be employed for phylogenetic inference of transmission histories, even...
Canine parvovirus is a member of the Carnivore protoparvovirus 1 species that, after a relatively recent origin, has reached a worldwide distribution. Like other ssDNA viruses, it is featured by a remarkable evolutionary rate and thus genetic variability. CPV-2 is responsible for a severe systemic i...
Healthcare-associated SARS-CoV-2 infections need to be explored further. Our study is an analysis of hospital-acquired infections (HAIs) and ambulatory healthcare workers (aHCWs) with SARS-CoV-2 across the pandemic in a Belgian university hospital. We compared HAIs with community-associated infectio...
To define bacterial aetiology of neonatal sepsis and estimate the prevalence of neonatal infection from maternal genital tract bacterial carriage among mother-newborn pairs. We carried out a cross-sectional study of newborns with clinical sepsis admitted to three hospitals in the Gambia neonatal war...
Influenza A virus (IAV) is widespread in wild bird reservoirs. Sixteen hemagglutinin subtypes are associated with wild waterfowl hosts; some subtypes are isolated infrequently, one of which is H12 IAV. In this study, we detected three H12 IAVs from and in Poyang Lake, China, in 2018, one of which...
Dengue is the fastest spreading arboviral disease, posing great challenges on global public health. A reproduceable and comparable global genotyping framework for contextualizing spatiotemporal epidemiological data of dengue virus (DENV) is essential for research studies and collaborative surveillan...
Hospital transmission of SARS-CoV-2 has proved difficult to control, with healthcare-associated infections troublesome throughout. To understand factors contributing to hospital transmission of infections, which is necessary for containing spread. An outbreak of 56 staff and patient cases of COVID-1...
The coxsackievirus A24 variant (CVA24v) has raised a remarkable concern because of its main etiological role in acute hemorrhagic conjunctivitis. We conducted a retrospective study to summarize CVA24v isolated from acute hemorrhagic conjunctivitis outbreaks and acute flaccid paralysis surveillance i...
Listeria monocytogenes is a life-threatening foodborne pathogen. Here, we report the genomic characterization of a nationwide dataset of 411 clinical and 82 food isolates collected in Taiwan between 2014 and 2019. The observed incidence of listeriosis increased from 0.83 to 7 cases per million popul...
Legionella pneumophila is the main cause of a severe pneumonic illness known as Legionnaires' disease and is a global public health threat. Whole-genome sequencing (WGS) can be applied to trace environmental origins of L pneumophila infections, providing information to guide appropriate intervention...
Methicillin-susceptible Staphylococcus aureus (MSSA) is a more prevalent neonatal intensive care unit (NICU) pathogen than methicillin-resistant S. aureus (MRSA). However, the introduction and spread of MSSA, the role of systematic decolonization, and optimal infection prevention and control strateg...
To reduce the high rates of morbidity and mortality caused by methicillin-resistant (MRSA) strains, it is essential to prevent their transmission. This can be achieved through molecular surveillance of the infecting strains, for which the detection of the entry of new strains, the analysis of antim...
Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome...
Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria....
Ducks, the natural reservoir of avian influenza virus (AIV), act as reassortment vessels for HPAI and low pathogenic avian influenza (LPAI) virus for domestic and wild bird species. In Bangladesh, earlier research was mainly focused on AIV in commercial poultry and live bird markets, where there is...
Invasive group B Streptococcus (GBS) infections are increasing among adults with underlying health conditions; however, clinical manifestations and serotype distribution remain unclear. This study investigated the molecular characteristics and antimicrobial resistance of invasive GBS in Korean adult...
Monkeypox, caused by the monkeypox virus (MPXV), is a zoonotic disease endemic mainly in West and Central Africa. As of 27 September 2022, human monkeypox has occurred in more than 100 countries (mostly in non-endemic regions) and caused over 66,000 confirmed cases, which differs from previous epide...
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results s...
Rhinovirus (RV) is a common cause of respiratory illness in all people, including those experiencing homelessness. RV epidemiology in homeless shelters is unknown. We analyzed data from a cross-sectional homeless shelter study in King County, Washington, October 2019-May 2021. Shelter residents or g...
is a Gram-negative, encapsulated, non-motile bacterium, which represents a global challenge to public health as one of the major causes of healthcare-associated infections worldwide. In the recent decade, the World Health Organization (WHO) noticed a critically increasing rate of carbapenem-resistan...
Viet Nam has high rates of antimicrobial resistance (AMR) but little capacity for genomic surveillance. This study used whole genome sequencing to examine the prevalence and transmission of three key AMR pathogens in two intensive care units (ICUs) in Hanoi, Viet Nam. A prospective surveillance stud...
In the last five years, the prevalence of monkeypox has been increasing both in the regions considered endemic for the disease (West and Central Africa) and worldwide. Indeed, in July 2022, the World Health Organization declared the ongoing global outbreak of monkeypox a public health emergency of i...
BackgroundTracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achiev...
Several individuals reported gastrointestinal symptoms following meals consumed in late January 2021 at a restaurant in western Finland. We conducted a retrospective cohort study and defined a case as a person who ate at the lunch restaurant between 27 and 29 January 2021 and had stomach pain, vomit...
Cherry leaf roll virus (CLRV) is an important plant pathogen that causes severe and detrimental effects on cherry and other fruit plants. Despite recent progress in plant pathology, molecular biology, and population genetics of CLRV, the spatiotemporal spread of this virus remains poorly studied. In...
Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-4...
In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. From January to June 2...
Since the first cases of SARS-CoV-2 infection in Wuhan in December 2019, this RNA virus gave rise to different viral lineages with different virological, epidemiological and immunological properties. Here we describe the dynamics of circulation of SARS-CoV-2 lineages in an Amazonian South American F...
The SARS-CoV-2 virus infection led to millions of deaths during the COVID-19 pandemic. Hundreds of workers from several other Brazilian cities, as well as from other countries, arrive daily in Macaé to work in the oil supply chain, making this city a putative hotspot for the introduction of new vira...
Clustered cases of Pseudomonas aeruginosa infection in immunocompromised patients' wards require rapid characterization of a potential epidemic to guide investigations and identify the potential source of contamination. To design and evaluate a rapid and simple typing method for P. aeruginosa in com...
Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring...
The Mycobacterium abscessus complex causes significant morbidity and mortality among patients with Cystic Fibrosis (CF). It has been hypothesized that these organisms are transmitted from patient to patient based on genomics. However, few studies incorporate epidemiologic data to confirm this hypoth...
The emergence of the SARS-CoV-2 B.1.617.2 lineage (Delta variant) in 2021 was associated with increased case numbers and test positivity rates, including a large number of infections in fully vaccinated individuals. Here, we describe the findings of an investigation conducted in Tompkins County, New...
Since 2010 the year when it was first reported in domestic ducks in China, highly pathogenic avian influenza (HPAI) H5N8 has caused several outbreaks in different countries. The first outbreak wave was documented in South Korea and Japan in 2014 and the second wave was reported in Asian and European...
Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readines...
The use of real-time genomic epidemiology has enabled the tracking of the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), informing evidence-based public health decision making. Ukraine has experienced four waves of the Coronavirus Disease 2019 (COVID-19) between sprin...
As recently demonstrated by the COVID-19 pandemic, large-scale pathogen genomic data are crucial to characterize transmission patterns of human infectious diseases. Yet, current methods to process raw sequence data into analysis-ready variants remain slow to scale, hampering rapid surveillance effor...
In the Netherlands, whole-genome sequencing (WGS) was implemented as routine typing tool for Salmonella Enteritidis isolates in 2019. Multiple locus variable-number tandem repeat analyses (MLVA) was performed in parallel. The objective was to determine the concordance of MLVA and WGS as typing metho...
Timelines of population-level effects of viruses on humans varied from the evolutionary scale of million years to contemporary spread of viral infections. Correspondingly, these events are exemplified by: (i) emergence of human endogenous retroviruses (HERVs) from ancient germline infections leading...
Universities are vulnerable to infectious disease outbreaks, making them ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures. Here, we analyze multimodal COVID-19-associated data collected during the 2020-2021 academic year at Colorado Mesa University...
Multiple instances of flight-associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission during long-haul flights have been reported during the COVID-19 pandemic. However, comprehensive investigations of passenger risk behaviours, before, during and after the flight, are sca...
The Global Polio Eradication Initiative uses an outbreak response protocol that defines type 2 Sabin or Sabin-like virus as those with 0-5 nucleotides diverging from their parental strain in the complete VP1 genomic region. Sabin or Sabin-like viruses share highly similar genome sequences, regardles...
The SARS-CoV-2 virus has shown a remarkable ability to evolve and spread across the globe through successive waves of variants since the original Wuhan lineage. Despite all the efforts of the last 2 years, the early and accurate prediction of variant severity is still a challenging issue which needs...
In this retrospective, single-center study, we conducted an analysis of 13,699 samples from different individuals obtained from the Federal Research Center of Fundamental and Translational Medicine, from 1 April to 30 May 2020 in Novosibirsk region (population 2.8 million people). We identified 6.49...
Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We a...
Candida auris is a recently described emerging pathogen in hospital settings. Five genetic clades have been delineated, with each clade being isolated from specific geographic regions. We here describe the first transmission between 2 patients (P0 and P1) of a clade I C. auris strain imported into o...
Amino acid sequences of immunodominant domains of hemagglutinin (HA) on the surface of influenza A virus (IAV) evolve rapidly, producing viral variants. HA mediates receptor recognition, binding and cell entry, and serves as the target for IAV vaccines. Glycosylation, a post-translational modificati...
The paper presents various issues related to the increasing drug resistance of and the occurrence and spread of multidrug-resistant clones. One of the most important is the incidence and evolution of resistance mechanisms of to beta-lactam antibiotics. Chromosomal resistance to penicillins and oxy...
In September 2021, a cluster of 6 patients with nosocomial coronavirus disease 2019 (COVID-19) were identified in a transplant unit. A visitor and 11 healthcare workers also tested positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2). Genomic sequencing identified 3 separate introd...
The emergence of multidrug-resistant (MDR) bacteria harboring tet(X4), bla or mcr-1 posed a serious threat to public health. Wild birds, especially migratory birds, were considered as one of important transmission vectors for antibiotic resistance genes (ARGs) globally, however, few studies were per...
Point-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) fo...
Novel variants continue to emerge in the SARS-CoV-2 pandemic. University testing programs may provide timely epidemiologic and genomic surveillance data to inform public health responses. We conducted testing from September 2021 to February 2022 in a university population under vaccination and indoo...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global public health threat. In this study, we employed whole-genome sequencing (WGS) to determine the genomic epidemiology of a longitudinal collection of clinical CRKP isolates recovered from a large public acute care hospital in Singapore. Ph...
Clostridioides difficile infections (CDIs) in Sweden are mostly hospital-associated (HA) with limited knowledge regarding community-associated (CA) infections. Here, we investigated the molecular epidemiology of clinical isolates of CA-CDI and HA-CDI in a Swedish county. Data and isolates (n = 156)...
The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a positive-stranded RNA genome. Current proteomic studies of SARS-CoV-2 mainly focus on the proteins encoded by its genomic RNA (gRNA) or canonical subgenomic RNAs (sgRNAs). Here, we systemat...
With the ongoing COVID-19 pandemic, the emergence of the novel Omicron variant in November 2021 has created chaos around the world. Despite mass vaccination, Omicron has spread rapidly, raising concerns around the globe. The Omicron variant has a vast array of mutations, as compared to another varia...
Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness characterized by respiratory symptoms, abortion and neurological disorders. It is common worldwide and causes severe economic losses to the equine industry. The present study was aimed at investigating the incide...
Since 2020, the COVID-19 pandemic represented an important worldwide burden. Well-structured surveillance by reliable and timely genomic data collection is crucial. In this study, a genomic monitoring analysis of all SARS-CoV-2 positive samples retrieved at the Fondazione Policlinico Universitario C...
Rollout of meningococcal serogroup A conjugate vaccine in Africa started in 2010, aiming to eliminate meningitis outbreaks, in meningitis belt countries. Since then, studies have been conducted, primarily using isolates, to assess the vaccine impact on the distribution of meningococcal strains in th...
is an emerging fungal pathogen causing outbreaks in healthcare facilities. Five distinctive genomic clades exhibit clade-unique characteristics, highlighting the importance of real-time genomic surveillance and incorporating genotypic information to inform infection prevention practices and treatmen...
Carbapenem resistant Acinetobacter baumannii have limited treatment options and a propensity to cause hospital outbreaks. In recent years an increase in their detection has been observed in New Zealand. This study aimed to describe the molecular epidemiology of these isolates. This study utilised ca...
The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are p...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in Wuhan, China, is the causative agent of the coronavirus disease 2019 (COVID-19). Since its first notification in São Paulo state (SP) on 26 February 2020, more than 22,300,000 cases and 619,000 deaths were reported...
Pseudomonas aeruginosa is a key opportunistic pathogen causing a wide range of community- and hospital-acquired infections in immunocompromised or catheterized patients. Here, we report the complete genome sequence of a multidrug-resistant (MDR) P. aeruginosa DMC30b to elucidate the genetic diversit...
During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic...
Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approac...
Lillian Musila highlights a paper by Quick et al., which reported the use of portable nanopore sequencing for on-site, real-time genomic surveillance during the 2014–2016 Ebola virus epidemic.
In the Northeast of Brazil, Ceará was the second state most impacted by COVID-19 in number of cases and death rate. Despite that, the early dynamics of the pandemic in Ceará was not yet well understood due the low genomic surveillance of SARS-CoV-2 in 2020. In this study, we analyze the circulating...
Most hospitals use traditional infection prevention (IP) methods for outbreak detection. We developed the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), which combines whole-genome sequencing (WGS) surveillance and machine learning (ML) of the electronic health record (E...
Foot and mouth disease (FMD) is a major economically important viral disease of cloven-hoofed livestock globally. The FMD virus (FMDV) spreads widely in confined, cool, and humid climatic conditions. Being an RNA virus, FMDV is genetically unstable, and its genome evolution is highly influenced by m...
Since the COVID-19 pandemic began in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved with many variants of concern emerging across the world. In order to monitor the evolution of these variants in Morocco, we analyzed a total of 2130 genomes o...
Methicillin-resistant Staphylococcus aureus (MRSA) causes severe community and hospital acquired infections. Identification of staphylococcal cassette chromosome mec (SCCmec), multilocus-sequence typing, and sequencing of S. aureus protein A (spa) gene are used for MRSA typing. The aim was to invest...
To analyse the genome sequences of four archival Acinetobacter nosocomialis clinical isolates (designated AC13, AC15, AC21 and AC25) obtained from Terengganu, Malaysia in 2011 to determine their genetic relatedness and basis of antimicrobial resistance. Antimicrobial susceptibility profiles of the A...
Variant of concern (VOC) SARS-CoV-2 alpha variant (B.1.1.7) was the dominant strain in the Netherlands between March 2021-June 2021. We describe three primary school outbreaks due to the alpha variant using whole genome sequencing with evidence of large-scale transmission among children, teachers an...
Since the beginning of the 21st century, humans have experienced three coronavirus pandemics, all of which were transmitted to humans via animals. Recent studies have found that porcine deltacoronavirus (PDCoV) can infect humans, so swine enteric coronavirus (SeCoV) may cause harm through cross-spec...
Since the declaration of SARS-CoV-2 outbreak as a pandemic, the United Arab Emirates (UAE) public health authorities have adopted strict measures to reduce transmission as early as March 2020. As a result of these measures, flight suspension, nationwide RT-PCR and surveillance of viral sequences wer...
To investigate the genotype and clinical characteristics of carbapenem-resistant Enterobacteriaceae (CRE) strains in southwest China and provide information on the treatment stopping the spread of the infection. The clinical information of CRE isolates was collected from 19 hospitals in 12 cities ac...
Brazil accounted for a total number of 1,276,194 reported cases of chikungunya fever between 2014 and 2022. Additionally, since 2015, the country has experienced an increasing death toll, in which the Northeast and Southeast regions appear to report the worst scenarios. Although the CHIKV transmissi...
Only one additional specific SNP in blaTEM-135 in penicillinase-producing Neisseria gonorrhoeae (PPNG) isolates is required for TEM-135 to evolve into an ESBL that is capable of degrading all extended-spectrum cephalosporins (ESCs). Identification of the blaTEM-135 gene was achieved by performing a...
This study provides a thorough investigation of a diverse set of antimicrobial resistant (AMR) isolates collected from a broad range of ready-to-eat (RTE) food in various geographic regions of Russia ranging from Pskov to Kamchatka. Thirty-five isolates were characterized using the whole genome seq...
After a limited first wave of community transmission in March 2020 and until 2022, Western Australia was largely free of COVID-19, with cases restricted to hotel quarantine, commercial vessels, and small, infrequent community clusters. Despite the low case load setting, sequencing of wastewater samp...
The coronavirus disease 2019 (COVID-19) pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with 7 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant BA.2 sublineage has increased rapidly in Europe and Asia since January 2022. Here, we report the epidemiological and genomic analysis of a large single-source BA.2 outbreak in a housing estate. We analyzed the epidemiol...
We describe rapid detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant using targeted spike single-nucleotide polymorphism polymerase chain reaction and viral genome sequencing. This case occurred in a fully vaccinated and boosted returning traveler with mild...
Omicron was detected in South Africa for the first time at the month of November 2021, from then it expanded swiftly over the world, outcompeting other SARS-CoV-2 variants such as Delta. The toxicity, resistance to antiviral medicines, transmissibility, and vaccine-induced immunity of newly develope...
Examining the neutralizing capacity of monoclonal antibodies (MAbs) used to treat COVID-19, as well as antibodies recovered from unvaccinated, previously vaccinated, and infected individuals, against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) remains crit...
The aim of this study was to investigate and obtain insights into the appearance, spread and impact of the Omicron variants and their sub-lineages in Cyprus by analyzing 611 high-coverage full-genome sequences for the period from November 2021 until April 2022. All viruses sequenced were identified...
We propose a novel, non-discriminatory classification of monkeypox virus diversity. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause of the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B....
The field of genomic epidemiology is rapidly growing as many jurisdictions begin to deploy whole-genome sequencing (WGS) in their national or regional pathogen surveillance programmes. WGS data offer a rich view of the shared ancestry of a set of taxa, typically visualized with phylogenetic trees il...
In less than a decade, population genomics of microbes has progressed from the effort of sequencing dozens of strains to thousands, or even tens of thousands of strains in a single study. There are now hundreds of thousands of genomes available even for a single bacterial species, and the number of...
Recent years have seen a remarkable increase in the practicality of sequencing whole genomes from large numbers of bacterial isolates. The availability of this data has huge potential to deliver new insights into the evolution and epidemiology of bacterial pathogens, but the scalability of the analy...
The SARS CoV-2 D614G variant circulated in Cuba in 2020. New viral variants were detected after the opening of the border in November 2020. We show the results of the genomic surveillance in Cuba from December 28, 2020, to September 28, 2021 and their relationship to the epidemiological situation in...
In the present study, we conducted surveillance of the strains present in clinical samples from six geographical regions of Mexico (22 states) from 2004 to 2011. The serotype dominance, virulence genes, presence of pandemic O3:K6 strains, and antibiotic resistance of the isolates were investigated....
The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of...
The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,13...
Staphylococcus aureus - both meticillin-resistant S. aureus (MRSA) and meticillin-susceptible S. aureus (MSSA) - is a major cause of neonatal infections. Infection control measures have not lowered the incidence of MSSA infections to the same degree as that of MRSA infections. To investigate the tra...
The circulation of respiratory viruses poses a significant health risk among those residing in congregate settings. Data are limited on seasonal human coronavirus (HCoV) infections in homeless shelter settings. We analysed data from a clinical trial and SARS-CoV-2 surveillance study at 23 homeless s...
There has been a growing body of evidence that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) shows enhanced transmissibility and increased viral loads compared to other variants. A recent study has even suggested that respiratory samples from people infec...
The Covid-19 pandemic has demonstrated the potential of genomic technologies for the detection and surveillance of infectious diseases. Pathogen genomics is likely to play a major role in the future of research and clinical implementation of genomic technologies. However, unlike human genetics, the...
Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) var...
Early detection of bacterial transmission and outbreaks in hospitals is important because nosocomial infections can result in health complications and longer hospitalization. Current practice to detect outbreaks uses genotyping methods amplified fragment length polymorphism (AFLP) and whole genome s...
Daptomycin is a cyclic lipopeptide used in the treatment of vancomycin-resistant Enterococcus faecium (VREfm). However, the development of daptomycin-resistant VREfm challenges the treatment of nosocomial VREfm infections. Resistance mechanisms of daptomycin are not fully understood. Here, we analyz...
As the COVID-19 pandemic continues into its third year, emerging data indicates increased risks associated with SARS-CoV-2 infection during pregnancy, including pre-eclampsia, intrauterine growth restriction, preterm birth, stillbirth, and risk of developmental defects in neonates. Here, we review c...
Hospital-onset (HO) methicillin-resistant Staphylococcus aureus (MRSA) infections have declined over the past decade due to infection control strategies; community-onset (CO) and healthcare-associated community-onset (HACO) MRSA, particularly USA300, has declined less. We examined the role of commun...
Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only approach to rapidly monitor and tackle emerging variants of concern (VOC) of the COVID-19 pandemic. Such scrutiny is crucial to limit the spread of VOC that might escape the immune protection conferred b...
Sequencing viruses in many specimens is hindered by excessive background material from hosts, microbiota, and environmental organisms. Consequently, enrichment of target genomic material is necessary for practical high-throughput viral genome sequencing. Hybridization probes are widely used for enri...
We conducted an abattoir-based cross-sectional study in the five administrative regions of Northern Ghana to determine the distribution of bovine tuberculosis (BTB) among slaughtered carcasses and identify the possibility of zoonotic transmission. Direct smear microscopy was done on 438 tuberculosis...
The evolution of the emerging SARS-CoV-2 variants carrying mutations in the spike protein raises concerns about the possibility of accelerated transmission in the ever-evolving COVID-19 pandemic worldwide. AY.4.2, a sublineage of the Delta variant, was considered a variant under investigation (VUI)...
gofasta comprises a set of command-line utilities for handling alignments of short assembled genomes in a genomic epidemiology context. It was developed for processing large numbers of closely related SARS-CoV-2 viral genomes and should be useful with other densely sampled pathogen genomic datasets....
To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-b...
Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the family Tephritidae, due to their wide host range and high...
Patients with Clostridioides difficile infection (CDI) who receive treatment at outpatient infusion centers (OICs) pose a risk for spore transmission. We investigated C. difficile contamination in the environment of CDI and non-CDI patients and evaluated the effectiveness of standard cleaning. This...
Human adenoviruses (HAdVs) are prevalent worldwide and are a common cause of respiratory tract infection in people of all ages. However, little is known about HAdV infection among children with severe acute respiratory infection (SARI). The present study retrospectively analysed the molecular typing...
Mycoplasma bovis (M. bovis) is an emerging major bovine pathogen, causing economic losses worldwide in the dairy and beef industry. Whole-genome sequencing (WGS) now allows high resolution for tracing clonal populations. Based on WGS, we developed the core genome multilocus sequence typing (cgMLST)...
Melioidosis and its causative bacterium Burkholderia pseudomallei are being found in unexpected locations and bacterial genotyping is providing new insights into global spread and where and how individuals are being infected. This review summarizes recent studies covering the epidemiology, diagnosis...
Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclea...
Phylodynamic methods reveal the spatial and temporal dynamics of viral geographic spread, and have featured prominently in studies of the COVID-19 pandemic. Virtually all such studies are based on phylodynamic models that assume-despite direct and compelling evidence to the contrary-that rates of vi...
The ongoing global pandemic has sharply increased the amount of data available to researchers in epidemiology and public health. Unfortunately, few existing analysis tools are capable of exploiting all of the information contained in a pandemic-scale data set, resulting in missed opportunities for i...
The One Health approach looks after animal welfare and demands constant monitoring of the strains that circulate globally to prevent outbreaks. Anaplasma marginale is the etiologic agent of bovine anaplasmosis and is endemic worldwide. This study aimed to analyze, for the first time, the genetic div...
Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in...
Genomic surveillance allows identification of circulating SARS-CoV-2 variants. We provide an update on the evolution of SARS-CoV-2 in Rhode Island (RI). All publicly available SARS-CoV-2 RI sequences were retrieved from https://www.gisaid.org. Genomic analyses were conducted to identify variants of...
In cases of outbreaks, food business operators face inspections, recall actions and delisting by retailers. This could have happened to an Austrian meat processor whose products have been associated with a cluster of seven cases of listeriosis spread over the years 2015-2017. Sequencing of clinical...
Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly...
Genomic surveillance of SARS-CoV-2 is critical in monitoring viral lineages. Available data reveal a significant gap between low- and middle-income countries and the rest of the world. The SARS-CoV-2 sequencing costs using the Oxford Nanopore MinION device and hardware prices for data computation i...
Methicillin-resistant Staphylococcus aureus (MRSA) is the leading cause of infection in hospitalized patients and can be prevalent in humans and various animal species. In European countries, MRSA isolates belonging to clonal complex 398 have been detected at high rates in pigs. However, the prevale...
Some single-centre studies have reported that MRSA carrying the staphylococcal cassette chromosome mec (SCCmec) type IV has been increasing in bloodstream infections (BSIs) in Japan. Therefore, we conducted nationwide surveillance for MRSA BSIs to investigate the extent of such change across Japan....
In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in different regions of Lebanon and from travelers crossing the L...
The emergence and global dissemination of Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) variants of concern (VOCs) have been described as the main factor driving the Coronavirus Disease 2019 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first perio...
Retrospective evaluation of past waves of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic is key for designing optimal interventions against future waves and novel pandemics. Here, we report on analysing genome sequences of SARS-CoV-2 from the first two waves of the epidemi...
Transmission is a driver of tuberculosis (TB) epidemics in high-burden regions, with assumed negligible impact in low-burden areas. However, we still lack a full characterization of transmission dynamics in settings with similar and different burdens. Genomic epidemiology can greatly help to quantif...
Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before Febr...
Seasonal epidemics of respiratory syncytial virus (RSV) is one of the leading causes of hospitalization and mortality among children. Preventive measures implemented to reduce the spread of SARS-CoV-2, including facemasks, stay-at-home orders, closure of schools and local-national borders, and hand...
Pseudomonas aeruginosa, a common opportunistic pathogen, is one of the leading etiological agents of nosocomial infections. Many previous studies have reported the nosocomial transmission and epidemiology of P. aeruginosa infections. However, longitudinal studies regarding the dynamics of P. aerugin...
The genetic features of foodborne Salmonella have changed in recent years as multidrug-resistant (MDR) strains have become prevalent among various serovars. The recent expansion of MDR Salmonella enterica serovar Indiana sequence type 17 (ST17) poses an increasing threat to global public health, as...
Klebsiella pneumoniae is a major cause of healthcare-associated infections. In this study, we aimed to develop a rapid and simple genotyping method that can characterize strains causing nosocomial infections. The PCR-based open reading frame (ORF) typing (POT) method consists of two multiplex PCR re...
This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020-December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the...
Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student m...
There is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in geriatric settings. We performed a retrospective cohort study including pat...
Brucellosis poses a significant burden to human and animal health worldwide. Robust and harmonized molecular epidemiological approaches and population studies that include routine disease screening are needed to efficiently track the origin and spread of Brucella strains. Core genome multilocus sequ...
Genetic evolution of Rift Valley fever virus (RVFV) in Africa has been shaped mainly by environmental changes such as abnormal rainfall patterns and climate change that has occurred over the last few decades. These gradual environmental changes are believed to have effected gene migration from macro...
With the emergence and spread of SARS-CoV-2 variants, genomic epidemiology and surveillance have proven invaluable tools for variant tracking. Here, we analyzed SARS-CoV-2 samples collected from personnel located at the US/NATO bases across Afghanistan. Sequencing and phylogenetic analyses revealed...
The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. To better understand the evolution of SARS-CoV-2 early in the pandemic in the Province of Cordoba, Argentina, we performed a comparative genomic analysis of SARS-CoV-2 strains detected in survivors and non-survivors of COVID-19. We also...
Vancomycin-resistant Enterococcus (VRE) can be carried in the gut for a long period and its carriage status is associated with subsequent infections. This study aimed to investigate the frequency of intestinal VRE carriage in intensive care patients in Beijing. A multicenter, retrospective cross-sec...
The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampli...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to represent a global health emergency as a highly transmissible, airborne virus. An important coronaviral drug target for treatment of COVID-19 is the conserved main protease (M). Nirmatrelvir is a potent M inhibitor and the ant...
New Zealand's COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with...
COVID-19 is a multi-system disorder with high variability in clinical outcomes among patients who are admitted to hospital. Although some cytokines such as interleukin (IL)-6 are believed to be associated with severity, there are no early biomarkers that can reliably predict patients who are more li...
In 2017, the New York State Department of Health investigated a large Klebsiella pneumoniae outbreak in a health care facility. A retrospective analysis was conducted to compare the use of multiple molecular typing methods for characterizing the outbreak. Forty-four isolates were characterized using...
From a historically rare serotype, subsp. Dublin slowly became one of the most prevalent in cattle and raw milk cheese in some regions of France. We present a retrospective genomic analysis of 480 . Dublin isolates to address the context, evolutionary dynamics, local diversity and the genesis pro...
Transmission and outbreaks of Staphylococcus aureus among retail food highlights the need to comprehensive analysis the molecular characteristic of Staphylococcus aureus in foods. However, the information about Staphylococcus aureus in north China is limited. In this study, 97 and 28 S. aureus strai...
Evolutionary analysis using viral sequence data can elucidate the epidemiology of transmission. Using publicly available SARS-CoV-2 sequence and epidemiological data, we developed discrete phylogeographic models to interrogate the emergence and dispersal of the Delta and Omicron variants in 2021 bet...
Digital health solutions, with apps, virtual care, and electronic medical records, are gaining momentum across all medical disciplines, and their adoption has been accelerated, in part, by the COVID-19 pandemic. Personal wearables, sensors, and mobile technologies are increasingly being used to iden...
Streptococcus uberis is one of the main causative agents of ovine mastitis, however little is known about this global, environmental pathogen and its genomic mechanisms of disease. In this study, we performed genomic analysis on 46 S. uberis isolates collected from mastitis-infected sheep in Sardini...
No abstract available
Yersinia pseudotuberculosis is an enteric pathogen causing mild enteritis that can lead to mesenteric adenitis in children and septicemia in elderly patients. Most cases are sporadic, but outbreaks have already been described in different countries. We report for the first time a Y. pseudotuberculos...
A crucial barrier to the routine application of whole-genome sequencing (WGS) for infection prevention is the insufficient criteria for determining whether a genomic linkage is consistent with transmission within the facility. We evaluated the use of single-nucleotide variant (SNV) thresholds, as we...
Over the past decade, the Pacific region has experienced many arboviral outbreaks, including dengue, chikungunya, and Zika viruses. Papua New Guinea (PNG) has a high burden of arboviral diseases, but there is a paucity of knowledge about the epidemiology and circulation of these viruses in the count...
is an important foodborne pathogen with diverse serotypes. In May 2021, we investigated a gastroenteritis outbreak that occurred in China, caused by O10:K4 infection. Based on the epidemiological curve, this outbreak was identified as a homologous exposure event. A case-control study demonstrated t...
The emergence of different variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in upsurges of coronavirus disease 2019 (COVID-19) cases around the globe. Pakistan faced the fourth wave of COVID-19 from July to August 2021 with 314,786 cases. To understand...
Extended spectrum β-lactamase (ESBL)-producing is a medically important pathogen that commonly causes human nosocomial infections. Since veterinary emergency and critical care services have also significantly progressed over the last decades, there are increasing reports of ESBL-producing causing...
Dengue infection is the most prevalent arthropod-borne viral disease in subtropical and tropical regions, whose primary vector is Aedes aegypti mosquitoes. The mechanisms of dengue virus (DENV) pathogenesis are little understood because we have no good disease models. Only humans develop symptoms (d...
This report describes SARS-CoV-2 genomic surveillance conducted by the Department of Defense (DoD) Global Emerging Infections Surveillance Branch and the Next-Generation Sequencing and Bioinformatics Consortium (NGSBC) in response to the COVID-19 pandemic. Samples and sequence data were from SARS-Co...
In low- and middle-income countries (LMIC) Staphylococcus aureus is regarded as one of the leading bacterial causes of neonatal sepsis, however there is limited knowledge on the species diversity and antimicrobial resistance caused by Gram-positive bacteria (GPB). We characterised GPB isolates from...
Four porcine circoviruses (PCVs) have been discovered over time and seem to share a common history, particularly for PCV-2 and -3. Despite being reported as apparently new viruses, rapidly emerging as a threat for the worldwide swine industry, they were then proven to have been circulating and coexi...
Clostridioides difficile is a major pathogen responsible for hospital-associated diarrhoea. This study investigated the molecular epidemiology and antibiotic resistance of C. difficile isolates in five Algerian hospitals. Between 2016 and 2019, faecal specimens were collected from in-patients and we...
Since its emergence in 2019, SARS-CoV-2 has spread and evolved globally, with newly emerged variants of concern (VOCs) accounting for more than 500 million COVID-19 cases and 6 million deaths. Continuous surveillance utilizing simple genetic tools is needed to measure the viral epidemiological diver...
Acinetobacter baumannii is a very important human pathogen. Nonetheless, we know very little about nonhuman isolates of A. baumannii. Here, we determine the genomic identity of 15 Scottish cattle and pig isolates, as well as their antibiotic and virulence genetic determinants, and compare them with...
The emergence of SARS-CoV-2 variants of concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAI...
The emergence of vector-borne pathogens in novel geographic areas is regulated by the migration of their arthropod vectors. Blacklegged ticks (Ixodes scapularis) and the pathogens they vector, including the causative agents of Lyme disease, babesiosis and anaplasmosis, continue to grow in their popu...
Evolutionary analyses of viral sequences can provide insights into transmission dynamics, which in turn can optimize prevention interventions. Here, we characterized the dynamics of HIV transmission within the Mexico City metropolitan area. HIV sequences from persons recently diagnosed at the large...
Viral genomics has become crucial in clinical diagnostics and ecology, not to mention to stem the COVID-19 pandemic. Whole-genome sequencing (WGS) is pivotal in gaining an improved understanding of viral evolution, genomic epidemiology, infectious outbreaks, pathobiology, clinical management, and va...
Enterococci are gram-positive, gastrointestinal (GI) tract commensal bacteria that have recently evolved into multidrug-resistant nosocomial pathogens. Enterococci are intrinsically hardy, meaning that they can thrive in challenging environments and outlast other commensal bacteria. Further adaptati...
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supple...
Beak and feather disease virus (BFDV) infects domestic and wild psittacine species and is able to cause progressive beak, claw and feather malformation and necrosis. In addition to having an impact on the health and welfare of domesticated birds, BFDV represents a significant threat to wild endanger...
Tsetse flies can transmit various Trypanosoma spp. that cause trypanosomiasis in humans, wild animals, and domestic animals. Amplicon deep sequencing of the 12S ribosomal RNA (rRNA) gene can be used to detect mammalian tsetse hosts, and the 18S rRNA gene can be used to detect all associated eukaryot...
Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family affecting babaco in all the provinces that produce this crop in Ecuador. BabMV was recently described but it has b...
Severe infections of virulent methicillin-resistant Staphylococcus aureus (MRSA) are a serious health problem. The present study aimed to investigate clonal spread, virulence and antimicrobial resistance rates of Bulgarian MRSA isolates in 2016-2020. Molecular identification and mecA gene detection...
The human Respiratory Syncytial Virus (hRSV) is the main causative agent of acute respiratory infections (ARI), such as pneumonia and bronchiolitis. One of the factors that lead to success in viral replication is the interaction of the M2-2 protein with the ribosomal complex. This interaction is res...
Dengue fever is caused by four related dengue virus serotypes, DENV-1 to DENV-4, where each serotype comprises distinct genotypes and lineages. The last major outbreak in Mexico occurred during 2012 and 2013, when 112,698 confirmed cases were reported (DENV-1 and DENV-2 were predominant). Following...
infections cause high morbidity and mortality in intensive care unit (ICU) patients. However, there are limited data on the changes of long-term epidemiology of imipenem resistance in bacteremia among pediatric ICU (PICU) patients. A retrospective review was performed on patients with bacteremia i...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a prevalent pathogen contributing to hospital infections. Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and core-genome MLST (cgMLST) are frequently used methods to illuminate the nosocomial transmission of CRAB. In...
The emergence and international spread of neurovirulent circulating vaccine-derived polioviruses (cVDPVs) across multiple countries in Africa and Asia in recent years pose a major challenge to the goal of eradicating all forms of polioviruses. Approximately 90% of all cVDPV outbreaks are caused by t...
To describe the genomic analysis and epidemiologic response related to a slow and prolonged methicillin-resistant (MRSA) outbreak. Prospective observational study. Neonatal intensive care unit (NICU). We conducted an epidemiologic investigation of a NICU MRSA outbreak involving serial baby and staf...
Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of March 2020, but cases remained low until Janua...
Previously, we showed that coagulation factors directly cleave SARS-CoV-2 spike and promote viral entry (Kastenhuber et al., 2022). Here, we show that substitutions in the S1/S2 cleavage site observed in SARS-CoV-2 variants of concern (VOCs) exhibit divergent interactions with host proteases, includ...
Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of var Typhi ( Typhi) contribute to disease in these countries which, given the MDR potential of H5...
This paper examines the construction of maternal responsibility in transgenerational epigenetics and its implications for pregnant women. Transgenerational epigenetics is suggesting a link between maternal behaviour and lifestyle during pregnancy and the subsequent well-being of their children. For...
Free online tools for bacterial genome analyses are available for local infection surveillance at hospitals. The tools do not require bioinformatic expertise and provide rapid actionable results. Within half a year carbapenemase producing was reported in clinical samples from three patients who had...
This retrospective multi-center matched cohort study assessed the risk for severe COVID-19 (combination of severity indicators), intensive care unit (ICU) admission, and in-hospital mortality in hospitalized patients when infected with the Omicron variant compared to when infected with the Delta var...
Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prosp...
Human Parainfluenza viruses (HPIV) comprise of four members of the genetically distinct genera of Respirovirus (HPIV1&3) and Orthorubulavirus (HPIV2&4), causing significant upper and lower respiratory tract infections worldwide, particularly in children. However, despite frequent molecular d...
Foot-and-mouth disease (FMD) affects the livestock industry and socioeconomic sustainability of many African countries. The success of FMD control programs in Africa depends largely on understanding the dynamics of FMD virus (FMDV) spread. In light of the recent outbreaks of FMD that affected the No...
In 2020, a new serotype of Vibrio parahaemolyticus O10:K4 emerged and caused several outbreaks and sporadic cases in Guangxi, China. Phylogenetic analysis indicated that those strains are new variants of the sequence type 3 pandemic clone. The new serotype may become dominant, warranting enhanced in...
Knowledge of contemporary genetic composition of dengue virus (DENV) in Africa is lacking. By using next-generation sequencing of samples from the 2017 DENV outbreak in Burkina Faso, we isolated 29 DENV genomes (5 serotype 1, 16 serotype 2 [DENV-2], and 8 serotype 3). Phylogenetic analysis demonstra...
BackgroundThere is a paucity of data on community-based infection (CDI) and how these compare with inpatient CDI.AimTo compare data on the populations with CDI in hospitals vs the community across 12 European countries.MethodsFor this point-prevalence study (July-November 2018), testing sites sent...
In some neonatal units, the screening of isolates for antimicrobial-resistant organisms is a matter of routine, with theoretical benefits including the prevention or early detection of outbreaks. This study sought to use whole-genome sequencing (WGS) retrospectively to characterize the genomic epide...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic revealed a worldwide lack of effective molecular surveillance networks at local, state, and national levels, which are essential to identify, monitor, and limit viral community spread. SARS-CoV-2 variants of concern (VOCs) suc...
Bars and restaurants are high-risk settings for SARS-CoV-2 transmission. A multistate outbreak after a bar gathering in Chicago, Illinois, USA, highlights Omicron variant transmissibility, the value of local genomic surveillance and interstate coordination, vaccination value, and the potential for r...
Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), is a significant threat to the global pig industry. In this study, a novel recombinant PRRSV, SD043, was isolated from a pig farm experiencing disease in 2019. Phylogenetic analysis revealed that SD043 belonged t...
Tourist occupancy in coastal environments threatens the stability of various coastal ecosystems and is thus a cause for concern for the environmental sector. As such, it is important to perform environmental monitoring in a way that analyses and quantifies the environmental impact of coastal ecosyst...
Klebsiella pneumoniae is a major cause of opportunistic healthcare-associated infections, which are increasingly complicated by the presence of extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance. We conducted a year-long prospective surveillance study of K. pneumoniae clinical isola...
We report two clusters of SARS-CoV-2 B.1.617.2 (Delta variant) infections in a group of 41 Indian nursing students who travelled from New Delhi, India, to Belgium via Paris, France. All students tested negative before departure and had a second negative antigen test upon arrival in Paris. Upon arriv...
Clostridioides difficile infection (CDI) is a form of antibiotic-associated infectious diarrhoea resulting in significant morbidity and mortality. Community-acquired disease in low-risk individuals is increasingly recognised. There are limited New Zealand data published. To determine the incidence a...
The aim of our study is to determine the discriminatory power of the Fourier transform infrared spectroscopy (FTIR), using multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) as molecular typing references. The study included seventeen isolates (OXA-23- and OXA-58-producin...
Prisons are susceptible to outbreaks. Control measures focusing on isolation and cohorting negatively affect wellbeing. We present an outbreak of coronavirus disease 2019 (COVID-19) in a large male prison in Wales, UK, October 2020 to April 2021, and discuss control measures.We gathered case-informa...
A key task of genomic surveillance of infectious viral diseases lies in the early detection of dangerous variants. Unexpected help to this end is provided by the analysis of deep sequencing data of viral samples, which are typically discarded after creating consensus sequences. Such analysis allows...
Infection caused by carbapenem-resistant (CRE) is a global public health problem. We performed whole-genome sequencing to investigate the molecular epidemiological characteristics of local CRE infections and understand the prevalence of hypervirulent carbapenem-resistant (CRKP). Analysis of multiL...
Hepatitis B virus (HBV) comprises 9 genotypes and multiple subgenotypes that depict differences in geographic distribution, clinical outcome and response to antiviral therapy. However, the molecular epidemiology of HBV geno/subgenotypes is globally scarce. In Spain, HBV genotype D seems to be more p...
Non-cystic fibrosis bronchiectasis (BE) is a chronic structural lung condition that facilitates chronic colonization by different microorganisms and courses with recurrent respiratory infections and frequent exacerbations. One of the main pathogens involved in BE is Pseudomonas aeruginosa. To determ...
Consecutive Polish regions have become endemic for NDM-1-producing Klebsiella pneumoniae ST11, followed by K. pneumoniae ST147. Since 2017 a significant increase in NDM-positive Enterobacter hormaechei cases has been observed. To investigate the origin and character of this increase in NDM-positive...
Healthcare-associated carbapenem-resistant (CRAB) infections are a serious threat associated with global epidemic clones and a variety of carbapenemase gene classes. In this study, we describe the molecular epidemiology, including whole-genome sequencing analysis and antimicrobial susceptibility pr...
Using a combination of data from routine surveillance, genomic sequencing, and phylogeographic analysis, we tracked the spread and introduction events of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants focusing on a large university community. Here, we sequenced and analyzed 67...
The present study was initiated to understand the proportion of predominant variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in postvaccination infections during the Delta dominated second wave of coronavirus disease 2019 (COVID-19) in the Mumbai Metropolitan Region (MMR) in...
Several human pathogens exhibit distinct patterns of seasonality and circulate as pairs. For instance, influenza A virus subtypes oscillate and peak during winter seasons of the world's temperate climate zones. Alternation of dominant strains in successive influenza seasons makes epidemic forecastin...
About two out of three Ethiopians are at risk of malaria, a disease caused by the parasites Plasmodium falciparum and Plasmodium vivax. Anopheles stephensi, an invasive vector typically found in South Asia and the Middle East, was recently found to be distributed across eastern and central Ethiopia...
In our center, previous infection prevention and control (IPC) resources were concentrated on multidrug-resistant organisms other than CRAB because the rate of CRAB was stable with no evidence of outbreaks. Triggered by an increase in the baseline rate of CRAB isolated in clinical cultures, we inves...
No abstract available
COVID-19 local outbreak response relies on subjective information to reconstruct transmission chains. We assessed the concordance between epidemiologically linked cases and viral genetic profiles, in the Baixo Vouga Region (Portugal), from March to June 2020. A total of 1925 COVID-19 cases were iden...
Industrial hygienists (IH) in the oil and gas business instituted an extraordinary number of safety protocols to limit spread of SARS-CoV-2 onto offshore platforms in the Gulf of Mexico. We used genomic surveillance to provide actionable information concerning the efficacy of their efforts. Over 6 m...
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARS-CoV-2 from imported cases admitted to the Guangzhou Eighth People's Hospital, which was appointed by the Guangdong provin...
The COVID-19 pandemic continues to pose a global health concern, despite the ongoing vaccination campaigns, due to the emergence and rapid spread of new variants of the causative agent SARS-CoV-2. These variants are identified and tracked via the marker mutations they carry, and the classification s...
An ongoing outbreak of syphilis in Australia, first reported in the state of Queensland in 2011, has led to increasing cases of congenital syphilis, including several deaths. Here, we applied multi-locus sequence typing (MLST) on available Treponema pallidum PCR-positive samples from the state of Qu...
The transmission patterns and genetic diversity of dengue virus (DENV) circulating in Africa remain poorly understood. Circulation of the DENV serotype 1 (DENV1) in Angola was detected in 2013, while DENV serotype 2 (DENV2) was detected in 2018. Here, we report results from molecular and genomic inv...
The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 1...
SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants of concern (VOCs) emerge there is also a need to identify the primary circulating variants in a...
The SARS-CoV-2 pandemic led to a huge increase in global pathogen genome sequencing efforts, and the resulting data are becoming increasingly important to detect variants of concern, monitor outbreaks, and quantify transmission dynamics. However, this rapid up-scaling in data generation brought with...
Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for ge...
From 24 December 2020 to 8 February 2021, 163 cases of SARS-CoV-2 Alpha variant of concern (VOC) were identified in Chieti province, Abruzzo region. Epidemiological data allowed the identification of 14 epi-clusters. With one exception, all the epi-clusters were linked to the town of Guardiagrele: 1...
Chlorhexidine is used widely to prevent the spread of bacteria in the hospital environment. However, bacteria are increasingly becoming tolerant to chlorhexidine. Here we investigated clinical characteristics, tolerance mechanisms, and molecular epidemiology of chlorhexidine-tolerant Pseudomonas aer...
Iron/siderophore uptake may play an important role in the biofilm formation and secretion of extracellular proteins in Pseudomonas aeruginosa isolates. In the present study, the role of siderophores, heme, and iron regulatory genes in the virulence of Pseudomonas aeruginosa isolates collected from w...
The geographic distribution of the hepatitis B virus (HBV) and the hepatitis D virus (HDV) genotypes is uneven. We reconstructed the temporal evolution of HBV and HDV in Yakutia, one of the regions of Russia most affected by HBV and HDV, in an attempt to understand the possible mechanisms that led t...
Carbapenemase-producing Klebsiella pneumoniae (CP-Kpn) are a major concern for nosocomial infections. We previously reported an intensive care unit (ICU) outbreak of CP-Kpn. This study investigated the transmission pattern and genetic characteristic of CP-Kpn in the hospital during the outbreak peri...
SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In this study, we compare the dynamics of two vari...
In 2022, the burden of cholera-an acute watery diarrheal disease caused by Vibrio cholerae serogroup O1 (or more rarely O139) bacteria, which produce cholera toxin-remains high in many African and Asian countries. In the last few years, microbial genomics has made it possible to define the bacterial...
Genomic surveillance using quality-assured whole-genome sequencing (WGS) together with epidemiological and antimicrobial resistance (AMR) data is essential to characterise the circulating Neisseria gonorrhoeae lineages and their association to patient groups (defined by demographic and epidemiologic...
To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS). SARS-Co...
Two cases of epidemic situation of serogroup B meningitis in infants in Shandong Province in 2021 were investigated. Samples of cases and their close contacts were collected for isolation, culture and identification of (). The isolates were subjected to multi-locus sequence typing, outer membrane p...
The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to bette...
Early disease detection is a prerequisite for enacting effective interventions for disease control. Strains of the bacterial plant pathogen have recurrently spread to new crops in new countries causing devastating outbreaks. So far, investigation of outbreak strains and highly resolved phylogenetic...
(Kp) has emerged as a global life-threatening pathogen owing to its multidrug resistance and hypervirulence phenotype. Several fatal outbreaks of carbapenem-resistant hypervirulent Kp have been reported recently. Hypermucoviscosity (HMV) is a phenotype commonly associated with hypervirulence of Kp,...
Native American individuals in the Southwestern USA experience a higher burden of invasive disease than the general population. However, little is known about carriage in these communities. A cross-sectional study was conducted to determine the carriage prevalence, risk factors and genomic epidemi...
Getah virus is an emerging mosquito-borne animal pathogen. Four phylogenetic groups of GETV, Group I (GI), GII, GIII and GIV, were identified. However, only the GETV GIII was associated with disease epidemics suggesting possible virulence difference in this virus group. Here, we compared the genetic...
Epidemiological surveillance of bacterial pathogens requires real-time data analysis with a fast turnaround, while aiming at generating two main outcomes: (1) species-level identification and (2) variant mapping at different levels of genotypic resolution for population-based tracking and surveillan...
Using georeferenced phylogenetic trees, phylogeography allows researchers to elucidate interactions between environmental heterogeneities and patterns of infectious disease spread. Concordant with the increasing availability of pathogen genetic sequence data, there is a growing need for tools to tes...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concerning for enhanced transmission, evasion of immune responses, or associated with severe disease have motivated the global increase in genomic surveillance. In the current study, large-scale whole-genome sequencing was perform...
Early diagnosis and treatment of diseases are crucial research areas of human health. For early diagnosis, one method that has proven efficient is the detection of biomarkers which can provide real-time and accurate biological information. Most biomarker detection is currently carried out at localis...
We investigated epidemiologic and molecular characteristics of healthcare-associated (HA) and community-associated (CA) Clostridioides difficile infection (CDI) among adult patients in Canadian Nosocomial Infection Surveillance Program hospitals during 2015-2019. The study encompassed 18,455 CDI cas...
Population genomic analysis is a powerful tool to understand the evolutionary history of pathogens and the factors contributing to the success or failure of lineages. These studies have significant implications for human health, as evident from our ongoing tracking of SARS-CoV-2. In their article, G...
Understanding the development of within the triatomine vector at the molecular level should provide novel targets for interrupting parasitic life cycle and affect vectorial competence. The aim of the current study is to provide new insights into triatomines immunology through the characterization o...
The scientific response to the COVID-19 pandemic has produced an abundance of publications, including peer-reviewed articles and preprints, across a wide array of disciplines, from microbiology to medicine and social sciences. Genomics and precision health (GPH) technologies have had a particularly...
Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and transmission of IAVs in Africa are scarce, limiting Afr...
The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatm...
Introduction: The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evolved into a worldwide outbreak, with significant molecular evolution over time. Large-scale phylodynamic studies allow to map the virus spread and inform preventive strategies. Aim: This study investig...
This study aimed to investigate sites for colonization and molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital. Bacterial specimens from surface and liquid samples (n = 165) located in five rooms were collected three times every 2 months, and an...
Porcine reproductive and respiratory syndrome (PRRS) is among the most devastating diseases affecting the pig industry. Despite vaccines having been available for decades, the remarkable genetic variability of this virus, leading to poor cross-protection, has limited their efficacy, and other measur...
Over 4 million SARS-CoV-2 genomes have been sequenced globally in the past 2 years. This has been crucial in elucidating transmission chains within communities, the development of new diagnostic methods, vaccines, and antivirals. Although several sequencing technologies have been employed, Illumina...
Ebola virus (EBV) disease (EVD) is a highly virulent systemic disease characterized by an aggressive systemic inflammatory response and impaired vascular and coagulation systems, often leading to uncontrolled hemorrhaging and death. In this study, the proteomes of 38 sequential plasma samples from 1...
The incidence of syphilis has increased markedly in the past decade in high-income countries, including Australia. To date, however, genomic studies of Treponema pallidum have focused mainly on the northern hemisphere. Here, we aimed to characterise the lineages of T pallidum driving the current syp...
SARS-CoV-2 virus sequencing has been applied to track the COVID-19 pandemic spread and assist the development of PCR-based diagnostics, serological assays, and vaccines. With sequencing becoming routine globally, bioinformatic tools are needed to assist in the robust processing of resulting genomic...
The massive increase in COVID-19 infection had generated a second wave in India during May-June 2021 with a critical pandemic situation. The Delta variant (B.1.617.2) was a significant factor during the second wave. Conversely, the UK had passed through the crucial phase of the pandemic from Novembe...
Global dissemination of K. pneumoniae clones poses health hazards to the public. Genomic epidemiology studies with comprehensive data set further revealed clone divergence, showing a high complexity in evolution. Moreover, clones carrying both acquired virulent and antimicrobial-resistant genes emer...
Current microbiological methods lack the resolution to accurately identify multidrug-resistant organism (MDRO) transmission, however, whole genome sequencing can identify highly-related patient isolates providing opportunities for precision infection control interventions. We investigated the feasib...
Several common conditions have been widely recognised as risk factors for COVID-19 related death, but risks borne by people with rare diseases are largely unknown. Therefore, we aim to estimate the difference of risk for people with rare diseases comparing to the unaffected. To estimate the correlat...
A 27-year-old female white-faced saki (Pithecia pithecia) died following an onset of vomiting and ptyalism. Necropsy revealed lesions of suppurative ventriculitis, choroid plexitis, periventricular encephalitis and meningitis with intralesional gram-positive coccobacilli and paired rods. The saki al...
Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. These are modulated by contributions from the...
The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e...
The risk of complications following surgical procedures is significantly increased in patients with SARS-CoV-2 infection. However, the mechanisms underlying these correlations are not fully known. Spinal cord injury (SCI) patients who underwent reconstructive surgery for pressure ulcers (PUs) before...
The classical swine fever virus is the etiologic agent of one of the diseases with the greatest impact on swine farming worldwide. An extensive area of Brazil is considered free of the disease, but some states in Northeast Brazil have registered outbreaks since 2001. The objective of this study was...
Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the COVID-19 pandemic. Nottingham-Indonesia Collaborati...
Human respiratory pathogens have repeatedly caused lethal outbreaks in wild great apes across Africa, leading to population declines. Nonetheless, our knowledge of potential genomic changes associated with pathogen introduction and spread at the human-great ape interface remains sparse. Here, we mad...
Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved us...
To study the epidemiological and pathogenic characteristics of isolated from outbreaks cases in Guangdong Province, 2017-2020. Epidemiological characteristics of 87 outbreak events caused by were analyzed. Strains were serotyped, and then analyzed by pulsed-field gel electrophoresis (PFGE). The...
Genomic surveillance during the coronavirus disease 2019 (COVID-19) pandemic has been key to the timely identification of virus variants with important public health consequences, such as variants that can transmit among and cause severe disease in both vaccinated or recovered individuals. The rapid...
SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019. The highly contagious B.1.617.2 (Delta) variant of concern (VOC) was first identified in October 2020 in India and subsequently disseminated worldwide, later becoming the dominant lineage in the US. Understanding the local transmissi...
H5Nx highly pathogenic avian influenza viruses (HPAIVs) have caused transboundary epizootics in poultry and wild birds. In 2016, the H5N6 subtype of clade 2.3.4.4e HPAIVs caused multiple outbreaks in Asia, including China, Japan, Korea, and Vietnam. However, the geographical spread pattern of 2.3.4....
The global spread of critical-priority antimicrobial-resistant Enterobacterales by food is a public health problem. Wild-caught seafood are broadly consumed worldwide, but exposure to land-based pollution can favor their contamination by clinically relevant antimicrobial-resistant bacteria. As part...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investig...
In two "départements" in the South-West of France, bovine tuberculosis (bTB) outbreaks due to Mycobacterium bovis spoligotype SB0821 have been identified in cattle since 2002 and in wildlife since 2013. Using whole genome sequencing, the aim of our study was to clarify badger contribution to bTB tra...
spp. are among the most prevalent foodborne pathogens. Rapid identification of etiologic agents during foodborne outbreaks is of great importance. In this study, we report a traceback investigation of a outbreak in China. Metagenomic sequencing of suspected food samples was performed on MinION and...
. Carbapenem-resistant (CRAB) is the primary pathogen causing hospital-acquired infections. The spread of CRAB is mainly driven by the dissemination of resistant clones, and in Latin America, International Clones IC-1 (also known as clonal complex CC1), IC-4 (CC15) and IC-5 (CC79) are the most prev...
During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated development of testing methods, and allowed timely tracking of novel SARS-CoV-2 variants. Yet...
The world has been dealing with the SARS-COV-2 pandemic since December 2019 and a lot of effort has focused on tracking the spread of the virus by gathering information regarding testing statistics and generating viral genomic sequences. Unfortunately, there is neither a single comprehensive resourc...
Lessons learnt from the COVID-19 pandemic include increased awareness of the potential for zoonoses and emerging infectious diseases that can adversely affect human health. Although emergent viruses are currently in the spotlight, we must not forget the ongoing toll of morbidity and mortality owing...
The population structure of a set of OXA-48-producing isolates belonging to sequence type 11 (ST11 Kp-OXA) and obtained from two hospitals in Madrid in the period from 2012 to 2015 was studied by genome sequencing. Overall, 97 ST11 Kp-OXA isolates were sequenced and their population structure and d...
The prevalence of vancomycin-resistant Enterococcus faecium has increased rapidly, and in Denmark, we are facing an endemic outbreak situation in hospitals. The aim of this study was to use whole-genome sequencing (WGS) and core genome multilocus sequencing typing (cgMLST) to determine the duration...
During a surveillance study conducted to assess the occurrence and genomic landscape of critical priority pathogens circulating at the human-animal-environment interface in Brazil, as part of the Grand Challenges Explorations-New Approaches to Characterize the Global Burden of Antimicrobial Resistan...
The outbreak of Coronavirus Disease 2019 (COVID-19) at the end of 2019 turned into a global pandemic. To help analyze the spread and evolution of the virus, we collated and analyzed data related to the viral genome, sequence variations, and locations in temporal and spatial distribution from GISAID....
The Society for Craniofacial Genetics and Developmental Biology (SCGDB) held its 44th Annual Meeting in a virtual format on October 18-19, 2021. The SCGDB meeting included presentation of the SCGDB Distinguished Scientists in Craniofacial Research Awards to Drs. Paul Trainor and Jeff Bush and four s...
Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission...
Despite of the fast development of highly effective vaccines to control the current COVID-19 pandemics, the unequal distribution and availability of these vaccines worldwide and the number of people infected in the world lead to the continuous emergence of Severe Acute Respiratory Syndrome coronavir...
Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the gen...
Understanding the molecular mechanisms of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is essential for the successful development of therapeutic strategies against the COVID-19 pandemic. Numerous studies have focused on the identification of host factors and cellular pathways in...
Striped skunks (Mephitis mephitis) densely populate the human-animal interface of suburbia throughout North America. Skunks share that habitat with numerous related mesocarnivores, where increased contact, competition for shared food and water sources and other stressors contribute to increased expo...
We sought to understand how the coronavirus disease 2019 (COVID-19) pandemic has affected the well-being, clinical training, and medical education for clinical trainees in medical genetics and genomics residency and fellowship programs. All clinical genetics trainees in the Accreditation Council for...
The role Staphylococcus aureus antimicrobial resistance genes and toxins play in disease severity, management and outcome in childhood is an emerging field requiring further exploration. A prospective multisite study of Australian and New Zealand children hospitalised with S. aureus bacteraemia (SAB...
Genomic surveillance in Uganda showed rapid replacement of severe acute respiratory syndrome coronavirus 2 over time by variants, dominated by Delta. However, detection of the more transmissible Omicron variant among travelers and increasing community transmission highlight the need for near-real-ti...
Tracing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or are not perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2...
Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory; it is a gathering point for travelers and transportation from the whole country. In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 Dec...
Genomic DNA preparation is a critical step for successful fingerprinting analysis by Pulsed Field Gel Electrophoresis (PFGE). This paper presents a simple and rapid protocol to prepare DNA samples from up to 24 bacterial isolates simultaneously. It involves performing the conventional PFGE sample pr...
Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) is a common clinical problem, leading to significant morbidity and mortality, and no effective pharmacotherapy exists. The problem of ARDS causing mortality became more apparent during the COVID-19 pandemic. Biotherapeutic produc...
Methicillin-resistant (MRSA) is an important pathogen in neonatal intensive care units (NICU) that confers significant morbidity and mortality. Improving our understanding of MRSA transmission dynamics, especially among high-risk patients, is an infection prevention priority. We investigated a clus...
PulseNet International (PNI) is a global network of 88 countries who work together through their regional and national public health laboratories to track foodborne disease around the world. The vision of PNI is to implement globally standardized surveillance using whole genome sequencing (WGS) for...
From 2003 onwards, three pandemics have been caused by coronaviruses: severe acute respiratory syndrome coronavirus (SARS-CoV); middle east respiratory syndrome coronavirus (MERS-CoV); and, most recently, SARS-CoV-2. Notably, all three were transmitted from animals to humans. This would suggest that...
Salmonella spp. is a major foodborne pathogen with a wide variety of serovars associated with human cases and food sources. Nevertheless, in Europe a panel of ten serovars is responsible for up to 80% of confirmed human cases. Clustering studies by single nucleotide polymorphism (SNP) core-genome ph...
Clostridioides difficile is a major cause of nosocomial diarrhea. Several "hypervirulent" lineages such as ribotype 027 (RT027) and RT078 are of high epidemiological importance, leading to outbreaks and more severe courses of disease. An active surveillance system targeting molecular epidemiology an...
The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of SARS-CoV-2 genomes across the Bronx from March-October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling r...
Multidrug-resistant (MDR) hypervirulent Klebsiella pneumoniae (hvKp) sequence type (ST) 23 (MDR-ST23-hvKp) is emerging in China. Despite its increasing importance, this pathogen has not yet been subject to detailed genomic interrogation. We identified 28 ST23 Kp isolated from three hospitals in Chin...
Equine influenza virus (EIV) is a highly contagious pathogen of equids, and a well-known burden in global equine health. EIV H3N8 variants seasonally emerged and resulted in EIV outbreaks in the United States and worldwide. The present study evaluated the pattern of cross-regional EIV H3N8 spread an...
The novel coronavirus SARS-CoV-2 is responsible for the ongoing COVID-19 pandemic and has caused a major health and economic burden worldwide. Understanding how SARS-CoV-2 viral proteins behave in host cells can reveal underlying mechanisms of pathogenesis and assist in development of antiviral ther...
To describe the undetected circulation of an epidemic BKC-1-producing Klebsiella pneumoniae ST442 clone, occasioning the first reported outbreak of the infrequent carbapenemase BKC-1. Six hundred and forty-seven K. pneumoniae isolates (2008-2017) with reduced susceptibility to carbapenems were scree...
The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in Ne...
To analyze the spread of a novel sequence type (ST1478) of vancomycin-resistant across Canadian hospitals. Retrospective chart review of patients identified as having ST1478 VRE bloodstream infection. Canadian hospitals that participate in the Canadian Nosocomial Infection Surveillance Program (CNI...
Genomic epidemiology is important to study the COVID-19 pandemic, and more than two million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challeng...
SARS-CoV-2 variants have been emerging and are shown to increase transmissibility, pathogenicity, and decreased vaccine efficacies. The objective of this study was to determine the distribution, prevalence, and dynamics of SARS-CoV-2 variants circulating in Brazzaville, the Republic of Congo (ROC)....
Outbreaks of SARS-CoV-2 in long-term care facilities (LTCFs) cause significant morbidity and mortality. Mapping viral transmission within and between facilities by combining genomic sequencing with epidemiologic investigations enables targeting infection-control interventions. We conducted weekly su...
Streptococcus agalactiae, also known as Lancefield Group B Streptococcus (GBS), is typically regarded as a neonatal pathogen; however, several studies have shown that the bacteria are capable of causing invasive diseases in non-pregnant adults as well. The majority of documented cases were from Sout...
Acute bacterial infections are often treated empirically, with the choice of antibiotic therapy updated during treatment. The effects of such rapid antibiotic switching on the evolution of antibiotic resistance in individual patients are poorly understood. Here we find that low-frequency antibiotic...
In 2016-2017, France experienced a devastating epidemic of highly pathogenic avian influenza (HPAI) H5N8, with more than 400 outbreaks reported in poultry farms. We analyzed the spatiotemporal dynamics of the epidemic using a structured-coalescent-based phylodynamic approach that combined viral geno...
During the COVID-19 pandemic within the United States, much of the responsibility for diagnostic testing and epidemiologic response has relied on the action of county-level departments of public health. Here we describe the integration of genomic surveillance into epidemiologic response within Humbo...
The coronavirus disease 2019 (COVID-19) pandemic has already affected all realms of public healthcare and, in particular, has led to increasing use of various antibiotics to treat possible bacterial coinfections even in cases for which such infections were not confirmed clinically. This could lead t...
The coronavirus disease 2019 (COVID-19) quickly swept over the world, becoming one of the most devastating outbreaks in human history. Being the first pandemic in the post-genomic era, advancements in genomics contributed significantly to scientific understanding and public health response to COVID-...
Multidrug-resistant Pseudomonas aeruginosa (MDRP) is a waterborne pathogen that occasionally causes hospital-acquired infection in immunocompromised or critically ill patients. Urine is frequently collected to evaluate renal function or to perform hormonal examinations, but the procedure involves ri...
Nanopore sequencing and phylodynamic modeling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Cost-effective bacterial genome sequencing and variant calling on nanopore platforms would greatly enhance...
serogroup 1 (Lp1) sequence type (ST) 23 is one of the most commonly detected STs in Italy where it currently causes all investigated outbreaks. ST23 has caused both epidemic and sporadic cases between 1995 and 2018 and was analysed at genomic level and compared with ST23 isolated in other countries...
The dissemination of carbapenem-resistant and third generation cephalosporin-resistant pathogens is a critical issue that is no longer restricted to hospital settings. The rapid spread of critical priority pathogens in Brazil is notably worrying, considering its continental dimension, the diversity...
Aedes aegypti [Linnaeus in Hasselquist; yellow fever mosquito] transmits several viruses that infect millions of people each year, including Zika, dengue, yellow fever, chikungunya, and West Nile. Pathogen transmission occurs during blood feeding. Only the females blood feed as they require a bloodm...
Stenotrophomonas maltophilia is an opportunistic bacterium, contributing to different hospital-acquired infections and can be acquired from different hospital setting sources. Epidemiological study of S. maltophilia in the hospital also demonstrates the intrahospital distribution of certain strains...
Pneumocystis jirovecii is an opportunistic fungus that causes Pneumocystis pneumonia (PCP) in immunocompromised hosts. Over an 11-month period, we observed a rise in cases of PCP among kidney-transplant recipients (KTR), prompting an outbreak investigation. Clinical and epidemiologic data were colle...
PCR ribotype (RT) 017 ranks among the most successful strains of in the world. In the past three decades, it has caused outbreaks on four continents, more than other ‘epidemic’ strains, but our understanding of the genomic epidemiology underpinning the spread of RT 017 is limited. Here, we perform...
Incidences of nosocomial infections mediated by New Delhi metallo-β-lactamase (NDM) enzyme-producing are increasing globally, resulting in a great burden to public health. The carbapenem-resistant (CRE) were collected from Henan, China during 2013-2016. The -positive strains were characterized usi...
Clostridioides difficile is an important pathogen of healthcare-associated gastrointestinal infections. Recently, an increased number of C. difficile infection (CDI) surveillance data has been reported from Asia. The aim of this review is to summarize the data on the prevalence, distribution and mol...
Lumpy skin disease virus (LSDV) is of high economic importance and has spread rapidly to many European and Asian countries in recent years. LSDV was introduced to China in 2019 and have caused severe outbreaks in several provinces. Here, we detected an LSDV strain (GD01/2020) from a cattle farm with...
Clostridioides difficile is the predominant pathogen responsible for antimicrobial associated diarrhea (AAD) and health care facility-associated infectious diarrhea. The role of C. difficile in China and its impact on public health have gained attention in recent years. Most clinical C. difficile is...
Limited genomic sampling in many high-incidence countries has impeded studies of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. We investigated SARS-CoV-2 tr...
Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associa...
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread worldwide. Many variants of SARS-CoV-2 have been reported, some of which have increased transmissibility and/or reduced susceptibility to vaccines. There is an urgent need for vari...
We recently carried out a metagenomic study to determine the fecal virome of infants during their first year of life in a semirural community in Mexico. A total of 97 stool samples from nine children were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In this w...
The Amazonas was one of the most heavily affected Brazilian states by the COVID-19 epidemic. Despite a large number of infected people, particularly during the second wave associated with the spread of the Variant of Concern (VOC) Gamma (lineage P.1), SARS-CoV-2 continues to circulate in the Amazona...
SARS-CoV-2 evolution threatens vaccine- and natural infection-derived immunity as well as the efficacy of therapeutic antibodies. To improve public health preparedness, we sought to predict which existing amino acid mutations in SARS-CoV-2 might contribute to future variants of concern. We tested th...
Cryptococcus gattii (C. gattii) is a fungal pathogen that once caused an outbreak of cryptococcosis on Vancouver Island, and had spread worldwide, while few data were available in China. In this study, seven clinical isolates of C. gattii VGII were collected from 19 hospitals, Multi-locus Sequence T...
A large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metageno...
Omics-based technologies have been largely adopted during this unprecedented global COVID-19 pandemic, allowing the scientific community to perform research on a large scale to understand the pathobiology of the SARS-CoV-2 infection and its replication into human cells. The application of omics tech...
This study aims to gather observational evidence of Whole Genome Sequencing's (WGS) impact in the pathogen identification, antimicrobial resistance profiling and transmission tracking from its users' observation within the diagnostic setting of the European reference laboratories for tuberculosis. S...
Avian pathogenic E. coli (APEC) cause high first week mortality (FWM) in broiler chickens worldwide. In order to investigate the epidemiologic aspects of colibacillosis in broiler flocks it is important to develop reliable and cost-effective sampling guidelines. In this context, it is particularly i...
Here, we report a first comprehensive genomic analysis of SARS-CoV-2 variants circulating in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with respect to genomic clades and mutational patterns. As of December 2021, a total of 1669 high-coverage whole-genome s...
At the end of 2019 Wuhan witnessed an outbreak of "atypical pneumonia" that later developed into a global pandemic. Metagenomic sequencing rapidly revealed the causative agent of this outbreak to be a novel coronavirus denoted SARS-CoV-2. To provide a snapshot of the pathogens in pneumonia-associate...
The disease burden attributable to opportunistic pathogens depends on their prevalence in asymptomatic colonisation and the rate at which they progress to cause symptomatic disease. Increases in infections caused by commensals can result from the emergence of "hyperinvasive" strains. Such pathogens...
To gain a deep insight into the additional drug-resistant profiles, genetic diversity, and transmission dynamics of rifampicin-resistant tuberculosis (RR-TB) circulating in Hunan province, drug susceptibility testing and whole-genome-sequencing were performed among RR-TB strains collected from Jan....
The SARS-CoV-2 P.1 lineage emerged in Amazonas (AM), North Brazil and its evolution has been dynamically reported associated with increased transmissibility and/or immune evasion. Here, we evaluated the lineages circulating in 29 cities in Rio Grande do Sul (RS), Southern Brazil between March 2020 a...
The COVID-19 pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with seven SARS-CoV-2 variants. Our study includes individuals with positive SARS-CoV-2 RT-PCR...
Bluetongue virus (BTV) is an arthropod-borne, segmented double-stranded RNA virus that can cause severe disease in both wild and domestic ruminants. BTV evolves via several key mechanisms, including the accumulation of mutations over time and the reassortment of genome segments.Additionally, BTV mus...
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, sel...
Modern HIV research depends crucially on both viral sequencing and population measurements. To directly link mechanistic biological processes and evolutionary dynamics during HIV infection, we developed multiple within-host phylodynamic models of HIV primary infection for comparative validation agai...
The COVID-19 pandemic has driven demand for integrated genomics, resulting in fast-tracked development of AusTrakka, Australia’s pathogen genomics platform. This facilitated rapid data sharing, democratised access to computational and bioinformatic resources and expertise, and achieved national real...
The Omicron variant of concern (VOC), first detected in Italy at the end of November 2021, has since spread rapidly, despite high vaccine coverage in the Italian population, especially in healthcare workers (HCWs). This study describes an outbreak of SARS-CoV-2 Omicron infection in 15 booster-vaccin...
Pathogen whole-genome sequencing has become an important tool for understanding the transmission and epidemiology of infectious diseases. It has improved our understanding of sources of infection and transmission routes for important healthcare-associated pathogens, including Clostridioides difficil...
Zika virus (ZIKV), a re-emerging virus, causes congenital brain abnormalities and Guillain-Barré syndrome. It is mainly transmitted by Aedes mosquitoes, but infections are also linked to sexual transmissions. Infectious ZIKV has been isolated, and viral RNA has been detected in semen over a year aft...
Genomic surveillance is a critical tool for tracking emerging variants of SARS-CoV-2 (the virus that causes COVID-19), which can exhibit characteristics that potentially affect public health and clinical interventions, including increased transmissibility, illness severity, and capacity for immune e...
More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for clas...
Inferring the dynamics of pathogen transmission during an outbreak is an important problem in infectious disease epidemiology. In mathematical epidemiology, estimates are often informed by time series of confirmed cases, while in phylodynamics genetic sequences of the pathogen, sampled through time,...
The rapid development of sequencing technology brings the explosive growth of pathogen genetic data. The combination of genomic data and phylogenetic method is being used to elaborate the origin and evolution of pathogens, the time and space distribution and parameter changes in the prevalence proce...
Staphylococcus aureus is a major bacterial human pathogen that causes a wide variety of clinical manifestations. The main aim of the presented study was to determine and optimize a novel sequencing independent approach that enables molecular typing of S. aureus isolates and elucidates the transmissi...
Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic c...
Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effec...
Worldwide, neonatal mortality remains high accounting for 47% of childhood deaths in 2019 and including an estimated 500 000 deaths from neonatal infections. While 42% of global neonatal deaths occur in sub-Saharan Africa, there is limited understanding of population-level burden and aetiology of ne...
To analyze the enterotoxins, enterotoxin genes, drug resistance and molecular typing of 41 isolates from 2 food-borne illness outbreaks on 21 August and 27 September 2020 in Guangzhou. A total of 41 isolates from 2 outbreaks were analyzed by multilocus sequence typing (MLST) and typing. The e...
Tuberculosis (TB) remains an important global health issue worldwide. Despite this scourge threatening many human lives, especially in developing countries, thus far, no advanced molecular epidemiology study using recent and more accurate tools has been conducted in Mali. Therefore, this study aimed...
The implementation of monoclonal antibody therapeutics during the COVID-19 pandemic altered the selective pressures encountered by SARS-CoV-2, raising the possibility of selection for resistant variants. Within-host viral evolution was reported in treated immunocompromised individuals but whether th...
Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181...
Disparities in SARS-CoV-2 genomic surveillance have limited our understanding of the viral population dynamics and may delay identification of globally important variants. Despite being the most populated country in Africa, Nigeria has remained critically under sampled. Here, we report sequences fro...
SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic a...
Brazil has the highest SARS-CoV-2 case-fatality rate in pregnant women in the Americas. In this study, clinical and virological findings of five mildly symptomatic pregnant women and their infected fetuses/newborns treated at a referral hospital for COVID19-pregnant women in Midwestern Brazil are re...
Vancomycin-resistant Enterococcus faecium (VREfm) cause a wide range of hospital infections. Ireland has had one of the highest invasive VREfm infection rates in Europe over the last decade, yet little is known about Irish VREfm. To investigate the population structure of Irish VREfm, explore divers...
Carbapenem-resistant (CRKP) is a major cause of clinical infection. However, carbapenemase (KPC)-producing ST15 strains are occasionally identified and have seldom been reported to cause hospital outbreaks in PR China. In this study, we describe nosocomial outbreaks caused by KPC-producing ST15...
Carbapenem-resistant are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here, we characterize carbapenem-resistant from Alexandria, Egypt, and place it in a regional context. Fifty-fo...
Haemophilus influenzae serotype a (Hia) can cause severe invasive disease, especially in young children. In 2018, 4 invasive Hia cases occurred in an Alaska community. We used whole-genome sequencing (WGS) to evaluate the relationship of the bacteria from this community and other Alaska patients wit...
is a critically important pathogen known for its widespread antibiotic resistance and ability to persist in hospital-associated environments. Whilst the majority of infections are hospital-acquired, infections from outside the hospital have been reported with high mortality. Despite this, little is...
Carbapenem-resistant members of the family Enterobacteriaceae are emerging as a global public-health threat and cause substantial challenges in clinical practice. There is a need for increased and continued genomic surveillance of antimicrobial resistance genes globally in order to detect outbreaks...
BackgroundSeveral SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains.AimWe aimed to assess the prevalence of co-circulating VOC in Italy and...
There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitoring antimicrobial resistance (AMR) and protecting the safety of people and animals. With the availability of smaller and more affordable sequencing platforms coupled with well-de...
Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanism...
Increasing incidence rates of Clostridium difficile infection (CDI) and outbreaks of emerging strains have highlighted the need for continuous monitoring and surveillance of CDI in Australia. Active surveillance captures all hospital-identified CDI cases in Western Australia (WA), where all C. diffi...
To enhance monitoring of high-burden foodborne pathogens, there is opportunity to combine pangenome data with network analysis. Salmonella enterica subspecies Enterica serovar Enteritidis isolates were referred to the New South Wales (NSW) Enteric Reference Laboratory between August 2015 and Decembe...
Biotechnological approaches have always sought to utilize novel and efficient methods in the prevention, diagnosis, and treatment of diseases. This science has consistently tried to revolutionize medical science by employing state-of-the-art technologies in genomic and proteomic engineering. CRISPR-...
We aimed to analyze the situation of the first two epidemic waves in Myanmar using the publicly available daily situation of COVID-19 and whole-genome sequencing data of SARS-CoV-2. From March 23 to December 31, 2020, there were 33,917 confirmed cases and 741 deaths in Myanmar (case fatality rate of...
The laboratory surveillance of bacillary dysentery is based on a standardised Shigella typing scheme that classifies Shigella strains into four serogroups and more than 50 serotypes on the basis of biochemical tests and lipopolysaccharide O-antigen serotyping. Real-time genomic surveillance of Shige...
Hunting can fundamentally alter wildlife population dynamics but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here, we present a study that leverages a unique landscape-scale quasi-experiment coupled with pathogen-transmission tracing, network simulati...
Vancomycin-resistant Enterococcus faecium (VREfm) is a major nosocomial pathogen. Identifying VREfm transmission dynamics permits targeted interventions, and while genomics is increasingly being utilised, methods are not yet standardised or optimised for accuracy. We aimed to develop a standardized...
Over the past 25 years, the powerful combination of genome sequencing and bioinformatics analysis has played a crucial role in interpreting information encoded in bacterial genomes. High-throughput sequencing technologies have paved the way towards understanding an increasingly wide range of biologi...
The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of 2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China. A few studies have reported the early SARS-CoV-2 epidemics in several large citi...
Outbreaks of community-acquired Pseudomonas aeruginosa are typically small and localized. We investigated an increase in community-acquired infections with P. aeruginosa in Cape Town, South Africa. Cases were defined as P. aeruginosa isolated from any clinical sample, and "wild-type" as those suscep...
The regional distribution and transmissibility of existing COVID-19 variants of concern (VOC) has led to concerns about increasing transmission, given the ability of VOCs to evade immunity as breakthrough infections become more prevalent. SARS-CoV-2 genomes ( = 277) were sequenced and analysed along...
In December 2018, PulseNet, the national laboratory network for enteric disease surveillance, identified an increase in Salmonella Typhimurium isolates with an uncommon pulsed-field gel electrophoresis pattern which was previously isolated from hedgehogs. CDC, state, and local health partners interv...
COVID-19 pandemic 2nd wave catastrophic effect in the state of Chhattisgarh, India, from where no exclusive genomic data yet published, has prompted us to undertake this study to unearth the causative variant. Whole-genome sequencing of SARS-CoV-2 isolated from COVID-19 infected nine vaccinated heal...
The incidence of Elizabethkingia anophelis bacteremia increased significantly in a tertiary hospital, Changhua Christian Hospital (CCH) since 2013. The infection density was 1.3 and 8.1 cases per 100,000 patient-days between 2005 and 2012 and 2013 and 2020, respectively ( < 0.05). During an outbreak...
We examined 185 complete, publicly available FII-33 plasmid sequences, characterizing their backbone and various insertions. The variable characteristic insertions facilitated evolutionary reconstruction for this plasmid group, beginning with the acquisition of a primary resistance region (PRR) over...
A comprehensive analysis of omics data can require vast computational resources and access to varied data sources that must be integrated into complex, multi-step analysis pipelines. Execution of many such analyses can be accelerated by applying the cloud computing paradigm, which provides scalable...
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rapidly became a global health challenge, leading to unprecedented social and economic consequences. The mechanisms behind the pathogenesis of SARS-CoV-2 are both unique and...
Microsporidia is a large group of eukaryotic obligate intracellular spore-forming parasites, of which 17 species can cause microsporidiosis in humans. Most human-infecting microsporidians belong to the genera Enterocytozoon and Encephalitozoon. To date, only five microsporidian species, including En...
A new variant of concern for SARS-CoV-2, Omicron (B.1.1.529), was designated by the World Health Organization on November 26, 2021. This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron. First, we found that the enrichment efficiency of vir...
Clostridioides difficile, which causes life-threatening diarrheal disease, presents an urgent threat to health care systems. In this study, we present a retrospective genomic and epidemiological analysis of C. difficile in a large teaching hospital. First, we collected 894 nonduplicate fecal samples...
Since the spread of the COVID-19 pandemic, the world paid attention to coronaviruses (CoVs) evolution and their diverged lineages because many researches studies supposed that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolutionarily developed from a lineage of bats CoVs. Th...
Porcine deltacoronavirus (PDCoV), a recently emerging pathogen, causes diarrhoea in pigs. A previous phylogenetic analysis based on spike genes suggested that PDCoV was divided into three different groups, including China, the United States, and Southeast Asia (SEA). SEA PDCoV, however, is genetical...
Tracking the evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through genomic surveillance programs is undoubtedly one of the key priorities in the current pandemic situation. Although the genome of SARS-CoV-2 acquires mutations at a slower rate compared with other RNA v...
Candida auris is an emerging yeast that is associated with antifungal resistance and healthcare-associated outbreaks. From 2012 to 2019, there were 24 known cases of C. auris colonization or infection in Canada. Isolates were from axilla/groin (n = 6), ear (n = 5), blood (n = 4), toe (n = 2), and a...
The structured coalescent allows inferring migration patterns between viral subpopulations from genetic sequence data. However, these analyses typically assume that no genetic recombination process impacted the sequence evolution of pathogens. For segmented viruses, such as influenza, that can under...
Sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. SARS-CoV-2 genomic sequences were gen...
The COVID-19 pandemic caused by the severe acute respiratory syndrome (SARS)-CoV-2 infection is a systemic disease and a major planetary health burden. While SARS-CoV-2 impacts host biology extensively, our knowledge of these alterations from a systems perspective remains incomplete. Moreover, there...
Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the United Kingdom's second pandemic...
The distribution of Clostridioides difficile strains and transmission dynamics in the United States are not well defined. Whole-genome sequencing across 2 Centers for Disease Control and Prevention Emerging Infections Program C. difficile infection (CDI) surveillance regions (Minnesota and New York)...
The present study describes a 19-year-old woman with systemic herpes simplex virus (HSV)-1 infection and hemophagocytic lymphohistiocytosis (HLH) postpartum, and a fatal course of neonatal herpesvirus infection. Functional investigation of cells from the mother demonstrated significantly impaired in...
COVID-19 vaccination has proven to be effective at preventing symptomatic disease but there are scarce data to fully understand whether vaccinated individuals can still behave as SARS-CoV-2 transmission vectors. Based on viral genome sequencing and detailed epidemiological interviews, we report a no...
For over a century, it has been reported that primary influenza infection promotes the development of a lethal form of bacterial pulmonary disease. More recently, pneumonia events caused by both viruses and bacteria have been directly associated with cardiac damage. Importantly, it is not known whet...
The argasid tick Ornithodoros erraticus is the main vector of tick-borne human relapsing fever (TBRF) and African swine fever (ASF) in the Mediterranean Basin. The prevention and control of these diseases would greatly benefit from the elimination of O. erraticus populations, and anti-tick vaccines...
M. intracellulare is a frequent causative pathogen of nontuberculous mycobacteria infection that causes infections in the respiratory tract, whose incidence is increasing in many countries. This study aimed at determining the VNTR-based genetic diversity of a collection of 39 M. intracellulare human...
We reviewed the molecular epidemiology of Clostridioides difficile infection (CDI) in Japan by reviewing articles in which typing analysis was performed on recovered C. difficile isolates. Most of the multicenter studies showed that the major prevalent PCR-ribotypes (RT018-related type, RT014, RT002...
The objective of this living systematic review is to synthesize the available evidence on the prevalence of types of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic variations in Africa. The burden of the coronavirus disease 2019 (COVID-19) pandemic on the health, well-being, an...
Increasing evidence of regional pathogen transmission networks highlights the importance of investigating the dissemination of multidrug-resistant organisms (MDROs) across a region to identify where transmission is occurring and how pathogens move across regions. We developed a framework for investi...
BackgroundEvidence supporting the effectiveness of single-room contact precautions (SCP) in preventing in-hospital acquisition of vancomycin-resistant enterococci (haVRE) is limited.AimWe assessed the impact of SCP on haVRE and their transmission.MethodsWe conducted a prospective, multicentre cohort...
Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the whole resistome of , a very important nosocomial pathogen. Here we analyse 1450+...
Antimicrobial resistance (AMR) is one of the most important health threats globally. The ability to accurately identify resistant bacterial isolates and the individual antimicrobial resistance genes (ARGs) is essential for understanding the evolution and emergence of AMR and to provide appropriate t...
Throughout the global COVID-19 pandemic, nosocomial transmission has represented a major concern for healthcare settings and has accounted for many infections diagnosed within hospitals. As restrictions ease and novel variants continue to spread, it is important to uncover the specific pathways by w...
infections may lead to clinical or subclinical mastitis in dairy animals when it invades the mammary gland. In this study, 51 strains were isolated from 305 milk samples that were collected from goats with mastitis in 13 provinces of China. The antimicrobial resistance of . was determined by disk...
The need for effective public health surveillance systems to track virus spread for targeted interventions was highlighted during the COVID-19 pandemic. It spurred an interest in the use of spatiotemporal clustering and genomic analyses to identify high-risk areas and track the spread of the SARS-Co...
The widespread use of antimicrobials and type b (Hib) vaccine worldwide has altered the epidemiological patterns of invasive . Nonetheless, little is currently known on the epidemiological characteristics of in Guiyang, Guizhou, China. To determine the serotype distribution, antimicrobial resistan...
Genomic surveillance and wastewater tracking strategies were used to strengthen the public health response to an outbreak of the SARS-CoV-2 Delta AY.25 lineage associated with a university campus in Arizona. Epidemiologic and clinical data routinely gathered through contact tracing were matched to S...
Genomic surveillance of SARS-CoV-2 has been essential to inform public health response to outbreaks. The high incidence of infection has resulted in a smaller proportion of cases undergoing whole genome sequencing due to finite resources. We present a framework for estimating the impact of reduced d...
Philaenus spumarius is a cosmopolitan species that has become a major threat to European agriculture being recognized as the main vector of the introduced plant pathogen Xylella fastidiosa, the agent of the "olive quick decline syndrome", a disease which is devastating olive orchards in southern Ita...
The COVID-19 pandemic caused by SARS-CoV-2 is exerting huge pressure on global healthcare. Understanding of the molecular pathophysiological alterations in COVID-19 patients with different severities during disease is important for effective treatment. In this study, we performed proteomic profiling...
In spite of the availability of vaccine, the health burden associated with the COVID-19 pandemic continues to increase. An estimated 5 million people have died with SARS-CoV-2 infection. Analysis of evolution and genomic diversity can provide sufficient information to reduce the health burden of the...
Zika is a vector-borne disease caused by an arbovirus (ZIKV) and overwhelmingly transmitted by . This disease is linked to adverse fetal outcomes, mostly microcephaly in newborns, and other clinical aspects such as acute febrile illness and neurologic complications, for example, Guillain-Barré syndr...
The Covid-19 pandemic has emerged as the leading public health challenge of our time (20th century). While vaccinations have finally blunted the death rate, concern has remained about more virulent forms highlighting the need for alternative approaches. Epidemiological studies indicate that physical...
Enterococcus species account for most of the human enterococcal HAI and multidrug-resistant infections and have become a major threat to modern public health. We examine the rise in the number of vancomycin resistant E. faecium blood stream and urinary tract infections in a COVID-19 department durin...
Chikungunya virus (CHIKV) is a single-stranded positive RNA virus that belongs to the genus and is transmitted to humans by infected and bites. In humans, CHIKV usually causes painful symptoms during acute and chronic stages of infection. Conversely, virus-vector interaction does not disturb the...
Genomic studies of Candida auris are underpinned by the generation of high-quality genome assemblies. These reference genomes have been essential for investigations of the evolution and epidemiology of this emerging fungal pathogen. In addition to genomic epidemiology studies of local outbreaks and...
The prevalence of phage 80/81 Staphylococcus aureus strains, the pandemic strains that were dominant in the 1950s, had declined in the 1960s and 1970s. However, these strains have reemerged in some countries in recent years. This study investigated the antibacterial resistance, virulence, and the ge...
Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Ira...
the limited number of equipped laboratories and the lack of expertise left Africa lagging behind in terms of contribution in genomic data generation. The COVID-19 pandemic has drawn the attention of all public health stakeholders so that it can be used as a marker of the efforts that public health s...
The timely release of SARS-CoV-2 first genomic sequences allowed the identification of the etiologic agent and development of diagnostic protocols. Genomic sequencing was a crucial step in generating data for driving laboratory response and detections of SARS-CoV-2 since the start of the COVID-19 pa...
Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) typing has been widely used for molecular epidemiological studies of tuberculosis (TB). However, genotyping tools for Mycobacterium tuberculosis (Mtb) may be limiting in some settings due to high cost and workload. In th...
The world is experiencing one of the most severe viral outbreaks in the last few years, the pandemic infection by SARS-CoV-2, the causative agent of COVID-19 disease. As of December 10th 2021, the virus has spread worldwide, with a total number of more than 267 million of confirmed cases (four times...
The COVID-19 pandemic has hit heavily many aspects of our lives. At this time, genomic research is concerned with exploiting available datasets and knowledge to fuel discovery on this novel disease. Studies that can precisely characterize the gene expression profiles of human hosts infected by SARS-...
The characterization of pathogenic bacteria by providing information regarding the identification and source-tracking of the causes of outbreaks is vital for the epidemiological investigations of foodborne diseases. The knowledge of transmission of () strains from the environment, directly or indir...
In recent years has been considered an important and frequent causative agent of health care-associated infections (HAIs), increasing the costs of hospitalization, morbidity, and mortality. Antibiotic resistance and biofilm formation are the most important obstacles in the treatment of infections c...
At the end of 2019, the COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection, seriously damaged world public health security. Several protein markers associated with virus infection have been extensively explored to combat the ever-increasing chall...
Multidrug-resistant organisms (MDRO), especially carbapenem-resistant organisms (CRO), represent a threat for newborns. This study investigates the colonization prevalence of these pathogens in a newborn unit at a Kenyan tertiary hospital in an integrated approach combining routine microbiology, who...
Healthcare-associated infections by carbapenem-resistant are difficult to control. Virulence and antibiotic resistance genes contribute to infection, but the mechanisms associated with the transition from colonization to infection remain unclear. We investigated the transition from carriage to infe...
New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuing to spread globally, contributing to the persistence of the COVID-19 pandemic. Increasing resources have been focused on developing vaccines and therapeutics that target the Spike glycoprotein of SARS-CoV-2. R...
Acinetobacter baumannii is an opportunistic gram-negative bacteria typically attributed to hospital-associated infection. It could also become multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR) during a short period. Although A. baumannii has been documented ex...
Multidrug-resistant Acinetobacter baumannii is an important causal pathogen of healthcare-associated infections, and colistin-resistant strains have recently emerged owing to the increased use of colistin. Using next-generation sequencing (NGS), a single whole-genome sequencing (WGS) protocol can id...
Global and local whole genome sequencing of SARS-CoV-2 enables the tracing of domestic and international transmissions. We sequenced Viral RNA from 37 sampled Covid-19 patients with RT-PCR-confirmed infections across the UAE and developed time-resolved phylogenies with 69 local and 3,894 global geno...
Brucellae are intracellular sneaky bacteria and they can elude the host's defensive mechanisms, resulting in therapeutic failure. Therefore, the goal of this investigation was to rapid identification of Brucella species collected from animals and humans in Saudi Arabia, as well as to evaluate their...
Hospital-acquired infections caused by carbapenem-resistant Gram-negative bacteria (CRGNB) have been increasingly reported worldwide and are associated with high rates of mortality especially in intensive care units(ICUs). Early identification through rectal surveillance cultures and implementation...
Orthohantaviruses are zoonotic pathogens of humans, unique among the bunyaviruses in not being transmitted by an arthropod vector. Tula orthohantavirus (TULV) is an old-world hantavirus, of yet unclear human pathogenicity, with few reported cases of clinically relevant human infection. So far, phylo...
The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national...
Genomic epidemiology plays an ever-increasing role in our understanding of and response to the spread of infectious pathogens. Phylogeography, the reconstruction of the historical location and movement of pathogens from the evolutionary relationships among sampled pathogen sequences, can inform poli...
Alfalfa mosaic virus (AMV) is the most pervasive epidemic virus affecting alfalfa production. However, detailed investigations on the molecular population genetics and evolutionary dynamics of AMV are scarce. This study aimed to report on a large-scale long-term survey of genetic variability in AMV...
Alfalfa mosaic virus (AMV) is an important plant virus causing considerable economic loss to alfalfa production. Knowledge of the evolutionary and demographic history of the pathogen is limited but essential to the development of effective and sustainable pathogen management schemes. In this study,...
The worldwide emergence and diffusion of extended-spectrum β-lactamase- (ESBL-KP) is of particular concern. Although ESBL-KP can inhabit the human gut asymptomatically, colonization with ESBL-KP is associated with an increased risk of ESBL-KP infection and mortality. In this study, we investigated t...
Everglades virus (EVEV) is a subtype (II) of Venezuelan equine encephalitis virus (VEEV), endemic in southern Florida, USA. EVEV has caused clinical encephalitis in humans, and antibodies have been found in a variety of wild and domesticated mammals. Over 29,000 females, the main vector of EVEV, we...
Africa accounts for 1.5% of the global coronavirus disease 2019 (COVID-19) cases and 2.7% of deaths, but this low incidence has been partly attributed to the limited testing capacity in most countries. In addition, the population in many African countries is at high risk of infection with endemic in...
The hepatitis C virus genotype 2 (HCV2) is endemic in Western and Central Africa. The HCV2 evolutionary origins remain uncertain due to the paucity of available genomes from African settings. In this study, we investigated the molecular epidemiology of HCV infections in rural Guinea, Western Africa,...
The COVID-19 pandemic is still in force, causing global public health challenges and threats. Although vaccination and herd immunity have proven to be the most efficient way to control the pandemic, massive and early testing of patients using the RT-qPCR technique is crucial for constant genomic sur...
Breakthrough SARS-CoV-2 infections have been reported in fully vaccinated individuals, in spite of the high efficacy of the currently available vaccines, proven in trials and real-world studies. Several variants of concern (VOC) have been proffered to be associated with breakthrough infections follo...
Metagenomic next-generation sequencing (mNGS) technology has been central in detecting infectious diseases and helping to simultaneously reveal the complex interplay between invaders and their hosts immune response characteristics. However, it needs to be rigorously assessed for clinical utility. Th...
Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has demonstrated its ability to rapidly and continuously evolve, leading to the emergence of thousands of different sequence variants, many with distinctive phenotypic properties. Fortunately, the broad application of next generation sequencin...
Phylogeographic analyses aim to extract information about pathogen spread from genomic data, and visualising spatio-temporal reconstructions is a key aspect of this process. Here we present SPREAD 4, a feature-rich web-based application that visualises estimates of pathogen dispersal resulting from...
An important unmet need revealed by the COVID-19 pandemic is the near-real-time identification of potentially fitness-altering mutations within rapidly growing SARS-CoV-2 lineages. Although powerful molecular sequence analysis methods are available to detect and characterize patterns of natural sele...
Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 var...
Senecavirus A (SVA) is a member of the genus in the family Picornaviridae that infects pigs and shows symptoms similar to foot and mouth diseases and other vesicular diseases. It is difficult to prevent, thus, causing tremendous economic loss to the pig industry. However, the global transmission ro...
The highly pathogenic virus SARS-CoV-2 has shattered the healthcare system of the world causing the COVID-19 pandemic since first detected in Wuhan, China. Therefore, scrutinizing the genome structure and tracing the transmission of the virus has gained enormous interest in designing appropriate int...
Since the initial reported discovery of SARS-CoV-2 in late 2019, genomic surveillance has been an important tool to understand its transmission and evolution. Here, we sought to describe the underlying regional phylodynamics before and during a rapid spreading event that was documented by surveillan...
Since the start of the COVID-19 pandemic, health policymakers globally have been attempting to predict an impending wave of COVID-19. India experienced a devastating second wave of COVID-19 in the late first week of May 2021. We retrospectively analyzed the viral genomic sequences and epidemiologica...
SARS-CoV-2 reinfection is defined as a new infection with a different virus variant in an individual who has already recovered from a previous episode of COVID-19. The first case of reinfection in the world was described in August 2020, since then, reinfections have increased over time and their inc...
Several variants of concern (VOCs) explain most of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic waves in Europe. We aimed to dissect the spread of the SARS-CoV-2 VOCs in the Canary Islands (Spain) between December 2020 and September 2021 at a micro-geographical level. We...
Severe acute respiratory syndrome (SARS-CoV-2) is responsible for the worldwide pandemic, COVID-19. The original viral whole-genome was sequenced by a high-throughput sequencing approach from the samples obtained from Wuhan, China. Real-time gene sequencing is the main parameter to manage viral outb...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. T...
With the spread of multiple drug-resistant bacteria, and have been detected in various bacteria worldwide. However, the simultaneous detection of and in has been rarely reported. This study identified an strain carrying both and . We investigated the genetic characteristics of these two re...
Puerto Rico has experienced the full impact of the COVID-19 pandemic. Since SARS-CoV-2, the virus that causes COVID-19, was first detected on the island in March of 2020, it spread rapidly though the island's population and became a critical threat to public health. We conducted a genomic surveillan...
is the causative agent of many enterotoxic diseases in humans and animals, and it is present in diverse environments (soil, food, sewage, and water). Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) have provided a general approach about genetic diversity of ; however, those studi...
Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional investigations to disclose genotype and antimicrobial susceptibility. We revi...
Monkeypox is a zoonotic disease with clinical manifestations similar to smallpox in humans. Since May 13, 2022, an increasing number of suspected and confirmed cases have been reported, affecting non-endemic regions across the globe. More strikingly, reports from the current outbreak reveal unique a...
The continuing emergence of new SARS-CoV-2 variants has perpetuated the current pandemic far beyond initial expectations. It is now likely that this virus is here to stay. Thus, a new infrastructure is required for monitoring and tracking of viral outbreaks which includes epidemiological and genomic...
Tick-borne encephalitis virus (TBEV) is the aetiological agent of tick-borne encephalitis, an infectious disease of the central nervous system that is often associated with severe sequelae in humans. While TBEV is typically classified into three subtypes, recent evidence suggests a more varied range...
Porcine Parvovirus Type 1 (PPV1) contributes to important losses in the swine industry worldwide. During a PPV1 infection, embryos and fetuses are targeted, resulting in stillbirth, mummification, embryonic death, and infertility (SMEDI syndrome). Even though vaccination is common in gilts and sows,...
Bovine leukemia virus (BLV), the causative agent of enzootic bovine leukosis, is currently one of the most important pathogens affecting the cattle industry worldwide. Determining where and in which host it originated, and how it dispersed across continents will provide valuable insights into its hi...
The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here, we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a severe acute respiratory syndrome coronav...
During 2014-2016, clade 2.3.4.4 H5N8 high pathogenicity avian influenza virus (HPAIV) caused the largest known avian influenza epidemic in South Korea. Based on data from earlier H5N8 outbreaks, primitive H5N8 virus in South Korea was classified into five subgroups: C1, C2, C3, C4, and C5. The prese...
Phylogeographic inference of the dispersal history of viral lineages offers key opportunities to tackle epidemiological questions about the spread of fast-evolving pathogens across human, animal and plant populations. In continuous space, i.e. when locations are specified by longitude and latitude,...
Nanopore sequencing has been widely used for the real-time detection and surveillance of pathogens with portable MinION. Nanopore adaptive sequencing can enrich on-target sequences without additional pretreatment. In this study, the performance of adaptive sequencing was evaluated for viral genome e...
Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology, and statistical inference. It has also experienced more intense application than ever before amid the SARS-CoV-2 pandemic. In light of this, we present a review of phylodynamic models beginning with foundationa...
During the first wave of infections, neurological symptoms in Coronavirus Disease 2019 (COVID-19) patients raised particular concern, suggesting that, in a subset of patients, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could invade and damage cells of the central nervous system...
The unprecedented severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) global sequencing effort has suffered from an analytical bottleneck. Many existing methods for phylogenetic analysis are designed for sparse, static datasets and are too computationally expensive to apply to densely sampl...
Hepatitis B is a potentially life-threatening liver infection caused by the hepatitis B virus (HBV). HBV-D1 is the dominant subgenotype in the Mediterranean basin, Eastern Europe, and Asia. However, little is currently known about its evolutionary history and spatio-temporal dynamics. We use Bayesia...
A global surge in SARS-CoV-2 cases is occurring due to the emergence of new disease variants, and requires continuous adjustment of public health measures. This study aims to continuously monitor and mitigate the impact of SARS-CoV-2 through genomic surveillance, to determine the emergence of varian...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other Eur...
Nosocomial infections caused by New Delhi metallo-β-lactamase (NDM)-producing bacteria are prevalent worldwide. However, such diseases caused by NDM-producing had never been reported. Our study aimed to elucidate the genomic characteristics of NDM-1-producing isolated from hospital patients. Bacte...
Certain rural and semiurban settings in the Unnao district, Uttar Pradesh, India observed an unprecedented increase in the detection of HIV cases during July 2017. Subsequent investigations through health camps and a follow-up case-control study attributed the outbreak to the unsafe injection exposu...
The recent outbreak of yellow fever (YF) in São Paulo during 2016-2019 has been one of the most severe in the last decades, spreading to areas with low vaccine coverage. The aim of this study was to assess the genetic diversity of the yellow fever virus (YFV) from São Paulo 2016-2019 outbreak, integ...
Genomic surveillance efforts for SARS-CoV-2 are needed to understand the epidemiology of the COVID-19 pandemic. Viral variants may impact routine diagnostic testing, increase viral transmissibility, cause differences in disease severity, have decreased susceptibility to therapeutics, and/or confer t...
Colistin is a last-resort treatment option for infections with multidrug-resistant Gram-negative bacteria. However, colistin resistance is increasing. A six-month prospective matched case-control study was performed in which 22 Dutch laboratories with 32 associated hospitals participated. Laboratori...
Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. By applying recent phylodynamic models that allow integration of individual...
On September 21, 2019, the Shenzhen and Dongguan Centers for Disease Control and Prevention received notification of a large cluster of suspected gastroenteritis involving primarily children who sought medical care at hospitals throughout two adjacent cities in China, Shenzhen, and Dongguan. A joint...
The genetic diversity of viral populations is a key driver of the spatial and temporal diffusion of viruses; yet, studying the diversity of whole genomes from natural populations still remains a challenge. Phylodynamic approaches are commonly used for RNA viruses harboring small genomes but have onl...
Methicillin-resistant (MRSA) is a leading cause of hospital-associated (HA) and community-associated (CA) infections globally. The multi-drug resistant nature of this pathogen and its capacity to cause outbreaks in hospital and community settings highlight the need for effective interventions, incl...
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to extra caution in workplaces to avoid the coronavirus disease 2019 (COVID-19). In the occupational environment, SARS-CoV-2 testing is a powerful approach in providing valuable information to detect, monitor,...
Sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains preliminary information on the phylodynamics and phylogeography of this new virus. A maximum clade credibility tree (MCCT) was constructed using available whole genome sequences of SARS-CoV-2 and highly similar whole...
The identification and tracking of SARS-CoV-2 infected patients in the general population are essential components of the global strategy to limit the COVID-19 viral spread, specifically for maintaining traceability and suppressing the resurgence of local outbreaks. Public health programs that inclu...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution plays a significant role in shaping the dynamics of the coronavirus disease 2019 pandemic. To monitor the evolution of SARS-CoV-2 variants, hrough international collaborations, we performed genomic epidemiology analyses on a week...
Large-scale SARS-CoV-2 molecular testing coupled with whole genome sequencing in the diagnostic laboratories is instrumental for real-time genomic surveillance. The extensive genomic, laboratory, and clinical data provide a valuable resource for understanding cases of reinfection versus prolonged RN...
The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus ep...
The increasing threat of emerging and re-emerging pathogens calls for a shared vision toward developing and maintaining global surveillance mechanisms to enable rapid characterization of pathogens, a foundational requirement for effective outbreak response. Efforts establishing new surveillance prog...
Infectious bronchitis (IB) virus (IBV) causes considerable economic losses to poultry production. The data on transmission dynamics of IBV in China are limited. The complete genome sequences of 212 IBV isolates in China during 1985-2020 were analyzed as well as the characteristics of the phylogeneti...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an enormous burden on the healthcare system worldwide as a consequence of its new emerging variants of concern (VOCs) since late 2019. Elucidating viral genome characteristics and its influence on disease severity and clinical outc...
Molecular surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is growing in west Africa, especially in the Republic of Senegal. Here, we present a molecular epidemiology study of the early waves of SARS-CoV-2 infections in this country based on Bayesian phylogeographic appro...
The existing panels of COVID-19 vaccines are based on the spike protein of an earlier SARS-CoV-2 strain that emerged in Wuhan, China. However, the evolving nature of SARS-CoV-2 has resulted in the emergence of new variants, thereby posing a greater challenge in the management of the disease. India f...
Inherited mutualists, parasites, and commensals occupy one of the most intimate ecological niches available to invertebrate-associated microbes. How this transmission environment influences microbial evolution is increasingly understood for inherited bacterial symbionts, but in viruses, research on...
A total of 1155 partial gene sequences of human immunodeficiency virus (HIV)-1 CRF07_BC were sampled between 1997 and 2015, spanning 13 provinces in Mainland China and risk groups [heterosexual, injecting drug users (IDU), and men who have sex with men (MSM)] to investigate the evolution, adaptatio...
Aim of this study was to reconstruct the phylogeography of virus (VARV) in the XX century, using 47 VARV whole genome sequences available in public databases, through two different methods for ancestral character reconstruction: a frequently used Bayesian framework and a fast maximum-likelihood (ML...
Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can poten...
are of major human health importance because they cause life-threatening nosocomial infections and often are highly resistant to antimicrobials. Specific multidrug-resistant lineages are implicated in hospital outbreaks globally. We retrospectively investigated a suspected outbreak of carbapenem-re...
Genetic analyses of fast-evolving pathogens are frequently undertaken to test the impact of covariates on their dispersal. In particular, a popular approach consists of parameterizing a discrete phylogeographic model as a generalized linear model to identify and analyse the predictors of the dispers...
The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), has been sequenced at an unprecedented scale leading to a tremendous amount of viral genome sequencing data. To assist in tracing infection pathways and desig...
Since 2015, plasmid-borne has been reported in various bacterial strains in the clinical setting globally. However, the transmission mechanisms of this gene in are not well defined. This study aimed to characterize the genomic features of a ST34 isolate, which carried a , mapped to a carbapenemas...
The COVID-19 pandemic has created an unprecedented need for epidemiological monitoring using diverse strategies. We conducted a project combining prevalence, seroprevalence, and genomic surveillance approaches to describe the initial pandemic stages in Betim City, Brazil. We collected 3239 subjects...
Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real ti...
ST127, a recently emerged global pathogen noted for high virulence gene carriage, is a leading cause of urinary tract and blood stream infections. ST127 is frequently isolated from humans and companion animals; however, it is unclear if they are distinct or related populations of ST127. We performed...
Mycolicibacterium fortuitum is an opportunistic pathogen associated with human and animal infection worldwide. Studies concerning this species are mainly represented by case reports, some of them addressing drug susceptibility with a focus on a specific geographic region, so there is a gap in relati...
In December 2019, a new severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China, causing coronavirus disease 2019. The present study investigated genetic profiles and variations of SARS-CoV-2 distributed in different regions of Saudi Arabia to begin to understand the pathogenesis...
Chikungunya virus (CHIKV) is an alphavirus transmitted by mosquitoes, which causes Chikungunya fever. Three CHIKV genotypes have been identified: West African, East-Central-South African and Asian. In 2014, CHIKV was detected for the first time in Mexico, accumulating 13,569 confirmed cases in the...
Rabies is a globally prevalent viral zoonosis that causes 59,000 deaths per year and has important economic consequences. Most virus spread is associated with the migration of its primary hosts. Anthropogenic dissemination, mainly via the transportation of rabid dogs, shaped virus ecology a few hund...
A large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of > 400 000 newly confirmed cases on 7 May 2021. Epidemiological inf...
Although Southeast Asia is one of the most leptospirosis afflicted regions, little is known about the diversity and molecular epidemiology of the causative agents of this widespread and emerging zoonotic disease. We used whole genome sequencing to examine genetic variation in 75 Leptospira strains i...
From 2018, IR Biotyper (IRBT; Bruker Daltonik GmbH, Germany) based on the Fourier transform infrared spectrophotometer has begun to be introduced as a new strain classification method in the field of clinical microbiological examination. We compared it with molecular epidemiology method to evaluate...
is a ubiquitous Gram-negative emerging pathogen that causes hospital-acquired infection in both immunocompromised and immunocompetent patients. It is a multi-drug-resistant bacterium; therefore, an effective subunit immunogenic candidate is of great interest to encounter the pathogenesis of this pat...
Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmissi...
An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection...
Vulvovaginal candidiasis (VVC) is frequent in women of reproductive age, but very limited data are available on the epidemiology in cases of VVC in China. The current study has been conducted to reveal the prevalence, species distribution of yeast causing VVC and molecular genetics of Candida albica...
The emergence of plasmid-mediated tigecycline resistance genes has attracted a great deal of attention globally. Currently, no comprehensive in-depth genomic epidemiology study of (X4)-bearing pathogens present of pork origin as the One Health approach has been performed. Herein, 139 fresh pork samp...
Considering the potential threat from emerging Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) variants and the rising COVID-19 cases, SARS-CoV-2 genomic surveillance is ongoing in India. We report herewith the isolation of the P.2 variant (B.1.1.28.2) from international travelers and...
The emergence and establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of interest (VOIs) and variants of concern (VOCs) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking...
Genomics-driven molecular epidemiology of pathogenic bacteria has largely been carried out through functionally neutral/inert sequences, mostly entailing polymorphic gene loci or repetitive tracts. However, it is very important to harness phenotypically relevant markers to assign a valid functional...
Viral disease poses a major barrier to sustainable aquaculture, with outbreaks causing large economic losses and growing concerns for fish welfare. Genomic epidemiology can support disease control by providing rapid inferences on viral evolution and disease transmission. In this study, genomic epide...
Resistance to commonly available antimicrobials is a major threat to the fight against endemic bacterial diseases in sub-Saharan Africa, with a majority of the population unable to afford alternative effective antimicrobial options for management of these diseases. Diseases such as typhoid, cholera,...
This work addresses the need for new chemical matter in product development for control of pest insects and vector-borne diseases. We present a barcoding strategy that enables phenotypic screens of blood-feeding insects against small molecules in microtiter plate-based arrays and apply this to disco...
The outbreak of the newly discovered human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has disrupted the normal life of almost every civilization worldwide. Studies have shown that the coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 can affect multiple hum...
To analyze the application of the metagenomics method in the identification of viral infectious agents that lead to diarrhea outbreaks. This study is a systematic review, which looked for publications on the following platforms: PubMed, Scientific Electronic Library Online (SciELO), LILACS and CAPES...
Convergence of resistance and virulence in Klebsiella pneumoniae is a critical public health issue worldwide. A multidrug-resistant CTX-M-15-producing K. pneumoniae (TIES-4900 strain) was isolated from a highly impacted urban river, in Brazil. The genome was sequenced by MiSeq Illumina platform and...
The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected t...
Urinary tract infection (UTI) develops after a pathogen adheres to the inner lining of the urinary tract. Cases of UTIs are predominantly caused by several Gram-negative bacteria and account for high morbidity in the clinical and community settings. Of greater concern are the strains carrying antimi...
Corona disease 2019 (COVID-19) affects multiple organ systems. Recent studies have indicated perturbations in the circulating metabolome linked to COVID-19 severity. However, several questions pertain with respect to the metabolome in COVID-19. We performed an in-depth assessment of 1129 unique meta...
This study aimed to explore associations between the molecular characterization of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and disease severity in ambulatory and hospitalized patients in two main Colombian epicentres during the first year of the coronavirus disease 2019 pandemic...
The public health value of whole genome sequencing (WGS) for spp. in England has been limited by a lack of information on sexual identity and behavior. We combined WGS data with other data sources to better understand Shigella flexneri transmission in men who have sex with men (MSM). WGS data for a...
Highly pathogenic (HP) H7N9 avian influenza virus (AIV) emerged in China in 2016. HP H7N9 AIV caused at least 33 human infections and has been circulating in poultry farms continuously since wave 5. The genetic divergence, geographic patterns, and hemagglutinin adaptive and parallel molecular evolut...
One of the most remarkable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) features is the significant number of mutations they acquired. However, the specific factors that drove the emergence of such variants since the second half of 2020 are not fully resolve...
The global spread and continued evolution of SARS-CoV-2 has driven an unprecedented surge in viral genomic surveillance. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine laboratory processes and resu...
Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs. Next-generation sequencing (NGS) provides an efficient and unbiased way to identify viral...
Porcine reproductive and respiratory syndrome (PRRS) is probably the most relevant viral disease affecting pig farming. Despite the remarkable efforts paid in terms of vaccination administration and biosecurity, eradication and long-term control have often been frustrated. Unfortunately, few studies...
Vaccination and the emergence of SARS-CoV-2 variants mark the second year of the pandemic. Variants have amino acid mutations at the spike region, a viral protein central in the understanding of COVID-19 pathogenesis and vaccine response. Variants may dominate local epidemics, as Gamma (P.1) in Braz...
Mosquito-borne diseases have a devastating impact on human civilization. A few species of Anopheles mosquitoes are responsible for malaria transmission, and while there has been a reduction in malaria-related deaths worldwide, growing insecticide resistance is a cause for concern. Aedes mosquitoes a...
As of May 1, 2016, use of oral poliovirus vaccine (OPV) type 2 for routine and supplementary immunization activities ceased after a synchronized global switch from trivalent OPV (tOPV; containing Sabin strain types 1, 2, and 3) to bivalent OPV (bOPV; containing Sabin strain types 1 and 3) subsequent...
Whole genome sequencing has been extensively used to describe infection outbreaks, although with limited application on Candida albicans and Candida parapsilosis.We retrospectively studied all patients admitted to the neonatal care unit diagnosed with candidemia caused by C. albicans (n = 46) or C....
Aetiology detection is crucial in the diagnosis and treatment of ventilator-associated pneumonia (VAP). However, the detection method needs improvement. In this study, we used Nanopore sequencing to build a quick detection protocol and compared the efficiency of different methods for detecting 7 VAP...
A new protocol step improves robustness and ease-of-use for mass spectrometry in the clinic, opening the door to mass deployment to monitor infectious agents.
Nasopharyngeal (NP) swabs are the standard for SARS-CoV-2 diagnosis. If less invasive alternatives to NP swabs (eg, oropharyngeal [OP] or nasal swabs [NS]) are comparably sensitive, the use of these techniques may be preferable in terms of comfort, convenience, and safety. This study compared the de...
The authors aimed to examine antibiotic resistance genes and representative virulence determinants among 100 isolates with an emphasis on capsular serotypes and clonality of some of the isolates. PCR amplification of (, , , and plasmid) and (NDM, OXA-48, KPC, CTX-M-15, VIM, IMP, SPM) was conduct...
Since the first cases of COVID-19 were documented in Wuhan, China in 2019, the world has witnessed a devastating global pandemic, with more than 238 million cases, nearly 5 million fatalities and the daily number of people infected increasing rapidly. Here we describe the currently available data on...
We performed an epidemiological investigation and genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) to define the source and scope of an outbreak in a cluster of hospitalized patients. Lack of appropriate respiratory hygiene led to SARS-CoV-2 transmission to patients and...
Newcastle disease virus (NDV) can infect over 250 bird species with variable pathogenicity; it can also infect humans in rare cases. The present study investigated an outbreak in feral pigeons in São Paulo city, Brazil, in 2019. Affected birds displayed neurological signs, and hemorrhages were obser...
Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures. We combined conventional surveillance with influenza A virus (IAV) genome se...
In this paper, we revealed the genetic structure and migration history of the Powassan virus (POWV) reconstructed based on 25 complete genomes available in NCBI and ViPR databases (accessed in June 2021). The usage of this data set allowed us to perform a more precise assessment of the evolutionary...
Other than genome structure, influenza C (ICV), and D (IDV) viruses with seven-segmented genomes are biologically different from the eight-segmented influenza A (IAV), and B (IBV) viruses concerning the presence of hemagglutinin-esterase fusion protein, which combines the function of hemagglutinin a...
Since its inception in late 2019, SARS-CoV-2 has been evolving continuously by procuring mutations, leading to emergence of numerous variants, causing second wave of pandemic in many countries including India in 2021. To control this pandemic continuous mutational surveillance and genomic epidemiolo...
The Covid-19 pandemic accelerated research and development not only in infectious diseases but also in digital technologies to improve monitoring, forecasting, and intervening on planetary and ecological risks. In the European Commission, the Destination Earth (DestinE) is a current major initiative...
The bacterial foodborne pathogen clonal complex 1 (-CC1) is the most prevalent clonal group associated with human listeriosis and is strongly associated with cattle and dairy products. Here, we analyze 2021 isolates collected from 40 countries, covering -CC1 first isolation to present days, to defi...
The spore-forming bacterium is the causative agent of American foulbrood (AFB), a devastating disease of honeybees (). In the present study, we used whole-genome sequencing (WGS) to investigate an extensive outbreak of AFB in northwestern Slovenia in 2019. A total of 59 . isolates underwent WGS, o...
Aedes aegypti and Ae. albopictus are vectors of numerous arboviruses that adversely affect human health. In mosquito vectors of disease, the bacterial microbiota influence several physiological processes, including fertility and vector competence, making manipulation of the bacterial community a pro...
Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied. A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-...
has caused widespread mortality in Indian shrimp aquaculture in recent years. However, there are insufficient genome data for the isolates from Indian shrimp vibriosis to analyze genetic diversity and track the acquisition of genetic features that could be involved in virulence and fitness. In this...
infection in humans, also known as psittacosis, is usually believed to be an uncommon disease which mainly presents as community-acquired pneumonia (CAP). It is usually sporadic, but outbreaks of infection may occasionally occur. In outbreaks, diagnosis and investigations were usually hampered by th...
is an emerging pathogenic fungal species found worldwide. Since April 2016, colonization/infection cases have been found in a general hospital in Shenyang, China. The genome-based phylogenetic studies of these isolates remain undefined. In the current study, the microbiological characteristics and...
Compared to the previous 2013-2014 outbreak, dengue 2016-2017 outbreak in New Caledonia was characterized by an increased number of severe forms associated with hepatic presentations. In this study, we assessed the virological factors associated with this enhanced severity. Whole-genome sequences we...
IMP-45, a variant of IMP-9, is one of the dominant metallo-β-lactamases (MBLs) in clinical carbapenem-resistant (CRPA) isolates in China. The aim of this study was to investigate the distribution and mechanism of dissemination of . MBL genes were detected by PCR in 173 non-duplicate CRPA isolates c...
Methicillin-resistant (MRSA) of the ST1-SCCIV lineage has been associated with community-acquired (CA) infections in North America and Australia. In Brazil, multi-drug resistant ST1-SCCIV MRSA has emerged in hospital-associated (HA) diseases in Rio de Janeiro. To understand these epidemiological di...
Analyses of HPAI H5 viruses from poultry outbreaks across a wide Eurasian region since July 2020 including the Russian Federation, Republics of Iraq and Kazakhstan, and recent detections in migratory waterfowl in the Netherlands, revealed undetected maintenance of H5N8, likely in galliform poultry s...
Shiga toxin-producing (STEC) is a zoonotic, foodborne gastrointestinal pathogen that has the potential to cause severe clinical outcomes, including haemolytic uraemic syndrome (HUS). STEC-HUS is the leading cause of renal failure in children and can be fatal. Over the last decade, STEC clonal compl...
Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying strain in Germany and show the value of contextual data. By screening about 10 000...
Performing whole genome sequencing (WGS) for the surveillance of antimicrobial resistance offers the ability to determine not only the antimicrobials to which rates of resistance are increasing, but also the evolutionary mechanisms and transmission routes responsible for the increase at local, natio...
Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses a...
Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria. We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimi...
Advanced genomics and sequencing technologies are increasingly becoming critical for global health applications such as pathogen and antimicrobial resistance (AMR) surveillance. Limited resources challenge capacity development in low- and middle-income countries (LMICs), with few countries having ge...
Avian influenza virus (AIV) subtypes H5N1 and H9N2 co-circulate in poultry in Bangladesh, causing significant bird morbidity and mortality. Despite their importance to the poultry value chain, the role of farms in spreading and maintaining AIV infections remains poorly understood in most disease-end...
is a clinically important pathogen implicated in many hospital-acquired infections. Its propensity to acquire broad-spectrum resistance has earned the organism its status as a severe public health threat requiring urgent control measures. While whole-genome sequencing-based genomic surveillance prov...
Mutations in the SARS-CoV-2 Membrane (M) gene are relatively uncommon. The M gene encodes the most abundant viral structural protein, and is implicated in multiple viral functions, including initial attachment to the host cell via heparin sulphate proteoglycan, viral protein assembly in conjunction...
Since spring 2020, Ukraine has experienced at least two COVID-19 waves and has just entered a third wave in autumn 2021. The use of real-time genomic epidemiology has enabled the tracking of SARS-CoV-2 circulation patterns worldwide, thus informing evidence-based public health decision making, inclu...
BACKGROUND: To describe the course and intervention of an hospital-wide IMI-Producing Enterobacter ludwigii outbreak. This was an outbreak interventional study, done at a tertiary care center in Tel-Aviv, Israel. Data was collected on the course of the outbreak and the demographic and clinical chara...
The SARS-CoV-2 alpha VOC (also known as lineage B.1.1.7) initially described in the autumn, 2020 in UK, rapidly became the dominant lineage across much of Europe. Despite multiple studies reporting molecular evidence suggestive of its circulation in Brazil, much is still unknown about its genomic di...
Aedes aegypti and Aedes albopictus are invasive mosquito species and significantly impact human health in southern China. Microbiota are confirmed to affect the development and immunity of mosquitoes. However, scientists have focused more on midgut microbiota of female mosquitoes and bacterial diffe...
Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) represent a serious threat to public health and their timely detection is essential for patient management and the prevention of nosocomial infections. Here, matrix-assisted laser desorption ionization time-of-flight mass spectrome...
Multi-drug-resistance (MDR) is a severe public health concern worldwide, and its containment is more challenging in developing countries due to poor antimicrobial resistance (AMR) surveillance and irrational use of antibiotics. The current study investigated 100 clinical E. coli isolates and reveale...
The hospital environment has been reported as a source of transmission events and outbreaks of carbapenemase-producing Enterobacterales. Interconnected plumbing systems and the microbial diversity in these reservoirs pose a challenge for outbreak investigation and control. A total of 133 clinical an...
The SARS-CoV-2 coronavirus pandemic has been an unprecedented challenge to global pandemic response and preparedness. With the continuous appearance of new SARS-CoV-2 variants, it is imperative to implement tools for genomic surveillance and diagnosis in order to decrease viral transmission and prev...
COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in Indi...
The increasing prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is a growing problem globally, particularly in low- to middle-income countries (LMICs). Previous studies have shown high rates of CRE colonisation among patients at hospitals in LMICs, with increased risk of hospital-acquired...
During routine industrial quarantine/premobilization procedures, four individuals who recently traveled from the Philippines tested positive for SARS-CoV-2. Subsequent genomic analysis showed that all four were infected with a relatively rare Variant of Interest (P.3, Theta) derived from a single or...
Plasmid-mediated, transmissible, tigecycline-inactivating enzyme Tet(X) has attracted considerable public attention. However, so far studies have not addressed its impact on public health and the ecosystem. Herein, we report the prevalence and molecular epidemiology of tet(X)-positive bacteria (TPB)...
SARS-CoV-2 isolates from long-term COVID-19 patients play a significant role in understanding the mechanisms of infection and virus persistence. This study describes a SARS-CoV-2 isolate from a 53-year-old woman from Apulia (Italy), who was COVID-19 positive for approximately four months. In this pa...
In recent years, a change in the epidemiology of meningococcal disease caused by Neisseria meningitidis serogroup W (MenW) has been observed worldwide, with the emergence of new sublineages associated with a higher rate of fatal cases. The present study intends to describe the epidemiology of invasi...
The appearance of emerging variants of SARS-CoV-2 carrying mutations into the spike protein has recently raised concern with respect to tracking their transmission and mitigating the impact in the evolving pandemic across countries. AY.4.2, a recently detected Delta variant sublineage, is considered...
We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1....
Coronavirus disease 2019 (COVID-19) has had high incidence rates at institutions of higher education (IHE) in the United States, but the transmission dynamics in these settings are poorly understood. It remains unclear to what extent IHE-associated outbreaks have contributed to transmission in nearb...
Emergence of SARS-CoV-2 with high transmission and immune evasion potential, the so-called variants of concern (VOC), is a major concern. We describe the early genomic epidemiology of SARS-CoV-2 recovered from vaccinated health care professionals (HCP). Our postvaccination COVID-19 symptoms-based su...
Current guidelines for patient isolation in COVID-19 cases recommend a symptom-based approach, averting the use of control real-time reverse transcription PCR (rRT-PCR) testing. However, we hypothesized that patients with persistently positive results by RT-PCR for severe acute respiratory syndrome...
Infection by multidrug-resistant (MDR) Acinetobacter baumannii is one of the major causes of hospital-acquired infections worldwide. The ability of A. baumannii to survive in adverse conditions as well as its extensive antimicrobial resistance make it one of the most difficult to treat pathogens ass...
In less than two years since SARS-CoV-2 emerged, the new coronavirus responsible for COVID-19, has accumulated a great number of mutations. Many of these mutations are located in the Spike protein and some of them confer to the virus higher transmissibility or partial resistance to antibody mediated...
Genomic surveillance of SARS-CoV-2 is paramount for understanding viral dynamics, contributing to disease control. This study analyzed SARS-CoV-2 genomic diversity in Rio Grande do Sul (RS), Brazil, including the first reported case in each Regional Health Coordination and cases from three epidemic...
The plague of 1630-1632 was one of the deadliest plague epidemics to ever hit Northern Italy, and for many of the affected regions, it was also the last. While accounts on plague during the early 1630s in Florence and Milan are frequent, much less is known about the city of Imola. We analyzed the fu...
African swine fever (ASF) is a highly infectious and fatal haemorrhagic disease of pigs that is caused by a complex DNA virus of the genus and African suids family. The disease is among the most devastating pig diseases worldwide including Africa. Although the disease was first reported in the 19t...
Staphylococcus aureus is a common pathogen causing hospital acquired infections (HAIs) in neonates. In this study, the epidemiology of methicillin-resistant S. aureus (MRSA) colonization and infections in a 30-bed, level III university-affiliated neonatal intensive care unit (NICU) located in a chil...
Salmonella enterica serovar Choleraesuis is a host-adapted serovar that causes serious infections in domestic pigs and wild boars. Here, we investigated an outbreak of salmonellosis in domestic pigs in Slovenia, 2018-2019. To assess the outbreak, 18 isolates from domestic pigs, wild boars, wild boar...
Since 2015, the United States has experienced a resurgence in the number of mumps cases and outbreaks in fully vaccinated populations. These outbreaks have occurred predominantly in close-quarter settings, such as camps, colleges, and detention centers. Phylogenetic analysis of 758 mumps-positive sa...
Healthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 and has become a major global pathogen in an astonishingly short period of time. The emergence of SARS-CoV-2 has been notable due to its impacts on residents in long-term care facilities (LTCFs). LTCF residents tend to poss...
Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes...
The sudden upsurge in the newly emerging COVID-19 variants acted as a catalyst for India to scale up the viral Genomic surveillance in order to understand the nature and trends of the newer variants of concern and strengthen public health interventions across the country. The Government of India has...
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the main reason for the increasing number of deaths worldwide. Although strict quarantine measures were followed in many countries, the disease situation is still intracta...
For epidemic prevention and control, the identification of SARS-CoV-2 subpopulations sharing similar micro-epidemiological patterns and evolutionary histories is necessary for a more targeted investigation into the links among COVID-19 outbreaks caused by SARS-CoV-2 with similar genetic backgrounds....
The rapid spread and huge impact of the COVID-19 pandemic caused by the emerging SARS-CoV-2 have driven large efforts for sequencing and analyzing the viral genomes. Mutation analyses have revealed that the virus keeps mutating and shows a certain degree of genetic diversity, which could result in t...
Single-cell sequencing is a biotechnology to sequence one layer of genomic information for individual cells in a tissue sample. For example, single-cell DNA sequencing is to sequence the DNA from every single cell. Increasing in complexity, single-cell multi-omics sequencing, or single-cell multimod...
In the last decade, incidences of carbapenem-resistant Acinetobacter baumannii have been increasingly reported worldwide. Consequently, A. baumannii was included in the World Health Organization's new list of critical pathogens, for which new drugs are desperately needed. The objective of this resea...
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Recently, bovine enterovirus (BEV) has caused several respiratory and gastrointestinal diseases outbreaks in cattle. Monitoring the epidemiological and pathogenic characteristics of this virus is crucial to controlling its spread. We isolated a BEV strain with typical cytopathic effects from the fae...
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Crown and root rot is the most important and destructive strawberry diseases in Korea as it causes substantial economic loss. In August 2020, a severe outbreak of crown and root rot on strawberries (Fragaria × ananassa Duch.) was observed in the greenhouse at Sangju, South Korea. Infected plantlets...
The emergence of carbapenem-resistant Pseudomonas aeruginosa is one of the most important challenges in a healthcare setting. The aim of this study is double-locus sequence typing (DLST) typing of bla positive P. aeruginosa isolates. Twenty-nine bla positive isolates were collected during three year...
The genetic diversity of foot-and-mouth disease virus (FMDV) poses a challenge to the successful control of the disease, and it is important to identify the emergence of different strains in endemic settings. The objective of this study was to evaluate the sampling of clinically healthy livestock at...
In June 2020, a large-scale food poisoning outbreak involving about 3000 elementary and junior high school students occurred in Yashio, Saitama, Japan. A school lunch was the only food stuff ingested by all of the patients. Escherichia coli serotype O7:H4 carrying the astA gene for enteroaggregative...
A special-care neonatal unit from a large public hospital in Malawi was noted as having more frequent, difficult-to-treat infections, and a suspected outbreak of multi-drug-resistant was investigated using genomic characterisation. All bloodstream infections (BSIs) from patients in the neonatal wa...
Many public health laboratories across the world have implemented whole-genome sequencing (WGS) for the surveillance and outbreak detection of foodborne pathogens. PulseNet-affiliated laboratories have determined that most single-strain foodborne outbreaks are contained within 0–10 multi-locus seque...
Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with...
The coronavirus disease COVID-19 has been the cause of millions of deaths worldwide. Among the SARS-CoV-2 proteins, the non-structural protein 1 (NSP1) has great importance during the virus infection process and is present in both alpha and beta-CoVs. Therefore, monitoring of NSP1 polymorphisms is c...
The outcome of SARS-CoV-2 infection is determined by multiple factors, including the viral, host genetics, age, and comorbidities. This study investigated the association between prognostic factors and disease outcomes of patients infected by SARS-CoV-2 with multiple S protein mutations. Fifty-one C...
Mutations in emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages can interfere with laboratory methods used to generate viral genome sequences for public health surveillance. We identified 20 mutations that are widespread in variant of concern lineages and affect widely us...
Fibropapillomatosis (FP) of sea turtles is characterised by cutaneous tumours and is associated with Chelonid herpesvirus 5 (ChHV5), an alphaherpesvirus from the family Herpesviridae. Here, we provide the first evidence of ChHV5-associated FP in endangered Green turtles () from Sabah, which is locat...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen subdivided into lineages termed sequence types (STs). Since the 1950s, successive waves of STs have appeared and replaced previously dominant lineages. One such event has been occurring in China since 2013, with commun...
Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec...
Wolbachia are maternally transmitted intracellular bacteria that can naturally and artificially infect arthropods and nematodes. Recently, they were applied to control the spread of mosquito-borne pathogens by causing cytoplasmic incompatibility (CI) between germ cells of females and males. The abil...
Whole-genome sequencing (WGS) has recently been used to investigate acquisition of Mycobacterium abscessus. Investigators have reached conflicting conclusions about the meaning of genetic distances for interpretation of person-to-person transmission. Existing genomic studies were limited by a lack o...
Serratia marcescens is an emerging opportunistic pathogen with high genetic diversity. This article describes the microbiological characteristics of isolates and the risk factors for infections caused by carbapenem-resistant S. marcescens. A retrospective study of patients colonized (n=43) and infec...
The number of bacterial genomes deposited each year in public databases is growing exponentially. However, efforts to use these genomes to track trends in antimicrobial resistance (AMR) have been limited thus far. We used 22,102 genomes from public databases to track AMR trends in nontyphoidal Salmo...
During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most c...
We report on a 15-year-long outbreak of bovine tuberculosis (bTB) in wildlife from a Brazilian safari park. A timeline of diagnostic events and whole-genome sequencing (WGS) of 21 Mycobacterium bovis isolates from deer and llamas were analyzed. Accordingly, from 2003 to 2018, at least 16 animals, fr...
African swine fever virus (ASFV) is one of the pathogens of highest concern worldwide. Despite different virus lineages co-circulating in several areas, dual infections in the same animal have been rarely observed, suggesting that ASF superinfections are infrequent events. Here we present the first...
Understanding the evolution of viral pathogens is critical to being able to define how viruses emerge within different landscapes. Host susceptibility, which is spread between different species and is a contributing factor to the subsequent epidemiology of a disease, is defined by virus detection an...
Verona Integron-encoded Metallo-beta-lactamase (VIM) is the most frequently-encountered carbapenemase in the healthcare-related pathogen Pseudomonas aeruginosa. In the Netherlands, a low-endemic country for antibiotic-resistant bacteria, no national surveillance data on the prevalence of carbapenema...
The availability of millions of SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus-2) sequences in public databases such as GISAID (Global Initiative on Sharing All Influenza Data) and EMBL-EBI (European Molecular Biology Laboratory-European Bioinformatics Institute) (the United Kingdom) allo...
The purpose of this study was to investigate the epidemiological, molecular, and clinical characteristics of MRSA t304/ST8 and t304/ST6 in Norway from 2008 to 2016. Clinical and epidemiological data were collected for each case included in the study. Strains were characterized by PCR, spa typing, an...
Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molecular typing. Long-read sequencing is more rapid and provides useful information about the g...
COVID-19 has swept globally and Pakistan is no exception. To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collecte...
A SARS-CoV-2 B.1.1.7 variant of concern (VOC) has been associated with increased transmissibility, hospitalization, and mortality. This study aimed to explore the factors associated with B.1.1.7 VOC infection in the context of vaccination. On March 2021, we detected SARS-CoV-2 RNA in nasopharyngeal...
is a pathogen of serious concern, often exhibiting multiple antibiotic resistance, frequently associated with hospital outbreaks in intensive care units. A prompt detection and tracking of these isolates is crucial. Reference methods for typing (pulsed-field gel electrophoresis, whole-genome sequenc...
Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public healt...
Clostridium perfringens (C. perfringens) is a common pathogenic microorganism present in nature, which can cause animal and human diseases, such as necrotizing enteritis (NE) in poultry. Little is known about the current prevalence status of C. perfringens from poultry farms of different types and r...
Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), in July 2021 contributed to an outbreak of over one thousand COVID-19 cases among residents and visitors. Most cases were fully vaccinated, many of whom were also symptomatic, prompting a comprehensive pu...
Carbapenem-resistant Enterobacterales (CRE) harboring blaKPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016-2019, a series of regional point-prevalence surveys identified increasing prevalence of blaNDM-containing CRE in multiple long-term acute care hospit...
Wastewater-based genomic surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus shows promise to complement genomic epidemiology efforts. Multiplex tiling PCR is a desirable approach for targeted genome sequencing of SARS-CoV-2 in wastewater due to its low cost and ra...
Human metapneumovirus (hMPV) is one of the important pathogens in infant respiratory tract infection. However, the molecular epidemiology of hMPV among children < 14 years of age hospitalized with severe acute respiratory infection (SARI) is unclear. We investigated the hMPV infection status and gen...
West Java Health Laboratory (WJHL) is one of the many institutions in Indonesia that have sequenced SARS-CoV-2 genome. Although having submitted a large number of sequences since September 2020, however, these submitted data lack advanced analyses. Therefore, in this study, we analyze the variant di...
Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats that threatens food security, small ruminant production and susceptible endangered wild ruminants. With policy directed towards achieving global PPR eradication, the establishment of cost-effective genomic...
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 diffe...
Digital transformation is currently impacting not only health care but also education curricula for medicine and life sciences. The COVID-19 pandemic has accelerated the deployment of digital technologies such as the Internet of Things and artificial intelligence in diverse fields of biomedicine. Ge...
Vector-borne diseases (VBDs) cause enormous health burden worldwide, as they account for more than 17% of all infectious diseases and over 700,000 deaths each year. A significant number of these VBDs are caused by RNA virus pathogens. Here, we used metagenomics and metabarcoding analysis to characte...
: In Coronavirus Disease 2019 (COVID-19), which is caused by the infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the clinical manifestations are primarily related to the pulmonary system. Under 10% of cases also develop gastrointestinal events such as diarrhea, nausea, v...
The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potential...
Since March 2020, 11 lineages of severe acute respiratory syndrome coronavirus 2 have been identified in Sergipe state, Northeast Brazil. During the first 6 months of coronavirus disease 2019 (COVID-19) outbreak, there was a higher frequency of B.1 (58.5%) and B.1.1.33 (17.1%) lineages. During the s...
The rapid increase in carbapenemase-producing Enterobacterales is a global health concern. During 2017-2020, a total of 44 Escherichia coli isolates co-harbouring bla and bla were collected from patients at 17 hospitals in Seoul and characterized based on antimicrobial susceptibility, resistance gen...
Few studies have assessed the clinical and bacterial characteristics of Pseudomonas aeruginosa (PA) bacteraemic pneumonia (BP) episodes. This study analysed all non-duplicate PA-BP episodes from a tertiary hospital in 2013-2017. Epidemiology, clinical data, antimicrobial therapy and outcomes were re...
In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cit...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to beco...
The majority of emerging infectious diseases originate in animals. Current routine surveillance is focused on known diseases and clinical syndromes, but the increasing likelihood of emerging disease outbreaks shows the critical importance of early detection of unusual illness or circulation of patho...
Porcine circovirus 4 (PCV4) was identified as a novel porcine circovirus in China in 2019. To investigate the prevalence and genetic characteristics of PCV2 and PCV4, 133 clinical samples (103 tissue samples and 30 serum samples) were collected from 30 different pig farms in Henan province of China,...
Healthcare workers are at increased risk of occupational transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We report 2 instances of healthcare workers contracting SARS-CoV-2 despite no known breach of personal protective equipment. Additional specific equipment cleaning w...
Arr is an ADP-ribosyltransferase enzyme primarily reported in association with rifamycin resistance, which has been used to treat tuberculosis in addition to Gram-positive infections and, recently, pan-resistant Gram-negative bacteria. The arr gene was initially identified on the Mycolicibacterium s...
Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknow...
Evolutionary analyses of well-annotated human immunodeficiency virus (HIV) sequence data can provide insights into viral transmission patterns and associated factors. Here, we explored the transmission dynamics of the HIV-1 subtype B epidemic across the San Diego (US) and Tijuana (Mexico) border reg...
Clostridioides difficile infections (CDIs) are among the most prevalent hospital-associated infections (HAIs), particularly for intensive care unit (ICU) patients. The risks for developing active CDI from asymptomatic carriage of C. difficile are not well understood. We identified asymptomatic C. di...
African swine fever virus (ASFV) is the etiological agent of the devastating disease African swine fever (ASF), for which there is currently no licensed vaccine or treatment available. ASF is defined as one of the most serious animal diseases identified to date, due to its global spread in regions o...
Genomic epidemiology, which links pathogen genomes with associated metadata to understand disease transmission, has become a key component of outbreak response. Decreasing costs of genome sequencing and increasing computational power provide opportunities to generate and analyse large viral genomic...
During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monito...
carbapenemase-producing KPC-CRPA) are rare in the United States. An outbreak of KPC-CRPA was investigated in Texas using molecular and epidemiologic methods and 17 cases of KPC-CRPA were identified. The isolates were genetically related and harbored the emerging multilocus sequence type 235, the fi...
Patients with invasive infections caused by methicillin-resistant Staphylococcus aureus (MRSA), especially those with an elevated minimal inhibitory concentration (MIC) of vancomycin (VA), are likely to have treatment failure and poor outcomes. The aim of this study was to delineate and correlate th...
The 2021 re-emergence of yellow fever in non-human primates in the state of Rio Grande do Sul (RS), southernmost Brazil, resulted in the death of many howler monkeys (genus ) and led the state to declare a Public Health Emergency of State Importance, despite no human cases reported. In this study, n...
Gonorrhea is a sexually transmitted infection of global concern. We investigated whole-genome sequencing (WGS) as a tool to measure and enhance partner notification (PN) in gonorrhea management. Between May and November 2018, all N. gonorrhoeae isolated from patients attending Leeds Sexual Health, U...
BackgroundIn the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data.AimWe applied genomic epidemiology to trace SARS-CoV-2 spread on an international, n...
Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to det...
We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the sa...
The advent of technologies allowing the global analysis of biological phenomena, referred to as "omics" (genomics, epigenomics, proteomics, metabolomics, microbiomics, radiomics, and radiogenomics), has revolutionized the study of human diseases and traced the path for quantitative personalized medi...
The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data are lacking. We isolated, sequenced, and analyzed 383 A(H1N1)pdm09 viral genomes from hospitali...
COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging...
Molecular typing methods are used to characterize the relatedness between bacterial isolates involved in infections. These approaches rely mostly on discrete loci or whole-genome sequencing (WGS) analyses of pure cultures. On the other hand, their application to environmental DNA profiling to evalua...
University settings have demonstrated potential for coronavirus disease (COVID-19) outbreaks; they combine congregate living, substantial social activity, and a young population predisposed to mild illness. Using genomic and epidemiologic data, we describe a COVID-19 outbreak at the University of Wi...
Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continue...
Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations' persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding...
Zika virus (ZIKV) infection has caused severe unexpected clinical outcomes in neonates and adults during the recent outbreak in Latin America, particularly in Brazil. Congenital malformations associated with ZIKV have been frequently reported; nevertheless, the mechanism of vertical transmission and...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other prevent...
SARS-CoV-2, the etiologic agent at the root of the ongoing COVID-19 pandemic, harbors a large RNA genome from which a tiered ensemble of subgenomic RNAs (sgRNAs) is generated. Comprehensive definition and investigation of these RNA products are important for understanding SARS-CoV-2 pathogenesis. Th...
Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in COVID-19 pandemic control and elimination efforts, especially by elucidating its global transmission network and illustrating its viral evolution. The deployment of multiplex PCR assays th...
We investigated possible nosocomial transmission of 3 invasive cases of Group B Streptococcus serotype III disease in newborns delivered in the same facility. All cases were of the same sequence type and clonal complex. Genomic variation was detected within the core genome and capsular region, indic...
The purpose of this study was to determine the phylogenetic relationships among the primary betanodavirus strains circulating in Tunisian coastal waters. A survey was conducted to investigate nodavirus infections at 15 European sea bass Dicentrarchus labrax and gilthead sea bream Sparus aurata farmi...
Dengue has become endemic in Pakistan with annual recurrence. A sudden increase in the dengue cases was reported from Rawalpindi in 2016, while an outbreak occurred for the first time in Peshawar in 2017. Therefore, a multi-center study was carried out to determine the circulating dengue virus (DENV...
Biting midges of the genus Culicoides Latreille are biological vectors of bluetongue virus (BTV), a member of family Reoviridae, genus Orbivirus. About 30 species of Culicoides have been identified as competent BTV vectors worldwide. Even though high seroprevalence of BTV has been reported among liv...
is one of the most common intracellular bacteria; it infects a wide variety of insects, other arthropods, and some nematodes. is ordinarily transmitted vertically from mother to offspring and can manipulate physiology and reproduction of their hosts in different ways, e.g., induce feminization, mal...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus responsible for the pandemic coronavirus disease 2019 (COVID-19), which has had a devastating impact on society. Here, we summarize proteomic research that has helped elucidate hallmark proteins associ...
Fast and effective methods are needed for sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome to track genetic mutations and to identify new and emerging variants during the ongoing pandemic. The objectives were to assess the performance of the SARS-CoV-2 AmpliSeq r...
Four enzymatic DNA library preparation kits were compared for sequencing Shiga toxin-producing E. coli. All kits produced high quality sequence data which performed equally well in the downstream analyses for surveillance and outbreak detection. Important differences were noted in the workflow user-...
To assess the differences in antimicrobial susceptibility of UK Bacteroides species across two distinct cohorts from 2000 to 2016. Strain identification was performed using matrix-assisted laser-desorption ionisation time of flight mass spectrometry (MALDI-TOF MS) or by partial 16S rRNA sequencing....
Typhoid fever is an invasive bacterial disease of humans that disproportionately affects low- and middle-income countries. Antimicrobial resistance (AMR) has been increasingly prevalent in recent decades in Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, limiting...
In December 2020, Italy experienced the first case of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) B.1.1.7 lineage. In January 2021, we identified 21 cases of this variant in Corzano, defining the first outbreak of SARS-CoV-2 B.1.1.7 lineage in Italy. The high transmissibility of the...
Genomic surveillance of the SARS-CoV-2 pandemic is crucial and mainly achieved by amplicon sequencing protocols. Overlapping tiled-amplicons are generated to establish contiguous SARS-CoV-2 genome sequences, which enable the precise resolution of infection chains and outbreaks. We investigated a SAR...
Outbreaks of MRSA occur in NICUs and may be difficult to control. We describe an outbreak of mupirocin-resistant MRSA, molecular epidemiology of isolates and control. Medical record review of personnel contact with infants. MRSA isolates were analyzed by whole genome sequencing (WGS); single nucleot...
At the end of 2020, several new variants of SARS-CoV-2-designated variants of concern-were detected and quickly suspected to be associated with a higher transmissibility and possible escape of vaccine-induced immunity. In Belgium, this discovery has motivated the initiation of a more ambitious genom...
Elevations of circulating branched-chain amino acids (BCAA) are observed in humans with obesity and metabolic comorbidities, such as insulin resistance. Although it has been described that microbial metabolism contributes to the circulating pool of these amino acids, studies are still scarce, partic...
COVID-19 has emerged as global pandemic with largest damage to the public health, economy and human psyche.The genome sequence data obtained during the ongoing pandemic are valuable to understand the virus evolutionary patterns and spread across the globe. Increased availability of genome informatio...
Recently, Escherichia coli producing extended-spectrum β-lactamases (ESBLs) have become a serious public-health problem, and food-producing animals (FPAs) have been suggested as a potential reservoir/source. This study aimed to compare ESBL-producing E. coli isolates from different sources. ESBL-pro...
Acinetobacter baumannii is a nosocomial pathogen that has emerged as a major threat in the health-care settings, particularly intensive care units (ICUs). The aim of this study was to investigate the prevalence of A. baumannii in the environment of intensive care and emergency units in 4 hospitals i...
Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, including over 582,764 fatalities. A set of...
Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021...
The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource in...
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two...
Vaccination generates a neutralizing immune response against SARS-CoV-2. The genomic surveillance is showing the emergence of variants with mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we report the neutralization potency against alpha,...
Hand, foot, and mouth disease (HFMD) is endemic in Malaysia, with the number of cases increasing. Sabah has experienced several HFMD outbreaks, but information on the epidemiology and molecular characteristics of responsible viruses is scarce. In this study, data of 17,574 reports of HFMD cases in S...
This study aimed to investigate the phylogenetic characterization and virulence traits of uropathogenic Escherichia coli (UPEC) isolated from kidney transplant patients (KTPs) as well as non-KTPs and analyze the clonal distribution of Extended spectrum β-lactamases (ESBLs)-producing UPEC containing...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is among the most concerning cause of healthcare-associated infections (HAI) due to its high level of antibiotic resistance and high mortality. In the era of the COVID-19 pandemic, the key priority of infection control committees is to contain the...
The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event. Our objectives were to perform a complete analysis of the sequential infections and communit...
Genomics, combined with population mobility data, used to map importation and spatial spread of SARS-CoV-2 in high-income countries has enabled the implementation of local control measures. Here, to track the spread of SARS-CoV-2 lineages in Bangladesh at the national level, we analysed outbreak tra...
From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of ind...
Since the 2000s, the distribution of bluetongue virus (BTV) has changed, leading to numerous epidemics and economic losses in Europe. Previously, we found a BTV-4 field strain with a higher infection rate of a vector than a BTV-1 field strain has. We reverse-engineered parental BTV-1 and BTV-4 stra...
The second plague pandemic started in Europe with the Black Death in 1346 and lasted until the 19th century. Based on ancient DNA studies, there is a scientific disagreement over whether the bacterium, , came into Europe once (Hypothesis 1) or repeatedly over the following four centuries (Hypothesis...
Phage therapy is an experimental therapeutic approach used to target multidrug-resistant bacterial infections. A lack of reliable data with regard to its efficacy and regulatory hurdles hinders a broad application. Here we report, for the first time, a case of vancomycin-resistant abdominal infecti...
, a multidrug-resistant yeast, can spread rapidly in ventilator-capable skilled-nursing facilities (vSNFs) and long-term acute care hospitals (LTACHs). In 2018, a laboratory serving LTACHs in southern California began identifying species of that were detected in urine specimens to enhance surveilla...
Vancomycin-resistant (VREfm) is a globally significant nosocomial pathogen with a rapidly increasing prevalence. The objectives were to investigate VREfm outbreak duration and study the additional impact that infection control bundle strategies (ICBSs) set up to curb coronavirus disease 2019 (COVID...
The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interventions are therefore hard to design. In this study, we sequenced 3468 unselected isolates...
Various hypotheses have been proposed regarding the origin of the plant pathogen Phytophthora cinnamomi. P. cinnamomi is a devastating, highly invasive soilborne pathogen associated with epidemics of agricultural, horticultural and forest plantations and native ecosystems worldwide. We conducted a p...
The genus includes a variety of pathogenic viruses that are transmitted by biting midges, mosquitoes and ticks. Some of the economically most relevant orbiviruses are endemic to Namibia, like the livestock-pathogenic Bluetongue and African horse sickness viruses. Here, we assessed the diversity of...
Seasonal influenza epidemics are associated with high mortality and morbidity in the human population. Influenza surveillance is critical for providing information to national influenza programmes and for making vaccine composition predictions. Vaccination prevents viral infections, but rapid influe...
The 10-valent conjugate vaccine (PCV10) was introduced into the Extended Program on Immunization in Madagascar. We assessed the impact of PCV10 on the targeted pneumococcal serotypes among children < 5 years of age at Centre Hospitalier Universitaire Mère Enfant Tsaralalàna. Between 2012 and Decembe...
COVID-19 is a worldwide public health emergency caused by SARS-CoV-2. Genomic surveillance of SARS-CoV-2 emerging variants is important for pandemic monitoring and informing public health responses. Through an interstate academic-public health partnership, we established Rhode Island's capacity to s...
is a leading cause of bloodstream infections. Developing interventions to reduce infections requires an understanding of the frequency of nosocomial transmission, but the available evidence is scarce. We aimed to detect and characterise transmission of and associated plasmids in a hospital setting...
The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, wh...
Data on how SARS-CoV-2 enters and spreads in a population are essential for guiding public policies. This study seeks to understand the transmission dynamics of SARS-CoV-2 in small Brazilian towns during the early phase of the epidemic and to identify core groups that can serve as the initial source...
In response to emerging infectious diseases, such as the recent pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is critical to quickly identify and understand responsible pathogens, risk factors, host immune responses, and pa...
No abstract available
Bovine coronavirus (BCoV) is associated with three distinct clinical syndromes in cattle that is, neonatal diarrhoea, haemorrhagic diarrhoea in adults (the so-called winter dysentery syndrome, WD) and respiratory infections in cattle of different ages. In addition, bovine-like CoVs have been detecte...
The world faces a great unforeseen challenge through the COVID-19 pandemic caused by coronavirus SARS-CoV-2. The virus genome structure and evolution are positioned front and center for further understanding insights on vaccine development, monitoring of transmission trajectories, and prevention of...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) manifests a broad spectrum of clinical presentations, varying in severity from asymptomatic to mortality. As the viral infection spread, it evolved and developed into many variants of concern. Understanding the impact of mutations in the S...
Despite compliance to extensive reprocessing protocols, duodenoscopes have been linked to outbreaks of susceptible and multi-drug resistant organisms (MDRO) due to persistent duodenoscope contamination. Duodenoscope-associated infections (DAIs) based on transmission of susceptible microorganisms are...
Nosocomial outbreaks of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are frequent despite implementation of conventional infection control measures. An outbreak investigation was undertaken using advanced genomic and statistical techniques to reconstruct likely transmission chains an...
Although Clostridioides difficile surveillance often identifies emerging strains, clinical outcome evaluations are rarely performed. Ribotype (RT) 106 is a commonly isolated C. difficile strain worldwide; however, studies investigating RT 106 clinical outcomes are limited. The purpose of this study...
Mycobacterium abscessus (MAB) is an emerging pathogen that leads to chronic lung infections. To date, the global population structure of non-cystic fibrosis (CF) MAB and evolutionary patterns of drug resistance emergence have not been investigated. Here we construct a global dataset of 1,279 MAB who...
In total, 50 Escherichia coli bloodstream isolates from the clinical laboratory and 12 E. coli isolates referred for pulsed-field gel electrophoresis (PFGE) were sequenced, assessed for clonality using core genome multilocus sequence typing (cgMLST), and evaluated for genomic susceptibility predicti...
The role of meticillin-resistant Staphylococcus aureus (MRSA) colonization of healthcare workers (HCWs), patients and the hospital environment in MRSA transmission in non-outbreak settings is poorly understood. To investigate transmission events (TEs) involving HCWs, patients and the environment und...
The pandemic generated by SARS-Cov-2 has caused a large number of cases and deaths in the world, but South America has been one of the continents that were most hard hit. The appearance of new variants causes concern because of the possibility that they may evade the protection generated by vaccinat...
is a dangerous bacterial pathogen possessing the ability to persist on various surfaces, especially in clinical settings, and to rapidly acquire the resistance to a broad spectrum of antibiotics. Thus, the epidemiological surveillance of within a particular hospital, region, and across the world is...
Carbapenem-resistant Acinetobacter baumannii (CRAB) infection outbreaks are difficult to control and sometimes require cohorting of CRAB-positive patients or temporary ward closure for environmental cleaning. We aimed at controlling the deadly 2018 CRAB outbreak in a 12 bed- intensive care unit (ICU...
Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace...
This study describes the epidemiology of listeriosis in New Zealand between 1999 and 2018 as well as the retrospective whole-genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cas...
Salmonella enterica serovar Typhimurium DT160 was the predominant cause of notified human salmonellosis cases in New Zealand from 2000 to 2010, before it was superseded by another S. Typhimurium strain, DT56 variant (DT56v). Whole genome sequencing and phenotypic testing were used to compare 109 DT1...
The mosquito Aedes albopictus is an important vector for many pathogens. Understanding the virome in Ae. albopictus is critical for assessing the risk of disease transmission, implementation of vector control measures, and health system strengthening. In this study, viral metagenomic and PCR methods...
To investigate the spread of (RYMV) along the Niger River, regular sampling of virus isolates was conducted along 500 km of the Niger Valley in the Republic of Niger and was complemented by additional sampling in neighbouring countries in West Africa and Central Africa. The spread of RYMV into and...
Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus . Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 pe...
To analyse nosocomial transmission in the early stages of the coronavirus 2019 (COVID-19) pandemic at a large multisite healthcare institution. Nosocomial incidence is linked with infection control interventions. Viral genome sequence and epidemiological data were analysed for 574 consecutive patien...
While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE...
Different coronaviruses have emerged due to their ability to infect, mutate and recombine multiple species and cell types, suggesting that these viruses will carry on to evolve and origin both veterinary and human diseases. So far, more than fifteen coronavirus-related diseases have been described i...
Vancomycin-resistant Enterococcus (VRE) is a rare bacterium in Japan, but an outbreak due to nosocomial transmission in medical facilities has been reported in recent years. Here, we report the outbreak of vanA vancomycin-resistant Enterococcus faecium (VREfm) in multiple wards of Nara Prefectural G...
To identify key factors of the expansion of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa (MPPA) in Poland, focusing on the role of clonal epidemic(s). MPPA isolates were typed by PFGE, followed by MLST. blaVIM/IMP MBL genes were amplified and sequenced within class 1 integrons. Their l...
During 2018-19, an increase of vanB vancomycin-resistant Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. vanA/vanB PCR performed directly on rectal swabs is accurate in detection of vanA; however, the positive predictive value for vanB-positive samples is low because of t...
The SARS-CoV-2 P.1 variant of concern (VOC) was first identified in Brazil and is now spreading in European countries. It is characterized by the E484K mutation in the receptor-binding domain, which could contribute to the evasion from neutralizing antibodies. In Italy, this variant was first identi...
Aleutian mink disease virus (AMDV) is one the most relevant pathogens of domestic mink, where it can cause significant economic losses, and wild species, which are considered a threat to mink farms. Despite their relevance, many aspects of the origin, evolution, and geographic and host spreading pat...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance has been vital in understanding the spread of coronavirus disease 2019 (COVID-19), the emergence of viral escape mutants, and variants of concern. However, low viral loads in clinical specimens affect variant calling f...
Duck hepatitis A virus (DHAV), an avian picornavirus, causes high-mortality acute disease in ducklings. Among the three serotypes, DHAV-1 is globally distributed, whereas DHAV-2 and DHAV-3 serotypes are chiefly restricted to Southeast Asia. In this study, we analyzed the genomic evolution of DHAV-1...
Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoron...
The application of next-generation sequencing extends from microbial identification to epidemiologic insight and antimicrobial resistance prediction. Despite this potential, the roadblock for clinical laboratories lies in implementation and validation of such complex technology and data analysis. He...
Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergenc...
Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2)....
Almost a year after the COVID-19 pandemic had begun, new lineages (B.1.1.7, B.1.351, P.1, and B.1.617.2) associated with enhanced transmissibility, immunity evasion, and mortality were identified in the United Kingdom, South Africa, and Brazil. The previous most prevalent lineages in the state of Ri...
has acquired resistance to several antimicrobial drugs, including last-resort antibiotics affecting, therefore, clinical efficacy and causing high rates of mortality. In this study, we investigate the whole genome sequence of a carbapenem-resistant strain isolated from the hospital environment in T...
The SARS-CoV-2 B.1.1.7 variant has increased sharply in numbers worldwide and is reported to be more contagious than the nonvariant. Little is known regarding the detailed clinical features of B.1.1.7 variant infection. Data on 74 COVID-19 cases from two outbreaks in two districts of Beijing, China...
SARS-CoV-2 nosocomial outbreaks in the first COVID-19 wave were likely associated with a shortage of personal protective equipment and scarce indications on control measures. Having covered these limitations, updates on current SARS-CoV-2 nosocomial outbreaks are required. We carried out an in-depth...
Candida auris is a human fungal pathogen classified as an urgent threat to the delivery of health care due to its extensive antimicrobial resistance and the high mortality rates associated with invasive infections. Global outbreaks have occurred in health care facilities, particularly, long-term car...
To determine the molecular strain typing and drug resistance pattern of serovar Typhi prevalent in Northwest Pakistan. A total of 2,138 blood samples of suspected typhoid patients from Northwest Pakistan were collected followed by identification of Typhi through biochemical, serological, and spec...
To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Alge...
Traditional methods of outbreak investigations utilize reactive whole genome sequencing (WGS) to confirm or refute the outbreak. We have implemented WGS surveillance and a machine learning (ML) algorithm for the electronic health record (EHR) to retrospectively detect previously unidentified outbrea...
The evolution and emergence of drug-resistant tuberculosis (TB) has been studied extensively in some contexts, but the ecological drivers of these two processes remain poorly understood. This study sought to describe the joint evolutionary and epidemiological histories of a novel multidrug-resistant...
(formerly subsp. ) is a common commensal and opportunistic pathogen of companion dogs. It carries a range of antimicrobial resistance genes and is an occasional zoonotic pathogen. Despite the potential insight offered by genome sequencing into the biology of , few genomes are currently available fo...
We discuss genomic detection of Schmallenberg virus in both Culicoides midges and affected ruminants during June 2018-December 2019, demonstrating its circulation in Israel. This region is a geographic bridge between 3 continents and may serve as an epidemiologic bridge for potential Schmallenberg v...
and the heterotypic synonym from dairy origin have recently been identified as a novel species based on 16S rRNA gene sequence analysis. type strain NCTC 7171 was used as the reference genome for determining and to be separate species. However, this taxonomic classification did not consider the...
The advancement of molecular techniques such as whole-genome sequencing (WGS) has revolutionized the field of bacterial strain typing, with important implications for epidemiological surveillance and outbreak investigations. This review summarizes state-of-the-art techniques in strain typing and exa...
This study was conducted to investigate mechanisms of cross-resistance to chlorine and peracetic acid (PAA) disinfectants by antibiotic-resistant bacteria. Our study evaluated chlorine and PAA based disinfection kinetics of erythromycin-resistant Enterococcus faecalis, meropenem-resistant Escherichi...
An outbreak of serotype 19A occurred among the residents of a relief facility. Pneumonia developed in 5 of 99 residents (attack rate, 5.1%). We obtained pharyngeal specimens from non-onset residents, and was isolated from 6 individuals (6.4%), 5 of whom had serotype 19A.
The bacterium Vibrio cholerae can colonize the human intestine and cause cholera, but spends much of its life cycle in seawater. The pathogen must adapt to substantial environmental changes when moving between seawater and the human intestine, including different availability of carbon sources such...
Here, we report on the increasing frequency of the SARS-CoV-2 lineage A.27 in Germany during the first months of 2021. Genomic surveillance identified 710 A.27 genomes in Germany as of 2 May 2021, with a vast majority identified in laboratories from a single German state (Baden-Wuerttemberg, = 572;...
The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large...
Although the development and increasingly widespread availability of effective and safe vaccines provides the greatest hope for the future recovery from the increasingly devastating COVID-19 pandemic, there are other preventive efforts that offer an immediate route to decreasing morbidity and mortal...
Dengue virus (DENV) is one of the most prevalent neglected tropical diseases, with half of the world's population at risk of infection. In Nepal, DENV was first reported in 2004, and its prevalence is increasing every year. The present study aimed to obtain and characterize the full-length genome se...
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of health care-associated (HA) and community-associated (CA) infections. USA300 strains are historically CA-MRSA, while USA100 strains are HA-MRSA. Here, we update an antibiotic prediction rule to distinguish these two genotypes b...
A total of 54 unique clinical Acinetobacter baumannii strains isolated from cerebrospinal fluid (CSF) together with 21 bloodstream isolates collected from five tertiary hospitals in East China between April 2013 and November 2016 were studied for antimicrobial susceptibility patterns and the prevale...
Acinetobacter baumannii has become one of the most important multidrug-resistant nosocomial pathogens all over the world. Nonetheless, very little is known about the diversity of A. baumannii lineages coexisting in hospital settings. Here, using whole-genome sequencing, epidemiological data, and ant...
Salmonella Panama was considered an invasive non-typhoidal Salmonella (iNTS) serovar. Comprehensive clinical, microbiological, and genomic studies on S. Panama are scarce. We aimed to characterize the clinical and microbiological characteristics of S. Panama infection. Virulence mechanism of S. Pana...
Bacillus cereus is a well-known pathogen for self-limited foodborne illness, and rarely an opportunistic pathogen associated with invasive infections among immunocompromised patients. Nosocomial outbreaks have been rarely reported. Between August and November 2019, four preterm neonates in neonatal...
Dual resistance to colistin and carbapenems is a milestone reached by certain extensively-drug resistant (XDR) Gram-negative bacteria. This study describes the first outbreak of XDR colistin- and carbapenem-resistant OXA-23-/NDM-1-producing Acinetobacter baumannii (CCRAB) in the European overseas te...
Burkholderia pseudomallei causes the severe disease melioidosis. Whole-genome sequencing (WGS)-based typing methods currently offer the highest resolution for molecular investigations of this genetically diverse pathogen. Still, its routine application in diagnostic laboratories is limited by the ne...
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for a pandemic response, but many laboratories do not have the resources to support population-level seq...
While China experienced a peak and decline in coronavirus disease 2019 (COVID-19) cases at the start of 2020, regional outbreaks continuously emerged in subsequent months. Resurgences of COVID-19 have also been observed in many other countries. In Guangzhou, China, a small outbreak, involving less t...
Microorganisms living in the midgut of Anopheles mosquitoes have been studied to fight vector-borne diseases, such as malaria. Studies on the microbiota of the Neotropical Anopheles darlingi, the most important Brazilian vector for malaria, have been reported for the same purpose. Our aims were to i...
An outbreak of Klebsiella pneumoniae producing the carbapenemase NDM-1 occurred in our ICU during the last COVID-19 wave. Twelve patients were tested positive, seven remained asymptomatic whereas 5 developed an infection. Resistome and in silico multilocus sequence typing confirmed the clonal origin...
Recent studies indicated that the monosubstituted deoxystreptamine aminoglycoside apramycin is a potent antibiotic against a wide range of MDR Gram-negative pathogens. To evaluate the in vitro activity of apramycin against carbapenem-resistant Klebsiella pneumoniae (CRKp) isolates from New York and...
High-frequency, rapid-turnaround severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, 2 SARS-CoV-2 outbreaks occurred among intercollegiate university athletic pr...
Q fever is a worldwide zoonosis caused by Coxiella burnetii (Cb). From January 2018 to November 2019, plasma samples from 2,382 patients with acute fever of unknown cause at a hospital in Zhuhai city of China were tested using metagenomic next-generation sequencing (mNGS). Of those tested, 138 patie...
The aim of this study was to determine the contribution of the contamination of the health care environment in the acquisition of carbapenem-resistant Klebsiella pneumoniae (CRKP) in a CRKP-prevalent setting. We performed a 3-month prospective study in a 20-bed medical intensive care unit (ICU) by c...
Genomic epidemiology of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has provided global epidemiological insight into the COVID-19 pandemic since it began. Sequencing of the virus has been performed at scale, with many countries depositing data into open access repositories to enable...
In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses c...
Third-generation cephalosporin-resistant Gram-negatives (3GCR-GN) and vancomycin-resistant enterococci (VRE) are common causes of multi-drug resistant healthcare-associated infections, for which gut colonisation is considered a prerequisite. However, there remains a key knowledge gap about colonisat...
Since the start of 2020, the world has been upended by the pandemic caused by the severe acute respiratory coronavirus type 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). It has not only led to a tragic loss of life and terrible economic costs but has also been met with...
The genus Flavivirus incorporates bona fide arboviruses, as well as others viruses with restricted replication in insect cells. Among the latter, a large monophyletic cluster of viruses, known as cISF (classical insect-specific flaviviruses), has been sampled in many species of mosquitoes collected...
The scale of the international efforts to sequence SARS-CoV-2 genomes is unprecedented. Early availability of genomes allowed rapid characterisation of the virus, thus kickstarting many highly successful vaccine development programmes. Worldwide genomic resources have provided a good understanding o...
More than a year after the first identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of the 2019 coronavirus disease (COVID-19) in China, the emergence and spread of genomic variants of this virus through travel raise concerns regarding the introduct...
As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genet...
A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the sourc...
Morbidity and mortality from typhoid and paratyphoid fever remain an important problem for public health authorities in developing countries. In countries with lower incidences, most cases occur in travelers who visit regions in which typhoid and paratyphoid fever are highly endemic. The aim was to...
Mutations accrued by SARS-CoV-2 lineage P.1-first detected in Brazil in early January, 2021-include amino acid changes in the receptor-binding domain of the viral spike protein that also are reported in other variants of concern, including B.1.1.7 and B.1.351. We aimed to investigate whether isolate...
Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and...
Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interp...
To unravel the source of SARS-CoV-2 introduction and the pattern of its spreading and evolution in the United Arab Emirates, we conducted meta-transcriptome sequencing of 1067 nasopharyngeal swab samples collected between May 9th and Jun 29th, 2020 during the first peak of the local COVID-19 epidemi...
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We p...
The emergence of new SARS-CoV-2 variants with enhanced transmissibility or decreased susceptibility to immune responses is a major threat to global efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Disparities in viral genomic surveillance capabilities and efforts have resulted in gap...
serovar Enteritidis is a major cause of foodborne infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool...
BACKGROUNDSARS-CoV-2 plasma viremia has been associated with severe disease and death in COVID-19 in small-scale cohort studies. The mechanisms behind this association remain elusive.METHODSWe evaluated the relationship between SARS-CoV-2 viremia, disease outcome, and inflammatory and proteomic prof...
After the introduction of pneumococcal conjugate vaccines for children, invasive pneumococcal disease caused by Streptococcus pneumoniae serotype 4 declined in all ages in Alberta, Canada, but it has reemerged and spread in adults in Calgary, primarily among persons who are experiencing homelessness...
Norovirus, often called winter vomiting bug, is the most common cause of outbreaks of acute gastroenteritis in all age groups all over the world. It was discovered in 1972; belong to the genus Norovirus in the family Caliciviridae. Based on genomic organization and phylogenetic analysis, the family...
This study investigated the evolution and epidemiology of the community-associated and multidrug-resistant clone European CC1-MRSA-IV. Whole-genome sequences were obtained for 194 European CC1-MRSA-IV isolates (189 of human and 5 of animal origin) from 12 countries, and 10 meticillin-susceptible pr...
Whole genome sequencing (WGS) surveillance and electronic health record data mining have the potential to greatly enhance the identification and control of hospital outbreaks. The objective was to develop methods for examining economic value of a WGS surveillance-based infection prevention (IP) prog...
Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 . isolates recovered from suspected paediatric meningitis case...
Livestock pigs and porcine norovirus could be candidate tools for future studies on the geographic isolation of norovirus. In this study, we provide the first evidence for geographic isolation of the host as a determinant of the distribution of subgenotypes of the porcine norovirus genogroup II (GII...
COVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneously achie...
Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to...
The unrestricted use of linezolid has been linked to the emergence of linezolid-resistant Staphylococcus epidermidis (LRSE). We report the effects of combined antibiotic stewardship and infection control measures on the spread of LRSE in an intensive care unit (ICU). Microbiological data were review...
Plant viruses trigger numerous responses in their insect vectors. Using iTRAQ-based quantitative proteomics analysis, early responses of the insect vector, the small brown planthopper (Laodelphax striatellus Fallén, SBPH), after acquiring Rice black-streaked dwarf virus (RBSDV) at 3 days and 5 days...
The Zika virus (ZIKV) epidemic of 2015/2016 spread throughout numerous countries. It emerged in mainland Latin America and spread to neighboring islands, including the Caribbean island of Barbados. Recent studies have indicated that the virus must have already been circulating in local mosquito popu...
Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provide...
Lupin cultivation worldwide is threatened by anthracnose, a destructive disease caused by the seed- and air-borne fungal pathogen Colletotrichum lupini. In this study we explored the intraspecific diversity of 39 C. lupini isolates collected from different lupin cultivating regions around the world,...
No abstract available
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of coronavirus disease-2019 (COVID-19), is a highly contagious pathogenic coronavirus to emerge and spread in human populations. Although substantial exertions have been laid to avert spread of COVID-19 by therapeuti...
Legionnaires' disease (LD) is a severe pneumonia caused by bacteria belonging to the genus . This is a major public health concern and infections are steadily increasing worldwide. Several sources of infection have been identified, but they have not always been linked to human isolates by molecular...
Carbapenem-resistant Enterobacter cloacae complex (CREC) is a new emerging threat to global public health. The objective of the study was to investigate the clinical characteristics and molecular epidemiology of CREC infections in the medical center of northeast China. Twenty-nine patients were infe...
During the COVID-19 pandemic, Thailand implemented a quarantine program at approved quarantine facilities for every international traveler. Here, we report an epidemiological and genomic investigation of a COVID-19 cluster consisting of seven healthcare workers (HCWs) at a quarantine facility and it...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta coronavirus that belongs to the Coronaviridae family. SARS-CoV-2 is an enveloped spherical-shaped virus. The ribonucleic acid (RNA) is oriented in a 5'-3'direction which makes it a positive sense RNA virus, and the RNA can be rea...
In this study, we aimed to investigate the molecular epidemiology and drug-resistance profiles of tuberculosis (TB) in Luodian, an area with highest TB incidence and limited healthcare resources in Guizhou, China. The passive case finding strategy was used to identify suspected pulmonary TB with sym...
The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of an unprecedented worldwide pandemic. Brazil demonstrates one of the highest numbers of confirmed SARS-CoV-2 cases, and São Paulo State is the epicenter of the pandemics in the country. Nevertheless, little is...
The ongoing COVID-19 pandemic has not only globally caused a high number of causalities, but is also an unprecedented challenge for scientists. False-positive virus detection tests not only aggravate the situation in the healthcare sector, but also provide ground for speculations. Previous studies h...
Clostridioides difficile BI/NAP1/ribotype 027 is an epidemic hypervirulent strain found worldwide, including in Latin America. We examined the genomes and exoproteomes of two multilocus sequence type (MLST) clade 2 C. difficile strains considered hypervirulent: ICC-45 (ribotype SLO231/UK[CE]821), is...
Acinetobacter baumannii (A. baumannii), an opportunistic, gram-negative pathogen, has evoked the interest of the medical community throughout the world because of its ability to cause nosocomial infections, majorly infecting those in intensive care units. It has also drawn the attention of researche...
Whole genome sequencing (WGS) analysis in tuberculosis allows the prediction of drug-resistant phenotypes, identification of lineages, and to better understanding of the epidemiology and transmission chains. Nevertheless the procedure has been scarcely assessed in Mexico, in this work we analyze by...
Standing amidst the COVID-19 pandemic, we have faced major medical and economic crisis in recent times which remains to be an unresolved issue till date. Although the scientific community has made significant progress towards diagnosis and understanding the disease; however, effective therapeutics a...
SARS-CoV-2 infection poses a global health crisis. In parallel with the ongoing world effort to identify therapeutic solutions, there is a critical need for improvement in the prognosis of COVID-19. Here, we report plasma proteome fingerprinting that predict high (hospitalized) and low-risk (outpati...
While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be us...
The catalytic subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) Nsp12 has a unique nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain that transfers nucleoside monophosphates to the Nsp9 protein and the nascent RNA. The NiRAN...
Advances in the epidemiological tracing of pathogen transmission have been largely driven by the increasing characterisation of whole-genome sequence data obtained at a finer resolution from infectious disease outbreaks. Dynamic models that integrate genomic and epidemiological data further enhance...
African swine fever (ASF) caused by the African swine fever virus (ASFV) is ranked by OIE as the most important source of mortality in domestic pigs globally and is indigenous to African wild suids and soft ticks. Despite two ASFV genotypes causing economically devastating epidemics outside the cont...
The global pandemic of coronavirus disease 2019 (COVID-19) has identified thousands of genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). On 31st May 2021, the Virus Evolution Working Group of the World Health Organization (WHO) announced its recommendations for revise...
Dengue fever, caused by the mosquito-borne dengue virus (DENV), has been endemic in Myanmar since 1970 and it has become a significant public health burden. It is crucial that circulating DENV strains are identified and monitored, and that their transmission efficiency and association with disease s...
Brucellosis is a highly contagious zoonosis that occurs worldwide. Whole-genome sequencing (WGS) has become a widely accepted molecular typing method for outbreak tracing and genomic epidemiology of brucellosis. Twenty-nine spp. (eight biovar 1 and 21 biovar 3) were isolated from lymph nodes, mil...
Ectromelia virus (ECTV), the causative agent of mousepox, has threatened laboratory mouse colonies worldwide for almost a century. Mousepox has been valuable for the understanding of poxvirus pathogenesis and immune evasion. Here, we have monitored in parallel the pathogenesis of nine ECTVs in BALB/...
The emergence and establishment of SARS-CoV-2 variants of interest (VOI) and variants of concern (VOC) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking potentially relevant Spike protein mutations. We ana...
Cholera has been present and recurring in Zambia since 1977. However, there is a paucity of data on genetic relatedness and diversity of the Vibrio cholerae isolates responsible for these outbreaks. Understanding whether the outbreaks are seeded from existing local isolates or if the outbreaks repre...
Gonorrhoea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are significant public health concerns globally. Nearly no gonococcal AMR data are available from Central Asia, and no data from Kyrgyzstan has been published. We examined, for the first time, AMR and molecular epidemiology of N....
To understand the epidemiological and etiologic characteristics of meningococcal meningitis in Xinjiang Uygur Autonomous Region (Xinjiang). The epidemiological data about the meningococcal meningitis cases in Xinjiang from 1960 to 2019 were collected from the China information system for disease co...
The continued endemicity of foot and mouth disease virus (FMDV) in East Africa has significant implications for livestock production and poverty reduction, yet its complex epidemiology in endemic settings remains poorly understood. Identifying FMDV dispersal routes and drivers of transmission is key...
Indirect (environmental) and direct (host-host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (te...
Antimicrobial-resistant bacteria and their antimicrobial resistance (AMR) genes can spread by hitchhiking in human guts. International travel can exacerbate this public health threat when travelers acquire AMR genes endemic to their destinations and bring them back to their home countries. Prior stu...
Following its emergence in late 2019, the spread of SARS-CoV-2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel...
Genome-wide analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains is essential to better understand infectivity and virulence and to track coronavirus disease 2019 (COVID-19) cases and outbreaks. We performed whole-genome sequencing of 27 SARS-CoV-2 strains isolated betwee...
An outbreak of aseptic meningitis occurred from June to August 2016, in Inner Mongolia Autonomous Region, China. To determine its epidemiological characteristics, etiologic agent, and possible origin, specimens were collected for virus isolation and identification, followed by molecular epidemiologi...
Since the first complete genome sequencing of SARS-CoV-2 in December 2019, more than 550,000 genomes have been submitted into the GISAID database. Sequencing of the SARS-CoV-2 genome might allow identification of variants with increased contagiousness, different clinical patterns and/or different re...
No abstract available
Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following its initial outbreak in the 19...
The COVID-19 pandemic has become a worldwide health crisis. So far, most studies have focused on the epidemiology and pathogenesis of this infectious disease. Little attention has been given to the disease sequelae in patients recovering from COVID-19, and nothing is known about the mechanisms under...
Lymphogranuloma venereum (LGV), the invasive infection of the sexually transmissible infection (STI) , is caused by strains from the LGV biovar, most commonly represented by -genotypes L2b and L2. We investigated the diversity in LGV samples across an international collection over seven years using...
is the leading cause of healthcare-associated infectious diarrhoea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare environments, and that the primary sites of transmission may be strain-dependent. We conducted a multisite geno...
Specific lineages of serogroup O1 are notorious for causing cholera pandemics, of which there have been seven since the 1800s. Much is known about the sixth pandemic (1899–1923) and the ongoing seventh pandemic (1961–present), but we know very little about the bacteriology of pandemics 1 to 5. More...
Background is one of the most frequent causes of bacterial gastroenteritis. outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing...
Methicillin-resistant Staphylococcus aureus (MRSA)-and now USA300 MRSA-is a significant intensive care unit (ICU) pathogen; healthcare worker (HCW) contamination may lead to patient cross-transmission. From September 2015 to February 2016, to study the spread of MRSA, we enrolled HCWs in 4 adult ICU...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the COVID-19 pandemic, continues to cause a significant public-health burden and disruption globally. Genomic epidemiology approaches point to most countries in the world having experienced many indep...
The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from...
No abstract available
Feline panleukopenia is a severe disease of cats caused by feline parvovirus (FPV), and marginally canine parvovirus (CPV). Despite being less rapid than CPV, FPV evolution deserves attention, especially since outbreaks of particular severity are currently reported. This apparently different virulen...
Surveillance studies for Staphylococcus aureus carriage are a primary tool to survey the prevalence of methicillin-resistant S. aureus (MRSA) in the general population, patients and healthcare workers. We have previously reported S. aureus carriage in various African countries, including Cape Verde....
Hard ticks act as arthropod vectors in the transmission of human and animal pathogens and are widely distributed in northern China. The aim of this study is to screen the important tick-borne pathogens (TBPs) carried by hard ticks in Inner Mongolia using metagenomic next-generation sequencing (mNGS)...
Rabies is a fatal yet vaccine-preventable disease. In the last two decades, domestic dog populations have been shown to constitute the predominant reservoir of rabies in developing countries, causing 99% of human rabies cases. Despite substantial control efforts, dog rabies is still widely endemic a...
An outbreak of diphtheria, declared in Yemen in October, 2017, is ongoing. We did a cross-sectional study to investigate the epidemiological, clinical, and microbiological features of the outbreak. Probable cases of diphtheria that were defined clinically and recorded through a weekly electronic dis...
The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak demonstrates the potential of coronaviruses, especially bat-derived beta coronaviruses to rapidly escalate to a global pandemic that has caused deaths in the order of several millions already. The huge efforts put in p...
Blastocystis is a common anaerobic colonic protist in humans with controversial pathogenicity. Clostridium difficile (C. difficile) is the commonest cause of infectious diarrhea in healthcare settings. The prevalence and subtype (ST) characteristics of Blastocystis in patients with C. difficile infe...
Infectious diseases are a major burden to global economies, and public and animal health. To date, quantifying the spread of infectious diseases to inform policy making has traditionally relied on epidemiological data collected during epidemics. However, interest has grown in recent phylodynamic tec...
The rise in human adenovirus (HAdV) infections poses a serious challenge to public health in China. Real-time (RT) sequencing provides solutions for achieving rapid pathogen identification during outbreaks, whereas high-throughput sequencing yields higher sequence accuracy. In the present study, we...
To study the epidemic features of hand-foot-mouth disease (HFMD) in mainland China through systematic review and meta-analysis so as to provide evidence for the future prevention and control of HFMD. Articles on the epidemic features of HFMD in mainland China, written in English or Chinese and relea...
Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We aimed to track molecular evolution and spread of Severe acute res...
Human fatalities caused by rabies are rarely reported in Jordan; however, domestic animals are more likely to fall victim to rabies compared to wild animals, at least this is the case in Jordan due to the presence of canine rabies. In this study, twelve brain samples from domestic and wild animals s...
The threat posed by novel pandemics in the future remains active. Equipping our routine laboratory with clinical metagenomics to detect unknown threats early on offers a considerable advantage and may be feasible and scalable with the ability to identify complicated infectious diseases in routine ca...
In 2018 to 2019, PCR for carbapenemases in routine Gram-negative isolates submitted to the National Microbiology Laboratory revealed an increase in IMP-type metalloenzyme-positive isolates, mostly among Whole-genome sequencing revealed that 23 harbored within a chromosomal Tn element. Phylogenomi...
COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent. To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 Af...
Effective systems for the analysis of molecular data are fundamental for monitoring the spread of infectious diseases and studying pathogen evolution. The rapid identification of emerging viral strains, and/or genetic variants potentially associated with novel phenotypic features is one of the most...
The benefits of wastewater-based epidemiology (WBE) for tracking the viral load of SARS-CoV-2, the causative agent of COVID-19, have become apparent since the start of the pandemic. However, most sampling occurs at the wastewater treatment plant influent and therefore monitors the entire catchment,...
The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike prot...
Meningococcal disease is a life-threatening illness caused by the human-restricted bacterium Neisseria meningitidis. Outbreaks in the USA involve at least two cases in an organization or community caused by the same serogroup within three months. Genome comparisons, including phylogenetic analysis a...
The COVID-19 pandemic has infected millions of people worldwide and many countries have been suffering from a large number of deaths. Acknowledging the ability of SARS-CoV-2 to mutate into distinct strains as an RNA virus and investigating its potential to cause reinfection is important for future h...
Hepatitis B virus genotype A (HBV-A) is disseminated in different countries around the world. It presents a high genetic diversity and is classified into seven subgenotypes (A1-A7). HBV-A1 and HBV-A2 are the most frequent and spread in almost all American countries. This study aimed to evaluate the...
Vaccines are powerful agents in infectious disease prevention but often designed to protect against some strains that are most likely to spread and cause diseases. Most vaccines do not succeed in eradicating the pathogen and thus allow the potential emergence of vaccine evading strains. As with most...
HoBi-like pestivirus, an emerging species within the Pestivirus genus, is an important pathogen associated with a variety of clinical manifestations of ruminants, especially cattle. HoBi-like pestiviruses were identified in several countries and from different hosts, and raised concerns with regard...
Although drinking water disinfection proved to be an effective strategy to eliminate many pathogens, bacteria can still show disinfection tolerance in drinking water distribution systems. To date, the molecular mechanisms on how environmental stress affects the tolerance of Pseudomonas aeruginosa to...
Leptospirosis is a zoonosis caused by pathogenic Leptospira spp. Cats have been reported to be infected with Leptospira spp. and shed the bacteria in the urine. However, the importance of cats as an infection source for humans remains unclear. In this study, Leptospira infection in cats in Okinawa P...
Over 950,000 whole-genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been determined for viruses isolated from around the world. These sequences are critical for understanding the spread and evolution of SARS-CoV-2. Using global phylogenomics, we show that mutatio...
A large number of insect-specific viruses (ISVs) have recently been discovered, mostly from hematophagous insect vectors because of their medical importance, but little attention has been paid to important plant virus vectors such as the whitefly Bemisia tabaci, which exists as a complex of cryptic...
Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data generated at an unprecedented rate. We present an updated version...
A novel circovirus designated "porcine circovirus type 4" (PCV4) was recently reported in pigs with severe clinical disease in Hunan Province, China. Relatively little is known about the molecular epidemiology of this recently discovered virus. In order to assess the prevalence of PCV4 infection in...
After the Zika virus (ZIKV) epidemic in the Americas in 2016, both Zika and dengue incidence declined to record lows in many countries in 2017-2018, but in 2019 dengue resurged in Brazil, causing ~2.1 million cases. In this study we use epidemiological, climatological and genomic data to investigate...
In December 2020, Italy began a national immunization campaign using the BNT162b2 coronavirus disease 2019 (COVID-19) mRNA vaccine, prioritizing healthcare workers (HCWs). Immune serum from vaccinated subjects seems (largely) to retain titres of neutralizing antibodies, even against severe acute res...
SARS-COV-2, Severe Acute Respiratory Syndrome (SARS), and the Middle East respiratory syndrome-related coronavirus (MERS) viruses are from the coronaviridae family; the former became a global pandemic (with low mortality rate) while the latter were confined to a limited region (with high mortality r...
Low-pathogenicity avian influenza viruses (LPAIV) introduced by migratory birds circulate in wild birds and can be transmitted to poultry. These viruses can mutate to become highly pathogenic avian influenza viruses causing severe disease and death in poultry. In March 2019, an H7N3 avian influenza...
Previous investigations have identified high rates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among residents and staff in care homes reporting an outbreak of coronavirus disease 2019 (COVID-19). We investigated care homes reporting a single suspected or confirmed case...
Several recent reports have raised concern that infected coworkers may be an important source of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) acquisition by healthcare personnel. In a suspected outbreak among emergency department personnel, sequencing of SARS-CoV-2 confirmed transmissio...
The Dutch province of Limburg borders the German district of Heinsberg, which had a large cluster of COVID-19 cases linked to local carnival activities before any cases were reported in the Netherlands. However, Heinsberg was not included as an area reporting local or community transmission per the...
Candida albicans bloodstream infection (BSI) is epidemiologically important because of its increasing frequency and serious outcome. Strain typing and delineation of the species are essential for understanding the phylogenetic relationship and clinical significance. Microsatellite CAI genotyping and...
The true frequency of hospital outbreaks of invasive group B streptococcal (iGBS; Streptococcus agalactiae) disease in infants is unknown. We used whole genome sequencing (WGS) of iGBS isolates collected during a period of enhanced surveillance of infant iGBS disease in the UK and Ireland to determi...
is a causal agent of bovine tuberculosis (bTB), one of the most important diseases currently facing the cattle industry worldwide. Tracing the source of infections of livestock is an important tool for understanding the epidemiology of bTB and defining control/eradication strategies. In this study,...
EV-D68 is an emerging enterovirus infection associated with severe acute respiratory illness (SARI), acute flaccid myelitis (AFM) and acute flaccid paralysis (AFP). While EV-D68 outbreaks and sporadic cases are reported globally, a single case has been reported from India. The present study aims to...
Tuberculosis is a leading public health priority in eastern Malaysia. Knowledge of the genomic epidemiology of tuberculosis can help tailor public health interventions. Our aims were to determine tuberculosis genomic epidemiology and characterize resistance mutations in the ethnically diverse city o...
Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated the virus, New Zealand experienced a second outbreak. Dur...
One health is a flexible concept with many facets, including the environment, community, and the nosocomial super-bacteria resistance network. We investigated the molecular prevalence of extended-spectrum-β-lactamase-producing (ESBL-EC) in workers, livestock, and the farm environment in Korea. ESBL...
The tp0548 gene, hypothesized to encode for an outer-membrane protein, was originally used in the enhanced Centers for Disease Control and Prevention typing for molecular typing of Treponema pallidum. It plays an important role in the molecular epidemiology of Treponema because it is not only an imp...
Ahmed Babiker's work focuses on the clinical and genomic epidemiology of multidrug-resistant health care-associated pathogens and other high-consequence pathogens. In this mSphere of Influence article, he reflects on how the paper "Tracking a Hospital Outbreak of Carbapenem-Resistant with Whole-Gen...
The assessment of Hospital-acquired infections due to multidrug-resistant bacteria involves the use of a variety of commercial and laboratory-developed tests to detect antimicrobial resistance genes in bacterial pathogens; however, few are evaluated for use in low- and middle-income countries. We us...
Marek's disease (MD) continues to threaten the sustainability of the world poultry industry. In this study, the sequences of the meq gene of 220 MDV strains isolated during the years 1964-2020 were analysed, including 50 from our group plus 170 isolates from the GenBank. Analyses, using phylogenetic...
With coronavirus disease 19 (COVID-19), we have witnessed a shift from public health to planetary health and a growing recognition of the importance of systems science in developing effective solutions against pandemics in the 21st century. COVID-19 and the history of frequent infectious outbreaks i...
Some mosquito species have significant public health importance given their ability to transmit major diseases to humans and animals, making them the deadliest animals in the world. Among these, the (.) genus is a vector of several viruses such as Dengue, Chikungunya, and Zika viruses that can caus...
Mosquitoes are major infectious disease-carrying vectors. Assessment of current and future risks associated with the mosquito population requires knowledge of the full repertoire of pathogens they carry, including novel viruses, as well as their blood meal sources. Unbiased metatranscriptomic sequen...
subsp. serovar Typhimurium DT104, a multidrug-resistant phage type, has emerged globally as a major cause of foodborne outbreaks particularly associated with contaminated beef products. In this study, we sequenced three Typhimurium DT104 strains associated with a 2009 outbreak caused by ground bee...
The COVID-19 pandemic was officially declared on March 11, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data...
Mosquitoes host and transmit numerous arthropod-borne viruses (arboviruses) that cause disease in both humans and animals. Effective surveillance of virome profiles in mosquitoes is vital to the prevention and control of mosquito-borne diseases in northwestern China, where epidemics occur frequently...
Since late 2019, the coronavirus disease 2019 (COVID-19) outbreak, caused by SARS-CoV-2, has rapidly evolved to become a global pandemic. Each country was affected but with a varying number of infected cases and mortality rates. Africa was hit late by the pandemic but the number of cases rose sharpl...
Enteroviruses are amongst the most common causes of aseptic meningitis. Between November 2018 and May 2019, an outbreak of enterovirus-associated aseptic meningitis cases was noted in the Western and Eastern Cape Provinces, South Africa. To describe the epidemiology and phylogeography of enterovirus...
Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest-hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. In Costa Rica, from the first detected case on March 6th to December 31st...
is a vector of " Liberibacter asiaticus (Las), associated with citrus greening disease. . exhibit at least two color morphotypes, blue and non-blue, the latter including gray and yellow morphs. Blue morphs have a greater capacity for long-distance flight and transmit Las less efficiently as compare...
No abstract available
The emergence of new bacterial pathogens is a continuing challenge for agriculture and food safety. Salmonella Typhimurium is a major cause of foodborne illness worldwide, with pigs a major zoonotic reservoir. Two phylogenetically distinct variants, U288 and ST34, emerged in UK pigs around the same...
In order to provide insights into the evolutionary and epidemiological viral dynamics during the current COVID-19 pandemic in South Eastern Italy, a total of 298 genomes of SARS-CoV-2 strains collected in the Apulia and Basilicata regions, between March 2020 and January 2021, were sequenced. The gen...
We identified an emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the western United States. Named B.1.427/B.1.429 to denote its two lineages, the varia...
Shiga toxin-producing Escherichia coli (STEC) can cause severe human illness, which are frequently linked to the consumption of contaminated beef or dairy products. However, recent outbreaks associated with contaminated flour and undercooked dough in the United States and Canada, highlight the poten...
Dengue fever was included in the top 10 global health threats announced by the World Health Organization (WHO) in early 2019. In some southern provinces of China, autochthonous outbreaks have also been reported over the last decade. An unexpected large outbreak of dengue fever was reported in Xishua...
Between November 2018 and October 2019, carbapenem-resistant Enterobacterales carrying New Delhi Metallo-β-lactamase (NDM) caused one of the largest and persistent outbreaks occurred in Italy and intensified surveillance measures have been taken in all Italian hospitals. In this study we analyzed ND...
High-resolution microbial strain typing is essential for various clinical purposes, including disease outbreak investigation, tracking of microbial transmission events and epidemiological surveillance of bacterial infections. The widely used approach for multilocus sequence typing (MLST) that is bas...
Multilocus sequence typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for , the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate popul...
No abstract available
Clostridioides difficile is a Gram positive spore-forming rod and mainly responsible for nosocomial diarrhea in developed nations. Molecular and antimicrobial surveillance is important for monitoring the strain composition including genotypes of high epidemiological importance such as ribotype 027 (...
Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be...
In 2016/2017, Washington State experienced a mumps outbreak despite high childhood vaccination rates, with cases more frequently detected among school-aged children and members of the Marshallese community. We sequenced 166 mumps virus genomes collected in Washington and other US states, and traced...
Visceral leishmaniasis (VL) is re-emerging in Armenia since 1999 with 167 cases recorded until 2019. The objectives of this study were (i) to determine for the first time the genetic diversity and population structure of the causative agent of VL in Armenia; (ii) to compare these genotypes with thos...
Brucellosis is a prevalent disease in Costa Rica (CR), with an increasing number of human infections. Close to half of homes in CR have one or more dogs, corresponding to ∼1.4 million canines, most of them in the Central Valley within or near the cities of San José, Heredia, and Alajuela. From 302 d...
Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequen...
Dengue virus (DENV) is a mosquito-borne viral pathogen that plagues many tropical-climate nations around the world, including Brazil. Molecular epidemiology is a growing and increasingly invaluable tool for understanding the dispersal, persistence, and diversity of this impactful virus. In this stud...
Pilus has been recently associated with pneumococcal pathogenesis in humans. The information regarding piliated isolates in Malaysia is scarce, especially in the less developed states on the east coast of Peninsular Malaysia. Therefore, we studied the characteristics of pneumococci, including the pi...
The SARS-CoV-2 pandemic has forced health authorities across the world to take important decisions to curtail its spread. Genomic epidemiology has emerged as a valuable tool to understand introductions and spread of the virus in a specific geographic location. Here, we report the sequences of 59 SAR...
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a nove...
Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or "drip" tips filled with extracellular bacteria of the species Orrella dioscoreae. This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and undergro...
Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of SARS-CoV-2 have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission du...
Deep sequencing of viral populations using next-generation sequencing (NGS) offers opportunities to understand and investigate evolution, transmission dynamics, and population genetics. Currently, the standard practice for processing NGS data to study viral populations is to summarize all the observ...
On 1 August 2018, the Democratic Republic of the Congo (DRC) declared its tenth Ebola virus disease (EVD) outbreak. To aid the epidemiologic response, the Institut National de Recherche Biomédicale (INRB) implemented an end-to-end genomic surveillance system, including sequencing, bioinformatic anal...
Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop's main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from...
(PUUV) has a wide distribution throughout Europe. Distinctive temporal patterns of spillover into the human population are related to population dynamics of the reservoir host, the bank vole (). As the rodent host is tied to specific habitats with small individual ranges, PUUV genetic diversity is a...
Paracoccidioidomycosis (PCM) is a systemic and endemic fungal infection in Latin American, mainly in Brazil. The majority of PCM cases occur in large areas in Brazil, comprising the South, Southeast and Midwest regions, with the latter demonstrating a higher incidence of the species Paracoccidioides...
New approaches to rapid, simple, diagnostic immunoassays that do not rely on centralized laboratory facilities are urgently needed for disease diagnosis and to inform treatment strategies. The recent and ongoing COVID-19 pandemic has emphasized that rapid diagnostics are needed to help guide govern...
To analyze the genomic epidemiological subtyping of carbapenem resistant (CRKP) isolated from a Third-class A hospital in Zhengzhou. From December 4, 2019 to January 10, 2020, 67 strains of CRKP were isolated from the samples submitted by the clinical departments of a Third-class A teaching hospit...
Biting midges in the genus Culicoides (Diptera; Ceratopogonidae) are vectors of pathogens that can cause diseases of major economic importance in humans and animals. Identifying host ranges of these biting midges might aid in understanding the complex epidemiology of such diseases, often involving r...
Genotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality of the sequence data obtained from these genotyping efforts depends on several factors, including the quantity/integrity of...
In August 2017, an increased incidence of Bareilly was detected in the Czech Republic. An investigation was conducted with Slovakia to confirm the outbreak and identify the source. Probable outbreak cases were defined as cases with laboratory-confirmed Bareilly reported in either of the national s...
Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to more easily obtained isolates from infected people. When no food isolate can be obtained, the source of the outbreak cannot be unambiguou...
No abstract available
The novel coronavirus SARS-CoV-2, the infective agent causing COVID-19, is having a global impact both in terms of human disease as well as socially and economically. Its heavily glycosylated spike glycoprotein is fundamental for the infection process, via its receptor-binding domains interaction wi...
Understanding of SARS-CoV-2 variants that alter disease outcomes are important for clinical risk stratification and may provide important clues to the complex virus-host relationship. To examine the association of identified SARS-CoV-2 variants, virus clades, and clade groups with disease severity a...
Advances in sequencing technologies have tremendously reduced the time and costs associated with sequence generation, making genomic data an important asset for routine public health practices. Within this context, phylogenetic and phylogeographic inference has become a popular method to study disea...
The spread of SARS-CoV-2 created a pandemic crisis with > 150,000 cumulative cases in > 65 countries within a few months. The reproductive number (R) is a metric to estimate the transmission of a pathogen during an outbreak. Preliminary published estimates were based on the initial outbreak in China...
A key lesson emerging from COVID-19 is that pandemic proofing planetary health against future ecological crises calls for systems science and preventive medicine innovations. With greater proximity of the human and animal natural habitats in the 21st century, it is also noteworthy that zoonotic infe...
Rats are an important maintenance host of Leptospira spp., the causative agents of leptospirosis, a zoonotic disease with worldwide distribution. Rats are traded as food in the Mekong Delta, where Cambodia exports tons of rats to Vietnam. Handling wild rats is a potential health risk, but the inform...
We analyzed the SARS-CoV-2 genome using our integrated genome analysis system and present the concept of a comprehensive approach to monitoring and surveillance of emerging variants. A total of 69 SARS-CoV-2 positive samples (with Ct value ≤ 28) were tested. Samples included in this study were sel...
In Marseille, France, following a first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in March-May 2020, a second epidemic phase occurred from June, involving 10 new variants. The Marseille-4 variant caused an epidemic that started in August and is still ongoing. The 1038 SAR...
Noroviruses are the leading cause of acute gastroenteritis and foodborne illness in the United States. Traditional Sanger sequencing of short genomic regions (~300-600 bp) is the primary method for differentiation of this pathogen; however, whole-genome sequencing (WGS) offers a valuable approach to...
The Asian tiger mosquito is contributing to the (re)-emergence of Chikungunya virus (CHIKV). To gain insights into the molecular underpinning of viral persistence, which renders a mosquito a life-long vector, we coupled small RNA and whole genome sequencing approaches on carcasses and ovaries of mo...
No abstract available
Infectious bronchitis of chicken is a high morbidity and mortality viral disease affecting the poultry industry worldwide; therefore, a better understanding of this pathogen is of utmost importance. The primary aim of this study was to obtain a deeper insight into the genomic diversity of field infe...
Following its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic resulting in unprecedented efforts to reduce transmission and develop therapies and vaccines (WHO Emergency Committee, 2020; Zhu et al., 2020). Rapidly generated viral geno...
Hypomyelination is a rare consequence of in utero bovine viral diarrhoea virus (BVDV) infection. We describe a BVDV outbreak in a naïve Holstein dairy herd in northern Italy, with an unusually high prevalence of calves with neurological signs, generalised tremors and ataxia. Histological analysis sh...
Viral genomic surveillance is vital for understanding the transmission of COVID-19. In Hong Kong, breakthrough outbreaks have occurred in July (third wave) and November (fourth wave) 2020. We used whole viral genome analysis to study the characteristics of these waves. We analyzed 509 SARS-CoV-2 gen...
is an emerging, multidrug-resistant fungal pathogen that has become a public health threat with an increasing incidence of infections worldwide. spreads easily among patients within and between hospitals. Infections and outbreaks caused by have been reported in the Middle East region including Oma...
No-touch disinfection systems like xenon- or mercury-based ultraviolet (UV) are now commonly being used for hospital room disinfection. However, serial exposure to UV light can potentially lead to the development of bacterial resistance. We sought to determine whether UV resistance develops due to s...
Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 who...
Information about the clinical and microbiological characteristics of IMP-producing Enterobacterales has been limited. Here, we describe an institutional outbreak of IMP-producing Enterobacter cloacae complex (ECC) involving multiple clades of ECC sequence type (ST) 78 strains. Antimicrobial suscept...
The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2 - th...
In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and readily available bioinformatics pipelines. In addition to virus discovery, these NGS technologies and bioinformatics resources ar...
We determined the whole DNA sequences of plasmids carrying a rare extended-spectrum β-lactamase gene (bla) to precisely understand the spread of resistance among nosocomial Serratia marcescens populations. Twenty non-duplicate ceftazidime-resistant S. marcescens nosocomial isolates (ceftazidime MICs...
Acinetobacter baumannii has emerged as one of the common multidrug resistance pathogens causing hospital-acquired infections. This study was conducted to elucidate the distribution of antimicrobial resistance genes in the bacterial population in Thailand. Multidrug-resistant A. baumannii (MDR A. bau...
Conventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms is...
The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patie...
Carbapenem-resistant (CRKP) is an important bacterium of nosocomial infections. In this study, CRKP strains, which were mainly isolated from fecal samples of 14 patients in three wards of the hospital in the Silesia Voivodship, rapidly increased from February to August 2018. Therefore, we conducted...
COVID-19 is highly transmissible; however, its severity varies from one individual to another. Variability among different isolates of the virus and among its receptor (ACE2) may contribute to this severity, but comorbidity plays a major role on disease prognosis. Many comorbidities have been report...
In 2016, Venezuela faced a large diphtheria outbreak that extended until 2019. Nasopharyngeal or oropharyngeal samples were prospectively collected from 51 suspected cases and retrospective data from 348 clinical records was retrieved from 14 hospitals between November 2017 and November 2018. Confir...
In 2003 to 2004, the first five VIM-2 metallo-β-lactamase (MBL)-producing (MPPA) isolates with an In4-like integron, In461 (--), on conjugative plasmids were identified in three hospitals in Poland. In 2005 to 2015, MPPA expanded much in the country, and as many as 80 isolates in a collection of 45...
Antimicrobial resistance (AMR) represents a profound global health threat. Reducing AMR spread requires the identification of transmission pathways. The extent to which hospital wards represent a venue for substantial AMR transmission in low- and middle-income countries settings is poorly understood...
Human metapneumovirus (HMPV) is an important cause of upper and lower respiratory tract disease in individuals of all ages. It is estimated that most individuals will be infected by HMPV by the age of five years old. Despite this burden of disease, there remain caveats in our knowledge of global gen...
Invasive fungal infections represent an expanding threat to public health. During the past decade, a paradigm shift of candidiasis from to non-albicans species has fundamentally increased with the advent of . was identified in 2009 and is now recognized as an emerging species of concern and under...
Bats can harbor zoonotic pathogens causing emerging infectious diseases, but their status as hosts for bacteria is limited. We aimed to investigate the distribution, prevalence and genetic diversity of Borrelia in bats and bat ticks in Hubei Province, China, which will give us a better understanding...
Leptospirosis is a ubiquitous zoonotic disease and a major clinical challenge owing to the multitude of clinical presentations and manifestations that are possibly attributable to the diversity of Leptospira, the understanding of which is key to study the epidemiology of this emerging global disease...
Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173...
The South Korean government effectively contained the coronavirus disease-2019 (COVID-19) outbreak primarily associated with a religious group. We conducted SARS-CoV-2 whole genome sequencing of 66 cases to investigate connections among the initial South Korean cases and the religious group outbreak...
The molecular epidemiology of the virus and mapping helps understand the epidemics' evolution and apply quick control measures. This study provides genomic evidence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introductions into Sri Lanka and virus evolution during circul...
is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the potential to bolster survei...
The rapid global spread and continued evolution of SARS-CoV-2 has highlighted an unprecedented need for viral genomic surveillance and clinical viral sequencing. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which ca...
Carbapenem-resistant (CRKP) is a critical-priority antibiotic resistance threat that has emerged over the past several decades, spread across the globe, and accumulated resistance to last-line antibiotic agents. While CRKP infections are associated with high mortality, only a subset of patients acq...
This study investigates enteric viruses in wastewater during an outbreak of acute hepatitis caused by hepatitis A virus (HAV) in a large metropolitan area. Emphasis is given to caliciviruses and HAV. Metagenomic analysis was performed to characterize enteric viruses excreted by the population of Det...
Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field has centered on viruses. Bacterial pathogens are seldom analyzed under such phylodynamic frameworks, due to their complex genome evolution and, until...
Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given locati...
Neisseria gonorrhoeae (NG) isolates with high-level azithromycin resistance (HL-AziR) have emerged worldwide in recent decades, threatening the sustainability of current dual-antimicrobial therapy. This study aimed to characterize the first 16 NG isolates with HL-AziR in Barcelona between 2016 and 2...
The World Health Organization (WHO) estimates that around 10 million people develop tuberculosis (TB) every year, with 1.5 million deaths attributed to TB in 2019 (World Health Organization, 2020). The majority of the disease burden occurs in low-income countries, where access to diagnostics and tai...
Recent genomic studies of methicillin-resistant (MRSA) have revealed genetic diversity in the various clonal lineages. Along with clinical concerns of MRSA infection, infection with heterogeneous vancomycin-intermediate (hVISA) is closely associated with treatment failure. In this study, we invest...
clonal complex 30 (CC30) has given rise to epidemics worldwide and is one of the most prevalent lineages in Argentina, represented by sequence type 30 methicillin-resistant SCC type IV (ST30-MRSA-IV). ST30-MRSA-IV has displaced previous prevalent clones in the country and demonstrated increased vir...
Over 200,000 whole genome sequences of SARS-CoV-2 have been determined for viruses isolated from around the world. These sequences have been critical for understanding the spread and evolution of SARS-CoV-2. Using global phylogenomics, we show that mutations frequently occur in the C-terminal end of...
Clostridioides difficile is an emerging One Health pathogen and a common etiologic agent of diarrhea, both in healthcare settings and the community. This bacterial species is highly diverse, and its global population has been classified in eight clades by multilocus sequence typing (MLST). The C. di...
Persistent plant viruses multiply and circulate inside insect vectors following the route of midgut-hemolymph-salivary gland. Currently, how viruses interact with insect vectors after they are released into hemolymph is not entirely clear. In this study, we found that the hemolymph and fat body (HF)...
Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including...
The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging t...
In 2021, the genetics and genomics community needs to communicate to policymakers how the field of human genetics and genomics is transforming biomedical research and medicine, including its essential role in combatting COVID-19. This is important for ensuring that policies enable a thriving scienti...
In November 2018, an outbreak of respiratory disease occurred in foals at an equestrian club in Changji, northern Xinjiang, China. We applied viral metagenomics to investigate this outbreak and identify potential pathogens involved in this equine respiratory syndrome. The metagenomics data revealed...
Sequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. SARS-CoV-2 genomic sequences were generated from positive samples collected, along with...
Paenibacillus larvae is the causative agent of the fatal American foulbrood disease in honeybees (Apis mellifera). Strain identification is vital for preventing the spread of the disease. To date, the most accessible and robust scheme to identify strains is the multilocus sequence typing (MLST) meth...
The investigation of migratory patterns during the SARS-CoV-2 pandemic before spring 2020 border closures in Europe is a crucial first step toward an in-depth evaluation of border closure policies. Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimat...
Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic e...
Knowledge gaps remain regarding SARS-CoV-2 transmission on flights. We conducted a retrospective cohort study to estimate risk of acquiring symptomatic SARS-CoV-2 on aircraft, to inform contact tracing and infection control efforts. We identified co-passengers of infectious passengers on 18 England-...
Members of the flea family Pulicidae have been the focus of many studies due to their significance as diseases vectors of medical and veterinary importance and their cosmopolitan distribution. They often exhibit variation in morphological features that can make correct species identification and man...
Streptococcus pyogenes has a variety of virulence factors and the predominant invasive strains differ according to specific emm types and geographical orientation. Although emm typing is commonly used as the gold standard method for the molecular characterisation, multilocus sequence typing (MLST) h...
Whole-genome sequencing (WGS) of allows rapid, accurate inferences about the sources, location and timing of transmission. However, in an era of heightened concern for personal privacy and science distrust, such inferences could result in unintended harm and undermine the public´s trust. We held in...
No abstract available
Ehrlichia chaffeensis causes human monocytic ehrlichiosis, and its principal vector is the Amblyomma americanum tick. The most frequently identified cases of ehrlichiosis come from the southeastern and south central states of the United States. In this study, a molecular typing system was developed...
In April 2018, Public Health England was notified of cases of Shigella sonnei who had eaten food from three different catering outlets in England. The outbreaks were initially investigated as separate events, but whole-genome sequencing (WGS) showed they were caused by the same strain. The investiga...
The global success of carbapenem-resistant pathogens has been attributed to large plasmids carrying bla genes circulating among high-risk clones. In this study, we sequenced the genome of a carbapenem-resistant Escherichia coli strain (Ec351) isolated from a human infection. Phylogenomic analysis ba...
Since December 2019, a new form of severe acute respiratory syndrome (SARS) from a novel strain of coronavirus (SARS coronavirus 2 [SARS-CoV-2]) has been spreading worldwide. The disease caused by SARS-CoV-2 was named Covid-19 and declared as a pandemic by the World Health Organization in March 2020...
This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN). For 10 days, 25 patients who receive...
Dengue fever is a mosquito-borne infectious disease that has caused major health problems. Variations in dengue virus (DENV) genes are important features of epidemic outbreaks. However, the associations of DENV genes with epidemic potential have not been extensively examined. Here, we assessed new g...
During the 2017 outbreak of severe dengue in Sri Lanka, dengue virus (DENV) serotypes 2, 3, and 4 were found to be co-circulating. Our previous study of 295 patients from the National Hospital Kandy in Sri Lanka between March 2017 and January 2018 determined that the dominant infecting serotype was...
No abstract available
During the SARS-CoV-2 pandemic, healthcare workers (HCWs) are being exposed to infection both at work and in their communities. Determining where HCWs might have been infected is challenging based on epidemiological data alone. At Akershus University Hospital, Norway, several clusters of possible in...
To describe an Acinetobacter baumannii outbreak among preterm neonates in a neonatal intensive care unit (NICU) in Serbia. A case-control study was conducted in the NICU at the Institute of Neonatology, Belgrade, Serbia. The case definition of A. baumannii bloodstream infection (BSI) was blood cultu...
Non-O157 STEC are increasingly linked to foodborne infections, yet little is known about the diversity and molecular epidemiology across locations. Herein, we used whole genome sequencing to examine genetic variation in 894 isolates collected from Michigan patients between 2001 and 2018. In all, 67...
Methicillin-resistant Staphylococcus aureus (MRSA) ST8-t008 of the pulsotype USA300 and the Latin American variant (USA300-LV) are the predominant virulent MRSA clonal lineages on the American continent. In Europe, the occurrence of USA300 or USA300-LV has often been related to international travel...
Since the outset of COVID-19, the pandemic has prompted immediate global efforts to sequence SARS-CoV-2, and over 450 000 complete genomes have been publicly deposited over the course of 12 months. Despite this, comparative nucleotide and amino acid sequence analyses often fall short in answering ke...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To study the lineage...
An outbreak of Legionella pneumonia occurred at a university hospital using copper-silver ionization for potable water disinfection. We present the epidemiological and laboratory investigation of the outbreak, and associated case-control study. Cases were defined by syndrome compatible with Legionel...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become fixed in a number of SARS-CoV-2 lineages. A subset of such mutations enable escape from neutralizing a...
The SARS-CoV-2 virus is the causative agent of the 2020 pandemic leading to the COVID-19 respiratory disease. With many scientific and humanitarian efforts ongoing to develop diagnostic tests, vaccines, and treatments for COVID-19, and to prevent the spread of SARS-CoV-2, mass spectrometry research,...
Until July 2016, vancomycin-resistantEnterococcus faecium (VREfm) was sporadically detected in Odense University Hospital, Denmark. After July 2016, the number of VREfm cases increased. This study aimed to apply a core genome multilocus sequence typing (cgMLST) scheme for E. faecium to type and anal...
Antimicrobial stewardship isn't strictly observed in most Egyptian hospitals, raising antibiotic resistance. Epidemiology of Egyptian MRSA isolates, or associations with resistance to other antibiotics remain largely unknown. We identified MRSA genotypes in Alexandria Main University Hospital (AMUH)...
Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods...
Infections caused by carbapenem-resistant (CR-Ab) have become increasingly prevalent in clinical settings and often result in significant morbidity and mortality due to their multidrug resistance (MDR). Here we present an integrated whole-genome sequencing (WGS) response to a persistent CR-Ab outbr...
Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs. To determine the variants of SARS-CoV-2 circulating in the state of Nevada, specimens from 200 COVID-19 patients were sequenced through our robust sequencing...
Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loa...
Genomic surveillance of viral isolates during the 2013-2016 Ebola virus epidemic in Western Africa, the largest and most devastating filovirus outbreak on record, revealed several novel mutations. The responsible strain, named Makona, carries an A-to-V substitution at position 82 (A82V) in the glyco...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every corner of the globe, causing societal instability. The resultant coronavirus disease 2019 (COVID-19) leads to fever, sore throat, cough, chest and muscle pain, dyspnoea, confusion, anosmia, ageusia and headache....
is an emerging MDR pathogen raising major concerns worldwide. In Italy, it was first and only identified in July 2019 in our hospital (San Martino Hospital, Genoa), where infection or colonization cases have been increasingly recognized during the following months. To gain insights into the introduc...
Conjunctivitis is a frequent ocular disorder caused by human adenoviruses (HAdVs). Only a few of the 45 HAdV-D species are associated with epidemic keratoconjunctivitis, including HAdV-D8. Nosocomial outbreaks due to HAdV-D8 have been rarely described, because keratoconjunctivitis cases are clinical...
Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of "last resort" there exists no alternative treatments...
Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (), a freshwater tel...
Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this wor...
Vancomycin-resistant enterococci (VRE) may cause nosocomial outbreaks. This article describes all VRE carriers that were identified in 2018 at Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands. To investigate the genetic relatedness of VRE isolates and the possibility of a common environmental...
Serratia marcescens is notorious for its increasing antimicrobial resistance and potential to cause outbreaks in neonatal intensive care units (NICUs). A promising tool in outbreak investigations is whole-genome sequencing (WGS). To describe a S. marcescens outbreak (2018-2019) in an NICU and discus...
The emergence of carbapenem resistance in represents a major global public health concern. Nosocomial outbreaks caused by multidrug-resistant are commonly reported to result in high morbidity and mortality due to limited treatment options. Between October 2019 and January 2020, two concurrent high...
This letter is the Human Genome Organisation's summary reaction to the 2020 COVID-19 pandemic. It identifies key areas for genomics research, and areas in which genomic scientists can contribute to a global response to the pandemic. The letter has been reviewed and endorsed by the HUGO Committee on...
We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method perfor...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a great threat to public health, being a causative pathogen of a deadly coronavirus disease (COVID-19). It has spread to more than 200 countries and infected millions of individuals globally. Although SARS-CoV-2 has structural/genomic s...
This study introduces an innovative methodological approach to identify potential drivers of structuring HIV-1 transmission clustering patterns between different subpopulations in the culturally and racially/ethnically diverse context of Houston, TX, the largest city in the Southern United States. U...
The genus demonstrates resistance to antibiotics and has been shown to spread in the hospital environment causing epidemic outbreaks among hospitalized patients. The objectives of the present study was to investigate the antibiotic resistance, biofilm formation, and clonality among strains. The st...
Streptococcus agalactiae is a contagious pathogen that causes bovine mastitis worldwide, resulting in considerable economic losses. In this study, we isolated 42 S. agalactiae strains in 379 milk samples from cows with subclinical mastitis on 15 dairy farms in 12 Chinese provinces. Analysis based on...
Streptococcus uberis is one of the most frequent mastitis-causing pathogens isolated from dairy cows. Further understanding of S. uberis genetics may help elucidate the disease pathogenesis. We compared the genomes of S. uberis isolates cultured from dairy cows located in distinctly different geogra...
Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) have continually grown as a global public health threat, with significant mortality rates observed across the world. We examined the clinical data from patients with CPE infections and their outcomes, concentrating on Klebsiella p...
Several bioinformatics pipelines have been developed to detect sequences from viruses that integrate into the human genome because of the health relevance of these integrations, such as in the persistence of viral infection and/or in generating genotoxic effects, often progressing into cancer. Recen...
is a Gram-negative bacterium that causes the sapronotic disease melioidosis. An outbreak in 2003 in the state of Ceara, Brazil, resulted in subsequent surveillance and environmental sampling which led to the recognition of as an endemic pathogen in that area. From 2003 to 2015, 24 clinical and 12 e...
The ability to cause plague in mammals represents only half of the life history of . It is also able to colonize and produce a transmissible infection in the digestive tract of the flea, its insect host. Parallel to studies of the molecular mechanisms by which is able to overcome the immune respons...
In severe bronchiolitis, it is unclear if delayed clearance or sequential infection of respiratory syncytial virus (RSV) or rhinovirus (RV) is associated with recurrent wheezing. In a 17-center severe bronchiolitis cohort, we tested nasopharyngeal aspirates (NPA) upon hospitalization and 3 weeks lat...
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90). Despite the early response, by November 2020, over 785,000 people in South Africa were in...
Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not dir...
Two London care homes experienced a second COVID-19 outbreak, with 29/209 (13.9%) SARS-CoV-2 RT-PCR-positive cases (16/103 residents, 13/106 staff). In those with prior SARS-CoV-2 exposure, 1/88 (1.1%) individuals (antibody positive: 87; RT-PCR-positive: 1) became PCR-positive compared with 22/73 (3...
In June-November 2020, SARS-CoV-2-infected mink were detected in 290 of 1,147 Danish mink farms. In North Denmark Region, 30% (324/1,092) of people found connected to mink farms tested SARS-CoV-2-PCR-positive and approximately 27% (95% confidence interval (CI): 25-30) of SARS-CoV-2-strains from huma...
, the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing infections demands effective preventive measures, antibiotic treatment...
Pregnant women can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet the incidence of perinatal infection is low. We hypothesized that this could be related to low expression of the membrane receptor for SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2), in the fetopl...
Objective This study compared the costs and patient movements of a new hospital protocol to discontinue contact precautions for patients with non-multiresistant methicillin-resistant Staphylococcus aureus (nmMRSA), based on whole-genome sequencing (WGS) of pathogens with current practice. Methods A...
Ending the hepatitis C virus (HCV) epidemic requires stopping transmission among networks of persons who inject drugs. Identifying transmission networks by using genomic epidemiology may inform community responses that can quickly interrupt transmission. We retrospectively identified HCV RNA-positiv...
vancomycin-resistant Enterococcus faecium (VREfm) is a major public health problem worldwide. The aim of our study was to determine the microbiological, epidemiological and molecular characteristics of VREfm isolated in north-central, eastern and western Algeria. a collection of 48 VREfm isolated fr...
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent...
Clostridioides difficile is the most common cause of nosocomial diarrhea. Ribotyping of cultured strains by a PCR-based test is used to study potential transmission between patients. We aimed to develop a rapid test that can be applied directly on fecal samples for simultaneous detection and ribotyp...
We introduce VERSO, a two-step framework for the characterization of viral evolution from sequencing data of viral genomes, which is an improvement on phylogenomic approaches for consensus sequences. VERSO exploits an efficient algorithmic strategy to return robust phylogenies from clonal variant pr...
To determine serogroups, multilocus sequence typing (MLST) of Listeria monocytogenes isolates and analyze clinical characteristics of these clones focusing on non-perinatal cases. From 2000 to 2015, we analyzed 123 human listeriosis cases at a medical center in northern Taiwan using PCR serogrouping...
The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate t...
The guts of blood-sucking insects host a community of bacteria that can shift dramatically in response to biotic and abiotic factors. Identifying the key factors structuring these microbial communities has important ecological and epidemiological implications. We used the yellow fever mosquito, Aede...
Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. C. difficile has also a highly diverse genome, which may contri...
Broad bean wilt virus 2 (BBWV-2), which belongs to the genus of the family , is an important pathogen that causes damage to broad bean, pepper, yam, spinach and other economically important ornamental and horticultural crops worldwide. Previously, only limited reports have shown the genetic variati...
A thorough knowledge of the presence and spatio-temporal distribution patterns of vector species are pivotal to assess the risk of mosquito-borne diseases in Europe. In 2018, a Culex larva was collected during routine monitoring activities to intercept exotic Aedes mosquito species in the port of An...
Coronavirus disease 2019 (COVID-19) pandemic is affecting millions of patients worldwide. The consequences of initial exposure to SARS-CoV-2 go beyond pulmonary damage, with a particular impact on lipid metabolism. Decreased levels in HDL-C were reported in COVID-19 patients. Since HDL particles dis...
No abstract available
No abstract available
The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy. The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet little is known of the intrinsic org...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive mea...
Rapid and reliable pathogen identification is compulsory to confirm ventilator-associated pneumonia (VAP) in order to initiate appropriate antibiotic treatment. In the present proof of concept, the effectiveness of rapid microorganism identification with a targeted bottom-up proteomics approach was...
Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also...
Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to unders...
The genotyping of pathogens within cystic fibrosis cohorts is an important process, enabling the detection of transmissible and clinically-important strains. Traditionally this has been via culture-dependent processes. However, culture-independent investigation of respiratory samples is becoming mor...
Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and to vancomycin has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can...
To characterize the clonal spread of carbapenem-resistant Klebsiella pneumoniae and Escherichia coli isolates between different healthcare institutions in Catalonia, Spain. Antimicrobial susceptibility was tested by disc diffusion. MICs were determined by gradient diffusion or broth microdilution. C...
Our ability to predict evolutionary trajectories of pathogens is one of the promising leverages to fight against the pandemic disease, yet few studies have addressed this question , due to the difficulty in monitoring the milestone evolutionary events for a given pathogen and in understanding the ev...
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was declared a pandemic infection in March 2020. As of December 2020, two COVID-19 vaccines have been authorized for emergency use by the U.S. Food and Drug Administrat...
The Northeast region of Brazil registered the second-highest incidence proportion of Chikungunya fever in 2019. In that year, an outbreak consisting of patients presenting with febrile disease associated with joint pain was reported by the public primary health care service in the city of Natal, in...
HIV-1 subtype CRF01_AE is the second most predominant strain in Bulgaria, yet little is known about the molecular epidemiology of its origin and transmissibility. We used a phylodynamics approach to better understand this sub-epidemic by analyzing 270 HIV-1 polymerase () sequences collected from per...
In the initial few months of the COVID-19 pandemic, two distinct strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) were identified (L and S strain) based on a tightly linked SNP between two widely separated nucleotides at location 8782 (ORF1ab T8517C) and position 28,144 (ORF8:...
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficienc...
Kenyan poultry consists of ~80% free-range indigenous chickens kept in small flocks (~30 birds) on backyard poultry farms (BPFs) and they are traded via live bird markets (LBMs). Newcastle disease virus (NDV) was detected in samples collected from chickens, wild farm birds, and other domestic poultr...
Given that accurately identifying pathogen vectors is vital for designing efficient mosquito control programs based on the proper surveillance of the epidemiologically important species, it has been suggested the complementary use of independently evolving genes and morphometric traits as a reliable...
Leishmaniasis is widely regarded as a vaccine-preventable disease, but the costs required to reach pivotal Phase 3 studies and uncertainty about which candidate vaccines should be progressed into human studies significantly limits progress in vaccine development for this neglected tropical disease....
Human infectious diseases are contributed equally by the host immune system's efficiency and any pathogens' infectivity. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the coronavirus strain causing the respiratory pandemic coronavirus disease 2019 (COVID-19). To understand the path...
The emergence of nonsusceptibility to ceftolozane/tazobactam and meropenem was evaluated among Pseudomonas aeruginosa (P. aeruginosa) lower respiratory tract isolates obtained from participants in the ASPECT-NP clinical trial. ASPECT-NP was a phase-3, randomised, double-blind, multicentre trial that...
The genus includes a range of mosquito-specific viruses in addition to well-known medically important arboviruses. Isolation and comprehensive genomic analyses of viruses in mosquitoes collected in Bolivia resulted in the identification of three novel flavivirus species. Psorophora flavivirus (PSFV...
The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis gene...
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of...
The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. MGD is the authoritative source for biological ref...
For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodat...
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensure...
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, upd...
The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes a...
The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most...
Phylodynamic inference is a pivotal tool in understanding transmission dynamics of viral outbreaks. These analyses are strongly guided by the input of an epidemiological model as well as sequence data that must contain sufficient intersequence variability in order to be informative. These criteria,...
is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal within...
High-level disinfection protects tens-of-millions of patients from the transmission of viruses on reusable medical devices. The efficacy of high-level disinfectants for preventing human papillomavirus (HPV) transmission has been called into question by recent publications, which if true, would have...
Phylogeographic inference allows reconstruction of past geographical spread of pathogens or living organisms by integrating genetic and geographic data. A popular model in continuous phylogeography-with location data provided in the form of latitude and longitude coordinates-describes spread as a Br...
There is an increasing concern about the role of animals as reservoirs of Clostridioides difficile. In this study, we investigated prevalence, antimicrobial resistance and zoonotic potential of C. difficile in dogs. Two-hundred and twenty-five dog faecal deposits were collected from trashcans in nin...
Vancomycin-resistant enterococci (VRE), particularly Enterococcus faecium (VREfm), can cause serious nosocomial infections, and have been responsible for healthcare-associated outbreaks. Spreading of VREfm can occur both clonally and by the dissemination of mobile genetic elements. To report prospec...
Helicobacter pylori is a human gastric carcinogen that is highly prevalent in Latin American. The prophages of H. pylori show a structured population and contribute to the diversity of this bacterium. However, H. pylori prophages present in American strains have not been described to date. In this s...
Dengue virus (DENV) is the most widespread arthropod-borne virus, with the number and severity of outbreaks increasing worldwide in recent decades. Dengue is caused by genetically distinct serotypes, DENV-1-4. Here, we present data on DENV-1, isolated from patients with dengue fever during an outbre...
Phylogenetic dating is one of the most powerful and commonly used methods of drawing epidemiological interpretations from pathogen genomic data. Building such trees requires considering a molecular clock model which represents the rate at which substitutions accumulate on genomes. When the molecular...
No abstract available
Metagenomic approaches have been key to successful tracing and outbreak management during the COVID-19 pandemic. How can we use this knowledge to better prepare, strategize and prevent future pandemics? [Formula: see text].
Streptococcus agalactiae (group B streptococcus) causes invasive disease in all age groups. In the Netherlands, the incidence of group B streptococcal sepsis in early infancy is increasing because of a specific genetic subtype, clonal complex (CC) 17-A1. We assessed the molecular epidemiology, incid...
Initial cases of coronavirus disease in Hong Kong were imported from mainland China. A dramatic increase in case numbers was seen in February 2020. Most case-patients had no recent travel history, suggesting the presence of transmission chains in the local community. We collected demographic, clinic...
Dengue virus (DENV) is the cause of one of the most prevalent neglected tropical diseases, and up to half of the world's population is at risk for infection. Recent results from clinical trials have shown that DENV vaccination can induce the development of severe dengue disease and/or prolong hospit...
Although Methicillin resistant Staphylococcus aureus (MRSA) is one of the major pathogens of healthcare associated infections, we had only sporadic cases in our intensive care unit (ICU) for years. To investigate the sudden increase in the number of MRSA cases in ICU. Descriptive study. From the 5th...
The current global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), led to the investigation with clinical, biochemical, immunological, and genomic characterization from patients to understand the pathophysiology of viral infect...
When harmful bacteria are detected in the final product at a food manufacturing plant, it is necessary to identify and eliminate the source of contamination so that it does not occur again. In the current study, the source of contamination was tracked using core genome multilocus sequence typing (cg...
Diphtheria is caused by a toxigenic bacterium Corynebacterium diphtheria which is being an emerging pathogen in India. Since diphtheria morbidity and mortality continues to be high in the country, the present study aimed to study the molecular epidemiology of C. diphtheriae strains from India. A tot...
Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021,...
Background The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the second wave of COVID-19 pandemic but, there is still a limited data on the genomic sequence of SARS-CoV-2 variants circulating in Nepal. Objective The objective of this study is to sequence the whole ge...
As whole-genome sequencing for pathogen genomes becomes increasingly popular, the typing methods of gene-by-gene comparison, such as core genome multilocus sequence typing (cgMLST) and whole-genome multilocus sequence typing (wgMLST), are being routinely implemented in molecular epidemiology. Howeve...
The molecular epidemiology and biological characteristics of associated with hemorrhagic pneumonia (HP) mink from five Chinese Provinces were determined. From 2017 to 2019, 85 strains were identified from 115 lung samples of mink suffering from HP. These samples were subjected to serotyping, antim...
Research indicates that Staphylococcus aureus colonization in the elderly with predisposing risks is associated with subsequent infection. However, the molecular epidemiology and risk factors for S. aureus colonization among residents and staff in nursing homes (NHs) in China remain unclear. A multi...
The U.S. Food and Drug Administration (FDA) created the GenomeTrakr Whole Genome Sequencing (WGS) Network in 2013, as a tool to improve food safety. This study presents an analysis of Whole Genome source tracking implementation on potential food contamination and related illnesses through theoretica...
As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insight...
SARS-CoV-2 pandemic has recently made the entire world come to a standstill. The number of cases in the world, especially India, have been increasing exponentially. The need of the hour is to assimilate as much data as possible to fast track the pipeline of bringing in new therapeutic tools against...
The emergence of carbapenem-resistant hypervirulent (CR-hvKP) strains has increased the threat posed by . Here, we described an outbreak of 32 CR-hvKP isolates from the emergency intensive care unit (EICU) of a teaching hospital in China. Thirty-two CRKp isolates were collected from six patients an...
The understanding of COVID-19, caused by the SARS-CoV-2, is essential to improve evidence-based public health policies. The effective reproductive number (Rt) in Peru was estimated using information from 113 complete genomes sequenced by the Instituto Nacional de Salud del Perú (INS), available in t...
We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to...
The surveillance of human salmonellosis in Belgium is dependent on the referral of human Salmonella isolates to the National Reference Center (NRC). Knowledge of current diagnostic practices and the coverage of the national Salmonella surveillance system are important to correctly interpret surveill...
Indonesia has the second largest tuberculosis (TB) burden globally. Attempts to scale-up TB control efforts have focused on TB households. However, in most high burden settings, considerable Mycobacterium tuberculosis (Mtb) transmission occurs outside TB households. A better understanding of transmi...
Understanding tuberculosis (TB) transmission chains can help public health staff target their resources to prevent further transmission, but currently there are few tools to automate this process. We have developed the Logically Inferred Tuberculosis Transmission (LITT) algorithm to systematize the...
Due to the critical condition and poor immunity of patients, the intensive care unit (ICU) has always been the main hospital source of multidrug-resistant bacteria. In recent years, with the large-scale use of antibiotics, the detection rate and mortality of carbapenem-resistant (CRKP) have gradual...
Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor i...
Infection by carbapenem-resistant (CRKp) hampers the treatment of elderly patients with lower respiratory tract infection (LRTI); however, relevant data with respect to the characteristics of CRKp in elderly patients with LRTIs are limited. In the present study, isolated from elderly patients with...
Dengue (DEN) is a neglected tropical disease, and surveillance of dengue virus (DENV) serotypes and genotypes is critical for the early detection of outbreaks. Risk factors for outbreaks include the emergence of new genotypes and serotype shifting. To understand the genomic and viral characteristics...
Individuals living in congregate settings, including those in group homes, have been disproportionately impacted by COVID-19 and may be at increased risk of exposure or infection due to underlying illness. In mid-May 2020, local public health officials responded to an outbreak of COVID-19 among staf...
To investigate the overall distributions of key virulence genes in , especially the hypervirulent -positive (Hv-(+)-KP). A total of 521 complete genomes of from GenBank were collected and analyzed. Multilocus sequence typing, molecular serotyping, antibiotic-resistance, virulence genes and plasmid...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was initially identified in China and currently worldwide dispersed, resulting in the coronavirus disease 2019 (COVID-19) pandemic. Notably, COVID-19 is characterized by systemic inflammation. However, the potential mechanisms of the "cyto...
The impact of host genomics on an individual's susceptibility, immune response, and risk of severe outcomes for a given infectious pathogen is increasingly recognized. As we uncover the links between host genomics and infectious disease, a number of ethical, legal, and social issues need to be consi...
Dengue virus, the etiological agent of dengue fever (DF) occurs in four genetically distinct serotypes (DENV1-4), being transmitted by female Aedes mosquitoes. DF incidence is increasing in Brazil, following vector dispersal, proliferation and DENV serotypes introduction, co-circulation and substitu...
While whole genome sequencing (WGS) may be more expensive than traditional testing and polymerase chain reaction (PCR), simple cost comparisons ignore the potential for WGS to reduce the societal costs of non-typhoidal Salmonella enterica through public health action to prevent illness. We determine...
Emerging infectious diseases (EIDs) caused by viruses are increasing in frequency, causing a high disease burden and mortality world-wide. The COVID-19 pandemic caused by the novel SARS-like coronavirus (SARS-CoV-2) underscores the need to innovate and accelerate the development of effective vaccina...
Today, whole genome sequencing (WGS)-based typing is the gold standard approach to detect outbreaks of Shiga toxin-producing Escherichia coli (STEC) and to differentiate them from sporadic cases. Here, we describe an optimized protocol to efficiently determine the genome sequences of STEC using shor...
Between 2018 and 2019, the incidence of chikungunya was approximately 15,000 cases across 60 provinces in Thailand. Here, the clinical presentations in chikungunya, emergent pattern, and genomic diversity of the chikungunya virus (CHIKV) causing this massive outbreak were demonstrated. A total of 1,...
Some early English language news coverage of COVID-19 epidemiology focused on studies that examined how SARS-CoV-2 (the coronavirus that causes COVID-19) was evolving at the genetic level. The use of phylogenetic methods to analyse pathogen genetic sequence data to understand disease dynamics is cal...
Outbreaks of a vesiculopustular disease in dairy cattle and milkers have been frequently reported in Brazil since 1999 when the vaccinia virus strain Cantagalo was first isolated in the State of Rio de Janeiro. However, the genomic diversity of the viral isolates associated with these outbreaks is n...
Since the COVID-19 epidemic is still expanding around the world and poses a serious threat to human life and health, it is necessary for us to carry out epidemic transmission prediction, whole genome sequence analysis, and public psychological stress assessment for 2019-nCoV. However, transmission p...
Campylobacter jejuni is an important foodborne pathogen with global distribution. We describe a genotyping study of a collection of C. jejuni (n=137) isolated from different broiler farms and from multiple sites along the processing line in a slaughterhouse in Argentina during 2011, 2012 and 2015. T...
The purpose of this study is to use whole genome sequencing (WGS) combined with epidemiological data to track a hospital infection of the carbapenem-resistant (CRKP), which affected 3 neonatal patients in the neonatal intensive care unit (NICU). The minimum inhibitory concentrations for the antimi...
The COVID-19 pandemic has inequitably impacted Indigenous communities in the United States. In this emergency state that highlighted existing inadequacies in US government and tribal public health infrastructures, many tribal nations contracted with commercial entities and other organization types t...
The year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid...
Whole genome sequencing (WGS) has had widespread use in the management of microbial outbreaks in a public health setting. Current models encompass sending isolates to a central laboratory for WGS who then produce a report for various levels of government. This model, although beneficial, has multipl...
Klebsiella pneumoniae is a major pathogen implicated in nosocomial infections. Extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae isolates are a public health concern. We aim to characterize the type of β-lactamases and the associated resistance mechanisms in ESBL-producing K. pneumoniae i...
Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial in...
Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or...
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily related to 2 other clinically relevant coronaviruses, SARS-CoV a...
is an opportunistic nosocomial pathogen that has increasingly become resistant to carbapenems worldwide. In the Philippines, rates of carbapenem resistance and multidrug resistance are above 50%. We undertook a genomic study of carbapenem-resistant in the Philippines to characterize the population...
We undertook an integrated analysis of genomic and epidemiological data to investigate a large health-care-associated outbreak of coronavirus disease 2019 (COVID-19) and to better understand the epidemiology of COVID-19 cases in Tasmania, Australia. Epidemiological data collected on COVID-19 cases n...
As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been...
Since the first reported case in December 2019, SARS-CoV-2 infections have become a major public health worldwide. Even with the increasing vaccination in several countries and relaxing of social distancing measures, the pandemic remains a threat especially due to the emergence of new SARS-CoV-2 var...
After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared...
The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance of SARS-CoV-2 is imperative for early detection of emerging variants, to trace the movement of variants, and to monitor effectiveness of countermeasures. Additionally, determini...
The global coronavirus disease 2019 (COVID-19) pandemic has demonstrated the range of disease severity and pathogen genomic diversity emanating from a singular virus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). This diversity in disease manifestations and genomic mutations has chal...
Brazil is the country with the second-largest number of deaths due to the coronavirus disease-2019 (COVID-19). Two variants of concern (VOCs), Alpha (B.1.1.7) and Gamma (P.1), were first detected in December 2020. While Alpha expanded within an expected rate in January and February 2021, its prevale...
Antimicrobial resistance (AMR) is an increasing and urgent issue for human health worldwide, as it leads to the reduction of available antibiotics to treat bacterial infections, in turn increasing hospital stays and lethality. Therefore, the study and genomic surveillance of bacterial carriers of re...
Porcine deltacoronavirus (PDCoV) is a highly transmissible intestinal pathogen that causes mild to severe clinical symptoms, such as anorexia, vomiting, and watery diarrhea in pigs. By comparing the genetic sequences of the spike glycoprotein between historical and current Taiwanese PDCoV strains, w...
The availability of accurate, reliable, and timely clinical data is crucial for clinicians, researchers, and policymakers so that they can respond effectively to emerging public health threats. This was typified by the recent SARS-CoV-2 pandemic and the critical knowledge and data gaps associated wi...
Since the start of the pandemic, SARS-CoV-2 has infected almost 200 million human hosts and is set to encounter and gain entry in many more in the coming months. As the coronavirus flourish, the evolutionary pressure selects those variants that can complete the infection cycle faster and reproduce i...
A new easy-to-use online bioinformatic tool analyzing whole genome sequences of healthcare associated bacteria was used by a local infection control unit to retrospectively map genetic relationship of isolates of carrying resistance genes to vancomycin in a hospital. Three clusters of isolates were...
Genomic epidemiology is a core component in investigating the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, the efficacy of control strategies in South Korea was evaluated using genomic epidemiology based on viral genome sequences of 2,065 SARS-CoV-2 case...
The diversity of lagoviruses () in Australia has increased considerably in recent years. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the evolutionary interactions among...
Peste des petits ruminants virus (PPRV) causes disease in domestic and wild ungulates, is the target of a Global Eradication Programme, and threatens biodiversity. Understanding the epidemiology and evolution of PPRV in wildlife is important but hampered by the paucity of wildlife-origin PPRV genome...
The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants...
The presence and dissemination of carbapenem-resistant (CRKP) often cause life-threatening infections worldwide, but the therapeutic option is limited. In this study, whole-genome sequencing (WGS) was applied to assess the epidemiological characteristics and transmission dynamics of CRKP isolates r...
The fitness of a pathogen is a composite phenotype determined by many different factors influencing growth rates both within and between hosts. Determining what factors shape fitness at the host population-level is especially challenging because both intrinsic factors like pathogen genetics and extr...
There is a global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Information on viral genomics is crucial for understanding global dispersion and for providing insight into viral pathogenicity and transmission. Here, we characterized the SARS-CoV-2 genomes isolated from fi...
is an opportunistic pathogen that often causes nosocomial infections resistant to treatment. Rates of antimicrobial resistance (AMR) are increasing, as are rates of multidrug-resistant (MDR) and possible extensively drug-resistant (XDR) infections. Our objective was to characterize the molecular epi...
Viral sequence data coupled with phylodynamic models have become instrumental in investigating the outbreaks of human and animal diseases, and the incorporation of the hypothesized drivers of pathogen spread can enhance the interpretation from phylodynamic inference. Integrating animal movement data...
Understanding of pandemics depends on the characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, Human Immunodeficiency Virus Type 1 (HIV-1) has geographically spread and genetically diversified into distinct...
The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the 'real-time' generation and sharing of SARS-CoV-2 genomic data. The rapid growth in virus genome data pro...
New Zealand, Australia, Iceland, and Taiwan all saw success in controlling their first waves of Coronavirus Disease 2019 (COVID-19). As islands, they make excellent case studies for exploring the effects of international travel and human movement on the spread of COVID-19. We employed a range of rob...
Staphylococci producing exfoliative toxins are the causative agents of staphylococcal scalded skin syndrome (SSSS). Exfoliative toxin A (ETA) is encoded by , which is harbored on a temperate bacteriophage ΦETA. A recent increase in the incidence of SSSS in North America has been observed; yet it is...
Azithromycin-nonsusceptible Neisseria gonorrhoeae strains are an emerging global public health threat. During 2015-2018, the prevalence of azithromycin-nonsusceptible gonococcal infection increased significantly in Argentina. To investigate the genomic epidemiology and resistance mechanisms of these...
The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coron...
Identification of the genomic diversity and the phylodynamic profiles of prevalent variants is critical to understand the evolution and spread of SARS-CoV-2 variants. We performed whole-genome sequencing of 54 SARS-CoV-2 variants collected from COVID-19 patients in Kolkata, West Bengal during August...
Rodonaja 1967, is an emerging, zoonotic filarial nematode parasite that causes ocular disease in dogs, cats, wild canids, and humans. It is the causative agent of ocular onchocercosis in canines with increasing incidence in both North America and the Old World during the early twenty-first century....
Tuberculosis (TB), an airborne infectious disease caused by complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of to the sub-region makes West Africa have an extra...
Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new app...
Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics o...
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the req...
Big Bayes is the computationally intensive co-application of big data and large, expressive Bayesian models for the analysis of complex phenomena in scientific inference and statistical learning. Standing as an example, Bayesian multidimensional scaling (MDS) can help scientists learn viral trajecto...
Uruguay is one of the few countries in the Americas that successfully contained the coronavirus disease 19 (COVID-19) epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to i...
Antimicrobial-resistant is a major threat to public health and is of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high. The Antimicrobial Resistance Surveillance Program (ARSP) has been capturing information on resistant gonorrhoea since 1996, but genomic e...
Methicillin-resistant (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to...
Even though the COVID-19 epidemic in China has been successfully put under control within a few months, it is still very important to infer the origin time and genetic diversity from the perspective of the whole genome sequence of its agent, SARS-CoV-2. Yet, the sequence of the entire virus genome f...
We have developed and implemented an undergraduate microbiology course in which students isolate, characterize, and perform whole genome assembly and analysis of from stream sediments and poultry litter. In the development of the course and over three semesters, successive teams of undergraduate st...
By tracking pathogen outbreaks using whole genome sequencing, medical microbiology is currently being transformed into genomic epidemiology. This change in technology is leading to the rapid accumulation of large samples of closely related genome sequences. Summarizing such samples into phylogenies...
Coronavirus SARS-CoV-2 is a novel coronavirus and the seventh that can infect human beings and result in severe and acute respiratory syndrome and deaths. Currently, the world is undergoing a global health emergency due to the SARS-CoV-2 pandemic. As of May 18, SARS-CoV-2 has spread to over two hund...
Humanity has seen numerous pandemics during its course of evolution. The list includes several incidents from the past, such as measles, Ebola, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS), etc. The latest edition to this is coronavirus disease 2019 (COVID-19...
The SARS-CoV-2 (SARS2) is the cause of the coronavirus disease 2019 (COVID-19) pandemic. One unique structural feature of the SARS2 spike protein is the presence of a furin-like cleavage site (FLC) which is associated with both viral pathogenesis and host tropism. Specifically, SARS2 spike protein b...
causes the American foulbrood (AFB), a highly contagious and devastating disease of honeybees. Whole-genome sequencing (WGS) has been increasingly used in bacterial pathogen typing, but rarely applied to study the epidemiology of . To this end, we used 125 genomes representative of a species-wide d...
Aedes aegypti mosquito-borne viruses including Zika (ZIKV), dengue (DENV), yellow fever (YFV), and chikungunya (CHIKV) have emerged and re-emerged globally, resulting in an elevated burden of human disease. Aedes aegypti is found worldwide in tropical, sub-tropical, and temperate areas. The characte...
Melioidosis is a neglected tropical disease with rising global public health and clinical importance. Melioidosis is endemic in Southeast Asia and Northern Australia and is of increasing concern in Malaysia. Despite a number of reported studies from Malaysia, these reports are limited to certain par...
Influenza A virus subtype H1N1 has caused global pandemics like the "Spanish flu" in 1918 and the 2009 H1N1 pandemic several times. H1N1 remains in circulation and survives in multiple animal sources, including wild birds. Surveillance during the winter of 2018-2019 in Korea revealed two H1N1 isolat...
Tomato mosaic virus (ToMV) is a tobamovirus affecting solanaceous crops worldwide. The process of its emergence, however, is poorly understood. Here, Bayesian phylogenetic framework was employed to reconstruct the phylogeography of ToMV in Eurasia. The results showed that the ToMV in Europe, Middle...
The global population is at present suffering from a pandemic of Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The goal of this study was to use artificial intelligence (AI) to predict blueprints for designing unive...
We present GeoBoost2, a natural language-processing pipeline for extracting the location of infected hosts for enriching metadata in nucleotide sequences repositories like National Center of Biotechnology Information's GenBank for downstream analysis including phylogeography and genomic epidemiology...
Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe a...
Clostridioides difficile infection (CDI) is a major healthcare-associated diarrheal disease. Consistent with trends across the United States, C. difficile RT106 was the second-most prevalent molecular type in our surveillance in Arizona from 2015 to 2018. A representative RT106 strain displayed robu...
Here, we describe the case of a COVID-19 patient who developed recurring ventilator-associated pneumonia caused by that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis revealed the AMR genotype, while immunological analysis revealed massiv...
Patients entering nursing facilities (NFs) are frequently colonized with antibiotic-resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission, we applied whole-genome sequencing to track the spread of 4 ARO species across regional NFs and evaluated patient-level...
Outbreaks of Rift Valley fever (RVF) occurred in Namibia in 2010 and 2011. Complete genome characterization was obtained from virus isolates collected during disease outbreaks in southern Namibia in 2010 and from wildlife in Etosha National Park in 2011, close to the area where RVF outbreaks occurre...
Using molecular techniques and bioinformatics tools, we studied the vector-host interactions and the molecular epidemiology of West Nile virus (WNV) in western Iran. Mosquitoes were collected during 2017 and 2018. DNA typing assays were used to study vector-host interactions. Mosquitoes were screene...
Salmonella Enteritidis, an important foodborne zoonosis, has a dramatically increased number of cases around the world. To explore the phylogenetic structure of Peruvian Salmonella Enteritidis strains and their relationship with an outbreak occurred in 2018, we analyzed a comprehensive strains of S....
Bluetongue virus (BTV) is an arbovirus (genus: ) that occurs worldwide. It infects domestic and wild ruminant species and can cause disease in livestock, producing high economic impact. Recently, it gained extra prominence throughout Europe, with disease occurring in regions traditionally free of BT...
The coronavirus disease 2019 (COVID-19) pandemic has disrupted global healthcare and economic systems throughout 2020 with no clear end in sight. While the pandemic continues to have deleterious effects across the globe, mechanisms for disrupting disease transmission have relied on behavioral contro...
The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main...
Pathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong pos...
New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide 'lockdown' of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected during th...
In 2010, Burkina Faso completed the first nationwide mass-vaccination campaign of a meningococcal A conjugate vaccine, drastically reducing the incidence of disease caused by serogroup A meningococci. Since then, other strains, such as those belonging to serogroups W, X and C, have continued to caus...
Canid alphaherpesvirus 1 (CHV-1) is a widespread pathogen of dogs with multiple associated clinical signs. There has been limited prior investigation into the genomics and phylogeny of this virus using whole viral genome analysis. Fifteen CHV-1 isolates were collected from animals with ocular diseas...
Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019, the situation evolved to pandemic level. Following China, Europe was the second epicenter of the pandemic. To better comprehend...
The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in...
Proteomics offers a wide collection of methodologies to study biological systems at the finest granularity. Faced with COVID-19, the most worrying pandemic in a century, proteomics researchers have made significant progress in understanding how the causative virus hijacks the host's cellular machine...
Dengue viruses (DENVs) are classified into four serotypes, each of which contains multiple genotypes. DENV genotypes introduced into the Americas over the past five decades have exhibited different rates and patterns of spatial dispersal. In order to understand factors underlying these patterns, we...
Bacteria of the genus Bartonella have been known as emerging zoonotic pathogens for several human diseases including cat scratch disease, Carrion's disease and trench fever. Numerous species of small mammals have been reported to play a role as a suitable reservoir to many pathogenic Bartonella. The...
Between 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. We aim to describe the spatiotemporal and molecular features of the three distinct epidemic waves and explore the role of vaccination campaigns...
Managing recovered COVID-19 patients with recurrent-positive SARS-CoV-2 RNA test results is challenging. We performed a population-based observational study to characterize the viral RNA level and serum antibody responses in recurrent-positive patients and evaluate their viral transmission risk. Of...
Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interactin...
The impact of SARS-CoV-2 on neonates remains largely unknown in low- and middle-income countries (LMICs). We provide an epidemiologic and clinical report of SARS-CoV-2 infections in neonates hospitalized in Bangladesh. Outborn neonates admitted to Dhaka Shishu Hospital, a tertiary-care referral hosp...
The emergence of SARS-CoV-2 has resulted in an ongoing global pandemic with significant morbidity, mortality, and economic consequences. The susceptibility of different animal species to SARS-CoV-2 is of concern due to the potential for interspecies transmission, and the requirement for pre-clinical...
Global dissemination of ciprofloxacin-resistant Kentucky has been observed over the past decades. In recent years, there have been reports of extended-spectrum β-lactamase (ESBL) producing . Kentucky. Routine surveillance at the European Centre for Disease Prevention and Control (ECDC) detected cas...
Early 2019, a chikungunya virus (CHIKV) outbreak hit the Democratic Republic of the Congo (DRC). Though seldomly deadly, this mosquito-borne disease presents as an acute febrile (poly)arthralgia often followed by long-term sequelae. Although is the primary vector, an amino acid substitution in the...
The recent emergence of a coronavirus (SARS-CoV-2), first identified in the Chinese city of Wuhan in December 2019, has had major public health and economic consequences. Although 61,888 confirmed cases were reported in Brazil by 28 April 2020, little is known about the SARS-CoV-2 epidemic in this c...
How severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections engage cellular host pathways and innate immunity in infected cells remains largely elusive. We performed an integrative proteo-transcriptomics analysis in SARS-CoV-2 infected Huh7 cells to map the cellular response to the i...
Due to its high case fatality rate, foodborne listeriosis is considered a major public health concern worldwide. We describe one of the largest listeriosis outbreaks in Germany with 83 cases of invasive listeriosis between 2013 and 2018. As part of the outbreak investigation, we identified a highly...
Taiwan experienced two waves of imported infections with Coronavirus Disease 2019 (COVID-19). This study aimed at investigating the genomic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Taiwan and compared their evolutionary trajectories with the global strains. We per...
In the present study, a total of 7793 samples from 5 different types of hosts were collected and tested, with a seroprevalence of 2.4% (184/7793). Although the seroprevalence of human and animal brucellosis is relatively low, numbers of human brucellosis cases reported have increased continuously fr...
is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of that cause diarrhe...
Hypervirulent Klebsiella pneumoniae(hvKp) is an increasingly important pathogen. Tracking its epidemiology and evolving antimicrobial resistance will facilitate care. A retrospective study was conducted in two hospitals. We collected the clinical data. Antimicrobial and virulence-associated phenotyp...
Whole-genome sequencing (WGS) can be used in genomic epidemiology investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted and efficient infection control interventions. We aimed to define a genetic relatedness cutoff, quantified as a number of single-nucleotide...
Coronavirus disease (COVID-19) in Colombia was first diagnosed in a traveler arriving from Italy on February 26, 2020. However, limited data are available on the origins and number of introductions of COVID-19 into the country. We sequenced the causative agent of COVID-19, severe acute respiratory s...
Melioidosis is a disease of significant public health importance that is being increasingly recognized globally. The majority of cases arise through direct percutaneous exposure to its etiological agent, In the Lao People's Democratic Republic (Laos), the presence and environmental distribution of...
The novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is causing an unprecedented pandemic, threatening planetary health, society, and economy. Genomic surveillance continues to be a critical effort toward tracking the virus and containing its spread, and more genomes from diverse...
Lineage 4/X-family of Mycobacterium tuberculosis is not very notorious, except for the CDC1551 strain. One strain of this family, named Ara50, caused one of the largest tuberculosis outbreaks of the Aragon region, Spain, during the 1990s and remained until 2018. These X-strains are characterised by...
Panton-Valentine leucocidin (PVL)-positive community-associated meticillin-resistant Staphylococcus aureus (CA-MRSA) is increasingly associated with infection outbreaks. To investigate multiple suspected PVL-positive CA-MRSA outbreaks using whole-genome sequencing (WGS). Forty-six suspected outbreak...
Salmonella spp. remains the most significant foodborne pathogen in south Brazil, but its epidemiology tends to change over time. Using official and surrogate data, a microbial subtyping model attributed different Salmonella serovars to laying hens, pigs, broilers, and turkeys from 2005 to 2015 in Ri...
The use of Whole genome sequencing (WGS) identified a multi-country outbreak of human listeriosis associated with consumption of frozen sweet corn produced in Hungary. The purpose of this report was to summarise information on the cases occurring in the UK which were part of this outbreak and outlin...
During August 7-16, 2020, a motorcycle rally was held in western South Dakota that attracted approximately 460,000 persons from across the United States to numerous indoor and outdoor events over a 10-day period. During August-September 2020, the Minnesota Department of Health (MDH) investigated a c...
The Caribbean and South American French Overseas Territories (CSAFOT) are the regions most heavily affected by the Human Immunodeficiency Virus type 1 (HIV-1) epidemic in France. Although dominated by HIV-1 subtype B, the detection of non-B subtypes and the great proportion of HIV-positive persons b...
Mucormycoses are invasive infections by species and other Mucorales. Over 10 months, four solid organ transplant (SOT) recipients at our centre developed mucormycosis due to (=2), (=1) or (=1), at a median 31.5 days (range: 13-34) post-admission. We performed whole genome sequencing (WGS) on 72...
Antibiotic resistance surveillance through regional and up-to-date testing of clinical isolates is a foundation for implementing effective empirical treatment. Surveillance data also provides an overview of geographical and temporal changes that are invaluable for guiding interventions. Still, due t...
Salmonella enterica, the causative agent of gastrointestinal diseases and typhoid fever, is a human and animal pathogen that causes significant mortality and morbidity worldwide. In this study, we examine the genomic diversity and phylogenetic relationships of 63 S. enterica isolates from human-deri...
During a meticillin-resistant Staphylococcus aureus contact tracing and screening investigation, two borderline oxacillin-resistant Staphylococcus aureus (BORSA)-positive screening cultures were encountered among neonatal intensive care unit (NICU) healthcare workers (HCWs). This finding led to furt...
Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first...
Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. This approach has been instrumental in understanding the emergence, spread, and evolution of a range of plant patho...
The control of re-occurring pandemic pathogens requires understanding the origins of new pandemic variants and the factors that drive their global spread. This is especially important for GII.4 norovirus, where vaccines under development offer promise to prevent hundreds of millions of annual gastro...
From 2013 onwards, the spread of novel H5N6 highly pathogenic avian influenza (HPAI) viruses in China has posed great threats to not only poultry industry but also human health. Since late-2016 in particular, frequent outbreaks of clade 2.3.4.4 H5N6 HPAI viruses among wild birds have promoted viral...
Potato virus Y (PVY) is a destructive plant pathogen that causes considerable losses to global potato and tobacco production. Although the molecular structure of PVY is well characterized, the evolutionary and global transmission dynamics of this virus remain poorly understood. We investigated the p...
The aim of this study was to assess the clinical utility of metagenomic next-generation sequencing (mNGS) on smear-negative extrapulmonary specimens collected in China. Specimens were tested by mNGS and other routine tests for tuberculosis (TB). The diagnostic accuracy of mNGS was calculated and com...
The high clinical burden of Clostridioides difficile infections merits rapid and sensitive identification of affected individuals. However, effective diagnosis remains challenging. Current best practice guidelines recommend molecular and/or direct toxin detection-based screening for symptomatic indi...
To develop RT-nPCR assays for amplifying partial and complete VP1 genes of human enteroviruses (HEVs) from clinical samples and to contribute to etiological surveillance of HEV-related diseases. A panel of RT-nPCR assays, consisting of published combined primer pairs for VP1 genes of HEV A-C and in-...
Infectious disease control is experiencing a paradigm shift, as pathogen sequencing technologies and digital applications are increasingly implemented for control of diseases such as tuberculosis, Ebola, and COVID-19. A new ethical framework should be a critical part of this emerging paradigm to ens...
Mycoplasma mycoides subsp. capri (Mmc) typically causes pneumonia, mastitis, arthritis, keratitis and septicaemia in goats. Mortality associated with Mmc in goat flocks is lower compared to Mycoplasma capricolum subsp. capripneumoniae-associated respiratory infections. Case fatality rates associated...
Serpentoviruses are an emerging group of nidoviruses known to cause respiratory disease in snakes and have been associated with disease in other non-avian reptile species (lizards and turtles). This study describes multiple episodes of respiratory disease-associated mortalities in a collection of ju...
Rickettsia felis is the causative agent of flea-borne spotted fever (FBSF), an emerging zoonosis. Although there is evidence of FBSF in Greece, fleas, the classic vectors of R. felis, have not been adequately studied. Thus, the aim of this study was to detect and characterize bacteria of genus Ricke...
is a leading cause of bacterial meningitis and sepsis worldwide and an occasional cause of meningococcal urethritis. When isolates are unavailable for surveillance or outbreak investigations, molecular characterization of pathogens needs to be performed directly from clinical specimens, such as cere...
Since the first reported severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in December 2019, coronavirus disease 2019 (COVID-19) has become a global pandemic, spreading to more than 200 countries and regions worldwide. With continued research progress and virus detection, SARS-C...
Spain has been one of the main global pandemic epicenters for coronavirus disease 2019 (COVID-19). Here, we analyzed >41 000 genomes (including >26 000 high-quality (HQ) genomes) downloaded from the GISAID repository, including 1 245 (922 HQ) sampled in Spain. The aim of this study was to investigat...
Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology. We devel...
There were 290 multidrug-resistant (MDR)-TB cases diagnosed in Singapore from 2006 to 2018. Eighty-one percent were foreign-born. Spoligotyping and MIRU-VNTR methods identified 108 patients in 24 clusters. The Beijing spoligotype accounted for 22 clusters. Whole genome sequencing (WGS) analysis redu...
The full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical characteristics in children. Whole-genome sequencing was performed on re...
Prevention and control of methicillin-resistant Staphylococcus aureus (MRSA) infections remain challenging. In-depth surveillance integrating patient and isolate data can provide evidence to better inform infection control and public health practice. We analyzed MRSA cases diagnosed in 2010 (n = 212...
Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome seque...
The Network for Genomic Surveillance in South Africa (NGS-SA) was formed to investigate the introduction and understand the early transmission dynamics of the SARS-CoV-2 epidemic in South-Africa. This paper presents the first results from this group, which is a molecular epidemiological study of the...
Since the early times, human beings have always been faced with deadly microbial infections, both bacterial and viral. Pathogens such as viruses are always evolving owing to the processes of antigenic shift and drift. Such viral evolution results in the emergence of new types and serovars that prove...
After the first case of coronavirus disease 2019 (COVID-19) in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating the emerging COVID-19 clusters by conducting active nationwide epidemiological surveill...
The efficacy of public health measures to control the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has not been well studied in young adults. We investigated SARS-CoV-2 infections among U.S. Marine Corps recruits who underwent a 2-week quarantine at home followed by a...
Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth invest...
serogroup O1 is responsible for epidemic and pandemic cholera and remains a global public health threat. This organism has been well established as a resident flora of the aquatic environment that alters its phenotypic and genotypic attributes for better adaptation to the environment. To reveal the...
Wolbachia bacteria are widely distributed throughout terrestrial arthropod species. These bacteria can manipulate reproduction and influence the vector competence of their hosts. Recently, Wolbachia have been integrated into vector control programmes for mosquito management. A number of supergroups...
Bovine coronavirus (BoCV) is an important pathogen of cattle, causing severe enteric disease and playing a role in the bovine respiratory disease complex. Similar to other coronaviruses, a remarkable variability characterizes both its genome and biology. Despite their potential relevance, different...
The General Population Cohort (GPC) in south-western Uganda has a low HIV-1 incidence rate (<1%). However, new infections continue to emerge. In this research, 3796 HIV-1 sequences (GPC: = 1418, non-GPC sites: = 1223, Central Uganda: = 1010 and Eastern Uganda: = 145) generated between 2003-2015...
Since spilling over into humans, SARS-CoV-2 has rapidly spread across the globe, accumulating significant genetic diversity. The structure of this genetic diversity and whether it reveals epidemiological insights are fundamental questions for understanding the evolutionary trajectory of this virus....
Carbapenem-resistant (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial suscep...
Outbreaks pose a significant risk to patient safety as well as being costly and time consuming to investigate. The implementation of targeted infection prevention and control measures relies on infection prevention and control teams having access to rapid results that detect resistance accurately, a...
Carbapenemase-producing and colistin resistant Klebsiella pneumoniae has become a worldwide healthcare problem. This study describes molecular characterization of carbapenemase-producing and colistin resistant clinical K. pneumoniae isolates.A total of 93 non-replicate carbapenem and colistin resist...
Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods. In this study, we assess how the core genome can be used to i...
Cases of Clostridiodes difficile infection (CDI) diagnosed after hospital discharge account for a substantial proportion of new infections. It is unclear whether post-discharge infections originate from hospital-based transmission. This was a Retrospective cohort study at a tertiary-care cancer cent...
Corynebacteritum straitum has been considered as an emerging multi-drug-resistant (MDR) pathogen. Isolation of MDR C. striatum as the only organism from respiratory samples from hospitalized patients is increasing in China. To elucidate the genomic epidemiology and evolution of C. striatum in China....
First Zika virus (ZIKV) positive case from North India was detected on routine surveillance of Dengue-Like Illness in an 85-year old female. Objective of the study was to conduct an investigation for epidemiological, clinical and genomic analysis of first ZIKV outbreak in Rajasthan, North India and...
Kenya experiences a substantial burden of dengue, yet there are very few DENV-2 sequence data available from this country and indeed the entire continent of Africa. We therefore undertook whole genome sequencing and evolutionary analysis of fourteen dengue virus (DENV)-2 strains sampled from Malindi...
SARS-CoV-2 emerged in 2019 and has become a major global pathogen. Its emergence is notable due to its impacts on individuals residing within long term care facilities (LTCFs) such as rehabilitation centers and nursing homes. LTCF residents tend to possess several risk factors for more severe SARS-C...
The oral cavity may comprise a significant reservoir for Staphylococcus aureus but the data on molecular epidemiology and clonal distribution of oral strains are really scarce. This study aimed to evaluate the clonal relatedness in S. aureus isolated from oral cavity and their relationship with carr...
Proteins and peptides serve as biomarkers in the context of multiple pathologies. The hypothesis that protein or peptide biomarkers may also be of value in the context of the Covid-19 pandemic appears self-evident. Proteome based biomarkers are not expected to display significant added value in the...
In December 2019, a new species of coronavirus (SARS-CoV-2) was identified in a number of patients presenting with pneumonias of unknown aetiology in WuHan Province, China. Early epidemiological indications were of a zoonotic origin: many of the initial patients confirmed contact with a local wet ma...
We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on March 2, 2020. Since w...
Streptococcus pyogenes is one of the Top 10 human infectious disease killers worldwide causing a range of clinical manifestations in humans. Colonizing a range of ecological niches within its sole host, the human, is key to the ability of this opportunistic pathogen to cause direct and post-infectio...
serotype Enteritidis ( Enteritidis) is a major cause of foodborne disease outbreaks worldwide. In 2018, two concurrent outbreaks of Enteritidis gastroenteritis in one district of South Africa were investigated. We describe the use of whole-genome sequencing (WGS) analysis of bacterial isolates to a...
To characterize genomes of Klebsiella pneumoniae ST11 NDM-1 responsible for a countrywide outbreak in Poland and compare them phylogenetically with other Polish and international ST11 strains. Seventy-one carbapenemase-producing K. pneumoniae ST11 isolates from Poland, including 66 representatives o...
With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 whole genome sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the...
In June 2017, the Pennsylvania Department of Health (PADOH) was notified of multiple norovirus outbreaks associated with 179 ill individuals who attended separate events held at an outdoor venue and campground over a month period. Epidemiologic investigations were unable to identify a single exposur...
Introduction: SARS-CoV-2 has been identified as the new coronavirus causing an outbreak of acute respiratory disease in China in December, 2019. This disease, currently named COVID-19, has been declared as a pandemic by the World Health Organization (WHO). The first case of COVID-19 in Colombia was...
Our current understanding of the natural evolution of RNA viruses comes largely from consensus level genetic analyses which ignore the diverse mutant swarms that comprise within-host viral populations. The breadth and composition of viral mutant swarms impact viral fitness and adaptation, and the ca...
The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This pandemic emerged during the era of genomic epidemiol...
Nipah virus (NiV) infection, often fatal in humans, is primarily transmitted in Bangladesh through the consumption of date palm sap contaminated by Pteropus bats. Person-to-person transmission is also common and increases the concern of large outbreaks. This study aimed to characterize the molecular...
Pneumocystis pneumonia (PCP) outbreaks may occur in solid organ transplant (SOT) patients. Transmissibility of Pneumocystis jirovecii among SOT and non-SOT patients has not been investigated. Ten SOT (ie, 4 heart, 4 kidney, 2 liver allograft recipients) and 11 non-SOT (ie, 7 HIV-infected, 3 hematolo...
Nosocomial acquisition and transmission of vancomycin-resistant Enterococcus faecium (VREfm) is the driver for E. faecium carriage in hospitalized patients, which, in turn, is a risk factor for invasive infection in immunocompromised patients. In the present study, we provide a comprehensive picture...
Metagenomic Next-Generation Sequencing (mNGS) is an emerging technique for microbial identification and diagnosis of infectious diseases. The clinical utility of mNGS, especially its real-world impact on antimicrobial treatment and patient outcome has not been systematically evaluated. We prospectiv...
Predicting the emergence of novel infectious diseases requires an understanding of how pathogens infect and efficiently spread in alternative naïve hosts. A pathogen's ability to adapt to a new host (i.e. host shift) oftentimes is constrained by host phylogeny, due to limits in the molecular mechani...
(.) is an important pathogen of cattle implicated in a broad range of clinical manifestations that adversely impacts livestock production worldwide. In the absence of a safe, effective commercial vaccine in Europe, the reported reduced susceptibility to antimicrobials for this organism has contribu...
Emerging and re-emerging infectious diseases due to RNA viruses cause major negative consequences for the quality of life, public health, and overall economic development. Most of the RNA viruses causing illnesses in humans are of zoonotic origin. Zoonotic viruses can directly be transferred from an...
In 1970, the seventh pandemic of cholera (7 P) reached both Africa and Europe. Between 1970 and 2011, several European countries reported cholera outbreaks of a few to more than 2,000 cases. We report here a whole-genome analysis of 1,324 7 P V. cholerae El Tor (7 PET) isolates, including 172 from a...
One of the most widely used methods to detect an acute viral infection in clinical specimens is diagnostic real-time polymerase chain reaction. However, because of the COVID-19 pandemic, mass-spectrometry-based proteomics is currently being discussed as a potential diagnostic method for viral infect...
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters....
Sustaining adequate nutritional needs of a population is a challenging task in normal times and a priority in times of crisis. There is no 'one-size-fits-all' solution that addresses nutrition. In relevance to the COVID-19 (coronavirus disease 2019) pandemic crisis, viral infections in general and R...
Nationally, there was a continuing downward trend in notifications of COVID-19. The daily average number of cases for this reporting period was 14 compared to an average of 23 cases per day in the previous fortnight. There were 192 cases of COVID-19 and 23 deaths this fortnight, bringing the cumulat...
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economic concern worldwide. There are currently large data sets available about the ORF5 gene of the virus, with thousands of sequences available, but little data are currently available on the full-length genome of PRRSV. We hyp...
International travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the United Arab Emirates (UAE), a major international travel...
International organizations advocate for the elimination of dog-mediated rabies, but there is only limited guidance on interpreting surveillance data for managing elimination programmes. With the regional programme in Latin America approaching elimination of dog-mediated rabies, we aimed to develop...
The coronavirus disease 2019 (COVID-19) pandemic is a global public health crisis. However, little is known about the pathogenesis and biomarkers of COVID-19. Here, we profiled host responses to COVID-19 by performing plasma proteomics of a cohort of COVID-19 patients, including non-survivors and su...
Since 2004, several outbreaks of highly pathogenic avian influenza (HPAI) have been reported in Cambodia. Until 2013, all H5N1 viruses identified in Cambodia belonged to clade 1 and its subclades. H5N1 HPAI viruses belonging to clade 2.3.2.1c have been dominant since the beginning of 2014, with vari...
Pseudorabies virus (PRV), the causative agent of Aujeszky's disease, has gained increased attention in China in recent years as a result of a recent outbreak of pseudorabies. The causative agent has a wide spectrum of hosts, including pigs, cattle, sheep, dogs, cats, bats, bears, and even some avian...
is notorious for acquiring antibiotic resistance and causing nosocomial infections worldwide. This study aimed to investigate the prevalence and molecular characteristics of isolates obtained from inpatients and the intensive care unit (ICU) environment of a pediatric hospital in Shanghai, China....
Methicillin-resistant Staphylococcus aureus (MRSA) belong to diverse genetic backgrounds that differ in antibiotic resistance. Knowledge of the local clonal composition of MRSA strains is important for patients' management and for designing effective control and eradication methods. The aim of this...
The COVID-19 pandemic has emerged as a global health emergency due to its association with severe pneumonia and relative high mortality. However, the molecular characteristics and pathological features underlying COVID-19 pneumonia remain largely unknown. To characterize molecular mechanisms underly...
Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps t...
Tick-Borne Encephalitis Virus (TBEV) is a dangerous arbovirus widely distributed in Northern Eurasia. The area of this pathogen changes over time. At the beginning of the 2000s, the Ixodes tick populations in Karelia increased. At the same time, the area of , the main vector of the Siberian TBEV sub...
Big data has become a central part of medical research, as well as modern life generally. "Omics" technologies include genomics, proteomics, microbiomics and increasingly other omics. These have been driven by rapid advances in laboratory techniques and equipment. Crucially, improved information han...
'Filth flies' facilitate the dispersal of pathogens between animals and humans. The objective was to study the intestinal colonization with antimicrobial resistant and enteropathogenic bacteria in 'filth flies' from Nigeria. Flies from Southern Nigeria were screened for extended-spectrum β-lactamase...
Human enteric adenovirus species F (HAdV-F) is one of the most common pathogens responsible for acute gastroenteritis worldwide. Brazil is a country with continental dimensions where continuous multiregional surveillance is vital to establish a more complete picture of the epidemiology of HAdV-F. Th...
To understand the etiological characteristics of an acute gastroenteritis outbreak. Real-time polymerase chain reaction (PCR) and bacteria cultures were performed for the samples, including stool samples from patients and cooks, environmental swabs, raw food material (chicken meat), collected durin...
SARS-CoV-2 has ushered a global pandemic with no effective drug being available at present. Although several FDA-approved drugs are currently under clinical trials for drug repositioning, there is an on-going global effort for new drug identification. In this paper, using multi-omics (interactome, p...
In the present work, two complete genome sequences of SARS-CoV-2 were obtained from nasal swab samples of Tunisian SARS-CoV-2 PCR-positive patients using nanopore sequencing. The virus genomes of two of the patients examined, a Tunisian soldier returning from a mission in Morocco and a member of ano...
To investigate the genetic context of colistin resistance in anmcr-9-harbouring Salmonella Typhimurium ST19 strain from swine in Brazil. Minimum inhibitory concentrations (MIC) to colistin were determined by broth microdilution. Whole-genome sequencing was performed on an Illumina MiSeq system, foll...
In a longitudinal study assessing the WHO strategy for yaws eradication using mass azithromycin treatment, we observed resurgence of yaws cases with dominance of a single JG8 sequence type and emergence of azithromycin-resistant Treponema pallidum subspecies pertenue (T p pertenue). Here, we analyse...
The aim of this study was to provide information about the spread and characteristics of the vancomycin-resistant Enterococcus faecium isolates (VREfm) in Turkey. Seventy-one nonduplicate consecutive isolates of VREfm were obtained from various clinical specimens of inpatients treated at university...
Since the first recognition that infectious microbes serve as the causes of many human diseases, physicians and scientists have sought to understand and control their spread. For the past 150+ years, these 'microbe hunters' have learned to combine epidemiological information with knowledge of the in...
Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-...
Viruses remain a major challenge in the fierce fight against diseases. There have been many pandemics caused by various viruses throughout the world over the years. Recently, the global outbreak of COVID-19 has had a catastrophic impact on human health and the world economy. Antiviral drug treatment...
Molecular epidemiology investigations are notoriously challenging in the leprosy field mainly because the inherent characteristics of the disease as well as its yet uncultivated causative agents, Mycobacterium leprae and M. lepromatosis. Despite significant developments in understanding the biology...
No abstract available
This paper describes a web based tool that uses a combination of sonification and an animated display to inquire into the SARS-CoV-2 genome. The audio data is generated in real time from a variety of RNA motifs that are known to be important in the functioning of RNA. Additionally, metadata relating...
Patients with signs of COVID-19 were tested with CDC approved diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from nasopharyngeal/nasal swabs. In order to determine the variants of SARS-CoV-2 circulating in the state of Nevada, 200 patient specimens from COVID-19 patients were sequenced through...
An outbreak of 59 cases of coronavirus disease (COVID-19) originated with 13 cases linked by a 7 h, 17% occupancy flight into Ireland, summer 2020. The flight-associated attack rate was 9.8-17.8%. Spread to 46 non-flight cases occurred country-wide. Asymptomatic/pre-symptomatic transmission in-fligh...
BackgroundEmerging antimicrobial resistance (AMR) challenges gonorrhoea treatment and requires surveillance.AimThis observational study describes the genetic diversity of isolates in Germany from 2014 to 2017 and identifies multi-antigen sequence typing (NG-MAST) genogroups associated with AMR or...
The cellular entry of severe respiratory syndrome coronavirus-2 (SARS-CoV-2) is mediated by interaction with the human angiotensin-converting enzyme 2 (ACE2), a receptor that is expressed on both lung and intestinal epithelial cells. We performed a quantitative proteomic analysis to investigate the...
During March 2017, a neonatal patient with severe diarrhoea subsequently developed septicaemia and died, with isolated as the causative microorganism. In keeping with infection control protocols, the coincident illness of an attending staff member and three other neonates with infection triggered...
To analyse the rectal carriage rate and the molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) recovered from patients upon hospital admission. Adult patients were screened at six German university hospitals from five different federal states upon hospital admission for rect...
MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control. Twenty-f...
Next-generation sequencing of pathogen quasispecies within a host yields data sets of tens to hundreds of unique sequences. However, the full data set often contains thousands of sequences, because many of those unique sequences have multiple identical copies. Data sets of this size represent a comp...
The outbreak of 2019-novel coronavirus disease (COVID-19), caused by SARS-CoV-2, started in late 2019; in a short time, it has spread rapidly all over the world. Although some possible antiviral and anti-inflammatory medications are available, thousands of people are dying daily. Well-understanding...
Understanding social and scientific drivers of antibiotic resistance is critical to help preserve antibiotic efficacy. These drivers include exposure to subinhibitory antibiotic concentrations in the environment and clinic. To summarize and quantify the relationship between subinhibitory fluoroquino...
is a human pathogen widely found in the environment, with birds being reported as possible natural hosts. During an epidemiological and genomic surveillance study conducted to monitor the occurrence of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales in South American wild birds, we i...
The first identification of autochthonous transmission of SARS-CoV-2 in Italy was documented by the Laboratory of Clinical Microbiology, Virology and Bioemergencies of L. Sacco Hospital (Milano, Italy) on 20th February 2020 in a 38 years old male patient, who was found positive for pneumonia at the...
The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Gen...
Stenotrophomonas maltophilia (S. maltophilia) is an important opportunistic pathogen that can be isolated in hospitals. With the abuse of broad spectrum antibiotics and invasive surgical devices, the rate of S. maltophilia infection is increasing every year. This study was an epidemiological analysi...
To investigate potential transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during a domestic flight within Australia, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed SARS-CoV-2 infection and symptom onset within 48 hou...
Leptospirosis is a widespread zoonosis with global impact, particularly among vulnerable populations in resource-poor settings in tropical countries. Rodents have been considered to be the main reservoir of the disease; however, a wide variety of mammals can act as hosts as well. Here we examine the...
ACE2 (angiotensin-converting enzyme 2) is a key component of the renin-angiotensin-aldosterone system. Yet, little is known about the clinical and biologic correlates of circulating ACE2 levels in humans. We assessed the clinical and proteomic correlates of plasma (soluble) ACE2 protein levels in hu...
Staphylococcus aureus is a widely recognized pathogen responsible for many serious diseases in both humans and animals. It is also one of the major causative agents of bovine mastitis. Methicillin-resistant S. aureus (MRSA), although relatively rare in this pathology, has been increasingly reported...
Candida tropicalis is a common human pathogenic yeast, and its molecular typing is important for studying the population structure and epidemiology of this opportunistic yeast, such as epidemic genotype, population dynamics, nosocomial infection, and drug resistance surveillance. In this study, the...
Motivated to find options for prevention or intervention, molecular epidemiology aims to identify the host and microbial factors that determine the transmission, manifestation and progression of infectious disease. The genotyping of cultivatable bacterial strains is performed by either anonymous fin...
An infestation of cat fleas in a research center led to the detection of two genotypes of Ctenocephalides felis biting humans in New Jersey, USA. The rarer flea genotype had an 83% incidence of Rickettsia asembonensis, a recently described bacterium closely related to R. felis, a known human pathoge...
As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an effective vaccine is critical. A promising approach for vaccine development is to generate, through codon pair deoptimization, an attenuated virus. This approach carries the advantage that it only requires limited...
No abstract available
Invasive listeriosis is a severe foodborne infection caused by Listeria(L.)monocytogenes. The aim of this investigation was to verify and describe a molecular cluster of listeriosis patients and identify factors leading to this outbreak. Whole genome sequencing and core genome multilocus sequence ty...
Nosocomial carbapenemase-producing Enterobacterieceae (CPE) infections constitute a major global health concern and are associated with increased morbidity and mortality. Rectal colonization with CPE is a risk factor for bacterial translocation leading to subsequent endogenous CPE infections. This p...
Molecular and genomic surveillance systems for bacterial pathogens currently rely on tracking clonally evolving lineages. By contrast, plasmids are usually excluded or analyzed with low-resolution techniques, despite being the primary vectors of antibiotic resistance genes across many key pathogens....
We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly da...
Progress of the omics platforms widens their application to diverse fields, including immunology. This enables a deeper level of knowledge and the provision of a huge amount of data for which management and fruitful integration with the past evidence requires a steadily growing computational effort....
Currently, hospitals have been forced to divert substantial resources to cope with the ongoing coronavirus disease 2019 (COVID-19) pandemic. It is unclear if this situation will affect long-standing infection prevention practices and impact on healthcare associated infections. Here, we report a noso...
is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify outbreaks and separate out sporadic isolate...
Merkel cell polyomavirus (MCPyV) is a common human skin pathogen, shows high seroprevalence and is considered the etiologic agent of Merkel cell carcinoma. However, studies which detect MCPyV DNA in blood products may reveal the importance of this virus for the transfusion medicine. In this study we...
The emergence of novel resistant markers hampers the efficacy of beta-lactam antibiotics to treat infections caused by micro-organisms carrying such resistances. This study investigated the antimicrobial susceptibility pattern, the carpapenem-associated determinants and the molecular epidemiology of...
Over the past two decades, has emerged as a leading cause of nosocomial infections worldwide. Of particular concern are panresistant strains, leading the World Health Organization (WHO) to designate carbapenem-resistant as a priority 1 (critical) pathogen for research and development of new antibi...
SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), can spread rapidly in high-risk congregate settings such as skilled nursing facilities (SNFs) (1). In Minnesota, SNF-associated cases accounted for 3,950 (8%) of 48,711 COVID-19 cases reported through July 21, 2020; 35% of SNF-as...
European bat lyssavirus 1 (EBLV-1) is a widespread lyssavirus across Europe, whose epizootic cycle is linked to a few bat species. Occasionally, EBLV-1 infection may occur in domestic animals and humans. EBLV-1 can be classified into two subtypes, where subtype EBLV-1a shows a wide geographic distri...
In this study, we compiled 84-year worth (1934-2017) of genomic and epidemiological data of foot-and-mouth disease virus (FMDV), and performed comprehensive analyses to determine its early origin and transmission route. We found that recombination is a key feature of FMDV, and that the genomic regio...
Enterobacter cloacae species is responsible for nosocomial outbreaks in vulnerable patients in neonatal intensive care units (NICU). The environment can constitute the reservoir and source of infection in NICUs. Herein we report the impact of preventive measures implemented after an Enterobacter clo...
We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping enables visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Subtyping thereby advances the developm...
The incidence and case-fatality rates (CFRs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, the etiological agent for Coronavirus Disease 2019 (COVID-19), have been rising unabated. Even though the entire world has been implementing infection prevention and control measur...
As corona virus disease 2019 (COVID-19) is a rapidly growing public health crisis across the world, our knowledge of meaningful diagnostic tests and treatment for severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is still evolving. This novel coronavirus disease COVID-19 can be diagnosed...
In the first quarter of the 21st century, we are already facing the third emergence of a coronavirus outbreak, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the coronavirus disease 2019 (COVID-19) pandemic. Comparative genomics can inform a deeper understanding of...
Between 2010 and 2013, an outbreak of serotype-1 sequence type 306 (ST306) invasive pneumococcal disease (IPD) occurred primarily in remote locations of Northern and Central Australia. This is a descriptive study of the epidemiology of the outbreak using nationwide IPD surveillance data, supplemente...
The outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed significant threats to international health. The genetic traits as well as evolutionary processes in this novel coronavirus are not fully characterized, and their roles i...
This study used whole-genome sequencing to analyze the first case of NDM-1-producing belonging to the novel sequence type 1465/CC216 recovered in Brazil. The study identified an unusual plasmid carrying gene, in which some genes of the Tn transposon were lost. Besides, on the chromosome, the strai...
The human pathogen Vibrio cholerae serves as a model organism for many important processes ranging from pathogenesis to natural transformation, which has been extensively studied in this bacterium. Previous work has deciphered important regulatory circuits involved in natural competence induction as...
Carbapenemase-producing Gram-negative bacteria cause infections that are difficult to treat and represent a rising threat to healthcare systems worldwide. This study analysed isolates of Escherichia coli (E. coli), a species associated with nosocomial-acquired and community-acquired infections, from...
Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very...
After 56 days without coronavirus disease 2019 (COVID-19) cases, reemergent cases were reported in Beijing, China on June 11, 2020. Here, we report the genetic characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequenced from the clinical specimens of 4 human cases and 2...
On 6 June 2019, the Norwegian Institute of Public Health was notified of more than 50 cases of gastroenteritis in Askøy. A reservoir in a water supply system was suspected as the source of the outbreak because of the acute onset and geographical distribution of cases. We investigated the outbreak to...
Genomic sequencing has significant potential to inform public health management for SARS-CoV-2. Here we report high-throughput genomics for SARS-CoV-2, sequencing 80% of cases in Victoria, Australia (population 6.24 million) between 6 January and 14 April 2020 (total 1,333 COVID-19 cases). We integr...
This month’s Genome Watch highlights how genomic surveillance can provide important information for identifying and tracking emerging pathogens such as SARS-CoV-2.
For the last decade, the New Jersey (NJ) Department of Health has reported between 42 and 144 new cases each year of "spotted fever group rickettsiosis" (SFGR), a statistic that reflects uncertainty regarding which rickettsial agents (Proteobacteria: Rickettsiaceae: ) are infecting NJ residents. To...
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown once again that coronavirus (CoV) in animals are potential sources for epidemics in humans. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen of swine with a worldwide distribution. Here, we implemen...
No abstract available
Further complications associated with infection by severe acute respiratory syndrome coronavirus 2 (a.k.a. SARS-CoV-2) continue to be reported. Very recent findings reveal that 20-30% of patients at high risk of mortality from COVID-19 infection experience blood clotting that leads to stroke and sud...
The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genom...
The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respi...
The genomic surveillance of porcine reproductive and respiratory syndrome virus (PRRSV) is based on sequencing of the ORF5 gene of the virus, which covers only 4% of the entire viral genome. It is expected that PRRSV whole-genome sequencing (WGS) will improve PRRSV genomic data and allow better unde...
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compromises the ability of military forces to fulfill missions. At the beginning of May 2020, 22 out of 70 Belgian soldiers deployed to a military education and training center in Maradi, Niger...
A novel coronavirus (SARS-CoV-2) emerged from China in late 2019 and rapidly spread across the globe, infecting millions of people and generating societal disruption on a level not seen since the 1918 influenza pandemic. A safe and effective vaccine is desperately needed to prevent the continued spr...
Some COVID-19 cases test positive again for SARS-CoV-2 RNA following negative test results and discharge, raising questions about the meaning of virus detection. Better characterization of re-positive cases is urgently needed. Clinical data were obtained through Guangdong's COVID-19 surveillance net...
Onchocerca lupi is a parasitic filarioid and the causative agent of canine ocular onchocercosis, a zoonotic disease of domestic dogs with sporadic reports in humans. A 13-year-old dog with no travel history outside of Israel was presented to an ophthalmology veterinary clinic in Israel with severe r...
is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We descri...
The genus has gained global attention in recent years as containing sporadic, worldwide, nosocomial pathogens. spp. are intrinsically multidrug resistant, primarily infect immunocompromised individuals, and are associated with high mortality (∼20 to 40%). As yet, gaps remain in our understanding o...
is a highly diverse genus consisting of over 2,600 serovars responsible for high-burden food- and waterborne gastroenteritis worldwide. Sensitivity and specificity of PCR-based culture-independent diagnostic testing (CIDT) systems for , which depend on a highly conserved gene target, can be affected...
The SARS-CoV-2 pathogen has established endemicity in humans. This necessitates the development of rapid genetic surveillance methodologies to serve as an adjunct with existing comprehensive, albeit though slower, genome sequencing-driven approaches. A total of 21,789 complete genomes were downloade...
The SARS-CoV-2 pandemic of 2020 is a prime example of the omnipresent threat of emerging viruses that can infect humans. A protocol for the identification of novel coronaviruses by viral metagenomic sequencing in diagnostic laboratories may contribute to pandemic preparedness. The aim of this study...
Genomic epidemiology can provide a unique, real-time understanding of SARS-CoV-2 transmission patterns. Yet the potential for genomic analyses to guide local policy and community-based behavioral decisions is limited because they are often oriented towards specially trained scientists and conducted...
Despite near-annual human outbreaks of Nipah virus (NiV) disease in Bangladesh, typically due to individual spillover events from the local bat population, only twenty whole-genome NiV sequences exist from humans and ten from bats. NiV whole-genome sequences from annual outbreaks have been challengi...
The detection of viral RNA by polymerase chain reaction (PCR) is currently the main diagnostic tool for COVID-19 ( 2019, 25 (3), 1). The PCR-based test, however, shows limited sensitivity, especially in the early and late stages of disease development ( 2020, 581, 465-469; 2020, 119 (6) 1123), an...
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters....
Dengue fever occurs worldwide and about 1% of cases progress to severe haemorrhage and shock. Dengue is endemic in Guatemala and its surveillance system could document long term trends. We analysed 17 years of country-wide dengue surveillance data in Guatemala to describe epidemiological trends from...
No abstract available
Most emerging pathogens of humans can infect multiple host species (Woolhouse & Gowtage-Sequeria, 2005). This simple fact has motivated multiple large-scale, comparative analyses of the drivers of pathogen sharing and zoonotic pathogen richness among hosts as well as the factors determining the zoon...
Invasive meningococcal disease (IMD) is a notifiable disease in Australia, and both probable and laboratory-confirmed cases of IMD are reported to the National Notifiable Diseases Surveillance System (NNDSS). In 2019, there were 206 notifications of IMD. Of these, 202 were laboratory-confirmed cases...
The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can b...
Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protoco...
The study aimed to explore the diversity of culturable microbiota colonizing the alimentary tract and outer surfaces of German cockroaches (Blattella germanica) captured in a health care facility. Microbial identification was conducted using Matrix Assisted Laser Desorption-Ionization Time-of-Flight...
Over 5 million people around the world have tested positive for the beta coronavirus SARS-CoV-2 as of May 29, 2020, a third of which are in the United States alone. These infections are associated with the development of a disease known as COVID-19, which is characterized by several symptoms, includ...
Deadly emerging infectious pathogens pose an unprecedented challenge to health systems and economies, especially across Africa, where health care infrastructure is weak, and poverty rates remain high. Genomic technologies are vital for enhancing the understanding and development of intervention appr...
Invasive Streptococcus agalactiae (Group B streptococci, GBS) infections result in a large burden of disease globally. Changes in clinical and molecular epidemiology, as well as antibiotic resistance patterns, are being described globally amongst GBS isolates. Very little is known about the characte...
Phylogeography is a popular way to analyze virus sequences annotated with discrete, epidemiologically-relevant, trait data. For applied public health surveillance, a key quantity of interest is often the state at the root of the inferred phylogeny. In epidemiological terms, this represents the geogr...
The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic...
Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of th...
Group B streptococcus (GBS) is a leading cause of serious infection in infants. Understanding its regional molecular epidemiology is helpful for regulating efficient prevention practice. A retrospective study was conducted to collected data from infants and pregnant women with culture-proven GBS dis...
Vibrio vulnificus is the leading cause of seafood-associated deaths worldwide. Despite the growing knowledge about the population structure of V. vulnificus, the evolutionary history and the ancestral relationships of strains isolated from various regions around the world have not been determined. U...
Early in its evolution, Enterococcus faecium acquired traits that allowed it to become a successful nosocomial pathogen. E. faecium inherent tenacity to build resistance to antibiotics and environmental stressors that allows the species to thrive in hospital environments. The continual wide use of a...
Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated...
The SARS-CoV-2 coronavirus is responsible for the current COVID-19 pandemic, with an ongoing toll of over 5 million infections and 333 thousand deaths worldwide within the first 5 months. Insight into the phylodynamics and mutation variants of this virus is vital to understanding the nature of its s...
Clostridioides difficile is one of the most important healthcare-associated pathogens. Recently, several new 027-like types have been found that all belong to the multilocus sequence typing (MLST) Clade 2. We report a rapidly spreading outbreak of C. difficile infections (CDI) due to a newly identif...
Porcine epidemic diarrhea virus (PEDV) is a fatal epizootic swine coronavirus that presents a financial threat to the global swine industry. Since the discovery of the low-pathogenic genotype 1b (G1b) in 2014, it has been responsible for sporadic outbreaks in South Korea. In this study, we identifie...
Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop...
Culture-independent diagnostics, such as metagenomic shotgun sequencing of food samples, could not only reduce the turnaround time of samples in an outbreak investigation, but also allow the detection of multi-species and multi-strain outbreaks. For successful foodborne outbreak investigation using...
Viruses are the most diverse and abundant microorganisms on earth, highly adaptive to a wide range of hosts. Viral diversity within invertebrate hosts has gained notoriety in recent years in public health as several such viruses have been of medical importance. serves as a vector for several viruse...
K57 (K57-KP) is associated with hypervirulence, but the basis and systematic data of K57-KP are limited. A retrospective study was conducted in 156 patients between January 2013 and January 2016. The clinical and molecular data, including antimicrobial susceptibility testing, multilocus sequence t...
Heritable microbes are an important component of invertebrate biology, acting both as beneficial symbionts and reproductive parasites. Whilst most previous research has focussed on the 'Wolbachia pandemic', recent work has emphasised the importance of other microbial symbionts. In this study, we pre...
São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbr...
Porcine reproductive and respiratory syndrome virus (PRRSV) remains widespread in the North American pig population. Despite improvements in virus characterization, it is unclear whether PRRSV infections are a product of viral circulation within production systems (local) or across production system...
To identify the epidemic clones of MRSA isolates at a hospital in shanghai. A total of 72 MRSA isolates have been isolated from a second grade hospital between 2017 and 2018, including 32 CA-MRSA isolates, 13 HA-MRSA isolates and 26 MRSA isolates from environment. In this study, MLST and PFGE typin...
Staphylococcus aureus is one of the major pathogens causing community-and healthcare-acquired infections. The presence of the virulence factor Panton-Valentine leukocidin (PVL) is associated with recurrent infection and clinical severity and generally regarded as a feature of community associated-me...
Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19 associated with increased neutrophil cou...
Coronavirus Disease 2019 (COVID-19) caused by a Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was first reported in Wuhan, China at the end of December 2019. SARS-CoV-2 is a highly pathogenic zoonotic virus and closely related to the Severe Acute Respiratory Coronavirus (SARS-CoV) and...
In Latin America, methicillin-resistantStaphylococcus aureus (MRSA) is a leading cause of nosocomial infections. Limited studies have addressed the molecular epidemiology of MRSA clones in Argentina, characterised by continuous human migratory movements. The aim of this study was to describe the MRS...
Congenital abnormalities cause serious fetal consequences. The term TORCH is used to designate the most common perinatal infections, where: (T) refers to toxoplasmosis, (O) means "others" and includes syphilis, varicella-zoster, parvovirus B19, zika virus (ZIKV), and malaria among others, (R) refers...
Coronaviruses (CoVs) are highly diverse single-stranded RNA viruses owing to their susceptibility to numerous genomic mutations and recombination. Such viruses involve human and animal pathogens including the etiologic agents of acute respiratory tract illnesses: severe acute respiratory syndrome co...
Since late December 2019, the coronavirus pandemic (COVID-19; previously known as 2019-nCoV) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been surging rapidly around the world. With more than 1,700,000 confirmed cases, the world faces an unprecedented economic, soci...
The Verax PGD rapid test for bacteria in platelets (PLTs) has been updated to simplify workflow and improve specificity and sensitivity by employing a novel sequential format. The performance of this updated version, called PGDprime, was evaluated to determine its suitability for use as an FDA-clear...
No abstract available
In a 2015 point-prevalence study, Clostridioides difficile 027, a hypervirulent ribotype, was absent from healthcare institutions in Switzerland. In late 2016, we detected an outbreak of C. difficile infection (CDI) with ribotype 027 occurring across several hospitals in the same hospital network. T...
As the COVID-19 pandemic is spreading around the world, the SARS-CoV-2 virus is evolving with mutations that potentially change and fine-tune functions of the proteins coded in its genome. Coronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of...
The carbapenems imipenem and meropenem play an important role in the empirical anti-infective treatment of critically ill patients. Carbapenem resistance in Haemophilus influenzae (Hi) has rarely been reported. We provide prevalence data for resistance to carbapenems from laboratory surveillance of...
No abstract available
To describe the burden, epidemiology and outcomes of co-infections and superinfections occurring in hospitalized patients with coronavirus disease 2019 (COVID-19). We performed an observational cohort study of all consecutive patients admitted for ≥48 hours to the Hospital Clinic of Barcelona for CO...
Coronaviruses have received global concern since 2003, when an outbreak caused by SARS-CoV emerged in China. Later on, in 2012, the Middle-East respiratory syndrome spread in Saudi Arabia, caused by MERS-CoV. Currently, the global crisis is caused by the pandemic SARS-CoV-2, which belongs to the sam...
Pathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet, there is no current consensus on how to measure genomic variation. To test the effect of the variant-identification approach...
Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genom...
Care homes have been disproportionately affected by the COVID-19 pandemic and continue to suffer large outbreaks even when community infection rates are declining, thus representing important pockets of transmission. We assessed occupational risk factors for SARS-CoV-2 infection among staff in six c...
A novel coronavirus (CoV), severe acute respiratory syndrome (SARS)-CoV-2, has infected >75 000 individuals and spread to >20 countries. It is still unclear how fast the virus evolved and how it interacts with other microorganisms in the lung. We have conducted metatranscriptome sequencing for bronc...
Sequence type 410 (ST410) of is an extraintestinal pathogen associated with multi drug resistance. In this study, we aimed to investigate the horizontal propagation pathway of a highrisk clone of ST410 that produces carbapenemase (KPC). blaKPCencoding and isolates were evaluated, and complete s...
No abstract available
The cruise ship was put under quarantine offshore Yokohama, Japan, after a passenger who disembarked in Hong Kong was confirmed as a coronavirus disease 2019 case. We performed whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from PCR clinical specime...
To study pathogenesis and toxicity of Staphylococcus aureus in foods, FORC_062 was isolated from a human blood sample and complete genome sequence has a type II SCCmec gene cluster and a type II toxin-antitoxin system, indicating an MRSA strain. Its mobile gene elements has many pathogenic genes inv...
Bacterial insecticidal proteins, such as the Bin toxin from Lysinibacillus sphaericus, could be used more extensively to control insecticide resistant mosquitoes. This study was aimed at identification of mosquito cell proteins binding Bin toxin. Results showed that purified toxin was toxic to Anoph...
Carbapenemase-producing Acinetobacter baumannii has been recognized as a critical priority pathogen by the World Health Organization. We hereby report the identification and the draft genome sequence of a carbapenem-resistant A. baumannii isolated from a patient with community-onset urinary tract in...
The emergence of novel coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 coronavirus, has necessitated the urgent development of new diagnostic and therapeutic strategies. Rapid research and development, on an international scale, has already generated assays for detecting SARS-CoV-2 RNA...
The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the li...
Serotyping has traditionally been considered the basis for surveillance of , but it cannot distinguish distinct lineages sharing the same serovar that vary in host range, pathogenicity and epidemiology. However, polyphyletic serovars have not been extensively investigated. Public health microbiology...
Twelve students experienced symptoms of acute respiratory infection (ARI) at a training base in Beijing from August 26 to August 30, 2015. We investigated the cause of this ARI outbreak. In partnership with the local center for disease control, we collected a total of twelve pharyngeal swab specimen...
Patients who died from COVID-19 often had comorbidities, such as hypertension, diabetes, and chronic obstructive lung disease. Although angiotensin-converting enzyme 2 (ACE2) is crucial for SARS-CoV-2 to bind and enter host cells, no study has systematically assessed the ACE2 expression in the lungs...
Post-donation illness can be described as appearance of clinical symptoms in blood donors after donation. The consequent call back of the donor to report these symptoms to the blood collection institution is considered a post-donation illness report (PDIR). The most suitable way to examine whether P...
serogroup O25b-sequence type 131 ( O25b/ST131) is known as a multidrug-resistant organism with high virulence potential and has received attention internationally. We aim to investigate the prevalence of O25b/ST131 and the distribution of , pathogenicity island (PAI) markers, phylogenetic groups, an...
Carbapenemase-producing Enterobacterales (CPE) have rapidly emerged in Europe, being responsible for nosocomial outbreaks. Following an outbreak in the burn unit of Ghent University Hospital, we investigated whether CPE can spread between toilets through drain water and therefrom be transmitted to p...
In this study, we explored the prevalence of oxacillin-susceptible -positive (OS-MRSA) in staphylococcal food poisoning outbreak isolates and foodborne isolates, and then investigated their molecular characteristics, classical staphylococcal enterotoxins (SEs), and drug resistance. Eight (2.9%) of...
The distributions of methicillin-susceptible Staphylococcus aureus (MSSA) are divers geographically with different genetic backgrounds. Data related to molecular characteristics of MSSA compare to methicillin-resistant Staphylococcus aureus (MRSA) is sparse. In this cross-sectional study, antimicrob...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is yet available as a treatment....
Staphylococcus aureus is a leading cause of broad-spectrum infections both in the community and within healthcare settings. Methicillin-resistant Staphylococcus aureus (MRSA) has become a global public health issue. The aim of this study was to examine the clinical and molecular characteristics of S...
Evaluation of a novel microsampling device for its use in clinical sample collection and biomarker analysis. Matching samples were collected from 16 healthy donors (ten females, six males; age 42 ± 20) via K2EDTA touch activated phlebotomy (TAP) device and phlebotomy. The protein profile difference...
To investigate the evolutionary and epidemiological dynamics of the current COVID-19 outbreak, a total of 112 genomes of SARS-CoV-2 strains sampled from China and 12 other countries with sampling dates between 24 December 2019 and 9 February 2020 were analyzed. We performed phylogenetic, split netwo...
H9N2 avian influenza viruses (AIV) has a worldwide geographic distribution and affects poultry of different types of production. H9N2 AIV was first reported in the Northeast of Algeria in April 2017, following an outbreak associated with high mortality, in broiler flocks. In the present study, we re...
Potyviruses are the largest group of plant infecting RNA viruses that cause significant losses in a wide range of crops across the globe. The majority of viruses in the genus are transmitted by aphids in a non-persistent, non-circulative manner and have been extensively studied vis-à-vis their stru...
In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China. The causative agent was identified as the species Severe acute respiratory syndrome-related coronavirus and was named SARS-CoV-2 (ref. ). By 16 April the virus had spread to 1...
Since the Shiga toxin-producing enteroaggregative Escherichia coli (Stx-EAEC) O104:H4 strain caused a massive outbreak across Europe in 2011, the importance of Stx-EAEC has attracted attention from a public health perspective. Two Stx-EAEC O86 isolates were obtained from patients with severe symptom...
In addition to an overall rise in vancomycin-resistant Enterococcus faecium (VREfm), an increase in certain strain types marked by sequence type (ST) and cluster type (CT) has been reported in Germany over the past few years. Outbreak analyses at Charité - Universitätsmedizin Berlin revealed the fre...
Increased knowledge about the role of horizontal gene transfer is key to improve our understanding of the spread of antimicrobial resistance (AMR) in human populations. We therefore studied the dissemination of the extended-spectrum-β-lactamase (ESBL) gene in isolates obtained from stool samples f...
is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant li...
No abstract available
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resoluti...
No abstract available
The ability of blood-feeding arthropods to successfully acquire and transmit pathogens of medical and veterinary importance has been shown to be interfered with, or enhanced by, the arthropod's native microbiome. Mosquitoes transmit viruses, protozoan and filarial nematodes, the majority of which co...
To evaluate the outbreak size and hospital cost effects of bacterial whole-genome sequencing availability in managing a large-scale hospital outbreak. We built a hybrid discrete event/agent-based simulation model to replicate a serious bacterial outbreak of resistant Escherichia coli in a large metr...
The molecular prevalence of human adenoviruses (HAdVs) in Datong city and molecular evolution of HAdV-C species is still obscure. Here, we explored the molecular prevalence of HAdVs by simultaneous sequencing of hexon and fiber. Then, the penton gene fragments of HAdV-C species were determined by se...
This opinion commentary on the coronavirus disease 2019 (COVID-19) pandemic brings together observations from Zimbabwe specifically, and Africa broadly, drawing from the fields of pharmacogenomics, precision herbal medicine, and responsible innovation so as to respond to the pandemic in ways that ar...
In January 2020, a novel betacoronavirus (family Coronaviridae), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of a cluster of pneumonia cases occurring in Wuhan City, Hubei Province, China. The disease arising from SARS-CoV-2 infection,...
Human noroviruses (HuNoVs) are the primary non-bacterial pathogens causing acute gastroenteritis worldwide. Here we reported a co-infection of HuNoVs with different genotypes during an outbreak of gastroenteritis in travelers. The aim was to trace the source and transmission patterns of the infectio...
The objective of this study was to characterize Polish penicillin-resistant, ampicillin-susceptible (PRASEF), increasingly reported to the National Reference Centre for Susceptibility Testing, Poland, to elucidate the path of emergence of such strains. A total of 136 isolates were examined by antim...
The recent coronavirus disease 2019 (COVID-19) pandemic has caused worldwide disruption which also extends to the arena of scientific meetings around the world. Here, we explore the lessons learned from moving two human genetics and genomics meetings quickly to an online format in early 2020. The ti...
The spread of multidrug-resistant (MDR) Klebsiella pneumoniae in the nosocomial setting represents a big challenge to infection control teams. We have recently developed a simple spectroscopic-based method with excellent accuracy, turnaround time and cost-effectiveness (Rodrigues et al. mSystems 202...
is well recognized as the leading cause of bacterial foodborne diarrheal disease worldwide with a very low outbreak reported in China. In May 2019, we investigated an outbreak of infections among students in a junior high school in Eastern China. Cases were interviewed to identify a common source o...
The worldwide emergence and clonal spread of carbapenem-resistant Acinetobacter baumannii (CRAB) is of great concern. The aim of this nationwide study was to investigate the prevalence of CRAB isolates in Serbia and to characterize underlying resistance mechanisms and their genetic relatedness. Non-...
Spiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, persistent manner by the beet leafhopper, Neoaliturus (Circulifer) tenellus (Baker), in Nort...
This study was conducted to acknowledge microbiological and clinical characteristics of hospital-acquired pneumonia (HAP) caused by carbapenem-resistant (CRKP). A retrospective, 1:1 matched (age, gender, specimen source, and ward) case-control study was conducted during 2015-2017 in a tertiary teac...
Japan has seen a substantial increase in syphilis cases since 2013 and Tokyo and Osaka prefectures accounted for about 40% of all cases in Japan. Therefore, focusing on these 2 prefectures, we assessed syphilis cases detected during 2017-2018, combining epidemiological information with molecular typ...
10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain...
The outbreak of Coronavirus Disease-2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has threatened health worldwide. As of the end of 2020, there were nearly 10 million confirmed cases and nearly 5 million deaths associated with COVID-19. Rapid and early labora...
Metagenomics revealed an impressive breadth of previously unrecognized viruses. Here, we report the virome of the Skuse mosquito, an important vector of pathogenic arboviruses in Australia. Mosquitoes were collected from three sites in the Kimberley region of Western Australia. Unbiased high-throug...
The Olive Quick Decline Syndrome by Xylella fastidiosa subspecies pauca is among the most severe phytopathological emergencies nowadays. In few years, the outbreak devastated olive groves in Apulia (Italy), potentially endangering the entire Mediterranean basin. This research aimed to develop a mult...
Carbapenem-resistant hypervirulent Klebsiella pneumoniae strains have recently come into existence worldwide; however, researchers in northeast China are not aware of their clinical features and molecular characteristics. Here, the molecular and virulent characteristics of 44 carbapenem-resistant K....
We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the other uses singleplex, nested reverse transcriptio...
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Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem globally, including in Indonesia. Whole-genome sequencing (WGS) analysis has rarely been used for the study of TB and MDR-TB in Indonesia. We evaluated the use of WGS for drug-susceptibility testing (DST) and to investigate t...
Cross-discipline collaboration among state and local health departments improved foodborne illness surveillance for a 2018 Salmonella enterica serovar Enteritidis outbreak in Massachusetts, USA. Prompt linking of epidemiologic and laboratory data and implementation of in-state whole-genome sequencin...
Invasive listeriosis is a severe foodborne infection in humans and is difficult to control. Listeriosis incidence is increasing worldwide, but some countries have implemented molecular surveillance programs to improve recognition and management of listeriosis outbreaks. In Germany, routine whole-gen...
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major health threat compromising the gonorrhoea treatment globally. AMR surveillance including whole genome sequencing (WGS)-based epidemiology provides ideal resolution to identify and describe AMR gonococcal clones, AMR determinants and...
A study reports on the suitability of the yeast as a platform for the assembly and maintenance of diverse RNA virus genomes, including SARS-CoV-2.
More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is...
To define characteristics of Klebsiella pneumoniae isolated from carriage and infections in mothers and their neonates belonging to a paediatric cohort in Madagascar. A total of 2000 mothers and their 2001 neonates were included. For each mother, vaginal and stool samples were collected at the birth...
Since 2012, the incidence of vancomycin-resistant Enterococcus faecium (VREfm) has increased dramatically in Copenhagen and vanA E. faecium has become endemic and polyclonal. To examine whether a patient with a positive VRE clinical sample had the same VREfm in a preceding screening sample (within 6...
and spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant and spp., particularly in the context of outbreaks of resistant strains amongst patients. Wit...
COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that th...
To investigate the relationship between Clostridium (Clostridioides) difficile strain characteristics and C. difficile infection (CDI) outcome. Between October and December 2017, 16 hospitals collected epidemiological data according to the European Centre for Disease Prevention and Control (ECDC) su...
Although the prevalence of brucellosis in Inner Mongolia Autonomous Region currently remains high, data available on the epidemiological of circulating Brucella abortus strains were limited. A total of 75 isolates obtained from cattle, sheep, and humans were analysed using both the classical method...
Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven pr...
Whole-genome sequencing (WGS) can provide useful information on methicillin-resistant Staphylococcus aureus (MRSA) transmission in hospitals. However, it is expensive and laborious, especially for environmental screening programs which generate large numbers of isolates. Multiplex PCR-reverse line b...
The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitativ...
As the COVID-19 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using MS-base...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery. We performed deep shotg...
Anthropic changes on the edges of the tropical forests may facilitate the emergence of new viruses from the sylvatic environment and the simultaneous circulation of sylvatic and urban viruses in the human population. In this study, we investigated the presence of arboviruses (arthropod-borne viruses...
is a pathogen of considerable public health importance. It was first reported in 2009. Five clades, determined by genomic analysis and named by the distinct regions where they were initially identified, have been defined. We previously completed a draft genome sequence of an African clade (clade III...
Coronavirus disease 2019 (COVID-19), caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has led to an unprecedented health and economic crisis worldwide. To develop treatments that can stop or lessen the symptoms and severity of SARS-CoV-2 infe...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is considered as a serious global threat. CRKPs occurred only sporadically in the Second Hospital of Shanxi Medical University. Our study aimed to investigate and control the first outbreak of CRKP in our hospital occurred between October 2017 and Au...
To determine whether pulsed-field gel electrophoresis (PFGE) accurately recognizes isolates belonging to clusters defined by techniques based on whole-genome sequencing (WGS) using Pseudomonas aeruginosa as a model. We selected 65 isolates of ST395 P. aeruginosa isolated in seven European hospitals...
Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial tool for fighting the COVID-19 pandemic. This dataset brief presents the exploration of a shotgun proteomics dataset acquired on SARS-CoV-2 infected Vero cells. Proteins from inactivated virus samples were extract...
Carbapenem-resistant Enterobacterales have become a major public-health issue worldwide. Here we report an outbreak caused by a clonal multidrug-resistant Proteus mirabilis strain producing VIM-4 metallo-β-lactamase (MBL) and TEM-2 β-lactamase in a Greek tertiary-care hospital. From July 2015 to Feb...
Efficient response to the pandemic through the mobilization of the larger scientific community is challenged by the limited reusability of the available primary genomic data. Here, the Genomic Standards Consortium board highlights the essential need for contextual genomic data FAIRness, for empoweri...
SARS-CoV-2 was first detected in the city of Wuhan, Hubei Province, China. In this report, we describe the complete genome sequence of the first imported SARS-CoV-2, detected in a Mexican patient who had traveled to Bergamo, Italy. Phylogenetic analysis showed that this isolate belongs to subclade A...
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Clusters of Salmonella Enteritidis cases were identified by the Minnesota Department of Health using both pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) single nucleotide polymorphism analysis from 1 January 2015 through 31 December 2017. The median turnaround time for obt...
Mycoplasma anserisalpingitidis is a waterfowl pathogen that mainly infects geese, can cause significant economic losses and is present worldwide. With the advance of whole genome sequencing technologies, new methods are available for the researchers; one emerging methodology is the core genome Multi...
Mammalian orthoreovirus (MRV), which can infect almost all mammals, is a zoonotic virus. In this study, six strains of type 2 MRV (MRV2) were isolated from 7 diarrhea piglets from a farm that had an outbreak of diarrhea in piglets in 2018, which tested negative for porcine epidemic diarrhea virus (P...
A global emergency due to the COVID-19 pandemic demands various studies related to genes and genomes of the SARS-CoV2. Among other important proteins, the role of accessory proteins are of immense importance in replication, regulation of infections of the coronavirus in the hosts. The largest access...
Since December 2019, the novel coronavirus SARS-CoV-2 has spread rapidly throughout China and keeps the world in suspense. Cardiovascular complications with myocarditis and embolism due to COVID-19 have been reported. SARS-CoV-2 genome detection in the heart muscle has not been demonstrated so far,...
In this study, five SARS-CoV-2 PCR assay panels were evaluated against the accumulated genetic variability of the virus to assess the effect on sensitivity of the individual assays. As of week 21, 2020, the complete set of available SARS-CoV-2 genomes from GISAID and GenBank databases were used in t...
For patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the damages to multiple organs have been clinically observed. Since most of current investigations for virus-host interaction are based on cell level, there is an urgent demand to probe tissue-specific...
Increasingly, public-health agencies are using pathogen genomic sequence data to support surveillance and epidemiological investigations. As access to whole-genome sequencing has grown, greater amounts of molecular data have helped improve the ability to detect and track outbreaks of diseases such a...
Mayaro virus (MAYV) is responsible for a mosquito-borne tropical disease with clinical symptoms similar to dengue or chikungunya virus fevers. In addition to the recent territorial expansion of MAYV, this virus may be responsible for an increasing number of outbreaks. Currently, no vaccine is availa...
Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA)...
St. Louis encephalitis virus (SLEV) is a flavivirus that circulates in an enzootic cycle between birds and mosquitoes and can also infect humans to cause febrile disease and sometimes encephalitis. Although SLEV is endemic to the United States, no activity was detected in California during the years...
Our aim was to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routinely used in the microbiology laboratory for bacterial identification, for bacterial typing in the setting of extended spectrum beta-lactamase producing Klebsi...
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the e...
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-Ma...
No abstract available
The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infected over 3300 healthcare workers in early 2020 in China. Little information is known about nosocomial infections of healthcare workers in the initial period. We analysed data from healthcare workers with nosoco...
No abstract available
The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clini...
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to disperse globally with worrisome speed, identifying amino acid variations in the virus could help to understand the characteristics of it. Here, we studied 489 SARS-CoV-2 genomes obtained from 32 countries from the Nextstra...
IntroductionInvasive meningococcal disease (IMD) is a rare condition with a high case fatality rate. While most patients suffer from one single episode in life, there is anecdotal evidence for recurrent infection.AimThe German National Reference Laboratory for Meningococci and (NRZMHi) analysed IMD...
We whole-genome sequenced 55 SARS-CoV-2 isolates from Germany to investigate SARS-CoV-2 outbreaks in 2020 in the Heinsberg district and Düsseldorf. While the genetic structure of the Heinsberg outbreak indicates a clonal origin, reflecting superspreading dynamics from mid-February during the carniva...
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Carbapenem-resistant Klebsiella pneumoniae (CR-KP) is an urgent public health issue in Italy. This pattern of resistance is due mainly to dissemination of carbapenemase genes. Molecular characterization of carbapenem-resistant Klebsiella pneumoniae (CR-KP) strains was performed over a three-year per...
During 2015-2016, Cape Verde, an island nation off the coast of West Africa, experienced a Zika virus (ZIKV) outbreak involving 7,580 suspected Zika cases and 18 microcephaly cases. Analysis of the complete genomes of 3 ZIKV isolates from the outbreak indicated the strain was of the Asian (not Afric...
Genome detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its...
Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) represent a major public health concern due to limited treatment options. Among invasive isolates of VREfm, ST117, ST80 and ST78 represent the most frequently detected STs by MLST in Germany. In this study, we investigated the ge...
De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacteri...
Between 2017 and 2018, several farms across Bulgaria reported outbreaks of H5 highly-pathogenic avian influenza (HPAI) viruses. In this study we used genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate t...
National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, ge...
Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing inference in an "online" fashion. Widely used Bayesian phyloge...
Streptococcus pyogenes is a well-known cause of postpartum infections and is causing significant morbidity and mortality. To describe measures taken to control an outbreak of postpartum infections caused by S. pyogenes emm75 on a maternity ward. Patients presenting postpartum with signs and symptoms...
Critical priority pathogens have globally disseminated beyond clinical settings, thereby threatening wildlife. Andean Condors (Vultur gryphus) are essential for ecosystem health and functioning, but their populations are globally near threatened and declining due to anthropogenic activities. During...
Rotavirus A is a dynamically evolving pathogen causing acute gastroenteritis in children during the first years of life. In the present study, we conducted a phylodynamic analysis based on the complete sequences of 11 segments of rotaviruses with the G4P[8] and G2P[4] genotypes isolated in Russia in...
The emergence of a novel coronavirus, SARS-CoV-2, in December 2019, progressed to become a world pandemic in a few months and reached South Africa at the beginning of March. To investigate introduction and understand the early transmission dynamics of the virus, we formed the South African Network f...
Early detection and effective treatment of severe COVID-19 patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control individuals. We then trained a machine learning model using proteomic and metabolomic measurements from a traini...
There is considerable public and scientific interest in the origin, spread, and evolution of SARS-CoV-2. Lu et al. recently conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local...
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for >100 years. Patients (n = 25...
is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant Here, we aimed to elucidate the baseline diversity of the wider New Hampshire populat...
Pre-clinical responses to fast-moving infectious disease outbreaks heavily depend on choosing the best isolates for animal models that inform diagnostics, vaccines and treatments. Current approaches are driven by practical considerations (e.g. first available virus isolate) rather than a detailed an...
GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for...
No abstract available
Human-use probiotics have recently been associated with clinical infections and antibiotic resistance transfer, raising public concern over their safety. However, despite their extensive application in aquaculture and animal husbandry, the safety of animal-use probiotics remains poorly described. We...
The COVID-19 epidemic was not the first coronavirus epidemic of this century and represents one of the increasing number of zoonoses from wildlife to impact global health. SARS CoV-2, the virus causing the COVID-19 epidemic is distinct from, but closely resembles SARS CoV-1, which was responsible fo...
Invasive community-acquired infections, including pyogenic liver abscesses, caused by hypervirulent Klebsiella pneumoniae (hvKp) strains have been well recognized worldwide. Among these, sporadic hvKp-related community-acquired pneumonia (CAP) is an acute-onset, rapidly progressing disease that can...
Rickettsia are obligate intracellular pathogens transmitted by arthropod vectors. The re-emergence of several rickettsioses imposes severe global health burden. In addition to the well-established rickettsial pathogens, newer rickettsial species and their pathogenic potentials are being uncovered. T...
Identification and characterization of viral genomes in vectors including ticks and mosquitoes positive for pathogens of great public health concern using metagenomic next generation sequencing (mNGS) has challenges. One such challenge is the ability to efficiently recover viral RNA which is typical...
Point-of-issue tests, such as the Verax Pan Genera Detection (PGD) test, can be used to mitigate the occurrence of septic reactions. Little is known about how widespread the adoption of the PGD test is across US hospitals. The Red Cross hemovigilance database was used to determine the numbers of PGD...
Linezolid is an antibiotic used to treat infections caused by multi-drug-resistant Gram-positive bacteria. Linezolid resistance in enterococci has been reported with increasing frequency, with a recent rise in resistance encoded by optrA, poxtA or cfr. To investigate a hospital outbreak of linezolid...
The successful sequencing of the novel coronavirus SARS-CoV-2 nucleic acid paved the way for exploration of omics systems science and integrative biology research approaches for combating this unprecedented planetary health challenge. Omics-scale studies on this viral infection are emerging rapidly...
Venezuelan equine encephalitis virus (VEEV) is an important pathogen of medical and veterinary importance in the Americas. In this report, we present the complete genome sequences of five VEEV isolates obtained from pools of Culex (Melanoconion) gnomatos (4) or Culex (Melanoconion) pedroi (1) from I...
The HIV-1 epidemic in Belgium is primarily driven by MSM. In this patient population subtype B predominates but an increasing presence of non-B subtypes has been reported. We aimed to define to what extent the increasing subtype heterogeneity in a high at risk population induces the formation and sp...
Novel coronavirus has wrecked medical and health care facilities claiming ∼5% death tollsglobally. All efforts to contain the pathogenesis either using inhibitory drugs or vaccines largelyremained futile due to a lack of better understanding of the genomic feature of this virus. In thepresent study,...
This study compared the phylogeography of MERS-CoV between hospital outbreak-associated cases and sporadic cases in Saudi Arabia. We collected complete genome sequences from human samples in Saudi Arabia and data on the multiple risk factors of human MERS-CoV in Saudi Arabia reported from 2012 to 20...
The incidence of Klebsiella pneumonia (Kp), which has often been found to produce, extended spectrum beta-lactamase (ESBL), is rising rapidly and poses a serious risk to neonates. To date, the mechanisms related to the spread of ESBL-Kp have not been fully elucidated. This study aimed to investigate...
A new coronavirus was recently discovered and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection with SARS-CoV-2 in humans causes coronavirus disease 2019 (COVID-19) and has been rapidly spreading around the globe. SARS-CoV-2 shows some similarities to other coronaviruses;...
Aging and comorbidities such as diabetes and vascular problems contribute to the increasing occurrence of chronic wounds. From the beginning of 2016, a marked increase in Arcanobacterium haemolyticum (ARH) in chronic wound cultures was noted among patients visiting a wound expertise centre in The Ne...
Salmonellosis is a leading bacterial cause of foodborne illness, and numerous Salmonella enterica serovars have been responsible for foodborne outbreaks. In the United States outbreaks are often linked to poultry and poultry-related products. The prevalence of Salmonella serovar Infantis has been in...
Surgical site infection (SSI) is the most common healthcare-associated infection. We report an outbreak of neurosurgical site infections caused by Serratia marcescens after craniotomy in a tertiary care hospital. Between August 6 and 21, 2018, five cases of early-onset SSI caused by S. marcescens af...
Neisseria meningitidis can cause sporadic cases and outbreaks of invasive disease, including meningitis and sepsis. The meningococcal serogroup C (MenC) is the second most common serogroup in Italy after MenB. In this study we have estimated the reproductive numbers and the demographic reconstructio...
Macrolide resistance in is emerging globally. There is paucity of data from sub-Saharan Africa where syndromic management is used to treat sexually transmitted infections (STIs). We conducted a molecular epidemiological study to determine the prevalence of azithromycin resistance and epidemic diver...
The COVID-19 pandemic is due to infection caused by the novel SARS-CoV-2 virus that impacts the lower respiratory tract. The spectrum of symptoms ranges from asymptomatic infections to mild respiratory symptoms to the lethal form of COVID-19 which is associated with severe pneumonia, acute respirato...
The spread of H5 highly pathogenic avian influenza viruses poses serious threats to the poultry industry, wild bird ecology and human health. Circulation of H5 viruses between poultry and wild birds is a significant public health threat in China. Thus, viral migration networks in this region need to...
Understanding interspecific viral transmission is key to understanding viral ecology and evolution, disease spillover into humans, and the consequences of global change. Prior studies have uncovered macroecological drivers of viral sharing, but analyses have never attempted to predict viral sharing...
To identify cell types in the male and female reproductive systems at risk for SARS-CoV-2 infection because of the expression of host genes and proteins used by the virus for cell entry. Descriptive analysis of transcriptomic and proteomic data. Academic research department and clinical diagnostic l...
The novel coronavirus SARS-CoV-2 was first detected in the Pacific Northwest region of the United States in January 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, w...
The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health. The new coronavirus responsible for this outbreak-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG13. Althoug...
This study sought to assess the genetic variability of isolated from bloodstream infections (BSIs) presenting at Concord Hospital, Sydney during 2013-2016. Whole-genome sequencing was used to characterize 81 isolates sourced from community-onset (CO) and hospital-onset (HO) BSIs. The cohort compri...
Whole-genome sequencing confirmed the presence of a Malassezia pachydermatis outbreak among neonates in a neonatal intensive care unit. This technology supports the importance of adhering to infection prevention measures.
Sugarcane mosaic virus (SCMV), a member of the genus Potyvirus in the family Potyviridae, is an important pathogen that causes mosaic diseases in maize, sugarcane, canna and other graminaceous species worldwide. Previously, several reports have showed the genetic variation and population structure o...
Reverse genetics has been an indispensable tool to gain insights into viral pathogenesis and vaccine development. The genomes of large RNA viruses, such as those from coronaviruses, are cumbersome to clone and manipulate in Escherichia coli owing to the size and occasional instability of the genome....
Filoviruses such as Ebola virus continue to pose a substantial health risk to humans. Advances in the sequencing and functional characterization of both pathogen and host genomes have provided a wealth of knowledge to clinicians, epidemiologists and public health responders during outbreaks of high-...
SARS-CoV-2 (Severe acute respiratory syndrome coronavirus-2) is evolving with the progression of the pandemic. This study was aimed to investigate the diversity and evolution of the coronavirus SARS-CoV-2 with progression of the pandemic over time and to identify similarities and differences of vira...
BackgroundBoth long- and short-term epidemiology are fundamental to disease control and require accurate bacterial typing. Genomic data resulting from implementation of whole genome sequencing in many public health laboratories can potentially provide highly sensitive and accurate descriptions of st...
In July 2018, a large outbreak of Legionnaires' disease (LD) caused by serogroup 1 (Lp1) occurred in Bresso, Italy. Fifty-two cases were diagnosed, including five deaths. We performed an epidemiological investigation and prepared a map of the places cases visited during the incubation period. All s...
Analysis of sequencing data for 143 - and -positive isolates from 13 European national collections and the public domain resulted in the identification of 15 previously undetected multi-country transmission clusters. For 10 clusters, cases had prior travel/hospitalisation history in countries outsi...
BackgroundCarbapenemase-producing are increasing worldwide. In recent years, an increase in OXA-244-producing isolates has been seen in the national surveillance of carbapenemase-producing organisms in Denmark.AimMolecular characterisation and epidemiological investigation of OXA-244-producing is...
In 2014, two residents of a long-term care facility (LTCF) developed invasive group A streptococcal (iGAS) infections with identical typing (emm 11), resulting in one death. The second resident recovered but had a subsequent episode of emm 11 iGAS infection 10 months later. This second episode was l...
No abstract available
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A 3-month outbreak of invasive group A Streptococcus disease at an eldercare facility, in which 5 persons died, was biphasic. Although targeted chemoprophylaxis contained the initial outbreak, a second phase of the outbreak occurred after infection control processes ended. To retrospectively investi...
No abstract available
Beginning in the 1960's, sowthistle yellow vein virus (SYVV) was the subject of pioneering research that demonstrated propagation of a plant virus in its insect vector. Since the 1980's there has been a paucity of research on SYVV, with historic isolates no longer maintained and no genomic sequence...
has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since t...
The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. Bluetongue virus serotype 8 (BTV-8), an arthropod-borne virus of ruminants, emerged in livestock in northern Europe in 2006, spreading to most European countries by 2009 an...
During 2009-2012, several outbreaks of avian influenza virus H9N2 were reported in Tunisian poultry. The circulating strains carried in their hemagglutinins the human-like marker 226L, which is known to be important for avian-to-human viral transmission. To investigate the origins and zoonotic poten...
Multi-drug resistant (MDR) Acinetobacter baumannii is one of the most important causes of nosocomial infections. The purpose of this study was to identify antibiotic resistance patterns, biofilm formation and the clonal relationship of clinical and environmental isolates of A. baumannii by Pulsed Fi...
Foodborne outbreaks caused by have become a significant public health problem worldwide. Applying genomic sequencing as a routine part of foodborne outbreak investigation remains in its infancy in China. We applied both traditional PFGE profiling and genomic investigation to understand the cause of...
Circulating vaccine-derived polioviruses (cVDPVs) can emerge in areas with low poliovirus immunity and cause outbreaks* of paralytic polio (1-5). Among the three types of wild poliovirus, type 2 was declared eradicated in 2015 (1,2). The use of trivalent oral poliovirus vaccine (tOPV; types 1, 2, an...
COVID-19, the disease caused by the novel SARS-CoV-2, a betacoronavirus structurally similar to SARS-CoV. Based on both structural and syndromic similarities with SARS-CoV, a hypothesis is formed on SARS-CoV-2 potential to affect the host's metabolism as part of its lifecycle. This hypothesis is eva...
species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lact...
The emergence of linezolid-resistant Enterococcus spp. (LRE) due to transferable resistance determinants is a matter of concern. To understand the contribution of the plasmid-encoded optrA and poxtA genes to the emergence of LRE, clinical isolates from different Spanish hospitals submitted to the Sp...
Clostridioides difficile is transmitted through endospores. Most disinfection procedures for these structures deploy high concentrations of chlorine-derived compounds such as sodium hypochlorite (NaOCl) and sodium dichloroisocyanurate (NaDCC). However, these substances are linked to undesirable publ...
Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated diarrhoea worldwide. In order to gain a better understanding about the molecular epidemiology of C. difficile in Beijing, China, molecular typing, antimicrobial susceptibility testing and drug resistance gene sequenc...
Tigecycline serves as one of the antibiotics of last resort to treat multidrug-resistant (including carbapenem-resistant) pathogens. However, the recently emerged plasmid-mediated tigecycline resistance mechanism, Tet(X), challenges the clinical efficacy of this class of antibiotics. In this study,...
Carbapenem resistance in is a public health threat. carbapenemase (encoded by alleles of the family) is one of the most common transmissible carbapenem resistance mechanisms worldwide. The dissemination of historically has been associated with distinct lineages (clonal group 258 [CG258]), a par...
Cefazolin has become a prominent therapy for methicillin-susceptible (MSSA) infections. However, an important concern is the cefazolin inoculum effect (CzIE), a phenomenon mediated by staphylococcal β-lactamases. Four variants of staphylococcal β-lactamases have been described based on serological...
No abstract available
Enterovirus B83 (EV-B83) is a new member of the enterovirus B group. Currently, there are only two full-length genomic sequences of EV-B83 in the GenBank database and few VP1 region sequences. The aetiology and epidemiology of EV-B83 is unclear. 24 stool specimens were collected from twelve AFP pati...
Assessment of the long-term population-level effects of HIV interventions is an ongoing public health challenge. Following the implementation of a Transmission Reduction Intervention Project (TRIP) in Odessa, Ukraine, in 2013-2016, we obtained HIV gene sequences and used phylogenetics to identify H...
Over the past recent years, Vibrio cholerae has been associated with outbreaks in sub-Saharan Africa, notably in Democratic Republic of the Congo (DRC). This study aimed to determine the genetic relatedness of isolates responsible for cholera outbreaks in eastern DRC between 2014 and 2017, and their...
Carbapenemase-producing Enterobacterales (CPE) pose an increasing threat to patient safety and healthcare systems globally. We present molecular epidemiology of CPE in Finland during 2012-2018 with detailed characteristics of CPE strains causing clusters during the same time period. All Finnish clin...
Two separate human outbreaks of serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of R...
Clostridium difficile infection (CDI), especially hospital-acquired Clostridium difficile infection (HA-CDI), continues to be a public health problem and has aroused great concern worldwide for years. This study aimed to elucidate the clinical and epidemiological features of HA-CDI and the character...
Multidrug-resistant bacteria pose a serious health threat, especially in hospitals. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) facilitates the spread of antibiotic resistance, virulence, and environmental persistence genes between nosocomial pathogens. We screened the genomes o...
Brucellosis, caused by Brucella abortus, is a major disease of cattle and humans worldwide distributed. Eradication and control of the disease has been difficult in Central and South America, Central Asia, the Mediterranean and the Middle East. Epidemiological strategies combined with phylogenetic m...
is an opportunistic bacterial pathogen most commonly associated with nosocomial infections, especially in intensive care unit (ICU) patients. Routine surveillance cultures for carbapenemase-producing Enterobacteriaceae have become a common practice for hospital infection prevention. The objective of...
: Since the emergence of infection in 2009, the disease has been reported from multiple countries within a decade. The infection is classified under urgent threat, as it is multi-drug resistant, causes high mortality, spreads easily in hospital setting and is difficult to identify. Whole-genome seq...
West Nile virus (WNV) lineage 2, and especially the Hungarian clade, predominates in Europe. Most of the Hungarian clade strains cluster into 2 groups: Central/South-West European and Balkan. Since there was not any study on WNV in mosquitoes in Bulgaria, the present study was designed to test Culex...
Tuberculosis (TB) is a significant public health problem in Ecuador with an incidence of 43 per 100,000 inhabitants and an estimated multidrug-resistant-TB prevalence in all TB cases of 9%. Genotyping of Mycobacterium tuberculosis (MTBC) is important to understand regional transmission dynamics. Thi...
Genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) identifies unsuspected transmission events and outbreaks. Used proactively, this could direct early and highly targeted infection control interventions to prevent ongoing spread. Here, we evaluated the cost-effectiveness of t...
Pneumocystis jirovecii is an opportunistic respiratory pathogen causing Pneumocystis pneumonia (PcP) in immunocompromised patients. The aim of this study was to investigate the genetic diversity of P. jirovecii isolates (n: 84) obtained from PcP patients using multilocus sequencing method based on m...
The current pandemic caused by the new coronavirus is a worldwide public health concern. To aboard this emergency, and like never before, scientific groups around the world have been working in a fast and coordinated way to get the maximum of information about this virus when it has been almost 3 mo...
In 2015 and 2016, meningococcal carriage evaluations were conducted at two universities in the United States following mass vaccination campaigns in response to serogroup B (NmB) disease outbreaks. A simultaneous carriage evaluation was also conducted at a university near one of the outbreaks, wher...
The worldwide distribution of carbapenem-resistant (CRAB) has become a global concern, particularly in countries where antibiotic prescription is not tightly regulated. However, knowledge of the genomic aspects of CRAB from many parts of the world is still limited. Here, 50 carbapenem-resistant is...
As an important insect vector, Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae) transmits the pathogen 'Candidatus Liberibacter asiaticus' (CLas) that is associated with citrus greening also known as Huanglongbing (HLB) disease. The bacterial endosymbionts have a potential...
To describe the first isolation and sequencing of SARS-CoV-2 in Australia and rapid sharing of the isolate. SARS-CoV-2 was isolated from a 58-year-old man from Wuhan, China who arrived in Melbourne on 19 January 2020 and was admitted to the Monash Medical Centre, Melbourne from the emergency departm...
SARS-CoV-2 is responsible for the present coronavirus pandemic and some suggestions were made about its possible artificial origin. We, therefore, compared SARS-CoV-2 with such known viruses that were prepared in the laboratory and other relevant natural strains to estimate their genetic relatedness...
On 20 November 2019, Lassa fever was diagnosed in a physician repatriated from Sierra Leone to the Netherlands. A second physician with suspected Lassa fever, repatriated a few days later from the same healthcare facility, was confirmed infected with Lassa virus on 21 November. Comprehensive contact...
Whole genome sequences of SARS-CoV-2 obtained from two patients, a Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient's sequence clustered with sequences from Germany while the tourist's sequence clustered...
Cholera continues to be an important public health concern in developing countries where proper hygiene and sanitation are compromised. This severe diarrheal disease is caused by the Gram-negative pathogen Vibrio cholerae belonging to serogroups O1 and O139. Cholera toxin (CT) is the prime virulence...
The pandemics caused by MDR Klebsiella pneumoniae are mostly due to the global dissemination of high-risk clonal complex 258 (CC258) and related IncF epidemic plasmids. However, the factors leading to the epidemiological advantages of CC258-IncF linkage remain obscure. The Clustered Regularly Inters...
No abstract available
A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genom...
Toll-like receptors (TLRs) are transmembrane proteins of the innate immune system, composed of the ectodomain involved in pathogen recognition and the intracellular Toll/interleukin-1 receptor (TIR) domain important for downstream signal transduction. Here, we analyze the genetic variability of TIR...
It has been performed worldwidely to explore the potential of animals that might be a reservoir for community associated human infections of Clostridioides difficile. Several genetically undistinguished PCR ribotypes of C. difficile from animals and human have been reported, illustrating potential t...
The spread of cholera in the midst of an epidemic is largely driven by direct transmission from person to person, although it is well-recognized that is also capable of growth and long-term survival in aquatic ecosystems. While prior studies have shown that aquatic reservoirs are important in the p...
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review,...
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investiga...
Clostridioides difficile is the leading cause of healthcare-associated diarrhea. Although the incidence of C. difficile-associated diarrhea is increasing worldwide, bacteremia due to C. difficile is relatively rare and represents the least frequent extra-colonic manifestation of C. difficile infecti...
The emergence of the novel betacoronavirus, recently renamed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised serious concerns due to the virus's rapid dissemination worldwide. Nevertheless, there is limited information about the genomic epidemiology of SARS-CoV-2 circulati...
Bacteria inside biofilms are more persistent and resistant to stress conditions found in the production environment of food processing plants, thus representing a constant risk for product safety and quality. Therefore, the aim of this study was to characterize, using 16S rRNA sequencing, the bacter...
Little is known about the population structure of vancomycin-resistant Enterococcus faecium (VREfm) in Latin America (LATAM). Here, we provide a complete genomic characterization of 55 representative Latin American VREfm recovered from 1998-2015 in 5 countries. The LATAM VREfm population is structur...
Newcastle disease is an important poultry disease that also affects Columbiform birds. The viruses adapted to pigeons and doves are referred to as pigeon paramyxoviruses 1 (PPMV-1). PPMV-1 are frequently isolated from pigeons worldwide and have the potential to cause disease in chickens. The complet...
Since its emergence and detection in Wuhan, China in late 2019, the novel coronavirus SARS-CoV-2 has spread to nearly every country around the world, resulting in hundreds of thousands of infections to date. The virus was first detected in the Pacific Northwest region of the United States in January...
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-2. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection. Although bats are proba...
is the second most prevalent gram-negative rod that causes nosocomial infections in hospitalized or otherwise immunocompromised patients. It can develop multiple drug resistance that results in limited treatment options and increased use of carbapenems. Various mechanisms are related to the developm...
During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the re...
Despite proactive measures to prevent raccoon rabies entering Canada from the United States, several incursions of this disease have occurred. The largest outbreak, first reported in December 2015 in the city of Hamilton, Ontario, has resulted in the reporting of 449 animal cases as of December 31,...
Whole genome sequencing (WGS) has revolutionized the genotyping of bacterial pathogens and is expected to become the new gold standard for tracing the transmissions of bacterial infectious diseases for public health purposes. Traditional genomic epidemiology often uses WGS as a verification tool, na...
Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without using a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We use gen...
sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (=69...
In Japan, only one outbreak of Salmonella enterica subsp. enterica serovar Chester (S. Chester) has been confirmed in 1999. We performed a single-center retrospective case review of S. Chester infections that occurred in a rural area of Japan in 2016 (n=8). Case 5 and 6 occurred in twin infants who...
The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses timely makes it a powerful tool for public health emergency response. Third-generation sequencing (TGS) offers advantages in speed and length of detection over second-generation sequencing (SGS). Here, we p...
Since the resurgence of chikungunya virus (CHIKV) in India in 2005, the Indian subcontinent sublineage of the Indian Ocean lineage (IOL) has continued transmission in India and also radiation from India causing additional outbreaks in surrounding countries. This study was undertaken for an in-depth...
This study presents the nationwide epidemiology of , using whole-genome sequencing of all culture-positive cases, which comprise roughly 40 % of all cases of gonorrhea reported in Norway from 2016 to 2017. Isolates were assigned to sequence types and Bayesian analysis clusters and variation in genes...
The purpose of the study was to investigate the molecular characteristics and genetic relatedness of the first reported cases of vancomycin-resistant enterococci (VRE) from the Tripoli Medical Center, Libya. In total, 43 VRE isolates were obtained from various clinical sites throughout the years 201...
From 1 January to 31 December 2018, thirty-six institutions around Australia participated in the Australian Enterococcal Sepsis Outcome Programme (AESOP). The aim of AESOP 2018 was to determine the proportion of enterococcal bacteraemia isolates in Australia that were antimicrobial resistant, and to...
Haemophilus influenzae reference laboratory from Portugal characterized the entire collection of 260 H. influenzae invasive isolates received between 2011 and 2018, with the purpose of updating the last published data (2002-2010). Capsular serotypes and antimicrobial susceptibility patterns were det...
Clostridium difficile is a leading causative agent of hospital-acquired and community-acquired diarrhea in human. This study aims to characterize the predominant C. difficile strains, RT001 and 126, circulating in Iranian hospitals in relation to resistant phenotypes, the antibiotic resistance genes...
Whole genome sequencing can be used to characterize and to trace viral outbreaks. Nanopore-based whole genome sequencing protocols have been described for several different viruses. These approaches utilize an overlapping amplicon-based approach which can be used to target a specific virus or group...
Bufavirus (BuV) can infect a variety of hosts, including human, bats, rats, dog, swine and shrew species and are suggested related to diarrhea disease. Porcine bufaviruses (PoBuV) were first detected in Hungarian pig farms in 2016. To determine the prevalence and genetic diversity of PoBuV in China,...
is the main species of the genus; however, non- (NBA) species causing infections have been described for the past years, as well as antimicrobial resistance. In this study, we describe the occurrence of two multidrug-resistant (MDR) IMP-1-producing isolates recovered from bloodstream infections in...
To analyze the genomic recombination of the serogroup O1 El Tor pandemic strains. A total of 292 complete or draft genome sequences of Vibrio cholerae O1 serogroup El Tor strains isolated from 1937 to 2015 were selected from National Biotechnology Information Center database. The genome alignment...
() has gained global notoriety as a significant nosocomial pathogen because it is frequently associated with multi-drug resistance and hospital-based outbreaks. There is a substantial difference in the incidence of infections between different countries and within Germany. However, its continuous...
Rabies is a deadly preventable viral disease that affects all warm-blooded animals and widespread in many regions including Africa. The disease remains of major public health importance in Uganda. The purpose of this study was to establish Knowledge, Attitude, Practice (KAP) of Rabies in Moyo and Nt...
Although cytomegaloviruses (CMVs) are species-specific, the study of nonhuman CMVs in animal models can help to inform and direct research aimed at developing a human CMV (HCMV) vaccine. Because the driving force behind the development of HCMV vaccines is to prevent congenital infection, the animal...
No abstract available
Lassa fever (LF) is a viral hemorrhagic fever that causes high morbidity and severe mortality annually. The disease is endemic to two geographically separate areas within tropical West Africa, one in Nigeria and the second predominantly in Sierra Leone-Guinea-Liberia-Mali. Lassa virus (LASV), the ca...
Strangles, caused by Streptococcus equi subspecies equi (S. equi) is an infectious disease of horses with worldwide distribution, but there are limited data available regarding strain variation using whole genome sequencing among and within outbreaks in the United States (US), and how US isolates co...
The aim of this study was to investigate the characteristics of carbapenem-resistant (CRKP) ST76 isolates collected during an outbreak in a hospital's intensive care unit and neurosurgery unit. Seventeen separate clinical isolates of CRKP were collected from patients from March 2016 to February 20...
For residents of long-term care facilities (LTCFs), antimicrobial-resistant bacteria (ARB) are a risk factor, yet their oral colonisation, potentially leading to aspiration pneumonia, remains unclear. This study was undertaken to survey the prevalence, phenotypic characteristics, and molecular epide...
Dengue fever, a mosquito-borne viral disease in humans, has been endemic in many Southeast Asian countries. Since its first outbreak in 1978 in Foshan, Guangdong province, China, dengue has been continually epidemic in recent years in Guangdong, which raised the concern whether dengue infection is e...
Tuberculosis (TB) is the most lethal infection among infectious diseases. The specific aim of this study was to establish panels of serum protein biomarkers representative of active TB patients and their household contacts who were either infected (LTBI) or uninfected (EMI-TB Discovery Cohort, Ponte...
An outbreak of dengue in Kudat, northern Sabah in 2016-2017 provided an opportunity to investigate the circulating serotypes of dengue viruses of cases at Hospital Kudat. Between September 2016 and December 2017, a total of 156 dengue positive sera (tested positive by either NS1 antigen, or IgM and...
BackgroundDiphtheria is a potentially fatal disease caused by toxigenic strains of or AimOur objective was to review the epidemiology of diphtheria in the United Kingdom (UK) and the impact of recent changes in public health management and surveillance.MethodsPutative human toxigenic diphtheria iso...
An outbreak of gastroenteritis with 83 cases occurred at a conference venue in November 2017 in Halland County, Sweden. Stool samples from two venue visitors and a symptomatic secondary case attributed to household transmission were PCR-positive for the gene, a target found in both spp. and entero...
Transmission of Enterobacterales in neonatal intensive care units (NICU) can cause outbreaks of colonization and invasive infections among neonates. Two clusters of nosocomial transmission of identified by MALDI-ToF mass-spectrometry were suspected at two NICUs in July and August 2016. To assess th...
During 2015-2018, seven schools in rural Vietnam experienced diphtheria outbreaks. Multilocus sequence types were the same within schools but differed between schools. Low vaccine coverage and crowded dormitories might have contributed to the outbreaks. Authorities should consider administering rout...
In industrialized countries, the leading cause of bacterial gastroenteritis is Campylobacter jejuni. However, outbreaks are rarely reported, which may reflect limitations of surveillance, for which molecular typing is not routinely performed. To determine the frequency of genetic clusters among pati...
Pharyngotonsillitis caused by (group A streptococci, or GAS) is among the most common infections treated with antibiotics in pediatric patients. This study aimed to analyse changes in molecular epidemiology and antibiotic susceptibility among GAS isolates in three study periods spanning 10 years.....
Pathogen-based factors associated with tuberculosis (TB) in eastern Sudan are not well defined. We investigated genetic diversity, drug resistance, and possible transmission clusters of Mycobacterium tuberculosis complex (MTBC) strains by using a genomic epidemiology approach. We collected 383 sputu...
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Klebsiella pneumoniae (KP) is an important pathogen involved in serious nosocomial infections all over the world. Here, we describe the first report on a blood-stream infection caused by an OXA-48/NDM-1 ST101-KP, in Italy. The patient was an Italian woman, transferred from Cairo Hospital to a Neuros...
To analyze the evolution and variation of SARS-CoV-2 during the epidemic starting at the end of 2019. We downloaded the full-length genome sequence of SARS-CoV-2 from the databases of GISAID and NCBI. Using the software for bioinformatics including MEGA-X, BEAST, and TempEst, we constructed the geno...
Worldwide, emerging and re-emerging infectious diseases (EIDs) are a major burden on public and animal health. Arthropod vectors, with mosquitoes being the main contributors of global disease, transmit more than 70% of the recognized EIDs. To assess new alternatives for arthropod-borne viral disease...
Ventilator-associated pneumonia (VAP) is one of the common serious infectious diseases encountered in the intensive care unit (ICU), which highly affects the healthcare cost and patient prognosis. VAP is caused by various antimicrobial-resistant aetiological agents and the clinical manifestations la...
The genotype F (HBV-F) is an autochthonous Native American strain of the hepatitis B virus. In this study, we reconstruct the HBV-F long-term evolution under a hypothesis of co-divergence with humans in Central and South America, since their entry into the region 14.5-16 thousand years ago. The Baye...
The discovery of a globally distributed porcine circovirus (; PCV-3) has led to intense research activity and the production of a large amount of molecular data. Different research groups have proposed several, not always concordant, genotypes for this virus. While such categories could aid an easie...
Japanese encephalitis (JE) remains a public health concern in several countries, and the mosquito plays a central role in its transmission cycle. mosquitoes harbor a wide range of viruses, including insect-specific viruses (ISVs), and can transmit a variety of arthropod-borne viruses (arboviruses)...
Among all cases of nosocomial pneumonia, Staphylococcus aureus is the second most prevalent pathogen (17.8%). In Europe, 29.9% of the isolates are oxacillin-resistant. The changing epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) nosocomial infections and the decreasing susceptibil...
Salmonella enterica serovar Enteritidis is a major cause of foodborne disease in Uruguay since 1995. We used a genomic approach to study a set of isolates from different sources and years. Whole genome phylogeny showed that most of the strains are distributed in two major lineages (E1 and E2), both...
• Cumulative confirmed cases in China were well fitted with Boltzmann function. • Potential total numbers of confirmed cases in different regions were estimated. • Key dates indicating minimal daily number of new confirmed cases were estimated. • Cumulative confirmed cases of 2003 SARS-CoV were well...
Rhabdoviruses are a large and ecologically diverse family of negative-sense RNA viruses (: ). These viruses are capable of infecting an unexpectedly wide variety of plants, vertebrates, and invertebrates distributed over all human-inhabited continents. However, only a few rhabdoviruses are known to...
Colistin is a last-resort antibiotic for the treatment of infections caused by multidrug and carbapenem-resistant Gram-negative bacteria. Colistin resistance has been emerging and multiple outbreaks have been reported in Europe and elsewhere. It has been most frequently reported in carbapenem-resist...
Molecular typing methods are useful for rapid detection and control of a disease. Recently, the use of high-resolution melting (HRM) for spa typing of MRSA isolates were reported. This technique is rapid, inexpensive and simple for genotyping and mutation screening in DNA sequence. The aim of this s...
Methicillin-resistant Staphylococcus aureus (MRSA) causes severe infectious diseases and can be life-threatening in healthcare-settings. MRSA is classified into health-care associated (HA)-MRSA strains and community acquired (CA)-MRSA strains based on genotype and phenotype. CA-MRSA has been reporte...
In a beef cattle facility an outbreak of abortions occurred over a 36-day period and included samples from two aborted (non-viable) fetuses and 21 post-abortion clinical cases. There are numerous etiologies, including clinical listeriosis. At the species level, Listeria monocytogenes is ubiquitous i...
Neonatal Staphylococcus aureus (S. aureus) bacteremia is an important cause of morbidity and mortality. In this study, we examined whether methicillin-susceptible S. aureus (MSSA) transmission and genetic makeup contribute to the occurrence of neonatal S. aureus bacteremia. A retrospective, single-c...
No abstract available
Urban development has major impacts on connectivity among wildlife populations and is thus likely an important factor shaping pathogen transmission in wildlife. However, most investigations of wildlife diseases in urban areas focus on prevalence and infection risk rather than potential effects of ur...
An ongoing outbreak of a novel coronavirus infection in Wuhan, China since December 2019 has led to 31,516 infected persons and 638 deaths across 25 countries (till 16:00 on February 7, 2020). The virus causing this pneumonia was then named as the 2019 novel coronavirus (2019-nCoV) by the World Heal...
In 2006, New Zealand had the highest notification rate of campylobacteriosis in the world, and poultry was considered the leading source of campylobacteriosis. Implementation of food safety interventions by the poultry industry led to a decrease in the campylobacteriosis notification rate. The aim i...
A respiratory outbreak associated with human adenovirus type 7 (HAdV-7) occurred among unvaccinated officer candidates attending initial military training. Respiratory infections associated with HAdV-7 can be severe, resulting in significant morbidity. Genomic sequencing revealed HAdV-7d, a genome t...
Non-toxigenic Vibrio cholerae isolates have been found associated with diarrheal disease globally, however, the global picture of non-toxigenic infections is largely unknown. Among non-toxigenic V. cholerae, ctxAB negative, tcpA positive (CNTP) isolates have the highest risk of disease. From 2001 to...
It is relevant to evaluate MDR-tuberculosis in prisons and its impact on the global epidemiology of this disease. However, systematic molecular epidemiology programs in prisons are lacking. A health-screening program performed on arrival for inmates transferred from Peruvian prisons to Spain led to...
Carbapenemase-resistant represents a major concern in hospital setting. The evolutionary history of carbapenem-resistant strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. A great increase carbapenem-resistant causing blood stre...
A septicaemic disease outbreak caused by Pasteurella multocida at a zoo in Western Australia (Zoo A) occurred in a resident group of squirrel gliders (Petaurus norfolcensis) following the introduction of two squirrel gliders imported from another zoo (Zoo B). P. multocida isolates obtained from the...
We investigated the epidemiological characteristics of drug resistance and virulence factors of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates from paediatric patients in Shanghai. CRKP strains were consecutively collected between January and December in 2018. Antimicrobial susceptibilit...
An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown. We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type isolates. A case was defined as laboratory-confirmed infection during the period from June 11...
In June 2017, an outbreak of Salmonella Kottbus infection was suspected in Germany. We investigated the outbreak with whole-genome sequencing (WGS) and a case-control study. Forty-six isolates from 69 cases were subtyped. Three WGS clusters were identified: cluster 1 (n = 36), cluster 2 (n = 5) and...
Serratia marcescens is a neglected opportunistic pathogen of public-health concern, especially due to its antimicrobial resistance features. Here we report the draft genome sequence of the first KPC-2 and SRT-2 co-producing S. marcescens strain (UCO-366) recovered from a catheter tip culture of a ho...
Cases of acute haemorrhagic conjunctivitis (AHC) caused by a coxsackie virus A24 variant (CV-A24v) in Mexico have been reported since 1987; however, no molecular data on the causative strains have been available. Here, we report the identification of the etiological agent responsible for the most re...
In recent years, numerous outbreaks of multidrug-resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing...
West Nile virus, Kunjin strain (WNV) is endemic in Northern Australia, but rarely causes clinical disease in humans and horses. Recently, WNV genomic material was detected in cutaneous lesions of farmed saltwater crocodiles (), but live virus could not be isolated, begging the question of the pathog...
The temporal switching of serotypes from serotype Ogawa to Inaba and back to Ogawa was identified in O1, which was responsible for seasonal outbreaks of cholera in Dhaka during the period 2015 to 2018. In order to delineate the factors responsible for this serotype transition, we performed whole-ge...
is a gut commensal of humans and animals but is also listed on the WHO global priority list of multidrug-resistant pathogens. Many of its antibiotic resistance traits reside on plasmids and have the potential to be disseminated by horizontal gene transfer. Here, we present the first comprehensive po...
Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment and outcomes. Here, we present a method called 'gen...
A longitudinal observational study was carried out to explore transmission dynamics and duration of infection of Streptococcus uberis. Quarter milk samples were collected aseptically for bacterial culture from all lactating cows once a month over a 10-mo period. Molecular typing of S. uberis mastiti...
Bovine ephemeral fever virus (BEFV) can cause bovine ephemeral fever and is an economically important arbovirus of cattle. To expand the knowledge of the molecular epidemiology of BEFV in southern China, the complete surface glycoprotein G gene of BEFV was sequenced from samples collected in five re...
IS6110 restriction fragment length polymorphism (RFLP) analysis is widely used for molecular epidemiological studies of tuberculosis. Role of spoligotyping and Fluorescent Amplified Fragment Length Polymorphism (FAFLP) was studied in low-copy number IS6110 strains of Mycobacterium tuberculosis compl...
The Kyasanur Forest Disease (KFD) has become a major public health problem in the State of Karnataka, India where the disease was first identified and in Tamil Nadu, Maharashtra, Kerala, and Goa covering the Western Ghats region of India. The incidence of positive cases and distribution of the Kyasa...
Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and ne...
Clostridioides difficile infections have become more frequently diagnosed and associated with greater disease severity, which has resulted in an increase burden on the healthcare system. These increases are attributed to the increased prevalence of hypervirulent strains encompassing select ribotypes...
Urogenital tuberculosis (TB) is rare in children and usually develops due to reactivation of the foci in the genitourinary tract after the latency period following initial infection. Urogenital TB in children has no pathognomonic clinical features that can result in overlooking or misdiagnosing this...
Healthcare associated infections (HAIs) are major cause of elevated mortality, morbidity, and high healthcare costs. Development of a vaccine targeting these pathogens could benefit in reducing HAIs count and excessive use of antibiotics. This work aimed to design a multi-epitope based prophylactic/...
Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysi...
Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and transmissibility despite the potential fitness cost associated with drug resis...
Mycobacterium tuberculosis complex (MTBC) is divided into several major phylogenetic lineages, with differential distribution globally. Using population-based data collected over a three year period, we performed 24-locus Mycobacterial Interspersed Repeat Unit - Variable Number Tandem Repeat (MIRU-V...
A number of serious human adenovirus (HAdV) outbreaks have been recently reported: HAdV-B7 (Israel, Singapore, and USA), HAdV-B7d (USA and China), HAdV-D8, -D54, and -C2 (Japan), HAdV-B14p1 (USA, Europe, and China), and HAdV-B55 (China, Singapore, and France). To understand the epidemiology of HAdV...
High transmissibility of FMDV and drop in productivity following infection, make FMD an important economically disease of livestock. According to the endemic nature of the disease in Iran, vaccines have been routinely applied, but not able to prevent frequent outbreaks. Circulation of different FMDV...
We report transcontinental expansion of Vibrio parahaemolyticus sequence type 36 into Lima, Peru. From national collections, we identified 7 isolates from 2 different Pacific Northwest complex lineages that surfaced during 2011-2016. Sequence type 36 is likely established in environmental reservoirs...
The molecular structure of circulating enteric fever pathogens was studied using hospital-based genomic surveillance in a tertiary care referral centre in South India as a first genomic surveillance study, to our knowledge, of blood culture-confirmed enteric fever in the region. Blood culture survei...
JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collecte...
No abstract available
In December 2016, Public Health England investigated an outbreak of campylobacteriosis in North West England, with 69 cases in total. Epidemiological, microbiological and environmental investigations associated the illness with the consumption of unpasteurised cows' milk from Farm X, where milk was...
Parechovirus (the Picornaviridae family), recently classified as Parechovirus A and formerly known as Human parechovirus (HPeV), can cause a wide range of human diseases. Over the past decade, several studies have reported HPeV epidemiology in different regions; however, information from Russia is l...
Mozambique is a high-burden tuberculosis (TB) country where TB/HIV co-infection and drug resistant TB (DR-TB) incidence is increasing. Whole genome sequencing (WGS) comprehensively describes the molecular epidemiology of TB, allows prediction of DR-TB phenotypes, lineages strains identification and...
The more quickly bacterial pathogens responsible for foodborne illness outbreaks can be linked to a vehicle of transmission or a source, the more illnesses can be prevented. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which p...
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated th...
The incidence of methicillin-resistant Staphylococcus aureus (MRSA) has increased sharply in Hospital District of Southwest Finland (HD). To understand reasons behind this, a retrospective, population-based study covering 10 years was conducted. All new 983 MRSA cases in HD from January 2007 to Dece...
The accurate identification of Taylorella equigenitalis strains is essential to improve worldwide prevention and control strategies for contagious equine metritis (CEM). This study compared 367 worldwide equine strains using multilocus sequence typing according to the geographical origin, isolation...
Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of bla carbapenemase-producing E. hormaechei. Using Illumina sequencing, we...
Hospital infection control requires timely detection and identification of organisms, and their antimicrobial susceptibility. We describe a hybrid modeling approach to evaluate whole genome sequencing of pathogens for improving clinical decisions during a 2017 hospital outbreak of OXA-181 carbapenem...
Haemophilus influenzae remains a common cause of illness in children worldwide. H. influenzae type b is the leading cause of bacterial meningitis in children before introduction of vaccination and is a common cause of pneumonia, epiglottis and septic arthritis. Since the implementation of the Hib co...
Dengue hemorrhagic fever is an acute viral infection transmitted by mosquitoes. In the 2017, a dengue epidemic occurred in Hanoi in a short time interval and many cases were serious with associated mortality. This was the largest and unusual dengue fever outbreak in the North of Vietnam over the pas...
Listeriosis is a foodborne illness characterized by a relatively low morbidity, but a large disease burden due to the severity of clinical manifestations and the high case fatality rate. Increased listeriosis notifications have been observed in Europe since the 2000s. However, the reasons for this i...
Whole-genome sequence (WGS) analyses were employed to investigate the genomic epidemiology of extensively drug-resistant strains, focusing on the carbapenem resistance-encoding determinants, mobile genetic support, clonal and epidemiological relationships. A total of ten isolates were obtained from...
Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic...
Streptococcus agalactiae are important pathogenic bacteria that cause severe infections in humans, especially neonates. The mechanism by which ST-17 causes invasive infections than other STs is not well understood. In this study, we sequenced the first genome of a S. agalactiae ST-17 strain isolated...
Carbapenem-resistant (CRAB) is an important opportunistic pathogen linked to a variety of nosocomial infections and hospital outbreaks worldwide. This study aimed at investigating and characterizing a CRAB outbreak at a large tertiary hospital in Lebanon. A total of 41 isolates were collected and a...
Aedes albopictus is naturally infected with Wolbachia spp., maternally transmitted bacteria that influence the reproduction of hosts. However, little is known regarding the prevalence of infection, multiple infection status, and the relationship between Wolbachia density and dengue outbreaks in diff...
Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen...
Streptococcus agalctiae (Group B Streptococcus, GBS) is a perinatal pathogen and a leading cause of neonatal infections worldwide. Serotype, sequence type, clonality, antibiotic resistance genes and surface protein profiles of GBS are scarce in Ethiopia, a reason that this study was planned to inves...
A rapid increase and dominance of G9P[8] Rotavirus A strains occurred in northern Vietnam between 2016 and 2018, during which period there appeared three G9P[8] strains possessing short RNA patterns. To understand how the first-ever G9P[8] strains possessing short RNA patterns were formed, next gene...
This report describes a survey of RNA and DNA viruses carried out in adult mosquitoes from Angola, raised under laboratory conditions from field-collected immature forms. This viral genomic survey was performed using different sets of primers targeting groups of arboviruses with a considerable impac...
Avian botulism is a serious neuroparalytic disease mainly caused by a type C/D botulinum neurotoxin produced by group III, one of the entwined bacterial species from the genospecies. Its isolation is very challenging due to the absence of selective media and the instability of the phage carrying t...
Bartonella is a genus of Gram-negative facultative intracellular Alphaproteobacteria of public health importance. Although they are known to mainly infect mammalian hosts with some blood-feeding arthropods having been confirmed as vectors, there is some evidence of Bartonella association with non-ma...
Birds are hosts for several zoonotic pathogens. Because of their high mobility, especially of longdistance migrants, birds can disperse these pathogens, affecting their distribution and phylogeography. We focused on Borrelia burgdorferi sensu lato, which includes the causative agents of Lyme borreli...
Over the last few decades, carbapenemase-producing has become a major cause of nosocomial infections all over the world. However, the genome identity of lineages of this species in Latin America has not been studied as much as in developed countries. Here, through a population genomics approach con...
Extraintestinal multidrug resistant Escherichia coli sequence type (ST) 131 is a worldwide pandemic pathogen and a major cause of urinary tract and bloodstream infections. The role of this pandemic lineage in multidrug resistance plasmid dissemination is still scarce. We herein performed a meta-anal...
Zika virus (ZIKV) is a negative sense RNA virus from the Flaviviridae family, which was relatively unknown until the first human epidemic in Micronesia, in 2007. Since then, it spread to French Polynesia and the Americas. Recife, the capital of Pernambuco state and epicenter of the Zika epidemic in...
The presence of infectious bronchitis virus (IBV) was identified for the first time in the poultry population in Poland at the end of the 1960s. From this time a few waves of epidemics caused by different IBV variants spread across the country. In order to gain more insight into the molecular epidem...
Acinetobacter baumannii is a major cause of ventilator-associated-pneumonia (VAP) worldwide due to its impressive propensity to rapidly acquire resistance elements to a wide range of antibacterial agents. We sought to explore the genomic features of this pathogen from a sputum specimen of a VAP male...
Genogroup II, genotype 4 noroviruses (GII.4 NoVs) are a leading cause of epidemic and sporadic acute non-bacterial gastroenteritis worldwide. In this study, we isolated a GII.4 NoV strain (designated 2015HN08) from a kid presenting with acute gastroenteritis and determined its near-complete genome s...
The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective trea...
The recent outbreaks of African swine fever (ASF) in China and Europe have threatened the swine industry globally. To control the transmission of ASF virus (ASFV), we developed the African swine fever virus database (ASFVdb), an online data visualization and analysis platform for comparative genomic...
In this work, we used a whole-genome sequencing (WGS) approach to study the features of KPC-producing (KPC-Kp) spreading in a large Italian long-term acute-care rehabilitation facility (LTACRF), and to track the dynamics of dissemination within this setting. Thirty-eight, non-replicated, KPC-Kp iso...
From September to October 2019, seven patients colonised or infected with a ceftazidime-avibactam (CZA)-resistant carbapenemase (KPC)-2-producing were detected in two intensive care units of a Greek general hospital. The outbreak strain was sequence type (ST)147 and co-produced KPC-2 and the novel...
We investigated the epidemiology of cholera in Taiwan during 2002-2018. Vibrio cholerae sequence type (ST) 75 clone emerged in 2009 and has since become more prevalent than the ST69 clone from a previous pandemic. Closely related ST75 strains have emerged in 4 countries and may now be widespread in...
Limited data regarding the epidemiology and susceptibility profiles of cryptococcosis are available in the Middle East. Our study aimed to evaluate the molecular diversity, mating types and antifungal susceptibility pattern of species (=14) isolated from 320 suspected patients with cryptococcosis....
The molecular epidemiology of Staphylococcus aureus strains causing staphylococcal scalded skin syndrome (SSSS) in the United States has not been described. We analyzed patient and S. aureus isolate characteristics associated with SSSS in children at Texas Children's Hospital. Patients with SSSS wer...
Resistance to meticillin and vancomycin in significantly complicates the management of severe infections like bacteraemia, endocarditis or osteomyelitis. Here, we review the molecular mechanisms and genomic epidemiology of resistance to these agents, with a focus on how genomics has provided insigh...
In recent years, has emerged as an important agent of hospital-acquired infections, such as pneumonia, urinary tract infection, septicaemia and meningitis, particularly in vulnerable patients. Compared to and , is less commonly associated with genes, yet few cases of plasmid transmission at the...
Genomic surveillance during ebolavirus outbreaks to elucidate transmission chains and develop diagnostic tests is delayed by the laborious development of variant-specific laboratory assays. We developed a new protocol combining 31 parallel PCR assays with Illumina/MinION-based sequencing, allowing g...
The COVID-19 pandemic has posed and is continuously posing enormous societal and health challenges worldwide. The research community has mobilized to develop novel projects to find a cure or a vaccine, as well as to contribute to mass testing, which has been a critical measure to contain the infecti...
the recent zoonotic coronavirus virus outbreak of a novel type (COVID-19) has necessitated the adequate understanding of the evolutionary pathway of zoonotic viruses which adversely affects human populations for therapeutic constructs to combat the pandemic now and in the future. we analyzed conserv...
The prevalence of causes an increased morbidity and mortality of inpatients, especially in Europe and North America, while data on infection (CDI) are limited in China. From September 2014 to August 2019, 562 isolates were collected from patients and screened for toxin genes. Multilocus sequence...
infections are the leading cause of bacterial gastroenteritis. In Europe, over 246,000 cases are confirmed annually. Infections are often transmitted contaminated food, such as poultry products, but water may be the source of infection as well. The aim of this study was to characterise a selection...
Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baum...
Between late 2017 and mid-2018, a chikungunya fever outbreak occurred in Mombasa, Kenya that followed an earlier outbreak in mid-2016 in Mandera County on the border with Somalia. Using targeted Next Generation Sequencing, we obtained genomes from clinical samples collected during the 2017/2018 Momb...
COVID-19 or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared throughout the World and currently affected more than 9 million people and caused the death of around 470,000 patients. The novel strain of the coronavirus disease is transmittable at a devastating rate with a high rat...
Invasive Streptococcus agalactiae (GBS) infections are increasingly common among neonates and the elderly. Therefore, GBS surveillance for better antibiotic treatment and prophylaxis strategies are needed. We retrospectively evaluated the clinical aspects of invasive infections and the phenotypic an...
A novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing Coronavirus Disease 2019 (COVID-19) pandemic. In this study, we performed a comprehensive epidemiological and genomic analysis of SARS-CoV-2 genomes from 10 patients in Shaoxing (Zhe...
Many outbreaks of complex (Bcc) infections are associated with contaminations in personal care products (PCPs). This study aimed to analyze a collection of Bcc isolates in PCPs and assess the susceptibility of preservatives, including dimethoxy dimethyl hydantoin (DMDMH), methylisothiazolinone-chlo...
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an outbreak of a pandemic worldwide. For better understanding the viral spike (S) protein variations and its potential effects on the interaction with the host immune system and al...
A new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] is currently causing a life-threatening pandemic. In this study, we report the complete genome sequencing and genetic characterisation of a SARS-CoV-2 detected in Manaus, Amazonas, Brazil, and the protocol we designed t...
More human deaths have been attributable to than any other pathogen, and the epidemic is sustained by ongoing transmission. Various typing schemes have been developed to identify strain-specific differences and track transmission dynamics in affected communities, with recent introduction of whole g...
Invasive Staphylococcus aureus infections are a common cause of morbidity and mortality in children. In the early 2000's the proportion of infections due the methicillin-resistant S. aureus (MRSA) increased rapidly. We described the clinical and molecular epidemiology of invasive S. aureus disease i...
Nosocomial infections arise from many microorganisms, including Staphylococcus aureus. The aim of this study is to determine the molecular epidemiology of circulating methicillin-resistant S. aureus (MRSA) clones among patients attending community and health-care facilities in Nova Friburgo, RJ, Bra...
An outbreak of bloodstream infection (BSI) caused by members of the Burkholderia cepacia complex (Bcc) took place from March 2012 until April 2014 involving thirteen patients. To describe an outbreak investigation of BSI Bcc and showing how genetic sequencing tools contributed to confirm the hypothe...
To study the molecular epidemiological characteristics of (SMA) isolated from patients in a pediatric teaching hospital in Shanghai so as to provide data for the prevention and treatment of SMA. Non-repetitive SMA strains were isolated from patients from January 2013 to December 2014. The cloning...
Mosquitoes of the genus transmit arboviruses of great importance to human health as dengue, chikungunya, Zika and yellow fever. The tiger mosquito can play an important role as arboviral vector, especially when is absent or present at low levels. Remarkably, the rapid worldwide spreading of the t...
EV-B93 is a novel serotype within the Enterovirus B species and is uncommon worldwide. Currently, only one full-length genomic sequence (the prototype strain) has been deposited in the GenBank database. In this study, three EV-B93 were identified, including one from an acute flaccid paralysis (AFP)...
Suddenly, many cases of fever with jaundice were reported from Sodala area at Jaipur. This outbreak of acute hepatitis at Jaipur Rajasthan was investigated for aetiology and subsequent phylogenetic analysis. Blood samples were collected from 106 symptomatic patients of acute hepatitis and 39 pregnan...
To describe the clinical features, outcomes, and molecular epidemiology of an outbreak of multidrug resistant (MDR) A. baumannii. We performed a retrospective analysis of all MDR A. baumannii isolates recovered during an outbreak from 2011 to 2015 in a tertiary care cancer hospital. Cases were class...
The outbreak of pneumonia caused by SARS-CoV-2 posed a great threat to global human health, which urgently requires us to understand comprehensively the mechanism of SARS-CoV-2 infection. Angiotensin-converting enzyme 2 (ACE2) was identified as a functional receptor for SARS-CoV-2, distribution of w...
Dengue virus (DENV) infection is endemic in Nepal. Although infection rates are reported annually, little information is available about the circulating viral serotypes and genotypes. Here, we report the results of a multicentre cross-sectional study of DENV serotypes and genotypes sampled from indi...
With the advent of whole-genome sequencing (WGS), comparative analysis has led to the use of core genome MLST (cgMLST) schemes for the high-resolution reproducible typing of bacterial isolates. In cgMLST, hundreds of loci are used for gene-by-gene comparisons of assembled genomes for studying the ge...
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has devastated health infrastructure around the world. Both ACE2 (an entry receptor) and TMPRSS2 (used by the virus for spike protein priming) are key proteins to SARS-CoV-2 cell entry, enabling progression to COVID-19 in humans. Comparati...
In 2009 and 2010, more than 6,000 cholera cases were recorded during these outbreaks with more than 80% of cases recorded in Lusaka province. After a five-year break, in 2016 an outbreak occurred in Lusaka, causing more than 1,000 cases of cholera. This study will strengthen the epidemiological info...
Knowledge of within-patient dynamics of resistance plasmids during outbreaks is important for understanding the persistence and transmission of plasmid-mediated antimicrobial resistance. During an outbreak of a Klebsiella pneumoniae carbapenemase-producing (KPC) K. pneumoniae, the plasmid and chromo...
Tuberculosis (TB) is an infectious disease, caused by , primarily affecting the lungs. The strain of the Haarlem family named M was responsible for a large multidrug-resistant TB (MDR-TB) outbreak in Buenos Aires. This outbreak started in the early 1990s and in the mid 2000s still accounted for 29%...
The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such major viral outbreaks demand early elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic...
The serotype and antimicrobial resistance of in adult patients have changed due to the application of antimicrobials and type b (Hib) vaccine worldwide. However, the epidemiologic characteristics of in Shanghai are still unavailable. To determine the serotype distribution, antimicrobial resistan...
The first hospital outbreak of carbapenemase-producing Enterobacteriaceae in Slovenia occurred in 2014-2016. Whole genome sequencing was used to analyse the population of carbapenem-resistant Klebsiella pneumoniae collected in Slovenia in 2014-2017, including OXA-48 and/or NDM-1 producing strains fr...
is an opportunistic pathogen associated with community-acquired and nosocomial infections. Since 2010, testing has been included into an existing diarrhea-syndrome surveillance system for estimating the prevalence of in diarrhea-syndrome patients, assessing antibiotic susceptibility, and investiga...
Little is known about the molecular epidemiology of Staphylococcus aureus in Chinese neonatal intensive care units (NICUs). We describe the molecular epidemiology of S. aureus isolated from neonates on admission to Beijing Children's Hospital. From May 2015-March 2016, nasal swabs were obtained on a...
is one of the main pathogens responsible for nosocomial infections, particularly in Intensive Care Units (ICUs). Due to the complexity of ecology, only powerful typing methods can efficiently allow its surveillance and the detection during expanding outbreaks. An increase in incidence was observed...
Production of the Panton-Valentine leukocidin (PVL) by Staphylococcus aureus is mediated via the genes lukS-PV and lukF-PV which are carried on bacteriophage ϕSa2. PVL is associated with S. aureus strains that cause serious infections and clones of community-associated methicillin-resistant S. aureu...
infection (CDI) is the most prevalent healthcare-associated infection in the United States and carries a significant healthcare system burden. As part of an ongoing, active surveillance system of throughout Texas, the objective of this study was to assess changes in ribotypes of clinical isolates...
Although exclusive breastfeeding has been linked to lower rates of postnatal HIV transmission compared to nonexclusive breastfeeding, mechanisms underlying this are unclear. Across a longitudinally sampled cohort of South African infants, we showed that exclusively breastfed (EBF) infants had altere...
Insects in the orders Hemiptera and Thysanoptera transmit viruses and other pathogens associated with the most serious diseases of plants. Plant viruses transmitted by these insects target similar tissues, genes, and proteins within the insect to facilitate plant-to-plant transmission with some degr...
Emerging and re-emerging RNA viruses pose significant public health, economic, and societal burdens. Hantaviruses (genus , family , order ) are enveloped, negative-sense, single-stranded, tripartite RNA viruses that are emerging zoonotic pathogens harbored by small mammals such as rodents, bats, mol...
Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high...
In December 2019, an acute respiratory disease caused by novel species of coronavirus (SARS-CoV-2), emerged in China and has spread throughout the world. On 11 March 2020, the World Health Organization (WHO) officially declared coronavirus disease 19 (COVID-19) a pandemic, severe coronavirus-mediate...
No abstract available
No abstract available
Methicillin-resistant (MRSA) is a common cause of severe and difficult to treat ocular infection. In this study, the population structure of 68 ocular MRSA isolates collected at Massachusetts Eye and Ear between January 2014 and June 2016 was assessed. By using a combination of multilocus sequence...
No abstract available
Several studies have shown the ubiquitous presence of bacteria in hospital surfaces, staff, and patients. Frequently, these bacteria are related to HAI (healthcare-associated infections) and carry antimicrobial resistance (AMR). These HAI-related bacteria contribute to a major public health issue by...
Acinetobacter baumannii is an opportunistic pathogen of intensive care unit (ICU) patients. A. baumannii colonizes many parts of the body including the gastrointestinal tract. Endemic and epidemic strains are polyclonal. There is no clarity on the origin of polyclonality of A. baumannii. The objecti...
Acinetobacter baumannii is a highly potent nosocomial pathogen that is associated with increased in-hospital mortality. Here, we investigated the changes in molecular characteristics of carbapenem-resistant A. baumannii (CRAB) isolated from the blood samples of patients admitted to a tertiary hospit...
Since the early time of space travel, planetary bodies undergoing chemical or biological evolution have been of particular interest for life detection missions. NASA's and ESA's Planetary Protection offices ensure responsible exploration of the solar system and aim at avoiding inadvertent contaminat...
has been responsible for a large number of clonal hospital outbreaks. However, some epidemiological changes have been observed since the emergence of CTX-M enzymes in . To analyse the transmission dynamics of Extended Spectrum β-Lactamase-producing (ESBL-Kp) in an acute care hospital. In 2015 a pro...
Modern genomic sequencing and bioinformatics approaches have detected numerous examples of DNA sequences derived from DNA and RNA virus genomes integrated into both vertebrate and insect genomes. Retroviruses encode RNA-dependent DNA polymerases (reverse transcriptases) and integrases that convert t...
A previous study demonstrates that most of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Brazilian strains fell in three local clades that were introduced from Europe around late February 2020. Here we investigated in more detail the origin of the major and most widely disseminated SA...
The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler...
Hyperinvasive strains of Neisseria meningitidis serogroup C have caused outbreaks of severe disease in Italy. Here, we report the analysis of the migration patterns of C:P1.5-1,10-8:F3-6:ST-11(cc11) meningococcal strains from different Italian regions collected between 2012 and 2017. N. meningitidis...
Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread o...
This study describes human immunodeficiency virus 1 (HIV-1) prevalence, associated factors, viral genetic diversity, transmitted drug resistance (TDR), and acquired drug resistance mutations (DRM) among a population of 522 men who have sex with men (MSM) recruited by the respondent-driven sampling (...
Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the disp...
() is ubiquitous among humans and one of the best-studied examples of an intimate association between bacteria and humans. Phylogeny and Phylogeography of strains are known to mirror human migration patterns and reflect significant demographic events in human prehistory. In this study, we analyzed...
is one of the most important foodborne pathogens around the world. In the last years, . serovar Infantis has become an important emerging pathogen in many countries, often as multidrug resistant clones. To understand the importance of in the broiler industry in Ecuador, we performed a study based...
The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have l...
The SARS-CoV-2 genome has been sequenced and the data is made available in the public domain. Molecular epidemiological investigators have utilized this information to elucidate the origin, mode of transmission, and contact tracing of SARS-CoV-2. The present review aims to highlight the recent advan...
Methicillin-resistant (MRSA) is a common healthcare-associated pathogen that remains a major public health concern. Sequence type 228 (ST228) was first described in Germany and spread to become a successful MRSA clone in several European countries. In 2000, ST228 emerged in Lausanne and has subsequ...
Nonparametric coalescent-based models are often employed to infer past population dynamics over time. Several of these models, such as the skyride and skygrid models, are equipped with a block-updating Markov chain Monte Carlo sampling scheme to efficiently estimate model parameters. The advent of p...
: Going forward, the routine implementation of genomic surveillance activities and outbreak investigation is to be expected. We sought to systematically identify the emerging ethical challenges; and to systematically assess the gaps in ethical frameworks or thinking and identify where further work i...
Extended-spectrum β-lactamase (ESBL)-producing pose significant treatment and infection prevention challenges. sequence type (ST) 131 associated with the gene has been the dominant lineage of ESBL-producing in the US and worldwide. In this study, our objective was to determine the β-lactamase p...
is a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common. Understanding the current prevalence and dynamics of lineages could inform...
India is endemic for enteric fever, and it is not known whether the variations in clinical manifestations between patients are due to host, environmental or pathogen factors.Blood culture surveillance was conducted at St. John's Medical College Hospital, Bangalore, between July 2016 and June 2017. C...
Echovirus 30 (E-30) has been investigated and reported worldwide and is closely associated with several infectious diseases, including encephalitis; myocarditis; and hand, foot, and mouth disease. Although many E-30 outbreaks associated with encephalitis have been reported around the world, it was n...
We performed an epidemiological surveillance of the Chikungunya (CHIKV) lineages in Bahia after the 2014 East/Central/South African (ECSA) genotype outbreak. Reverse-transcription polymerase chain reaction (RT-PCR), viral isolation, and phylogenetic analyses were conducted on serum samples from 605...
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic b...
In Europe HAV infection occurs mainly among specific risk groups, such as consumers of specific food. Sexual transmission of HAV has been demonstrated, particularly among Men-Who-Have-Sex-With-Men (MSM), causing MSM-specific outbreaksin Europe. Here we report a molecular epidemiologic and phylodynam...
Since its first introduction into China in 2009, influenza A/H1N1pdm virus has undergone a rapid expansion and replaced the classical seasonal A(H1N1) virus. To characterize the ongoing evolution and national transmission dynamics of this virus, we analyzed 335 complete genome, 1259 HA, and 1043 NA...
Understanding the dynamics of pathogen transfer in aquaculture systems is essential to manage and mitigate disease outbreaks. The goal of this study was to understand recent transmission dynamics of salmonid alphavirus (SAV) in Norway. SAV causes significant economic impacts on farmed salmonids in E...
Emerging and endemic animal viral diseases continue to impose substantial impacts on animal and human health. Most current and past molecular surveillance studies of animal diseases investigated spatio-temporal and evolutionary dynamics of the viruses in a disjointed analytical framework, ignoring m...
is associated with both hospital-acquired infections and community-acquired pneumonia (CAP). Here, we describe a novel strain of in a case of CAP in a previously healthy rural villager from Central Eastern China. isolated from the patient (LS01) was compared to well-characterized pathogenic strain...
producing extended-spectrum β-lactamases (ESBLs) causes nosocomial infections worldwide. The present study aimed to determine the molecular subtyping characteristics and antibiotic resistance mechanisms of ESBL-producing strains collected during an outbreak. Moreover, we attempted to reveal the fin...
Whole-genome sequencing (WGS) is used increasingly in public-health laboratories for typing and characterizing foodborne pathogens. To evaluate the performance of existing bioinformatic tools for prediction of antimicrobial resistance (AMR) and serotypes of , WGS-based genotype predictions were com...
Low pathogenic avian influenza (LPAI) virus of subtype H9N2 is the most frequently detected subtype among domestic poultry and is a public health concern because of its zoonotic potential. Due to the multiple and complex routes of LPAIV H9N2 between geographic regions, little is known about the spat...
The amphipod is a high-risk carrier of parasites that impact wildlife in its non-native range. Studies using the mitochondrial genes, Cytochrome Oxidase Sub-Unit 1 (cox1) and small-subunit ribosomal RNA gene (16S), provide some nucleotide detail for understanding the evolution and phylogeography of...
Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics...
Salmonella enterica serovar Wangata is an important pathogen in New South Wales (NSW), Australia. The incidence of S. Wangata is increasing and transmission is suspected to be via a non-food source. A recent outbreak investigation of sources of S. Wangata recovered isolates from humans, domestic ani...
The chikungunya East/Central/South/Africa virus lineage (CHIKV-ECSA) was first detected in Brazil in the municipality of Feira de Santana (FS) by mid 2014. Following that, a large number of CHIKV cases have been notified in FS, which is the second-most populous city in Bahia state, northeastern Braz...
Campylobacter spp. is the most common gastrointestinal pathogen worldwide with a very low reported incidence in China. In April 2018, one 36 cases of diarrhea outbreak occurred in a high school in Beijing after a trip to another province in Southern China. The investigation for the enteric pathogen...
Infectious bursal disease virus (IBDV) is an economically relevant and widespread pathogen that produces immunosuppression in young chickens. IBDV is genetically classified into seven genogroups (G1-G7), where the traditional classic, variant and very virulent strains correspond to G1, G2 and G3, re...
Respiratory syncytial virus (RSV), a leading cause of lower respiratory tract infections, is classified in two major groups (A and B) with multiple genotypes within them. Continuous changes in spatiotemporal distribution of RSV genotypes have been recorded since the identification of this virus. How...
Rapid advances in DNA sequencing technology ("next-generation sequencing") have inspired optimism about the potential of human genomics for "precision medicine." Meanwhile, pathogen genomics is already delivering "precision public health" through more effective investigations of outbreaks of foodbor...
Inexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole...
is one of the few commensal bacteria that can even cause large epidemics of invasive meningococcal disease (IMD). serogroup C belonging to the hypervirulent clonal complex 11 (cc11) represents an important public health threat worldwide. We reconstructed the dispersal patterns of hypervirulent meni...
Outbreaks of infections by , particularly subspecies , are increasingly reported worldwide. Several multilocus sequence typing (MLST) protocols for grouping international outbreak strains have been developed but not yet directly compared. Using the three-gene (, , and ), seven-gene (, , , , , , and...
Community acquired-methicillin resistant (MRSA) clones, including ST1, ST8, and ST30 are reported worldwide. However, data among Korean children are limited. Thus, we investigated the molecular characteristics of among children in Korea. isolated from Korean children diagnosed with skin and soft...
Streptococcus pneumoniae is one of the most common bacteria causing community-acquired pneumonia and meningitis. The use of 7-valent pneumococcal conjugate vaccine (PCV7) has reduced the incidence of pneumococcal disease while changing pneumococcal population through herd immunity and non-vaccine pn...
We report the detection and gene coding sequences of three novel species found in six dead farmed white-tailed deer in the United States. Phylogenetic analyses indicate that the new orbiviruses are genetically closely related to the Guangxi, Mobuck, Peruvian horse sickness, and Yunnan orbiviruses,...
spores can survive in the environment in either mono- or mixed-species biofilms. However, no previous studies have investigated chemical disinfection of spores embedded in biofilms. Thus, the purpose of this study was to assess the effectiveness of hospital disinfectants against spores embedded w...
We study the problem of computing the probability distribution of phylogenetic trees that commonly arise in areas ranging from epidemiology to macroevolution. We focus on homogeneous birth death trees with incomplete sampling and consider observations from three distinct sampling schemes. First, ind...
We report the full-genome sequence of a Dengue serotype-1 virus (DENV-1) isolated from a traveler returning in July 2019 to Italy from Democratic Republic of Congo (DRC), which is currently affected by Ebola and measles outbreaks. The sequence shows high similarity with two 2013 strains isolated in...
Carbapenemase-producing (CPE) are an increasingly common cause of healthcare-associated infections and may occasionally be identified in patients without extensive healthcare exposure. is the most frequently detected carbapenemase gene in within Australia, but little is known about the mechanisms...
Clostridioides difficile typing is invaluable for the investigation of both institution-specific outbreaks as well as national surveillance. While the epidemic ribotype 027 (RT027) has received a significant amount of resources and attention, ribotype 106 (RT106) has become more prevalent throughout...
Melioidosis is a tropical infectious disease which is being increasingly recognised throughout the globe. Infection occurs in humans and animals, typically through direct exposure to soil or water containing the environmental bacterium Burkholderia pseudomallei. Case clusters of melioidosis have bee...
A structured survey of the cystic fibrosis pathogens Achromobacter, Pandoraea and Ralstonia species from thirteen sentinel hospitals throughout England was undertaken by Public Health England. One isolate per patient of these genera collected from CF patients during the seven-month survey period in...
The porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of porcine reproductive and respiratory syndrome (PRRS). Disease outbreaks caused by NADC30-like PRRSV strains were a bit prevalent in China in recent years. In the present study, two newly emerged PRRSV strains,...
The burden of meningitis in low-and-middle-income countries remains significant, but the infectious causes remain largely unknown, impeding institution of evidence-based treatment and prevention decisions. We conducted a validation and application study of unbiased metagenomic next-generation sequen...
The increased incidence of Clostridioides difficile infection (CDI) and the emergence of highly virulent types highlight the need of microbiological characterization to gain insight CDI epidemiological changes. This paper, reporting data obtained by the Istituto Superiore di Sanità Central Laborator...
Streptococcus uberis, a major mastitis pathogen associated with intramammary infections (IMI), can be found ubiquitously in the cow's environment. Although Strep. uberis is reported to be susceptible to most antimicrobials, in practice poor responses to treatment and recurrent mastitis are observed....
Livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 may be transmitted and cause morbidity and mortality in hospitals. The economic cost of stopping hospital transmission of LA-MRSA CC398 is poorly described. Early detection of transmission may limit the...
Here we present a personalized viral genomics approach to investigating a rare case of perinatal herpes simplex virus 1 (HSV-1) transmission that ended in death of both mother and neonate. We sought to determine whether the virus involved in this rare case had any unusual features that may have cont...
Three severe acute gastroenteritis patients were identified within a 5-h period in a sentinel hospital enrolled in the foodborne pathogen surveillance project in Beijing. All patients had high fever (over 38.5°C), diarrhea, abdominal pain, vomiting, and headache. Ten grams of fresh patient stool sam...
The recent reemergence of yellow fever virus (YFV) in Brazil has raised serious concerns due to the rapid dissemination of the virus in the southeastern region. To better understand YFV genetic diversity and dynamics during the recent outbreak in southeastern Brazil, we generated 18 complete and nea...
About 15,000 hospitalizations due to group A Rotavirus gastroenteritis (RVA) are recorded each year in Italy. In the present study, we report the seasonal distribution and molecular characterization of RVA in pediatric and adult hospitalized patients in the period September 2015-April 2018 in Pavia...
Clostridium (Clostridioides) difficile infections (CDIs) are among the most frequent healthcare-associated infections in Serbia. In 2013, Serbia participated in the European Clostridium difficile Infection Surveillance Network (ECDIS-Net) who launched a pilot study to enhance laboratory capacity and...
: Antimicrobial resistance (AMR) played an important role in the initial outbreaks of infection (CDI) in the 1970s. ribotype (RT) 017 has emerged as the major strain of in Asia, where antimicrobial use is poorly regulated. This strain has also caused CDI outbreaks around the world for almost 30 y...
Methicillin-resistant Staphylococcus aureus (MRSA) are a major cause of healthcare and community- associated infections due to their ability to express a variety of virulence factors. We investigated 209 MRSA isolates obtained from 1 January to 31 December 2016 using a combination of phenotypic and...
Tuberculosis remains a major public health challenge globally with increasing risks for inter-transmission between pastoralists and cattle in Nigeria. This study was aimed at using molecular tools to establish zoonotic transmission of tuberculosis between pastoralists and their cattle in Ebonyi Stat...
Since carbapenems have been used for the treatment of infections in medical settings, multidrug-resistant containing resistance for carbapenems has become a major cause of nosocomial infections worldwide. Information on carbapenemase-producing isolates at community hospitals, including long-term c...
Infections as a result of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) are considered infections with a high public health burden. In this study, we aimed to identify incidences of and risk factors for healthcare-associated infections (HAIs) after rectal colonization with ESBL-p...
Wild waterfowl birds are known to be the main reservoir for a variety of avian influenza viruses of different subtypes. Some subtypes, such as H2Nx, H8Nx, H12Nx, and H14Nx, occur relatively rarely in nature. During 10-year long-term surveillance, we isolated five rare H12N5 and one H12N2 viruses in...
The objective of this study was to determine clinical-epidemiological characteristics of the patients and the genetic characteristics of carbapenemase KPC-3-producing Klebsiella pneumoniae isolates belonging to sequence type ST258. The eligible study population was all patients with isolates detecte...
Fluctuations in the clonal composition of Group A Streptococcus (GAS) have been associated with the emergence of successful lineages and with upsurges of invasive infections (iGAS). This study aimed at identifying changes in the clones causing iGAS in Portugal. Antimicrobial susceptibility testing,...
Currently, norovirus (NoV) is associated with one-fifth of all acute gastroenteritis (AGE) cases worldwide. The NoV GII.17_2014 variant has been associated with gastroenteritis outbreaks in several Asian countries, replacing the previously dominant Sydney 2012 variant. There is limited data about ci...
Effective control of avian diseases in domestic populations requires understanding of the transmission dynamics facilitating viral emergence and spread. In 2016-17, Italy experienced a significant avian influenza epidemic caused by a highly pathogenic A(H5N8) virus, which affected domestic premises...
We report an outbreak of invasive pneumococcal disease and pneumococcal pneumonia among shipyard workers, in Turku, Southwest Finland. In total, 31 confirmed and six probable cases were identified between 3 May and 28 November 2019. serotypes 12F, 4 and 8 were isolated from blood cultures of 25 cas...
Streptococcus suis is an emerging agent of zoonotic bacterial meningitis in Asia. We describe the epidemiology of S. suis cases and clinical signs and microbiological findings in persons with meningitis in Bali, Indonesia, using patient data and bacterial cultures of cerebrospinal fluid collected du...
According to the government of China, reported cases of pertussis have increased remarkably and are still increasing. To determine the genetic relatedness of Bordetella pertussis strains, we compared multilocus variable-number tandem-repeat analysis (MLVA) results for isolates from China with those...
To determine the prevalence of Staphylococcus aureus from hospital-acquired pneumonia (HAP) in Italy and the susceptibility to ceftobiprole and comparators of MSSA and MRSA isolates. A secondary objective was to characterize the clonality and acquired resistance and virulence genes of MRSA. Consecut...
Infection and colonization with multi-resistant Acinetobacter baumannii causes therapeutic and economic problems in the nosocomial setting. Due to the sensitivity issue of screening schemes for A. baumannii, it is difficult to implement adequate transmission prevention measures. The high discriminat...
We report the full polyprotein genomic sequence of a West Nile virus strain isolated from Eurasian magpies dying with neurologic signs in Greece. Our findings demonstrate the local genetic evolution of the West Nile virus strain responsible for a human disease outbreak in the country that began in 2...
A 17-month-old boy in India with severe acute respiratory infection was laboratory confirmed to have avian influenza A(H9N2) virus infection. Complete genome analysis of the strain indicated a mixed lineage of G1 and H7N3. The strain also was found to be susceptible to adamantanes and neuraminidase...
PFGE is the 'gold standard' method for bacterial subtyping. However, many strains are non-typable by this approach because of DNA degradation by nucleases action. To evaluate a modified PFGE protocol for typing nosocomial isolates of . Twenty- five isolates previously exposed to DNA degradation wer...
The genus Anaplasma currently comprises 6 bacterial species mostly pathogenic to animals and/or human, including the zoonotic species Anaplasma phagocytophilum, the causative agent of tick-borne fever (TBF) of ruminants, and of granulocytic anaplasmosis of horses, dogs and human. Recently, novel pot...
Bovine viral diarrhea virus type 1 (BVDV-1) is prevalent worldwide and causes significant economic loss in animal husbandry. Since its first report in the 1980s in China, several genotypes of BVDV-1 had been reported, but an in-depth phylogenetic analysis on the BVDV isolates from China is lacking....
, a leading cause of gastroenteritis worldwide, has been frequently isolated from recreational rivers and streams in New Zealand, yet the public health significance of this is unknown. This study uses molecular tools to improve our understanding of the epidemiology and sources of in recreational wa...
Neonatal sepsis is a great challenge for clinicians and infection control practitioners, especially in facilities with limited resources. Carbapenem-resistant Klebsiella pneumoniae (CRKP) is rapidly increasing and carriages a major threat to neonates. We aimed to examine phenotypes causing neonatal...
The present study aimed to elucidate the prevalence of Clostridioides difficile in Japanese retail food products. For this purpose, retail food samples (242 fresh vegetables and 266 retail meat samples: 89 chicken meat; 28 chicken liver; 200 pork meat; 24 pig liver; 127 beef meat) were collected fro...
The porcine circovirus type 3 (PCV3) becomes an important causative agent of swine disease since its discovery in 2016. PCV3 infection exhibits a wide range of clinical syndromes causing substantial economic losses in swine industry. Previous studies have reported the detection of numerous known vir...
Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131...
Whole-genome sequencing (WGS) of is increasingly used as part of infection prevention practices. In this study, we established a long-read technology-based WGS screening program of all first-episode methicillin-resistant (MRSA) blood infections at a major urban hospital. A survey of 132 MRSA genom...
Molecular epidemiology of HIV-1 infection in treatment-naive HIV-1 infected persons from Croatia was investigated. We included 403 persons, representing 92.4% of all HIV-positive individuals entering clinical care in Croatia in 2014-2017. Overall prevalence of transmitted drug resistance (TDR) was e...
Enterotoxigenic Escherichia coli (ETEC) is one of the most common diarrheal pathogens in the low- and middle-income regions of the world, however a systematic examination of the genomic content of isolates from Chile has not yet been undertaken. Whole genome sequencing and comparative analysis of a...
The most recent documented Australian outbreak of enterovirus A71 (EV-A71) occurred in Sydney from 2012 to 2013. Over a four-month period more than 100 children presented to four paediatric hospitals with encephalitic presentations including fever and myoclonic jerks. The heterogeneous presentations...
Enterovirus D68 (EV-D68) causes respiratory tract infections and neurologic manifestations. We compared the clinical manifestations from 2 EV-D68 outbreaks in 2014 and 2018 and a low-activity period in 2016 among hospitalized children in central Ohio, USA, and used PCR and sequencing to enable phylo...
We characterized exposures and demographics of Middle East respiratory syndrome coronavirus cases reported to the Saudi Arabia Ministry of Health during July 1-October 31, 2017, and June 1-September 16, 2018. Molecular characterization of available specimens showed that circulating viruses during th...
The order Mucorales is an ancient group of fungi classified in the subphylum Mucoromycotina. Mucorales are mainly fast-growing saprotrophs that belong to the first colonizers of diverse organic materials and represent a permanent part of the human environment. Several species are able to cause human...
While respiratory viral infections are recognized as a frequent cause of illness in hematopoietic stem cell transplantation (HSCT) recipients, HCoV-OC43 infections have rarely been investigated as healthcare-associated infections in this population. In this report, HCoV-OC43 isolates collected from...
High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and b...
This report describes transmission of a ET12 strain (ET12-Bc) at the Toronto Adult Cystic Fibrosis (CF) Centre occurring from 2008 to 2017. Epidemiological and genomic data from 11 patients with CF were evaluated. Isolates were analysed using whole genome sequencing (WGS). Epidemiological investiga...
Certification of global eradication of indigenous wild poliovirus type 2 occurred in 2015 and of type 3 in 2019. Since the launch of the Global Polio Eradication Initiative (GPEI) in 1988 and broad use of live, attenuated oral poliovirus vaccine (OPV), the number of wild poliovirus cases has decline...
First appearing in 2011 in Northern Europe, Schmallenberg virus (SBV), an of the Simbu serogroup, is associated with clinical disease mainly in ruminants such as cattle, sheep and goats. The clinical signs are characterized by abortion and congenital deformities in newborns. The virus is transmitte...
Unpasteurized milk can contain harmful bacteria such as Listeria monocytogenes. In 2016, the US Food and Drug Administration notified the Centers for Disease Control and Prevention (Atlanta, GA) that L. monocytogenes isolated from unpasteurized chocolate milk from a Pennsylvania dairy was closely re...
Infectious bronchitis virus (IBV) infection in chickens can lead to an economically important disease, namely, infectious bronchitis (IB). New IBV variants are continuously emerging, which complicates vaccination-based IB control. In this study, five IBVs were isolated from clinical samples submitte...
We conducted a longitudinal study to evaluate changes in the clinical presentation and epidemiology of Staphylococcus aureus bacteremia (SAB) in an academic, US medical center. Consecutive patients with monomicrobial SAB were enrolled from January 1995 to December 2015. Each person's initial bloodst...
To characterize outbreaks of invasive Group B Streptococcal (iGBS) disease in hospitals. Systematic review using electronic databases to identify studies describing iGBS outbreaks/clusters or cross-infection/acquisition in healthcare settings where 'cluster' was defined as ≥2 linked cases. PROSPERO...
Avian malaria is a mosquito-borne disease caused by Plasmodium spp. protozoa, and penguins are considered particularly susceptible to this disease, developing rapid outbreaks with potentially high mortality. We report on an outbreak of avian malaria in Magellanic penguins (Spheniscus magellanicus) a...
The structure and connectivity of wildlife host populations may influence zoonotic disease dynamics, evolution and therefore spillover risk to people. Fruit bats in the genus Pteropus, or flying foxes, are the primary natural reservoir for henipaviruses-a group of emerging paramyxoviruses that threa...
Colombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to desc...
Multilocus variable number tandem repeat analysis (MLVA) technique has wide applications in studying phylogenies and short-term epidemiology of pathogens. The technique has been extensively used worldwide in molecular epidemiology of Brucella genus. Only one study on this aspect is reported from Ind...
In 2018, the World Health Organization identified the Zika virus (ZIKV) as a pathogen that should be prioritized for public health research due to its epidemic potential. In this study, whole-genome sequencing (WGS) of travel-acquired ZIKV infections was used to examine the limitations of phylogenet...
Clostridioides difficile is considered the main pathogen responsible for hospital-acquired infections. This prospective study determined the prevalence, molecular epidemiological characteristics, and risk factors for C. difficile infection (CDI) and C. difficile colonization (CDC) among patients in...
A potential mechanism for the global distribution of waterborne pathogens is through carriage by the migratory waterbirds. However, this mode of transmission has yet been confirmed epidemiologically. Here, we conducted whole genome sequencing of Vibrio spp. collected from waterbirds, sediments, and...
Three cases of pneumonia caused by Legionella pneumophila serogroup 1 (Lp1) in immunosuppressed patients with repeated hospitalization were suspected as a healthcare-associated cluster. The environmental investigation did not reveal the presence of legionellae in the hospital patient rooms. Water sa...
Human enteroviruses and human parechoviruses are associated with a broad range of diseases and even severe and fatal conditions. For human cosaviruses, the etiological role is yet unknown. Little is known about the circulation of non-polio enteroviruses, human parechoviruses, and human cosaviruses i...
Since acellular vaccines (ACV) were introduced in Australia, epidemic Bordetella pertussis strains changed from single nucleotide polymorphism (SNP) cluster II to SNP cluster I. Our previous proteomic analysis identified potential proteomic adaptations in the whole cell and secretome of SNP cluster...
Mosquitoes harbor an extensive diversity of 'insect-specific' RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes, little is known about the diversity and evolutionary history of RNA viruse...
The spread of colistin resistance gene at the animal-human interface remains largely unknown. This work aimed to investigate the molecular characteristics of two extended-spectrum-β-lactamase (ESBL)-producing strains with , i.e., strains H8 and H9, isolated from the same mink farmer. In this study...
In this study, we report the draft genome sequence of a multidrug-resistant (MDR)Escherichia coli strain recovered from stool sample of an outpatient infant girl with acute diarrheal infection in Mexico. Antimicrobial susceptibility testing and PCR-based detection of diarrheagenic E. coli (DEC) were...
Streptococcus pyogenes (Group A streptococci: GAS) are known to cause a wide variety of human illnesses, some of which can be life-threatening. Usually, penicillin is the first-choice agent for the treatment of GAS infections. For patients with penicillin or beta-lactam antibiotics allergies, macrol...
For over four decades, Clostridium difficile has been a significant enteric pathogen of humans. It is associated with the use of antimicrobials that generally disrupt the microbiota of the gastrointestinal tract. Previously, it was thought that C. difficile was primarily a hospital-acquired infectio...
Aeromonads are mainly opportunistic pathogens; however, many species are emerging as important human pathogens. Therefore, monitoring these bacteria and their accurate characterization of its species is highly important. Aeromonas Aer593 strain was recovered from a diarrhoea outbreak and did not gro...
Sweden is investigating an outbreak of monophasic Typhimurium. Eighty-two nationally-distributed cases have been confirmed, with date of symptom onset between 28 August and 29 October. Cases were 51 years of age on average (range: 0-89) and the majority of cases were female (62%). A case-control st...
Helicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human, H. pylori is used as a tool to trace human migration. However, there are few studies about the relationship between phylogeography of H. pylori and its host human....
Bacillus cereus isolates causing an outbreak in the neonatal intensive care unit were investigated using whole-genome sequencing. The outbreak coincided with construction work performed adjacent to the neonatal intensive care unit and ceased after strict sealing of the construction area. We found th...
Legionellosis was diagnosed in an immunocompromised 3-year-old girl in Canada. We traced the source of the bacterium through co-culture with an ameba collected from a hot tub in her home. We identified Legionella pneumophila serogroup 6, sequence type 185, and used whole-genome sequencing to confirm...
Invasive group B Streptococcus (GBS) remains a leading cause of illness and death among infants globally. We conducted prospective and retrospective laboratory-based surveillance of GBS-positive cultures from infants <3 months of age in 18 hospitals across China during January 1, 2015-December 31, 2...
To describe the population structure, molecular epidemiology and genetic context of blaKPC-2-bearing Klebsiella pneumoniae. Isolates (n = 157) were retrospective, phenotypically carbapenem-resistant blaKPC-positive K. pneumoniae, collected from public hospitals. WGS was performed on the Illumina pla...
To evaluate the correlation of O-antigen serotypes with resistance profiles and high-risk clones in a Spanish nationwide survey. Up to 30 consecutive healthcare-associated Pseudomonas aeruginosa isolates were collected during October 2017 from each of 51 hospitals (covering all Spanish regions) with...
In 2015 and 2016 Poland recorded rapid proliferation of New Delhi MBL (NDM)-producing Enterobacterales, with at least 470 and 1780 cases, respectively. We addressed the roles of the Klebsiella pneumoniae ST11 NDM-1 outbreak genotype, already spreading in 2012-14, and of newly imported organisms in t...
Cryptococcus neoformans and Cryptococcus gattii species complexes have a worldwide distribution; however, there is geographical variation in the prevalence of different molecular types. Additionally, antifungal susceptibility differences between molecular types have been demonstrated. This study inv...
A nosocomial case of Legionella pneumophila pneumonia likely caused by a serogroup 3 strain was detected by a urinary antigen test in Spain in 2018. Although Legionella bacteria could not be isolated from respiratory samples, molecular methods implicated the sink faucet of the patient's room as the...
Inferring past population dynamics over time from heterochronous molecular sequence data is often achieved using the Bayesian Skygrid model, a nonparametric coalescent model that estimates the effective population size over time. Available in BEAST, a cross-platform program for Bayesian analysis of...
The secondary in-hospital epidemiological investigation for drug-resistant Pseudomonas aeruginosa infections was conducted to evaluate the in-hospital situation and identify any associations between exoenzyme genotypes and other genotypes and antimicrobial resistance characteristics, at the Universi...
Emerging of very virulent infectious bursal disease virus (vvIBDV) genotype in poultry flocks in Morocco were characterized. VP2 sequence analysis showed that the strains of Moroccan vvIBDV genotypes clustered separately from classic and vaccine strains reference of IBDV. The full-length genome of f...
The hepatitis C virus (HCV) has remarkable genetic diversity and exists as eight genotypes (1 to 8) with distinct geographic distributions. No complete genome sequence of HCV subtype 2b (HCV-2b) is available from Latin American countries, and the factors underlying its emergence and spread within th...
In 2016, Mali reported a bacterial meningitis outbreak consisting of 39 suspected cases between epidemiologic weeks 9 and 17 with 15% case fatality ratio in the health district of Ouéléssebougou, 80 kilometers from the capital Bamako. Cerebrospinal fluid specimens from 29 cases were tested by cultur...
Whole-genome sequencing (WGS) is invaluable for studying the epidemiology of meningococcal disease. Here we provide a perspective on the use of WGS for meningococcal molecular surveillance and outbreak investigation, where it helps to characterize pathogens, predict pathogen traits, identify emergin...
Infectious bursal disease virus (IBDV), the agent of an immunosuppressive and sometimes lethal disease in chickens, is causing recurrent outbreaks in broiler chickens in Egypt. In particular, an antigenically modified isolate of very virulent IBDV (vvIBDV) called 99323 was detected in Egypt nearly t...
Borrelia turcica, a member of the reptile-associated Borrelia clade, is vectored by Hyalomma aegyptium. The only suggested reservoir hosts of B. turcica are tortoises of the genus Testudo. Borrelia turcica has been described to occur in several Southeastern European countries including Turkey, Roman...
Influenza A virus causes annual epidemics in humans and is associated with significant morbidity and mortality. Haemagglutinin (HA) and neuraminidase (NA) gene sequencing have traditionally been used to identify the virus genotype, although their utility in detecting outbreak clusters is still uncle...
In a cohort of 480 patients admitted to an acute care hospital, 68 (14%) had positive perirectal cultures for toxigenic Clostridioides difficile on admission. Of the 11 patients (2%) diagnosed with healthcare-associated C. difficile infections, 3 (27%) had genetically related admission and infection...
During the period from April 2012 to May 2013, 13 newborns (1 to 4 weeks of age) and 1 child in a pediatric hospital ward in Germany were colonized with producing an extended-spectrum beta-lactamase (ESBL) (CTX-M-15). A microbiological source-tracking analysis with human and environmental samples w...
We aimed to characterise gonorrhoea transmission patterns in a diverse urban population by linking genomic, epidemiological and antimicrobial susceptibility data. isolates from patients attending sexual health clinics at Barts Health NHS Trust, London, UK, during an 11-month period underwent whole-...
Plasmid-encoded extended-spectrum β-lactamase and AmpC gene-carrying Escherichia coli (ESBL/AmpC E. coli) is an increasing cause of human infections worldwide. Increasing carbapenem and colistin resistance further complicate treatment of these infections. The aim of this study was to assess the occu...
Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target...
Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian r...
The hepatitis delta virus (HDV) is a globally distributed agent, and its genetic variability allows for it to be organized into eight genotypes with different geographic distributions. In South America, genotype 3 (HDV-3) is frequently isolated and responsible for the most severe form of infection....
Microbial communities residing in the nose play important roles in human health and disease. We report marked differences in nasal microbiota between a rural community and an industrial setting located near a major urban city. Nasal samples were collected from 19 healthy male subjects: 9 samples fro...
Genomic surveillance that combines bacterial sequencing and epidemiological information will become the gold standard for outbreak detection, but its clinical translation is hampered by the lack of automated interpretation tools. We performed a prospective pilot study to evaluate the analysis of met...
Although hypervirulent (hvKp) has been associated with severe community-acquired infections that occur among relatively healthy individuals, information about hvKp infections in health care settings remains limited. Here, we systematically analyzed the clinical and molecular characteristics of iso...
The molecular epidemiology and antimicrobial resistance of Clostridioides difficile were studied in South Korea in 2017 as part of a National Surveillance System. From February to May 2017, all non-duplicate isolates of C. difficile were recovered from patients who were suspected to have C. difficil...
Carbapenem-resistant (CRKP) is an antibiotic resistance threat of the highest priority. Given the limited treatment options for this multidrug-resistant organism (MDRO), there is an urgent need for targeted strategies to prevent transmission. Here, we applied whole-genome sequencing to a comprehens...
Group A rotavirus (RVA) genotype G12 has spread globally and has become one of the most prevalent genotypes of rotavirus in Africa. To understand the drivers for its genetic diversity and rapid spread we investigated the Bayesian phylogeography, viral evolution and population demography of Rotavirus...
Proteus mirabilis is ubiquitous in soil and water. It is an important catheter-associated urinary tract pathogen and has reportedly been associated with antimicrobial-resistant infections. This study reports the draft genome of a multidrug-resistant P. mirabilis isolated from raw retail chicken meat...
Linezolid (LZD)-resistant Staphylococcus epidermidis (LRSE) are increasing, and are mainly associated with outbreaks in hospital wards with high LZD consumption. To investigate the frequency of LRSE in a tertiary hospital in the context of LZD use. The frequency of LRSE and the data on LZD usage [ex...
Mycobacterium bovis is the main causative agent of bovine tuberculosis (bTB) being among the animal-adapted Mycobacterium tuberculosis complex. Herds can also be infected with non-tuberculous mycobacteria (NTM) causing a negative effect on the economy and on animal and human health through zoonotic...
Extended-spectrum β-lactamase (ESBL)-producing isolates are known to tolerate superior quinolone antimicrobials compared with other antibacterial agents. Among the clones belonging to sequence type (ST) 131 by multilocus sequence typing, the involvement of the H30-Rx subclone has been reported worl...
Resistance to colistin, a last resort antibiotic, has emerged in India. We investigated colistin-resistant Klebsiella pneumoniae(ColR-KP) in a hospital in India to describe infections, characterize resistance of isolates, compare concordance of detection methods, and identify transmission events. Re...
The worldwide emergence of multidrug-resistant uropathogens has resulted in the revival of old antibiotics such as nitrofurantoin (NIT) for the treatment of uncomplicated urinary tract infections (UTIs). This study aimed to identify determinants of NIT resistance and to investigate the genetic diver...
Leptospirosis is a zoonotic disease caused by a bacterium of the genus Leptospira that affects domestic animals, including cattle. Despite of this importance in livestock, little is known about the epidemiology of leptospirosis in cattle in Brazil and other tropical countries. In this context, the o...
Salmonella outbreaks in childcare facilities are relatively rare, most often occurring secondary to contaminated food products or poor infection control practices. We report an outbreak of Salmonella Saintpaul at a pre-school facility in Ayrshire, Scotland with atypical clinical and epidemiological...
Lassa virus is genetically diverse with several lineages circulating in West Africa. This study aimed at describing the sequence variability of Lassa virus across Nigeria and inferring its spatiotemporal evolution. We sequenced and isolated 77 Lassa virus strains from 16 Nigerian states. The final d...
is an important zoonotic pathogen. Serotype 2 and sequence type (ST) 1 are the most frequently reported strains in both infected humans and pigs. ST7 is only endemic to China, and it was responsible for outbreaks in 1998 and 2005 in China. In the present study, 38 sporadic ST7 strains, which mostly...
In 2014, two genetically-linked cases of carbapenemase-producing Enterobacteriaceae (CPE) were detected at the Canberra Hospital (TCH), prompting an investigation and response that appeared to contain transmission. We report a 2017 retrospective investigation into cases of CPE in the Australian Capi...
Transmission of vector-borne virus by insects is a complex mechanism consisting of many different processes; viremia in the host, uptake, infection and dissemination in the vector, and delivery of virus during blood-feeding leading to infection of the susceptible host. Bluetongue virus (BTV) is the...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates (carrying the carbapenemase gene bla) of sequence type 16 caused hospital-acquired bloodstream infection or gut colonization in two patients in an intensive care unit (ICU). It was hypothesized that handwashing sinks were the source, and all...
Variation in disease incidence in wildlife is often assumed to reflect environmental or demographic changes acting on an endemic pathogen. However, apparent endemicity might instead arise from spatial processes that are challenging to identify from traditional data sources including time series and...
Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced twenty-one full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2...
Candida auris (C. auris) has globally emerged as a multidrug-resistant pathogen. While it is known that there are four geographic clades, little is known about its genomic epidemiology in the Southeast Asian region. Laboratory identification can be challenging but the VITEK2 system (version 8.01 sof...
Equine herpesvirus 1 (EHV-1) is an Alphaherpesvirus infecting not only horses but also other equid and non-equid mammals. It can cause respiratory distress, stillbirth and neonatal death, abortion, and neurological disease. The different forms of disease induced by EHV-1 infection can have dramatic...
Bluetongue disease of ruminants is a typical insect-borne disease caused by bluetongue virus (BTV) of the genus Orbivirus (family Reoviridae) and transmitted by some species of Culicoides (Diptera: Ceratopogonidae). Recently, the detection of BTV in yaks in high altitude meadows of the Shangri-La di...
An alarming rise in reported Lassa fever cases continues in west Africa. Liberia has the largest reported per capita incidence of Lassa fever cases in the region, but genomic information on the circulating strains is scarce. The aim of this study was to substantially increase the available pool of d...
This study provides a phylogeographic insight into the population diversity of strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and...
In May 2016, an unusual outbreak with the Panton-Valentine leukocidin-positive human variant of meticillin-resistant (MRSA) clonal complex 398 occurred among mothers and infants in the maternity unit of a Danish hospital. MRSA sharing genotypic and phenotypic characteristics was confirmed in 36 cas...
Background is a leading global cause of bacterial gastroenteritis, motivating research to identify sources of human infection. Population genetic studies have been increasingly applied to this end, mainly using multilocus sequence typing (MLST) data.ObjectivesThis review aimed to summarise approache...
Non-pandemic variants of the Human Immunodeficiency Virus Type 1 (HIV-1) subtype B accounts for a significant fraction of HIV infections in several Caribbean islands, Northeastern South American countries and the Northern Brazilian states of Roraima and Amazonas. In this paper, we used a comprehensi...
Bacterial wilt (BW) caused by the species complex (RSSC) is a serious threat to potato production in Uganda. However, little is known about the extent of the disease and the type of the pathogen strains involved. A nationwide survey was conducted to study BW prevalence and incidence in potato, and...
The identification of a new circovirus ( 3, PCV-3) has raised a remarkable concern because of some analogies with (PCV-2). Preliminary results suggest an extremely recent PCV-3 emergence and high mutation rate. Retrospective studies prove its circulation at least since the early 1990s, revealing th...
Repeated outbreaks of Hand, foot and mouth disease (HFMD) infections have been observed in recent decades and dominated by various enteroviral serotypes. In particular, enterovirus 71 (EV-A71), coxsackievirus A16 (CV-A16) and coxsackievirus A6 (CV-A6) dominated the prevalence of HFMD infections alte...
Phylodynamic analyses using pathogen genetic data have become popular for making epidemiological inferences. However, many methods assume that the underlying host population follows homogenous mixing patterns. Nevertheless, in real disease outbreaks, a small number of individuals infect a disproport...
Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of partic...
A recent preliminary study from our group found that extended-spectrum cephalosporin-resistance determinants can be detected in the majority of composite fecal samples collected from Alberta feedlot cattle. Most notably, genes were detected in 46.5% of samples. Further isolate characterization iden...
GII.4 noroviruses are a major cause of acute gastroenteritis. Their dominance has been partially explained by the continuous emergence of antigenically distinct variants. To gain insights into the mechanisms of viral emergence and population dynamics of GII.4 noroviruses, we performed large-scale ge...
With the aim to elucidate gonococcal antimicrobial resistance (AMR)-risk factors, we undertook a retrospective analysis of the molecular epidemiology and AMR of 104 Neisseria gonorrhoeae isolates from clinical samples (urethra, rectum, pharynx and cervix) of 94 individuals attending a sexually trans...
The surveillance of health care-associated infection (HAI) is an essential element of the infection control program. While whole-genome sequencing (WGS) has widely been adopted for genomic surveillance, its data processing remains to be improved. Here, we propose a three-level data processing pipeli...
Shiga toxin-producing (STEC) and the STEC subgroup enterohemorrhagic cause intestinal infections with symptoms ranging from watery diarrhea to hemolytic-uremic syndrome (HUS). A key tool for the epidemiological differentiation of STEC is serotyping. The serotype in combination with the main virule...
Molecular typing such as spa typing is used to control and prevent Staphylococcus aureus widespread in hospitals and communities. Hence, the aim of this study was to find the most common types of S. aureus strain circulating in Shiraz via spa and SCCmec typing methods. Total of 159 S. aureus isolate...
Candida auris has recently emerged as a global cause of multidrug resistant fungal outbreaks. An outbreak occurred at a tertiary care center in London in 2016. Transmission characteristics, interventions, patient outcomes and cost of resources are described. Outbreak interventions included patient i...
is a major enteric pathogen known to cause gastroenteritis in human adults. Although major outbreak cases are frequently reported, only limited whole-genome sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of outbreak-associated st...
Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmenta...
To characterize the resistance patterns of uropathogenic (UPEC) in a Tertiary Teaching Hospital in Iran, we conducted a descriptive epidemiology study using molecular techniques. The subjects consisted of patients having acute urinary tract infection, who were enrolled in the study from 2014 to 201...
Leptospirosis presents a complex and dynamic epidemiology. Bovine leptospirosis has been described as a major infectious disease impairing reproductive efficiency. Although infections by Leptospira interrogans, L. santarosai and L. borgpetersenii are frequently reported in cattle, the presence of L....
Biting midges ( species) are vectors of arboviruses and were responsible for the emergence and spread of (SBV) in Europe in 2011 and are likely to be involved in the emergence of other arboviruses in Europe. Improved surveillance and better understanding of risks require a better understanding of t...
Sentinel hospital surveillance was instituted in Australia to detect the presence of pandemic group A Streptococcus strains causing scarlet fever. Genomic and phylogenetic analyses indicated the presence of an Australian GAS emm12 scarlet fever isolate related to United Kingdom outbreak strains. Nat...
We investigated a large multistate outbreak that occurred in the United States in 2015-2016. Epidemiologic, laboratory, and traceback studies were conducted to determine the source of the infections. We identified 907 case-patients from 40 states with illness onset dates ranging from July 3, 2015 to...
The interplay between food production animals, humans and the environment with respect to the transmission of drug-resistant pathogens is widely debated and poorly understood. Pandemic uropathogenic ST131-H30, with conserved fluoroquinolone and cephalosporin resistance, are not frequently identifie...
Foodborne salmonellosis causes approximately 1 million illnesses annually in the United States. In the summer of 2017, we investigated four multistate outbreaks of Salmonella infections associated with Maradol papayas imported from four Mexican farms. PulseNet initially identified a cluster of Salmo...
No abstract available
It is known that antibiotic usage is associated with the development of Clostridioides difficile infection (CDI), especially clindamycin, third-generation cephalosporins, and fuoroquinolones. Antibiotic resistance rates to many antibiotics varies a lot by study. We performed a study focused on antib...
Invasive meningococcal disease (IMD) is one of the leading causes of bacterial meningitis and septicemia in Israel. The purpose of the study was to describe the IMD in the Tel Aviv District and to identify specific populations who could benefit from vaccine introduction. In the Tel Aviv District, th...
Microsporidia are composed of a highly diverse group of single-celled, obligate intracellular fungi that colonize an extremely wide range of other eukaryotes, among which Enterocytozoon bieneusi is the most common species responsible for human microsporidiasis. Genotyping of E. bieneusi based on seq...
Information on the epidemiology of C. difficile infection (CDI) in South-East Asian countries is limited, as is data on possible animal reservoirs of C. difficile in the region. We investigated the prevalence and molecular epidemiology of C. difficile in piglets and the piggery environment in Thaila...
Carbapenem-resistant (CRKP) strains belonging to sequence type 258 (ST258) are frequent causes of hospital-associated outbreaks and are a major contributor to the spread of carbapenemases. This genetic lineage emerged several decades ago and remains a major global health care challenge. In this stu...
Indigenous typhoid fever was continuing to be identified in Taiwan which has not been endemic for the enteric fever for more than 20 years. The source and transmission by which the local patients acquired typhoid and the population structure of the indigenous typhoid strains remain not well characte...
There has been a considerable upsurge of extensive, treatment recalcitrant, dermatophytosis presenting as tinea corporis and tinea cruris in India since the past few years. Genome analysis of Trichophytonspecies causing severe superficial dermatophytosis in North India confirmed a unique clade relat...
Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both s...
BackgroundEnding the HIV pandemic must involve new tools to rapidly identify and control local outbreaks and prevent the emergence of recombinant strains with epidemiological advantages.AimThis observational study aimed to investigate in France a cluster of HIV-1 cases related to a new circulating r...
BackgroundTwo epidemiologically-unrelated clusters of carbapenemase (KPC)-producing were detected among several healthcare facilities (HCF) in Finland by routine surveillance using whole genome sequencing (WGS).AimThe objective was to investigate transmission chains to stop further spread of the r...
In spring 2016, Greece reported an outbreak caused by a previously undescribed subsp. serotype (antigenic formula 11:z41:e,n,z15) via the Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD), with epidemiological evidence for sesame products as presum...
We describe two outbreaks of multidrug-resistant (MDR) I 4,[5],12:i:- infection, occurring in 2015 to 2016, linked to pork products, including whole roaster pigs sold raw from a single Washington slaughter and processing facility (establishment A). Food histories from 80 ill persons were compared w...
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology...
Near 60% of new HIV infections in the United Kingdom are estimated to occur in men who have sex with men (MSM). Age-disassortative partnerships in MSM have been suggested to spread the HIV epidemics in many Western developed countries and to contribute to ethnic disparities in infection rates. Under...
Klebsiella pneumoniae is an important human pathogen, able to accumulate and disseminate a variety of antimicrobial resistance genes. Resistance to colistin, one of the last therapeutic options for multi-drug-resistant bacteria, has been reported increasingly. Colistin-resistant K. pneumoniae (ColRK...
While the molecular epidemiology of extended-spectrum-b-lactamase (ESBL)-producing E. coli is well known in Europe due to effective surveillance networks and substantial literature, data for Africa are less available, especially in Djibouti. We studied 31 isolates of ESBL-producing E. coli from Djib...
Klebsiella pneumoniae is an opportunistic pathogen accounting for 5-7% of hospital acquired infections. The emergence of carbapenem-resistant Klebsiella pneumoniae has been increasing rapidly over recent years causing many therapeutic problems worldwide. This study aimed to research the antimicrobia...
In 2017 Ontario experienced the largest mumps outbreak in the province in 8 years, at a time when multiple outbreaks were occurring across North America. Of 259 reported cases, 143 occurred in Toronto, primarily among young adults. Routine genotyping of the small hydrophobic gene indicated that the...
Since 2009, increases in the incidence of invasive meningococcal disease have occurred in the United Kingdom due to a sublineage of the Neisseria meningitidis serogroup W ST-11 clonal complex (hereafter, the "original UK strain"). In 2013, a descendent substrain (hereafter, the "2013 strain") became...
A child developed hydrocephalus. Sixteen months later, it was discovered to be a complication of coccidioidal meningitis. The infection's source was uncertain until genomic analysis of the fungal isolate identified its origin to be a visit to Beeville, Texas. Improved national reporting of cases of...
Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between ongoing in-hospital transmission of the virus and new introductions from the community, and it is challen...
Before kidney transplantation, donors and recipients are routinely screened for viral pathogens using specific tests. Little is known about unrecognized viruses of the urinary tract that potentially result in transmission. Using an open metagenomic approach, we aimed to comprehensively assess virus...
On 29 April 2015, the Florida Department of Health in Miami-Dade County (DOH Miami-Dade) was notified by a local dermatologist of 3 patients with suspected nontuberculous mycobacterial (NTM) infection after receiving tattoos at a local tattoo studio. DOH Miami-Dade conducted interviews and offered t...
A variety of methods based on coalescent theory have been developed to infer demographic history from gene sequences sampled from natural populations. The 'skyline plot' and related approaches are commonly employed as flexible prior distributions for phylogenetic trees in the Bayesian analysis of pa...
Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To unders...
To characterise the genotypic profiles of methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates from companion animals and to investigate their association with those from humans in Japan. Non-duplicated MRSA clinical isolates recovered between July 2016 and January 2018 were analysed...
Infections caused by Corynebacterium diphtheriae remain endemic in many countries. Since the implementation of the DTP (Diphtheria-Tetanus-Pertussis) vaccination program in 1977, only sporadic diphtheria cases have been reported in Thailand. In 2012, a diphtheria outbreak occurred in rural Thailand...
Mosquitoes are the most important invertebrate viral vectors in humans and harbor a high diversity of understudied viruses, which has been shown in many mosquito virome studies in recent years. These studies generally performed metagenomics sequencing on pools of mosquitoes, without assessment of th...
Enterocytozoon bieneusi and Giardia duodenalis are important opportunistic enteric zoonotic pathogens that cause diarrhoea and intestinal diseases in animals and humans. China is the largest producer of pigs, but whether Tibetan pigs, a unique pig breed in Tibet, are infected with E. bieneusi and G....
The rise of antimicrobial resistance in uropathogens has complicated the management of urinary tract infections (UTIs), particularly in patients who are afflicted by recurrent episodes of UTIs. Antimicrobial-resistant (AR) uropathogens persistently colonizing individuals at asymptomatic time points...
is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of , which contributes to its long-term persistence and transmission in hospitals. In this study, a total of 192 isolate...
Carbapenemase-producing (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016. Suspected CPE were referred to the stat...
We applied metagenomic next-generation sequencing (mNGS) to detect Zaire Ebola virus (EBOV) and other potential pathogens from whole-blood samples from 70 patients with suspected Ebola hemorrhagic fever during a 2014 outbreak in Boende, Democratic Republic of the Congo (DRC) and correlated these fin...
Staphylococcus aureus has been recognised as one of the important zoonotic pathogens. However, knowledge about the epidemiology and genetic characteristics of S. aureus in rabbits was limited. The aim of this study was to determine the characteristics of 281 S. aureus isolated from dead rabbits of n...
Bufavirus (BuV), a recent discovery virus of the family Parvoviridae, has been suggested to be a potential causative agent of diarrhea in humans. The prevalence of BuV has been demonstrated mostly in fecal specimens of diarrheic patients. Little is known about the presence of BuV in the environmenta...
The Zika epidemic in the Americas has challenged surveillance and control. As the epidemic appears to be waning, it is unclear whether transmission is still ongoing, which is exacerbated by discrepancies in reporting. To uncover locations with lingering outbreaks, we investigated travel-associated Z...
Frozen raw breaded chicken products (FRBCP) have been identified as a risk factor for Salmonella infection in Canada. In 2017, Canada implemented whole genome sequencing (WGS) for clinical and non-clinical Salmonella isolates, which increased understanding of the relatedness of Salmonella isolates,...
Cyprinid herpesvirus 2 (CyHV-2) infection is detrimental to gibel carp health and may result in severe economic loss in freshwater aquaculture. However, information regarding the interaction of this pathogen with the aquatic environment is scarce. In this study, quantitative polymerase chain reactio...
Dengue virus (DENV) is the most prevalent arbovirus in terms of human public health importance globally. In addition to DENV epidemiological surveillance, genomic surveillance may help investigators understand the epidemiological dynamics, geographic distribution, and temporal patterns of DENV circu...
Knowledge on basic characteristics of Mycobacterium tuberculosis (MTB) is helpful to understand the disease epidemiology and support the prediction of clinical outcome of the disease. The aim of this study was to detect the genotypes and genotypic characters of clinical Mycobacterium tuberculosis (M...
Outbreaks of vancomycin-resistant enterococcus (VRE) are a serious problem in hospitals. Inferring the transmission route is an important factor to institute appropriate infection control measures; however, the methodology has not been fully established. To reconstruct and evaluate the transmission...
The aim of this study was to investigate the mechanisms of fosfomycin resistance and epidemiological characteristics in fosfomycin-resistant enterococci in China. A collection of 761 enterococcal clinical isolates from a teaching hospital in Wenzhou, China were studied. The fosfomycin susceptibility...
The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2017 survey was the fifth year to focus on blood stream infections, and included Enterobacterales, and...
An outbreak of an uncommon emm type (emm66.0) of group A streptococcus (GAS) occurred in England and Wales between January 2016 and May 2017, involving 52 individuals who were homeless or injecting drugs users. In order to investigate the outbreak, epidemiological and network analysis were performed...
Kenya is endemic for cholera with different waves of outbreaks having been documented since 1971. In recent years, new variants of Vibrio cholerae O1 have emerged and have replaced most of the traditional El Tor biotype globally. These strains also appear to have increased virulence, and it is impor...
Due to the migration or transboundary spread of domestic and wild animals, peste des petits ruminants virus posed a high potential threat to them. In this study, we initially detected that a class of animal named Procapra przewalskii was infected with peste des petits ruminants virus (PPRV ChinaGS20...
Hand, foot, and mouth disease (HFMD) is endemic in the Pacific region, especially in mainland China. The case-fatality ratio of HFMD is increasing steadily. Knowledge of the changing epidemiology of HFMD in different regions is necessary for implementing appropriate intervention strategies. In this...
Klebsiella infections are reported from neonatal intensive care units (NICUs) worldwide, but data on their incidence and genetic diversity remain scarce. We determined the incidence and genetic diversity of Klebsiella infections in NICU patients in Rio de Janeiro. This was a prospective study includ...
Microbiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition)...
A cluster of seven cases of skin and wound infections caused by a multiply resistant meticillin-resistant Staphylococcus aureus (MRSA) were detected in a small-town community in South Yorkshire. Initial microbiological investigations showed that all isolates belonged to a spa type observed rarely in...
There have been few available data that presented a direct comparison between polymerase chain reaction ribotype (RT) distribution of Clostridioides difficile strains from C. difficile infection (CDI) and colonization. To understand the epidemiology of CDI in a hospital setting, we compared RTs of C...
Globally, bacterial vector-borne disease (VBD) exerts a large toll on dogs in terms of morbidity and mortality but nowhere is this more pronounced than in the tropics. Tropical environments permit a burgeoning diversity and abundance of ectoparasites some of which can transmit an extensive range of...
The aim of this study was to describe the epidemiology and clinical impact of carbapenem-non-susceptible Pseudomonas aeruginosa (CNPA) in intensive care units (ICUs) of the national referral hospital of Indonesia. Adult patients admitted to ICUs were prospectively included. Pseudomonas aeruginosa we...
Model-based phylodynamic approaches recently employed generalized linear models (GLMs) to uncover potential predictors of viral spread. Very recently some of these models have allowed both the predictors and their coefficients to be time-dependent. However, these studies mainly focused on predictors...
To describe an outbreak of bacteremia caused by vancomycin-sensitive Enterococcus faecalis (VSEfe). An investigation by retrospective case control and molecular typing by whole-genome sequencing (WGS). A tertiary-care neonatal unit in Melbourne, Australia. Risk factors for 30 consecutive neonates wi...
Clostridium difficile, the causal agent of antibiotic-associated diarrhea, has a complex epidemiology poorly studied in Latin America. We performed a robust genomic and phenotypic profiling of 53 C. difficile clinical isolates established from diarrheal samples from either intrahospital (IH) or comm...
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes Chikungunya fever. CHIKV entered Mexico through the state of Chiapas in October 2014. To fully understand the Chikungunya fever outbreak that occurred in southern Chiapas during 2015, we evaluated 22 PCR-confirmed CHIKV-positive pa...
-borne arboviruses have spread globally with outbreaks of vast impact on human populations and health systems. The West African archipelago of Cape Verde had its first outbreak of Dengue in 2009, at the time the largest recorded in Africa, and was one of the few African countries affected by the Zik...
Multidrug-resistant Shigella isolates have recently emerged as a serious public health threat worldwide. In particular, overseas travel is a risk factor for acquisition of antimicrobial-resistant Shigella strains. To explore the role of travel in the spread of cefotaxime-resistant Shigella sonnei in...
Salmonellae represent one of the most common bacterial infection reagents in both humans and animals. For detection and epidemiological elucidation of Salmonella infections, determination of Salmonella serotypes and differentiation between different Salmonella isolates is crucial. In the first part...
Background is a leading cause of healthcare-associated diarrhoea in middle and high-income countries. Up to 2018, there has been no systematic, annual surveillance for infections (CDI) in France.AimsTo provide an updated overview of the epidemiology of CDI in France between 2010 and 2017 based on f...
In September 2017, a cluster of monophasic Typhimurium isolates was identified at the National Reference Laboratory for Enteropathogenic Bacteria in Norway. We investigated the cluster to identify the source and implement control measures. We defined a case as a person with laboratory-confirmed sal...
colonizes the human oropharynx and transmits mainly via asymptomatic carriage. Actual outbreaks of meningococcal meningitis are comparatively rare and occur when susceptible populations are exposed to hypervirulent clones, genetically distinct from the main carriage isolates. However, carriage isola...
Fecal colonization with carbapenem-resistant Enterobacteriaceae (CRE) is a risk factor for bacterial translocation resulting in subsequent endogenous infections. The purpose of this study is to investigate the prevalence of CRE strains colonization in stool samples of outpatient in a tertiary pediat...
We investigated an outbreak of listeriosis detected by whole-genome multilocus sequence typing and associated with packaged leafy green salads. Nineteen cases were identified in the United States during July 5, 2015-January 31, 2016; isolates from case-patients were closely related (median differenc...
We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. Of the 151 pools analyzed, 17 tested positive for Zika virus RNA; infectious Zika virus was successfully isolated from 1 of the larvae pools (31N) in...
We implemented subgenomic and whole-genome sequencing to support the investigation of a large hepatitis A virus outbreak among persons experiencing homelessness, users of illicit drugs, or both in California, USA, during 2017-2018. Genotyping data helped confirm case-patients, track chains of transm...
The majority of norovirus outbreaks in the United States occur in healthcare facilities. With the growing population of immunocompromised hosts who are in frequent contact with healthcare facilities, norovirus is not only a threat to hospitals and nursing homes but also to these individuals. This re...
NDM-producing Enterobacteriaceae clinical isolates remain uncommon in the European region. We describe the emergence and broad dissemination of one successful NDM-1-producing Klebsiella pneumoniae clone in Greek hospitals. During a 4 year survey (January 2013-December 2016), 480 single-patient carba...
Modern phylodynamic methods interpret an inferred phylogenetic tree as a partial transmission chain providing information about the dynamic process of transmission and removal (where removal may be due to recovery, death, or behavior change). Birth-death and coalescent processes have been introduced...
This study reports on a surveillance in an Italian hospital focused on carbapenemase-producing (CP-Ec). Eighteen isolates (nine from clinical specimens and nine from rectal swab) were characterized for antibiotic susceptibilities, typing features, main carbapenemase, extended-spectrum ß-lactamases...
The outstanding ability of to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a...
We report bla-harboring carbapenem-resistant Klebsiella pneumoniae in an emerging sequence type 307 lineage in a traveler returning from Puerto Rico to the Dominican Republic. Phylogenetic analyses indicate regional dissemination of this highly drug-resistant clone across the Americas, underscoring...
Staphylococcus lugdunensis is a significant pathogen that causes community-acquired and nosocomial infections. The high prevalence of oxacillin-resistant S. lugdunensis (ORSL) is of major concern. Resistance to β-lactams is caused by acquisition of the staphylococcal cassette chromosome mec (SCCmec)...
IntroductionTwo hantavirus species, Puumala (PUUV) and Dobrava-Belgrade (DOBV) virus (genotype Kurkino), are endemic in Germany. Recent PUUV outbreaks raised questions concerning increasing frequency of outbreaks and expansion of PUUV endemic areas.AimsTo describe the epidemiology of human PUUV and...
Staphylococcus aureus repeat (STAR) elements are abundant repeat sequences that are highly variable in numbers and locations within the genome of S. aureus. The evolutionary variation of these repeats occurs rapidly over time and may correlate with their evolutionary lineage. Therefore, the aim of t...
Stenotrophomonas maltophilia, which is able to form a biofilm, has mostly been related to catheters when it is the agent in hospital infections; these infections generally present as bacteremia and pneumonia, which may progress with complications and result in death. The study included 153 S. maltop...
Tuberculosis is a chronic debilitating infectious disease causing a severe challenge to public health, especially in developing countries. The aim of this study was to examine genetic diversity in Mycobacterium tuberculosis strains circulating in the Balochistan region of Pakistan. One hundred isola...
To screen diagnostic specimens for the presence of hantavirus genomes or to identify new hantaviruses in nature, the pan-hanta L-PCR assay, a broadly reactive nested reverse transcription polymerase chain reaction (RT-PCR) assay targeting the L segment, is highly preferred over other assays because...
No abstract available
Escherichia coli (E. coli) causes urinary tract infections, pneumonia, surgical site infections, and bloodstream infections and is the important pathogen for both community-acquired and healthcare-associated infections. To investigate the clonality of E. coli is important for infection control and p...
Acinetobacter baumannii is a nosocomial pathogen increasingly affecting the critically ill patients and represents a major public health challenge. Carbapenem-resistant A. baumannii (CRAB) is found to be associated with International Clones (ICs) and different classes of carbapenemases. The objectiv...
Staphylococcus pseudintermedius is the leading cause of pyoderma in dogs and the frequent use of antimicrobial treatment is associated to the development of resistance to nearly all classes of antibiotics. Despite S. pseudintermedius significance, our understanding of the molecular mechanism of β-la...
Listeria monocytogenes causes severe diseases in humans, including febrile gastroenteritis and systemic infections that has a high mortality despite antibiotic treatment. This pathogen may cause massive outbreaks associated to the consumption of contaminated food products, which highlight its import...
Epidemiology of Clostridioides difficile (syn. Clostridium difficile) infection (CDI) in Bangladesh is poorly understood. This study assessed the epidemiology of CDI in hospitalized patients and hospital environmental contamination of toxigenic C. difficile at two large urban Bangladesh hospitals. T...
In 2016-2017, there was an increase in the number of paediatric invasive pneumococcal disease (IPD) cases caused by serotype 12F in Chiba Prefecture, Japan. Serotype 12F is one of the major causative serotypes of IPD following the introduction of pneumococcal conjugate vaccine 13 (PCV13), and outbr...
Many pathogens that caused devastating disease throughout human history, such as , , and , remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously unde...
The transmission of methicillin-resistant Staphylococcus aureus (MRSA) between humans and animals has been identified in a number of countries. In this study, MRSA in urban rodents and shrews in a community was investigated. Further, comparisons of MRSA isolates from rodents, shrews, and humans were...
Porcine circovirus type 2 (PCV2) is an important pathogen that causes significant economic losses in the swine industry worldwide. Five major PCV2 genotypes have been identified, including PCV2a, PCV2b, PCV2c, PCV2d, and PCV2e. To investigate the prevalence and phylodynamics of the different PCV2 ge...
is an important nosocomial pathogen. The objective of this study was to determine the proportion of infections due to patient-to-patient transmission by analyzing the molecular epidemiology of patients who acquired , using perianal surveillance cultures in a large 2-year intensive care unit (ICU) p...
This study reports the results of diagnostic and molecular typing methods for 18 isolates obtained from outbreaks of infectious coryza in commercial layer flocks in the Netherlands. Isolation, biochemical identification, species-specific PCR tests and classical serotyping were performed. In additio...
Klebsiella variicola is considered an emerging pathogen in humans and has been described in different environments. K. variicola belongs to Klebsiella pneumoniae complex, which has expanded the taxonomic classification and hindered epidemiological and evolutionary studies. The present work describes...
Horizontal gene transfer (HGT) has changed the way we regard evolution. Instead of waiting for the next generation to establish new traits, especially bacteria are able to take a shortcut via HGT that enables them to pass on genes from one individual to another, even across species boundaries. The t...
Syphilis is a sexually transmitted infection caused by Treponema pallidum subspecies pallidum and may lead to severe complications. Recent years have seen striking increases in syphilis in many countries. Previous analyses have suggested one lineage of syphilis, SS14, may have expanded recently, ind...
Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant public health threat and was listed on the World Health Organization's 2017 list of high-priority pathogens for which new treatments are urgently needed. Treatment options for invasive VREfm infections are very limited, and...
The emergence of carbapenem-resistant (CRKP) has posed a great threat to public health. Among 133 nonduplicated CRKP isolates collected between September 2016 and November 2017 in a tertiary hospital in China, 89 (89/133, 66.9%) and 31 (31/133, 23.3%) were positive for and . Multilocus sequence ty...
A hospital outbreak of e carbapenemase (KPC)-producing (KPN) linked with an index case of community-acquired infection occurred in an urban tertiary care hospital in Seoul, South Korea. Therefore, we performed an outbreak investigation and whole genome sequencing (WGS) analysis to trace the outbrea...
Clostridioides difficile has become the leading nosocomial Gram-positive pathogen in the developed countries. In Lithuania, the national surveillance program for C. difficile started in 2017. Enzyme immunoassay, the real-time PCR system, and culture are used for laboratory confirmation of C. diffici...
Enteroviruses (EVs) are the major cause of hand, foot, and mouth disease (HFMD) and herpangina in children. In this study, we conducted a molecular investigation of EVs in throat swab samples from children in Hangzhou, China with a diagnosis of HFMD or herpangina. EVs were detected using one-step re...
Hospital-care workers (HCWs) are at risk for MRSA carriage, subsequent infection and potential transmission of nosocomial infection. Epidemiological typing of MRSA among HCWs would provide data that can be used for control measures. This is a cross sectional study that involved 92 participants from...
TEM-52 extended-spectrum β-lactamases (ESBLs) have been detected in members of the Enterobacteriaceae isolated from human and non-human reservoirs, mainly in European countries. Here we report the first draft genome of a multidrug-resistant TEM-52b-positive Escherichia coli isolated from a companion...
Vibrio parahaemolyticus is the leading bacterial cause of seafood-associated gastroenteritis worldwide. Moreover, infections and outbreaks caused by V. parahaemolyticus has kept increasing over the last two decades. In this study, we investigated the genetic diversity, virulence factors and farm-to-...
The phytobiome, defined as plants and all the entities that interact with them, is rich in viruses, but with the exception of plant viruses of crop plants, most of the phytobiome viruses remain very understudied. This review focuses on the neglected portions of the phytobiome, including viruses of o...
Between April 2016 and September 2017, four cases of group B meningococcal disease were reported among sixth-form college students in Bristol, UK. Culture and non-culture whole genome sequencing was utilised and demonstrated that the four genomes of the responsible ST-41 strains clustered closely on...
Chikungunya virus (CHIKV) is considered a public health problem due to its rapid spread and high morbidity. This study aimed to determine the genetic diversity and phylogenetic relationships of CHIKVs in Colombia. A descriptive and retrospective study was carried out using sera of patients infected...
Fleas are important vectors of zoonotic disease. However, little is known about the natural diversity and abundance of flea viruses, particularly in the absence of disease associations, nor the evolutionary relationships among those viruses found in different parasitic vector species. Herein, we pre...
The ongoing Ebola virus outbreak in the Ituri and North Kivu Provinces of the Democratic Republic of the Congo, which began in July, 2018, is the second largest ever recorded. Despite civil unrest, outbreak control measures and the administration of experimental therapies and a vaccine have been ini...
Sri Lanka is a country where the molecular epidemiology of Mycobacterium tuberculosis (MTB) is poorly explored. Therefore, this study was performed to identify circulating lineages/sub-lineages of MTB and their transmission patterns. DNA was extracted from 89 isolates of MTB collected during 2012 an...
Invasive group A streptococcal (iGAS) infection in the peripartum setting is a rare but devastating disease occasionally occurring as a health care-associated infection (HAI). Current guidelines suggest enhanced surveillance and streptococcal isolate storage after a single case of iGAS, as well as a...
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human...
Whole genome sequencing (WGS) of Streptococcus pyogenes linked to invasive disease has been used to identify and investigate outbreaks. The clinical application of WGS in real-time for outbreak control is seldom employed. A fatal case of bacteraemia at a national orthopaedic hospital prompted an out...
In September, 2017, human monkeypox re-emerged in Nigeria, 39 years after the last reported case. We aimed to describe the clinical and epidemiological features of the 2017-18 human monkeypox outbreak in Nigeria. We reviewed the epidemiological and clinical characteristics of cases of human monkeypo...
The small hive beetle (SHB) is an opportunistic parasite that feeds on bee larvae, honey, and pollen. While SHBs can also feed on fruit and other plant products, like its plant-feeding relatives, SHBs prefer to feed on hive resources and only reproduce inside bee colonies. As parasites, SHBs are ine...
The discovery in 2009 of a new species of yeast, Candida auris, heralded the arrival of a novel emerging human infectious disease. This review highlights the unique characteristics of C. auris that have lled to it being of public health concern worldwide, namely public health concern, namely its glo...
is a Gram-negative, nonfermenting, environmental bacillus that is an important cause of nosocomial infections, primarily associated with the respiratory tract in the immunocompromised population. Aiming to understand the population structure, microbiological characteristics and impact of allelic var...
Vancomycin-resistant enterococci are an important cause of healthcare-associated infections and are inherently resistant to many commonly used antibiotics. Linezolid is the only drug currently approved by the US Food and Drug Administration to treat vancomycin-resistant enterococci; however, resista...
No abstract available
This study characterizes a large Mycoplasma pneumoniae outbreak observed in Kymenlaakso in Southeastern Finland during August 2017-January 2018. The first part of the investigation included 327 patients, who sought healthcare consultation at local GPs or hospitals due to clinical symptoms, and were...
IntroductionSequence-based typing of hepatitis A virus (HAV) is important for outbreak detection, investigation and surveillance. In 2013, sequencing was central to resolving a large European Union (EU)-wide outbreak related to frozen berries. However, as the sequenced HAV genome regions were only p...
The prevalence of infections caused by OXA-48-like carbapenemase-producing organisms in Ireland has increased dramatically since 2011 and is an urgent public health issue. Genome-based high-resolution genotyping was used to analyse clinical isolates submitted to the Irish Carbapenemase-Producing Ent...
In 2018, a cluster of pediatric human parechovirus (HPeV) infections in 2 neighboring German hospitals was detected. Viral protein 1 sequence analysis demonstrated co-circulation of different HPeV-3 sublineages and of HPeV-1 and -5 strains, thereby excluding a nosocomial outbreak. Our findings under...
Salmonella enterica serotype I 4,[5],12:i:- has been increasingly isolated from swine. However, its pathogenic potential is not well characterized. Analysis of swine cases confirmed a strong positive association between isolation of I 4,[5],12:i:- and lesions of enteric salmonellosis and suggested a...
We describe a sexual network consisting of 1 nonbinary-gendered participant and 2 male and 4 female participants in Australia, 2018. Six of 7 participants had oropharyngeal gonorrhea in the absence of urogenital gonorrhea. This observation supports a new paradigm of gonorrhea transmission in which o...
We examined whole-genome-sequenced Campylobacter jejuni and C. coli from 2012-2015 isolated from birds and human stool samples in North East Scotland for the presence of antimicrobial resistance genes. We found that sequence type (ST) 5136 (clonal complex 464) was the most prevalent multidrug-resist...
During March 13-June 23, 2018, anthrax-like cutaneous lesions attributed to the Bacillus cereus group of organisms developed in 12 newborns in India. We traced the source of infection to the healthcare kits used for newborn care. We used multilocus sequence typing to characterize the 19 selected str...
Studies on Aspergillus fumigatus azole resistance in cystic fibrosis patients are scarce despite the fact that it is the most frequently isolated fungus from respiratory samples from these individuals. To evaluate resistance prevalence, investigate mechanisms of resistance and explore the relationsh...
Ceftriaxone resistance in Neisseria gonorrhoeae is a major public health concern globally because a high-dose (1 g) injection of ceftriaxone is the only remaining option for empirical monotherapy of gonorrhoea. The ceftriaxone-resistant gonococcal strain FC428, cultured in Osaka in 2015, is suspecte...
To undertake a Spanish nationwide survey on Pseudomonas aeruginosa molecular epidemiology and antimicrobial resistance. Up to 30 consecutive healthcare-associated P. aeruginosa isolates collected in 2017 from each of 51 hospitals were studied. MICs of 13 antipseudomonal agents were determined by bro...
From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium (VSEfm) was investigated, transmission events between hospitals were identifie...
Elizabethkingia spp are Gram-negative bacteria associated with neonatal meningitis. In 2015-2016, an outbreak of Elizabethkingia anophelis infection that involved 63 patients and 18 deaths occurred in Wisconsin. Despite a multistate investigation, as of September 2016 the source remained undetermine...
Novel highly pathogenic porcine reproductive and respiratory syndrome viruses (PRRSVs) have attracted increasing attention owing to their continual high emergence and recent re-emergence. Recently, lineage 3 PRRSVs, belonging to the type 2 viruses, with novel characteristics and increased virulence...
The global emergence of epidemic Clostridium difficile PCR ribotype (RT) 027 prompted enhanced surveillance of emerging strains. Recently, there have been reports of severe C. difficile infection in Australia caused by an unusual strain of C. difficile not seen previously. Identified as PCR RT251, t...
Chlorination can contribute to the enrichment of specific antibiotic resistance genes (ARGs) in drinking water, but the underlying molecular ecological mechanisms remain unknown, which may hinder the assessment and control of the resulting health risks. In this study, metagenomic assembly and Resfam...
In 2015, Singapore had the first and only reported foodborne outbreak of invasive disease caused by the group B Streptococcus (GBS; Streptococcus agalactiae). Disease, predominantly septic arthritis and meningitis, was associated with sequence type (ST)283, acquired from eating raw farmed freshwater...
The routine use of whole-genome sequencing (WGS) as part of enteric disease surveillance is substantially enhancing our ability to detect and investigate outbreaks and to monitor disease trends. At the same time, it is revealing as never before the vast complexity of microbial and human interactions...
Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features...
Tick-borne rickettsial diseases are caused by pathogens acquired from hard ticks. In particular, Rickettsia slovaca, a zoonotic infectious bacterium causing tick-borne lymphadenopathy (TIBOLA), is transmitted by the vectors Dermacentor spp. that can be found all over Europe. Although recent studies...
Leptospirosis is one of the most important neglected tropical bacterial diseases worldwide. However, there is limited information on the genetic diversity and host selectivity of pathogenic Leptospira in wild small mammal populations. Jiangxi Province, located in southern China, is a region highly e...
No abstract available
Salmonella enterica serovar Enteritidis is a cause of both poultry- and egg-associated enterocolitis globally and bloodstream-invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa (sSA). Distinct, multi-drug resistant genotypes associated with iNTS disease in sSA have recently been d...
Clostridioides difficile is the major etiologic agent of nosocomial bacterial diarrhoea and pseudomembranous colitis. The pathogenesis of C. difficile infection (CDI)involves two cytotoxic enzymes (TcdA, TcdB) that cause colonic epithelial damage, fluid accumulation and enteritis. CDI has been demon...
Animals such as domestic dogs and zoo animals reside in close proximity to humans and could contribute to the dissemination of Clostridioides difficile spores which are common in the community environment. The purpose of this study was to assess C. difficile colonization in domestic dogs attending a...
To assess the epidemiological features of 76 Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) isolates recovered from three hospitals in Buenos Aires, Argentina, during 2015-2017. Antimicrobial susceptibilities were determined according to CLSI Clinical and Laborato...
Whole-genome sequencing (WGS) has become a significant tool in investigating foodborne disease outbreaks and some countries have incorporated WGS into national food control systems. However, WGS poses technical challenges that deter developing countries from incorporating it into their food safety m...
Lineage 2 West Nile virus (WNV) strains have been implicated in severe encephalitis outbreaks in humans and equines residing in Europe. WNV molecular characterization is important for the development of diagnostic assays, as well as for obtaining molecular information, which is necessary for epidemi...
(, ) is an intraovarially transmitted symbiont of insects able to exert striking phenotypes, including reproductive manipulations and pathogen blocking. These phenotypes make a promising tool to combat mosquito-borne diseases. Although is present in the majority of terrestrial arthropods, includin...
Next-generation sequencing, coupled with the development of user-friendly software, has achieved a level of accessibility that is revolutionizing the way we approach epidemiological investigations. We can sequence pathogen genomes and conduct phylogenetic analyses to assess transmission, identify fr...
To study the molecular-epidemiological characteristics of Brucella species isolated from different countries, using the multiple locus tandem-repeat (MLVA) analysis. Eleven variable-number tandem-repeat (VNTR) loci were selected. VNTR strains of Brucella isolated from 48 different countries in 1953...
Noroviruses evolve by antigenic drift and recombination, which occurs most frequently at the junction between the non-structural and structural protein coding genomic regions. In 2015, a novel GII.P16-GII.4 Sydney recombinant strain emerged, replacing the predominance of GII.Pe-GII.4 Sydney among US...
In this study, we aimed to identify DENV-2 subtypes in Aedes aegypti pools collected between 2011 and 2017 in a rural area of Northern Cordoba, Colombia ("La Balsa"). RT-PCR was performed to analyze the capsid/pre-membrane region (C-PrM). Sequencing and phylogenetic bayesian inference using referenc...
Foodborne disease surveillance in the United States is at a critical point. Clinical and diagnostic laboratories are using culture-independent diagnostic tests (CIDTs) to identify the pathogen causing foodborne illness from patient specimens. CIDTs are molecular tests that allow doctors to rapidly i...
The aim of this study was to analyze the alarming spread of NDM-1- and OXA-48-co-producing Klebsiella pneumoniae clinical isolates, collected between October 2016 and January 2018 in a neonatal intensive care unit of the University Hospital, Catania, Italy, through whole genome sequencing. All confi...
Acinetobacter baumannii (A. baumannii) is the world's most significant opportunistic pathogen that causes nosocomial infections; there is widespread health concern due to its ability to acquire multidrug resistance. This study reports a new variety of A. baumannii L13 isolated from Tarim River in Xi...
Between 1991 and 2014 the per capita notification rate of salmonellosis in Australia increased from 31.9 to 69.7 cases per 100,000 people. Salmonella Typhimurium accounted for nearly half the human cases until the end of 2014. In this study, we used cluster analysis tools to compare S. Typhimurium i...
Clostridioides difficile infection (CDI) is a major concern in hospital settings. Antimicrobial resistance is a key contributing factor in CDI outbreaks. This study analysed the antimicrobial susceptibility and PCR ribotypes (RTs) of 745 C. difficile isolates collected at a single institution over 5...
Chikungunya virus (CHIKV) is an emerging pathogen around the world and causes significant morbidity in patients. A single amino acid mutation in the envelope protein of CHIKV has led to a shift in vector preference towards . While mosquitoes are known to mount an antiviral immune response post-infec...
PCR ribotyping and antimicrobial susceptibility testing were used to characterize 940 Clostridioides (Clostridium) difficile isolates collected from 26 U S. hospitals over three time periods from 2011 to 2017. The proportion of ribotype (RT) 027 isolated during the three surveys decreased significan...
The aim of the study was to analyze the epidemiology of and investigate the genetic characteristics of carbapenem-resistant (CRAB) isolates isolated from blood cultures in a regional hospital in Hong Kong. Twenty blood culture isolates were collected from a regional hospital in Hong Kong from 201...
From April to October 2017, 27 cases of Hepatitis A (HA), 22 male and 5 female, were reported in Cosenza (South Italy). The median age of cases was 32 years (range 3-49 years). Out of 21 male adults, 14 were identified as men who have sex with men (MSM). Phylogenetic analysis was conducted in 15 cas...
In April 2019, a cross-border outbreak of O3 was identified in Sweden and Denmark and confirmed using whole genome sequencing. Close cross-border collaboration with representatives from human and food authorities helped direct resources and investigations. Combined epidemiological and trace-back in...
In 2015, a suspected cluster of two invasive meningococcal disease (IMD) cases of serogroup W (MenW) occurred in elderly care home residents in England over 7 months; case investigations followed United Kingdom guidance. An incident control team reviewed epidemiological information. Phenotyping of...
We report national surveillance of Legionnaires' disease in China. Urine samples from 11 (3.85%) of 286 patients with severe pneumonia of unknown cause were positive for the Legionella pneumophila serogroup 1 antigen. We isolated Legionella strains from 7 patients. Improved diagnostic testing is nee...
No abstract available
In August 2015, 17 neonates with Enterobacter cloacae (E. cloacae) colonization were identified in a neonatal intensive care unit (NICU) in Germany. Two developed severe brain abscesses. Despite temporary NICU closure in September, another infant with E. cloacae colonization was detected in October...
The Gram-negative bacterium Klebsiella pneumoniae is a frequent pathogen causing outbreaks in neonatal intensive care units. Some Enterobacteriaceae can acquire the ability to sequester iron from infected tissue by secretion of iron-chelating compounds such as yersiniabactin. Here we describe an out...
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathog...
We performed Leptospira culture analysis of 76 clinical samples collected from animals and of six soil samples for the investigation of a leptospirosis outbreak in southern Thailand in 2017. Leptospires were recovered from a kidney sample (a fatal canine leptospirosis case) and from all the soil sam...
Pseudomonas aeruginosa is the second most prevalent opportunistic pathogen causing nosocomial infections in Mexico. This study evaluated antibiotic resistance, production of virulence factors and clonal diversity of P. aeruginosa strains isolated from patients undergoing nosocomial infections in pub...
To determine the prevalence of New Delhi metallo-β-lactamase (NDM)-producing Gram-negative pathogens isolated from children's samples. Carbapenem-resistant clinical isolates (n = 117) were confirmed by VITEK 2 compact system, matrix-assisted laser desorption ionization-time of flight and multilocus...
Understanding the dynamics of foot-and-mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programmes in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wil...
is a common inhabitant of coastal estuaries, and can accumulate to high levels in the shellfish that populate those waters. Human gastrointestinal infection occasionally follows ingestion of raw oysters, and it can lead to extended closures of implicated oyster beds with serious economic consequence...
Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide. Mainly isolated from stool samples, C. jejuni can also become invasive. C. jejuni belongs to the commensal microbiota of a number of hosts, and infection by this bacterium can sometimes be traced back to exposure t...
Rabies is a fatal disease caused by infection with rabies virus (RABV), and human rabies is still a critical public-health concern in China. Although there have been some phylogenetic studies about RABV transmission patterns, with the accumulation of more rabies sequences in recent years, there is a...
Quantitative knowledge about which natural and anthropogenic factors influence the global spread of plague remains sparse. We estimated the worldwide spreading velocity of plague during the Third Pandemic, using more than 200 years of extensive human plague case records and genomic data, and analyze...
In this pilot study, we used shotgun metagenome sequencing (SMS) strategy on bronchoalveolar lavage (BAL) samples from hospitalized patients with suspected ventilate-associated pneumonia (VAP) in order to explore its potential for improving detection of ventilator-associated-pneumonia (VAP) etiology...
Enterococcus faecalis as part of the normal floras of human gastrointestinal and genitourinary tracts are an important cause of nosocomial infections. The present study aimed to investigate the prevalence of genes encoding antimicrobial resistance and genetic relatedness of clinical isolates of E. f...
In Brazil, A. baumannii has been described as nosocomial pathogens causing hospital-acquired infections. Current WGS technologies have been useful in identifying of genetic features between Acinetobacter isolates. Here, we report the draft genome sequence of OXA-23 producing A. baumannii CCBH15815 c...
Whole-genome sequencing is increasingly adopted in clinical settings to identify pathogen transmissions, though largely as a retrospective tool. Prospective monitoring, in which samples are continuously added and compared to previous samples, can generate more actionable information. To enable prosp...
Avian avulavirus (commonly known as avian paramyxovirus-1 or APMV-1) can cause disease of varying severity in both domestic and wild birds. Understanding how viruses move among hosts and geography would be useful for informing prevention and control efforts. A Bayesian statistical framework was empl...
is a nosocomial pathogen associated with drug resistance and outbreaks in intensive care units. In a 5-month period in 2017, we experienced an increased incidence of cultures for carbapenem-resistant (CR-KA) from an adult cardiothoracic intensive care unit (CICU) involving 15 patients. Phylogenomic...
No abstract available
Salmonella spp are a major cause of food-borne outbreaks in Europe. We investigated a large multi-country outbreak of Salmonella enterica serotype Enteritidis in the EU and European Economic Area (EEA). A confirmed case was defined as a laboratory-confirmed infection with the outbreak strains of S E...
Phlebotomine sand flies are generalist vectors with significant implications for public health. They are able to transmit phleboviruses that cause sand fly fever, headaches, or meningitis in humans. Albania is a country in Southeast Europe with a typical Mediterranean climate which provides convenie...
The purpose of this study was to analyze the antibiotic resistance and genetic diversity of 27 enterococci (, , , and ) isolated from wild bird species. Resistance to lincomycin was most common, followed by erythromycin, ciprofloxacin, tetracyclines, high level of aminoglycoside, and -lactam antibio...
Shiga-toxin-producing Escherichia coli (STEC) infection is an important global cause of foodborne disease. To date however, genomics-based studies of STEC have been predominately focused upon STEC collected in the Northern Hemisphere. Here, we demonstrate the population structure of 485 STEC isolate...
Clostridioides difficile is a ubiquitous, diarrhoeagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of C. difficile cases have been attribute...
Klebsiella pneumoniae is an opportunistic pathogen associated with nosocomial infections worldwide. Isolates with a K. pneumoniae carbapenemase (KPC)-producing phenotype show reduced susceptibility to first-choice antibiotics. Between 2012-2013, the largest public tertiary-care hospital in Quito (Ec...
is a clinically relevant pathogen and a frequent cause of hospital-acquired (HA) and community-acquired (CA) urinary tract infections (UTI). The increased resistance of this pathogen is leading to limited therapeutic options. To investigate the epidemiology, virulence, and antibiotic resistance prof...
Whole-genome sequencing (WGS) has yielded new insights into the transmission patterns of healthcare facility-onset Clostridioides difficile infection (HO-CDI). WGS results prompted a focused diagnostic stewardship program, which was associated with a significant and sustained decrease in HO-CDI at l...
In Cambodia, little epidemiological data of hepatitis C virus (HCV) is available. All previous studies were limited to only small or specific populations. In the present study, we performed a characterization of HCV genetic diversity based on demography, clinical data, and phylogenetic analysis of H...
Multidrug-resistant Mycobacterium tuberculosis (MDR-TB) is a severe health threat to human beings; however, the epidemic and molecular characteristics exist along with the change in the geographic environment and genealogy. Jiangxi province is located in southeast China, which is a high-MDR-TB burde...
To better understand the molecular epidemiology of MRSA and to assess the utility of 19-target binary typing we undertook large-scale epidemiological surveillance of MRSA from invasive and non-invasive clinical specimens, and screening swabs. Binary typing was performed on clinical MRSA isolates col...
In 2017, we identified a Clostridium difficile strain HKCD4 that caused community-acquired fulminant colitis in a previously healthy child. Phylogenetically, it belonged to clade 2, sequence type 67 and was resistant to fluoroquinolone and tetracycline. The strain was pathogenicity locus and binary...
In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and r...
Foodborne diseases are still a major health issue in Lebanon, although some steps have been taken forward in food safety. To this purpose, PulseNet Lebanon, a foodborne diseases tracking network, was established in 2009, through the collaboration between the Ministry of Public Health (MoPH) and the...
A prevalence study in two nursing homes (one each in the Netherlands and Ireland) found four (11%) Dutch and six (9%) Irish residents colonized with 11 extended-spectrum beta-lactamase-producing Escherichia coli, 10 of which contained CTX-M-15. Four Dutch isolates, from three residents of the same w...
Hypervirulent typically presents as a community-acquired infection causing a liver abscess. It is often associated with A and A genes and confers a mucoid phenotype. Our aim was to evaluate the clinical presentation and antibiotic resistance of hypervirulent (hvKP) of health care-associated origin...
Zika virus (ZIKV) has been isolated from many mosquito species in nature, but it is believed that the main vectors in urban environments are species of the genus Aedes. Here, we detected and isolated ZIKV in samples from Aedes aegypti, Aedes taeniorhynchus and Culex quinquefasciatus, collected durin...
Prosthetic joint infections (PJIs) are rare but feared complications following joint replacement surgery. Cutibacterium acnes is a skin commensal that is best known for its role in acne vulgaris but can also cause invasive infections such as PJIs. Some phylotypes might be associated with specific di...
The 2nd St. Petersburg Symposium on Tuberculosis and Mycobacteria: Molecular Approach, was held in St. Petersburg, Russia on 5-6 December 2018. A special issue of Infection, Genetics and Evolution will publish articles based on the selected presentations. In this paper, I will discuss some of the ho...
Over 60 years ago clinical patterns resembling tick-borne rickettsioses have been described for the first time in Kazakhstan. Since 1995 the incidence of clinical cases of tick-borne rickettsioses in humans seems to be rising but studies on epidemiological data regarding the occurring etiological ag...
The large diversity of new tick-borne phleboviruses, and the negative impacts of the virulent viruses on human/animal health have led to a growing interest in their analysis. In this report, new insights are brought out into the diversity of putative phleboviruses circulating in Portugal (both the c...
Moraxella catarrhalis is a common agent causing upper and lower respiratory tract infections, particularly of ventilated patients. The bacteria are transmitted between humans by direct and indirect contacts. However, reports of nosocomial outbreaks by this pathogen are scarce. To analyse M. catarrha...
While the international spread of multidrug-resistant (MDR) strains is an acknowledged public health threat, a broad and more comprehensive examination of the global spread of MDR-tuberculosis (TB) using whole-genome sequencing has not yet been performed. In a global dataset of 5310 . whole-genome...
Using metagenomic analysis, we identified a novel picornavirus in young preweaned lambs with neurologic signs associated with severe nonsuppurative encephalitis and sensory ganglionitis in 2016 and 2017 in the United Kingdom. In situ hybridization demonstrated intralesional neuronotropism of this vi...
We investigated a cluster of Mycobacterium fortuitum and M. goodii prosthetic joint surgical site infections occurring during 2010-2014. Cases were defined as culture-positive nontuberculous mycobacteria surgical site infections that had occurred within 1 year of joint replacement surgery performed...
To characterize the antimicrobial susceptibility, molecular epidemiology and carbapenem resistance mechanisms in Pseudomonas aeruginosa isolates recovered from respiratory tract samples from patients with ventilator-associated pneumonia enrolled in the MagicBullet clinical trial. Isolates were colle...
Although case series of talaromycosis have been reported in China, their detailed clinical and microbiological characteristics have never been systematically profiled. In this study, we report the clinical characteristics, molecular epidemiology, rapid identification and antifungal susceptibilities...
Bacillus cereus is associated with foodborne illnesses characterized by vomiting and diarrhea. Although some B. cereus strains that cause severe extraintestinal infections and nosocomial infections are recognized as serious public health threats in healthcare settings, the genetic backgrounds of B....
Acute post-streptococcal glomerulonephritis (APSGN) is a postinfectious immune-mediated kidney disease associated with group A (GAS). The prevalence of APSGN varies within and between countries and is influenced by socioeconomic, host, and bacterial factors. The disease is more prevalent in develop...
No abstract available
Pseudomonas aeruginosa is one of the most common nosocomial pathogens, known with a wide resistance to antimicrobials. Carbapenemases producing Pseudomonas aeruginosa is a growing global public health concern as this pathogen is easily transmissible among patients. Metallo-Beta-lactamases is the mos...
Several Romanian hospitals have noted increasing isolation of Providencia stuartii strains in recent years, with an alarming rate of carbapenem resistance. In order to provide molecular epidemiological data regarding their dissemination, 77 P. stuartii strains collected from five hospitals located i...
Clostridium difficile ribotype-027, ribotype-078, and ribotype-017 are virulent and epidemic lineages. Trehalose metabolism variants in these ribotypes, combined with increased human trehalose consumption, have been hypothesised to have contributed to their emergence and virulence. 5232 previously w...
Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some...
Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the...
The emergence of multidrug-resistant (MDR) has become a serious worldwide medical problem. This study was designed to clarify the genetic and epidemiological properties of MDR strains isolated from hospitals in Myanmar. Forty-five MDR isolates obtained from different patients in seven hospitals i...
The frequency of epidemics caused by Dengue viruses 1-4, Zika virus and Chikungunya viruses have been on an upward trend in recent years driven primarily by uncontrolled urbanization, mobility of human populations and geographical spread of their shared vectors, Aedes aegypti and Aedes albopictus. I...
Determining infectious cross-transmission events in healthcare settings involves manual surveillance of case clusters by infection control personnel, followed by strain typing of clinical/environmental isolates suspected in said clusters. Recent advances in genomic sequencing and cloud computing now...
Ralstonia picketti, Ralstonia mannitolilytica, and Ralstonia insidiosa have recently been regarded as emerging pathogens of infectious diseases, in particular as the pathogens responsible for nosocomial infection in immunocompromised patients. R. insidiosa differs from R. picketti and R. mannitolily...
Infectious bursal disease virus (IBDV) is a very important pathogen to poultry production and it is classified into three main groups: classical virulent (cvIBDV), very virulent (vvIBDV) and antigenic variants (avIBDV). This last group is composed by five different genetic lineages (recently classif...
Endogenous and exogenous infection of the biliary tract could occur during endoscopic retrograde cholangiopancreatography. Bile samples of patients with hepatobiliary diseases, and swab samples of elevator channel samples of duodenoscope and washing instruments were prepared simultaneously and cultu...
Swine brucellosis due to Brucella suis biovar 2 (bv2) is enzootic in wild boar and hare in continental Europe and may cause major economic losses to the pig industry, mainly in free-ranged pig farms. The high nucleotide identity found among the B. suis biovar 2 isolates has long hindered the full un...
Recently, protocols for amplicon based whole genome sequencing using Nanopore technology have been described for Ebola virus, Zika virus, yellow fever virus and West Nile virus. However, there is some debate regarding reliability of sequencing using this technology, which is important for applicatio...
Methicillin-resistant Staphylococcus aureus (MRSA) can be classified into hospital-acquired MRSA (HA-MRSA) and community-associated MRSA (CA-MRSA), based on the associated epidemiological risk factors and their SCCmec types. We therefore studied the diversity and distribution of SCCmec elements amon...
Chicken meat represents an important source of Campylobacter infections of humans world-wide. A better understanding of Campylobacter epidemiology in commercial chicken flocks will facilitate the development of more effective intervention strategies. We developed a gene-specific parallel sequencing...
Although HIV-1 subtype A has predominated in Russia since the end of the 20th century, other viral variants also circulate in this country. The dramatic outbreak of HIV-1 subtype G in 1988-1990 represents the origin of this variant spreading in Russia. However, full genome sequencing of the nosocomi...
We examine non-typhoidal Salmonella (S. Typhimurium or STM) epidemics as complex systems, driven by evolution and interactions of diverse microbial strains, and focus on emergence of successful strains. Our findings challenge the established view that seasonal epidemics are associated with random se...
No abstract available
No abstract available
The 2018 Ebola virus disease (EVD) outbreak in Équateur Province, Democratic Republic of the Congo, began on May 8, and was declared over on July 24; it resulted in 54 documented cases and 33 deaths. We did a retrospective genomic characterisation of the outbreak and assessed potential therapeutic a...
The real-time generation of information about pathogen genomes has become a vital goal for transmission analysis and characterisation in rapid outbreak responses. In response to the recently established genomic capacity in the Democratic Republic of the Congo, we explored the real-time generation of...
Non-typhoidal Salmonella (NTS) bacteremia is a significant cause of morbidity and mortality worldwide. It is considered to be an emerging and neglected tropical disease in Africa. We studied this in two tertiary hospitals-Al Farwaniya and Al Amiri-in Kuwait, a subtropical country, from April 2013-Ma...
Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. To summarize the eviden...
The Washington State Department of Health Public Health Laboratories (WAPHL) has tested 11,501 samples between 2007 and 2017 for a foodborne disease using a combination of identification, serotyping, and subtyping tools. During this period there were 8037 total clinical and environmental samples tes...
While conducting rotavirus gastroenteritis surveillance in Vietnam, two G3P[8] rotavirus A specimens possessing an identical short RNA electropherotype were detected. They were RVA/Human-wt/VNM/0232/2016/G3P[8] and RVA/Human-wt/VNM/0248/2016/G3P[8], and recovered from 9 and 23 months old boys, respe...
Mycobacterium bovis is a notorious infectious agent leading to serious economic losses for cattle farms worldwide. Analysis of the widely spreading genotypes is vital for tracing infections, understanding transmission dynamics, and controlling the cluster growth. This study aimed to evaluate the dis...
Livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) is an increasingly important public health concern worldwide; however, data on LA-MRSA from Asian countries is scarce. As such, a comprehensive molecular epidemiological survey of S. aureus along a pork production chain and in...
In the Netherlands, three commercial poultry farms and two hobby holdings were infected with highly pathogenic avian influenza (HPAI) H5N6 virus in the winter of 2017-2018. This H5N6 virus is a reassortant of HPAI H5N8 clade 2.3.4.4 group B viruses detected in Eurasia in 2016. H5N6 viruses were also...
Foot-and-mouth disease (FMD) is a major livestock disease with direct clinical impacts as well as indirect trade implications. Control through vaccination and stamping-out has successfully reduced or eradicated the disease from Europe and large parts of South America. However, sub-Saharan Africa rem...
Event-based social media monitoring and pathogen whole genome sequencing (WGS) will enhance communicable disease surveillance research and systems. If linked electronically and scanned systematically, the information provided by these technologies could be mined to uncover new epidemiological patter...
Extended multi-locus sequence typing (eMLST) methods have become popular in the field of genomic epidemiology. Before eMLST methods can be applied in epidemiological investigations, the selection of a suitable scheme is critical. The core genome scheme (cgMLST) has become the most popular eMLST appr...
Numerous nosocomial infections including urinary tract infection (UTI) have been reported to be linked to Pseudomonas aeruginosa (P. aeruginosa). This bacterium is one of the most common pathogen colonized in the urinary tract. The main purpose of this study was to evaluated the presence of antibiot...
Beginning in late 2016 Brazil faced the worst outbreak of Yellow Fever in recent decades, mainly located in southeastern rural regions of the country. In the present study we characterize the Yellow Fever Virus (YFV) associated with this outbreak in São Paulo State, Brazil. Blood or tissues collecte...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) increasingly cause high-mortality outbreaks in hospital settings globally. Following a patient fatality at a hospital in Beijing due to a blaKPC-2-positive CRKP infection, close monitoring was put in place over the course of 14 months to characterize...
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clones other than Clonal Complex (CC)398, as CC1, have been isolated in pigs in some countries, and appeared to be prevalent in Italy. The aim of this study was to evaluate the capability of Sequence Type (ST)1, CC1, LA-MRSA...
Hemorrhagic pneumonia in mink is a fatal disease caused by Very little is known about in relation to genotype and the mechanisms underlying antimicrobial resistance in mink. A total of 110 samples were collected from mink from Chinese mink farms between 2007 and 2015. Samples underwent molecular...
The objective of this study was to investigate a sudden increase in methicillin-resistant Staphylococcus aureus (MRSA) cases primarily in one maternity ward at the Center for Children's and Women's Health at Linköping University Hospital, Sweden. Approximately 300 individuals including patients, the...
In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collec...
In 2016 and 2017, we characterized outbreaks caused by Streptococcus agalactiae serotype III sequence type (ST) 283 in Nile tilapia farms in Brazil. Whole-genome multilocus sequence typing clustered the fish isolates together with the zoonotic ST283 and other STs related to cases in humans, frogs, d...
We collected sputum samples and cough plates from 15 cystic fibrosis patients in the Netherlands who were colonized with Aspergillus fumigatus; we recovered A. fumigatus of the same genotype in cough aerosols and sputum samples from 2 patients. The belief that transmission of A. fumigatus from cysti...
We describe a novel virus, designated Ntepes virus (NPV), isolated from sand flies in Kenya. NPV has the characteristic phlebovirus trisegmented genome architecture and is related to, but distinct from, Gabek Forest phlebovirus. Diverse cell cultures derived from wildlife, livestock, and humans were...
Rates of Clostridioides (Clostridium) difficile infection (CDI) are higher in North Wales than elsewhere in the UK. We used WGS to investigate if this is due to increased healthcare-associated transmission from other cases. Healthcare and community C. difficile isolates from patients across North Wa...
Clostridioides difficile is a major cause of nosocomial infectious diarrhea in hospitalized patients throughout the world. We aimed to characterize C. difficile isolates among hospitalized patients, hospital staffs, and hospital environment samples obtained in three tertiary care hospitals of Iran w...
Klebsiella pneumoniae sequence type (ST) 307 is an emerging global antimicrobial drug-resistant clone. We used whole-genome sequencing and PCR to characterize K. pneumoniae ST307 with oxacillinase (OXA) 181 carbapenemase across several private hospitals in South Africa during 2014-2016. The South Af...
Human Endogenous Retrovirus type K (HERV-K) is the only HERV known to be insertionally polymorphic; not all individuals have a retrovirus at a specific genomic location. It is possible that HERV-Ks contribute to human disease because people differ in both number and genomic location of these retrovi...
The phylogenetically closely related Shigella species and enteroinvasive Escherichia coli (EIEC) are responsible for millions of episodes of bacterial dysenteriae worldwide. Given its distinct epidemiology and public health relevance, only Shigellae are subject to mandatory reporting and follow-up b...
is an opportunistic bacterial pathogen. It is notorious for its increasing antimicrobial resistance and its potential to cause outbreaks of colonization and infections, predominantly in neonatal intensive care units (NICUs). There, its spread requires rapid infection control response. To understand...
In total, 95 Acinetobacter baumannii isolates recovered from patients from two hospitals in Cochabamba, Bolivia were studied. The presence of class D and B β-lactamases was investigated using polymerase chain reaction, and antimicrobial susceptibility testing was performed by agar dilution and broth...
This study investigated the molecular epidemiology of carbapenem-resistant and (ANAP). Clinical isolates of spp. collected by the biennial nationwide Taiwan Surveillance of Antimicrobial Resistance program from 2010 to 2014 were subjected to species identification, antimicrobial susceptibility te...
The prevalence of methicillin-susceptible Staphylococcus aureus (MSSA) bloodstream infections (BSIs) has increased in many countries, including Ireland. This study aimed to investigate the molecular epidemiology of MSSA causing BSIs in Irish hospitals between 2006 and 2017, when MSSA BSIs increased,...
Hantaviruses (order Bunyavirales, family Hantaviridae) are important zoonotic pathogens. Because of the great diversity of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. To understand the mechanisms behind the evolutionary history of han...
Hepatitis B virus (HBV) infection is a leading cause of severe chronic liver disease worldwide. The HBV epidemiology in Latin American countries is complex and the data is still scanty and fragmentary. The aim of this study was to investigate the distribution of HBV genotypes in Paraguay and to esti...
In Argentina, there has been an abrupt increase in KPC-2-producing Klebsiella pneumoniae (K. pneumoniae). Tucumán is a multi-border area, so the rapid dissemination of carbapenem-resistant K. pneumoniae is a clinically relevant problem for the region. This study aimed to investigate the epidemiologi...
Dengue virus is the most prevalent arbovirus in Mexico, and although the diversity of this virus has been studied, the vast majority of sequences have been derived from viruses isolated from the human host. In this work, we aimed to sequence and to analyze DENVs derived from wild mosquitoes captured...
G12 rotaviruses were first detected in Spain (Gipuzkoa province) in December 2004. After four years with no detections, G12 strains re-emerged in the 2010-2011 epidemic season, when the first European epidemic circulation of this genotype was observed in Gipuzkoa. G12 rotaviruses were also the domin...
Colistin resistance mediated by mcr-1-harbouring plasmids is an emerging threat in Enterobacteriaceae, like Salmonella. Based on its major contribution to the diarrhoea burden, the epidemic state and threat of mcr-1-harbouring Salmonella in community-acquired infections should be estimated. This ret...
Between October 2016 and June 2017, a C57BL/6J mouse colony that was undergoing a pre- and perinatal methyl donor supplementation diet intervention to study the impact of parental nutrition on offspring susceptibility to disease was found to suffer from an epizootic of unexpected deaths. Necropsy re...
An outbreak of disease characterized by skin ulcers, fin rot and mortality was observed a few days after the transfer of Atlantic salmon (Salmo salar) from a freshwater smolt production facility to a land-based seawater post-smolt site. Dead and moribund fish had severe skin and muscle ulcers, often...
Domestic ruminants are regarded as the major reservoir of Shiga toxin-producing Escherichia coli (STEC) closely related to human infection. A total of 363 ovine carcasses were swabbed in an Algiers city slaughterhouse for research on STEC. First of all, screening of the STECs was carried out by a mu...
No abstract available
The implementation of an integrated molecular surveillance (IMS) of tuberculosis (TB) is of high priority for TB control. IMS is defined as the systematic inclusion of molecular typing results in the national TB surveillance system. Although not standardized, an IMS of TB is already implemented in s...
Treatment with antibiotics leads to the selection of isolates with increased resistance. We investigated if evolution towards resistance was associated with virulence changes, in the context of P. aeruginosa ventilator-associated pneumonia (VAP). Four patients were selected because they had multiple...
Utilization of contact networks has provided opportunities for assessing the dynamic interplay between pathogen transmission and host behavior. Genomic techniques have, in their own right, provided new insight into complex questions in disease ecology, and the increasing accessibility of genomic app...
Highly pathogenic avian influenza A(H5N8) clade 2.3.4.4 spread in France during 2016-2017. We assessed the biosecurity and avian influenza virus infection status of 70 backyard flocks near H5N8-infected commercial farms. One flock was seropositive for clade 2.3.4.4. Backyard flocks linked to commerc...
Enterococcus faecium is ranked worldwide as one of the top ten pathogens identified in healthcare-associated infections (HAI) and is classified as one of the high priority pathogens for research and development of new antibiotics worldwide. Due to molecular biology techniques' higher costs, the appr...
The aim of this study was to investigate the spread of the bla gene among Klebsiella pneumoniae and to illustrate the mechanism of dissemination of K. pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) ST11 in China. A total of 354 K. pneumoniae isolates were collected from four hospitals in...
Outbreaks of infection occur more often than they are reported in most developing countries, largely due to poor diagnostic services. A species bacteremia outbreak in a newborn unit with high mortality was recently encountered at a location being surveilled for childhood bacteremia. These surveilla...
To describe cases of dengue virus (DENV) concurrent infections in patients from both local and international traveler visiting Bali, Indonesia. During a hospital-based study, 260 patients (from 161 local and 99 international traveler patients) were recruited. Among them, 190 were positive by DENV RT...
The increasing clinical importance of human infections (frequently severe) caused by PCR ribotype 078 (RT078) was first reported in 2008. The severity of symptoms (mortality of ≤30%) and the higher proportion of infections among community and younger patients raised concerns. Farm animals, especial...
Clostridioides (Clostridium) difficile is the leading cause of healthcare-associated infectious diarrhea in the developed world. Retrospective studies have shown a lower incidence of C. difficile infection (CDI) in Japan than in Europe or North America. Prospective studies are needed to determine if...
To investigate the antimicrobial resistance and molecular epidemiology of foodborne (.) in Pudong New District of Shanghai. Four kinds of raw food samples were collected in retail circulation sites in Pudong from 2012 to 2016. Cold enrichment method was used to isolate and further detection of b...
To understand the epidemiological characteristics of brucellosis in Hainan province. Automatic microbial identification system of Vitek 2 compact was used for the preliminary identification of 16 brucellosis cases in Hainan province from 2012 to 2017, and further confirmation was performed with tra...
Detection of tuberculosis laboratory cross-contamination using whole-genome sequencing. A total of 22 M. tuberculosis strains with high genotypic homology from one hospital were collected during the drug resistance surveillance. Genome sequencing and epidemiological investigation were conducted to d...
Mycobacterium abscessus is an emerging pathogen in cystic fibrosis (CF) lung disease. Hospital transmission of M. abscessus has been described. This paper details the investigation into possible cross-transmission of M. abscessus locally at our paediatric hospital CF centre, and the subsequent infec...
Transfer of hepatitis C virus (HCV) infection from a donor to a new recipient is associated with a bottleneck of genetic diversity in the transmitted viral variants. Existing data suggests that one, or very few, variants emerge from this bottleneck to establish the infection (transmitted founder [T/...
Hand, foot and mouth disease (HFMD) is responsible for a heavy economic and social burden in the Asia-Pacific region. Previous studies have shown that coxsackievirus A6 (CVA6) and coxsackievirus A10 (CVA10) have become the predominant agents of HFMD in mainland China in recent years, replacing enter...
Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon...
The first outbreak of vancomycin-resistant Enterococcus faecium (VREfm) in Western Australia was recorded in 2001. A state-wide infection control effort that oversaw patient screening and transfers successfully terminated the outbreak within six months; however, the outbreak re-emerged two years lat...
Rotavirus C (RVC) causes enteric disease in multiple species, including humans, swine, bovines, and canines. To date, the evolutionary relationships of RVC populations circulating in different host species are poorly understood, owing to the low availability of genetic sequence data. To address this...
We report the use of next generation sequencing (NGS) for investigating an outbreak of 13 cases of Serratia marcescens blood stream infections in a non-Neonatal Intensive Care Unit (non-NICU) setting in a tertiary care hospital in India over 5 months. Thirteen cases of sepsis due to S. marcescens we...
Human enteroviruses of species A (EV-A) are the leading cause of hand-foot-and-mouth disease (HFMD). EV-A71 is frequently implicated in HFMD outbreaks and can also cause severe neurological manifestations. We investigated the molecular epidemiological processes at work and the contribution of geneti...
Arboviruses continue to be a significant global health concern. The unbiased metagenomic analyses of mosquito-borne and mosquito-specific viruses are useful to understand viral diversity and for the surveillance of pathogens of medical and veterinary importance. Metagenomic analysis was conducted on...
Wolbachia is a genus of obligate intracellular bacteria found in nematodes and arthropods worldwide, including insect vectors that transmit dengue, West Nile, and Zika viruses. Wolbachia's unique ability to alter host reproductive behavior through its temperate bacteriophage WO has enabled the devel...
The incidence of nosocomial infections due to carbapenem-resistant Klebsiella pneumoniae is increasing worldwide. Whole-genome sequencing (WGS) can help elucidate the transmission route of nosocomial pathogens. We combined WGS and epidemiological data to analyze an outbreak of New Delhi metallo-β-la...
The primary method of molecular subtyping for the identification and investigation of outbreaks has been pulsed-field gel electrophoresis (PFGE). In some cases, this technique has not been able to show discrimination between the unrelated strains that can be achieved by whole genome sequencing (WGS)...
Clostridioides difficile is a colonizer of the human gut; asymptomatic colonization has been reported to be more common in infants and is highly variable across regions even with no symptoms of diarrhea or death. Antibiotic treatment strategies might increase the antibiotic resistance of C. difficil...
Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae. However, generating full scaffolds of N. gonorrhoeae genomes from short r...
Extended-spectrum beta-lactamase (ESBL) and plasmidic AmpC (pAmpC) producing Escherichia coli are found in the poultry production even without antibiotic use. The spread of these bacteria has been suggested to occur via imported parent birds, enabling transmission to production level broilers vertic...
Although Pseudomonas aeruginosa has a non-clonal epidemic population structure, recent studies have provided evidence of the existence of epidemic high-risk clones. The aim of this study was to assess the molecular epidemiology of P. aeruginosa isolates responsible for infections in French ICUs, reg...
In 2015, Bristol (South West England) experienced a large increase in cases of meticillin-resistant (MRSA) infection in people who inject drugs (PWID). We aimed to characterise and estimate the prevalence of MRSA colonisation among PWID in Bristol and test evidence of a clonal outbreak. PWID recrui...
Hepatitis E virus (HEV) genotype 4 (HEV-4) is an emerging cause of acute hepatitis in China. Less is known about the clinical characteristics and natural history of HEV-4 than HEV genotype 3 infections in immunocompromised patients. We report transmission of HEV-4 from a deceased organ donor to 5 tr...
Cronobacter sakazakii has been documented as a cause of life-threating infections, predominantly in neonates. We conducted a multicenter study to assess the occurrence of C. sakazakii across Europe and the extent of clonality for outbreak detection. National coordinators representing 24 countries in...
Attention to environmental sources of Mycobacterium avium complex (MAC) infection is a vital component of disease prevention and control. We investigated MAC colonization of household plumbing in suburban Philadelphia, Pennsylvania, USA. We used variable-number tandem-repeat genotyping and whole-gen...
To investigate transmission of drug-resistant strains of Mycobacterium tuberculosis in Tunisia, we performed whole-genome sequencing on 46 multidrug-resistant strains isolated during 2012-2016. Core-genome multilocus sequence typing grouped 30 strains (65.2%) into 3 clusters, indicating extensive re...
To investigate the risk of colonization with ESBL-producing Escherichia coli (ESBL-Ec) in humans in Vietnam associated with non-intensive chicken farming. Faecal samples from 204 randomly selected farmers and their chickens, and from 306 age- and sex-matched community-based individuals who did not r...
This study was set to determine the genetic linkage and the clonal relationship between vancomycin-resistant Enterococcusfaecium (VREfm) isolates in three hospitals of Ahwaz city. In this study, 1050 samples were collected from various rectal swabs, hands of health care workers, environmental surfac...
The genus Acinetobacter comprises many species that can cause infectious diseases. Despite their importance as nosocomial pathogens, the clinical distributions of individual species or clones are not well understood. In this study, we aimed to characterize 13 Acinetobacter strains isolated from bloo...
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common nosocomial pathogens, causing mild to severe infections. This study aimed to determine the genotypic and phenotypic characteristics of clinical MRSA isolates collected from a teaching hospital from 2014 - 2015. These isolat...
Discrete phylogeography using software such as BEAST considers the sampling location of each taxon as fixed; often to a single location without uncertainty. When studying viruses, this implies that there is no possibility that the location of the infected host for that taxa is somewhere else. Here,...
Vibrio cholerae is the causative agent of cholera, a globally important human disease for at least 200 years. In 2009-2011, the first recorded cholera outbreak in Papua New Guinea (PNG) occurred. We conducted genetic and phenotypic characterization of 21 isolates of V. cholerae, with whole-genome se...
Acinetobacter baumannii causes severe, fulminant, community-acquired pneumonia (CAP) in tropical and subtropical regions. We compared the population structure, virulence and antimicrobial resistance determinants of northern Australian community-onset A. baumannii strains with local and global strain...
Pakistan ranks 5th among the world's highest tuberculosis (TB) burden countries and 6th among the countries with the highest prevalence of drug-resistant TB. However, insufficient data are available on the genetic structure of M. tuberculosis strains circulating in this country. The objective of thi...
Intra-familial infection, mother-to-child infection, is considered to be one of the main routes of transmission for Helicobacter pylori, in developed countries such as Japan. A major role for intra-familial spread in the pathogenicity of H. pylori is now beyond controversy, although the major route...
In this study, we investigated the diversity of drug-resistant Mycobacterium tuberculosis isolates from families who own cattle in the Eastern Cape Province of South Africa using spoligotyping and mycobacterial interspersed repetitive-unit-variable number tandem repeat (MIRU-VNTR) typing. The Mycoba...
Flexible endoscopes are difficult to decontaminate, and endoscope-associated infections are increasing. This report describes an outbreak of multi-drug resistant Pseudomonas aeruginosa identified following an increase in incidence of clinical infections associated with flexible ureteroscopy at a ter...
The aim of this study was to characterise the molecular drivers of multidrug resistance in Proteus mirabilis isolated from Algerian community and hospital patients. A total of 166 P. mirabilis isolates were collected from two hospitals and eight private laboratories from four cities (Khemis Miliana,...
A Dyella-like bacterium was previously isolated from the planthopper Hyalesthes obsoletus (Hemiptera). Based on its 16S rRNA gene sequence, strain DHo was assigned to the family Rhodanobacteraceae with Dyella and Frateuria as its closest relatives. The closest 16S rRNA gene sequences were Frateuria...
Echovirus 30 (E30) is an important causative agent of aseptic meningitis worldwide. Despite this, the global and regional dispersion patterns, especially in South America, are still largely unknown. We performed an in-depth analysis of global E30 population dynamics, by using the VP1 sequences of 79...
Emergence of DS-1-like-G1P[8] rotavirus in Asia have been recently reported. We report for the first time the detection and the whole genome phylogenetic analysis of DS-1-like-G1P[8] strains in America. From 2013 to 2017, a total of 4226 fecal samples were screened for rotavirus by ELISA, PAGE, RT-P...
Schistosomiasis is frequently detected in persons entering Europe. In 2017, we detected a Schistosoma mansoni-Schistosoma haematobium hybrid parasite infection in a migrant boy from Côte d'Ivoire entering France. Because such parasites might be established in Europe, as illustrated by an outbreak on...
Meticillin-susceptible and -resistant Staphylococcus aureus (MSSA and MRSA) are responsible for outbreaks in intensive care units. MSSA infections have the same morbidity and mortality rate as MRSA infections but are studied less often. Whole-genome sequencing (WGS) is used increasingly for outbreak...
Epstein-Barr virus (EBV) is an etiological agent for gastric cancer with significant worldwide variations. Molecular characterizations of EBV have shown phylogeographical variations among healthy populations and in EBV-associated diseases, particularly the cosegregated BamHI-I fragment and XhoI rest...
Staphylococcal surface protein sasX is a colonization mediating virulence factor in ST239 methicillin-resistant Staphylococcus aureus (MRSA) strains, which potentially contribute to its successful establishment. We aimed to study the presence and dissemination of sasX in clinical MRSA isolates and a...
To analyze the molecular epidemiology and to compare between the major methicillin resistant Staphylococcus aureus biotypes for association with patient characteristics who had an implant for closed fracture and developed early post-operative wound infections (POWI) in a tertiary care hospital of In...
Elizabethkingia species are ubiquitous bacteria that uncommonly cause human infection. Elizabethkingia anophelis was first identified in 2011 from the mosquito Anopheles gambiae. The currently available bacterial typing systems vary greatly with respect to labour, cost, reliability, and ability to d...
To investigate the occurrence of vancomycin-resistant enterococci (VRE) isolated from patients in Peking Union Medical College Hospital, Beijing, China from 2011 to 2017, and to evaluate their resistance mechanisms and genetic relatedness. All isolates were identified using matrix-assisted laser des...
Disinfection regimes are considered the most solid strategy to reduce microbial risks in drinking water, but their roles in shaping the antibiotic resistome are poorly understood. This study revealed the alteration of antibiotic resistance genes (ARGs) profiles, their co-occurrence with mobile genet...
Poultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterized from western jackdaws ( = 91, 43%), mallard ducks ( = 82, 76%), and pheasan...
Buruli ulcer is a neglected tropical disease of skin and subcutaneous tissue caused by infection with the pathogen Many critical issues for disease control, such as understanding the mode of transmission and identifying source reservoirs of , are still largely unknown. Here, we used genomics to rec...
Advances in genomics and computing are transforming the capacity for the characterization of biological systems, and researchers are now poised for a precision-focused transformation in the way they prepare for, and respond to, infectious diseases. This includes the use of genome-based approaches to...
The bacterium Spiroplasma ixodetis is a maternally inherited endosymbiont primarily described from ticks but also found widespread across other arthropods. While it has been identified as a male-killing agent in some insect species, the consequences of infection with S. ixodetis in ticks are entirel...
Methicillin-resistant Staphylococcus aureus (MRSA) transmission dynamics in the emergency department (ED) are not well defined; environmental surfaces may serve as reservoirs for transmission. This study investigates the effect of patients with a history of MRSA colonization or infection on subseque...
Cholera has affected Haiti with damping waves of outbreaks since October 2010. However, mechanisms behind disease persistence during lull periods remain poorly understood. By mid 2014, cholera transmission seemed to only persist in the northern part of Haiti. Meanwhile, cholera appeared nearly extin...
Bacteria belonging to the Burkholderia cepacia complex (Bcc) are among the most important pathogens isolated from cystic fibrosis (CF) patients and in hospital acquired infections (HAI). Accurate identification of Bcc is questionable by conventional biochemical methods. Clonal typing of Burkholderia...
Exponentially increasing amounts of unprocessed bacterial and viral genomic sequence data are stored in the global archives. The ability to query these data for sequence search terms would facilitate both basic research and applications such as real-time genomic epidemiology and surveillance. Howeve...
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe set...
In recent years, approaches to tracking the spread of meticillin-resistant Staphylococcus aureus (MRSA) as part of outbreak management have used conventional DNA-based methods, including pulsed-field gel electrophoresis and spa typing. However, when a predominant clone is present, these methods may...
Clostridium difficile infection (CDI) is a leading cause of hospital-associated infections. Antibiotic stewardship, environmental disinfection, and reduction of transmission via health care workers are the major modes of CDI prevention within hospitals. The aim of this study was to evaluate the role...
Acinetobacter baumannii is an opportunistic pathogen causing various nosocomial infections. The spread of multidrug-resistant A. baumannii is a major public health problem. The aim of this study was to investigate the molecular epidemiology and the genetic support of multidrug-resistant A. baumannii...
No abstract available
Although fishing communities (FCs) in Uganda are disproportionately affected by HIV-1 relative to the general population (GP), the transmission dynamics are not completely understood. We earlier found most HIV-1 transmissions to occur within FCs of Lake Victoria. Here, we test the hypothesis that HI...
No abstract available
Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of vision threatening ocular infections. This study aimed to determine the prevalence and antimicrobial susceptibility pattern of MRSA and their genotypic characterization in ocular infections. The study period was from January...
Many mosquitoes harbour Wolbachia symbionts that could affect the biology of their host in different ways. Evolutionary relationships of mosquitoes' Wolbachia infection, geographical distribution and symbiont prevalence in many mosquito species are not yet clear. Here, we present the results of Wolb...
The molecular epidemiology of 38 non-duplicate toxigenic Clostridioides (previously Clostridium) difficile isolates from inpatients from a hospital in Brazil during a 6-year period (2012-2017) were investigated by multilocus sequence typing (MLST) and ribotyping. These isolates were classified into...
The transmission dynamics of Mycobacterium tuberculosis (Mtb) using various genotyping tools has been studied globally and a particular tool for genotyping Mtb is the mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR). Tuberculosis (TB) remains an important public...
Since first isolation in 1947 from the Zika forest in Uganda, Zika virus (ZIKV) has been principally known as a benign agent associated with sporadic human infections in a restricted number of African countries. However, during 2015-2016, an Asian lineage of ZIKV caused an unprecedentedly large outb...
This study reported a hospital outbreak due to an extensively drug-resistant (XDR) OXA-72-producing strain of Acinetobacter baumannii (A. baumannii). The isolates were found to be genotypically indistinguishable by whole-genome multiple locus sequence typing, and to belong to the international clona...
MALDI-TOF mass spectrometry (MS) may be used as a rapid typing method for nosocomial pathogens. Here, we evaluated MALDI-TOF MS for discrimination of hospital outbreak-related clusters of Serratia marcescens and carbapenemase-producing Citrobacter freundii. Thirty-three S. marcescens isolates collec...
We describe a nosocomial outbreak of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) ST59-SCCmec type V in a neonatal intensive care unit (NICU) in Hong Kong. In-depth epidemiological analysis was performed by whole-genome sequencing (WGS) of the CA-MRSA isolates collected...
The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subse...
Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases o...
The epidemiological shift in MRSA distribution from healthcare-related facilities to the general population is distressing and requires continuous monitoring to manage and control the rate of incidences. The retrospective relationship between genetic and phenotypic variability of methicillin-resista...
Sequence type 1193 (ST1193) is a new emerging global clone of Escherichia coli. The main goal of this study was to determine the prevalence and molecular characteristics of ST1193 among clinical isolates of extended-spectrum β-lactamase (ESBL)-producing E. coli from University Hospital of Erlangen,...
The majority of vancomycin-resistant Enterococcus faecium (VREfm) in Australia is of the vanB genotype. An outbreak of vanA VREfm emerged in our haematology/oncology unit between November 2014 and May 2015. The first case of daptomycin non-susceptible E. faecium (DNSEfm) detected was a patient with...
The definition of hypervirulent Klebsiella pneumoniae (hvKp), traditionally regarded as hypermucoviscosity, is controversial. However, data based on both phenotype (hypermucoviscous) and genetic (aerobactin) criteria are limited. A retrospective study was conducted in 175 geriatric patients between...
Geographical differences can manifest in different spectra of microorganisms and patterns of antibiotic resistance. Considering this, Enterobacteriacae isolated from septicemic neonates from a tertiary care centre in Agartala, India were studied with focus on carbapenem resistance. Two hundred non-d...
This study investigated the recent emergence of multidrug-resistant Panton-Valentine leukocidin (PVL)-negative CC1-MRSA-IV in Ireland and Germany. Ten CC1-MSSA and 139 CC1-MRSA isolates recovered in Ireland between 2004 and 2017 were investigated. These were compared to 21 German CC1-MRSA, 10 Romani...
Reports of raw meat pet food containing zoonotic foodborne bacteria, including Salmonella, Escherichia coli, and Listeria monocytogenes, are increasing. Contaminated raw pet food and biological waste from pets consuming those diets may pose a public health risk. The U.S. Food and Drug Administration...
Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation...
We generated genome sequences from 218 cases of Ebola virus disease (EVD) in Sierra Leone (SLE) during 2014⁻2015 to complement available datasets, particularly by including cases from a period of low sequence coverage during peak transmission of Ebola virus (EBOV) in the highly-affected Western Area...
The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, inclu...
Seoul virus (SEOV) is the etiologic agent of hemorrhagic fever with renal syndrome. It is carried by brown rats (Rattus norvegicus), a commensal rodent that closely cohabitates with humans in urban environments. SEOV has a worldwide distribution, and in Europe, it has been found in rats in UK, Franc...
Tuberculosis (TB) is a serious re-emergent public health problem in the UK. In response to rising case incidence a National TB Strain-Typing Service based on molecular strain-typing was established. This facilitates early detection and investigation of clusters, targeted public health action, and pr...
In Thailand a proventricular dilation disease (PDD)-like syndrome commonly occurs in captive psittacine birds. The etiology, however, has been unknown to date and studies to detect parrot bornaviruses have never been performed in Southeastern Asia. Therefore, 111 psittacines (22 different species) i...
Human adenoviruses (HAdVs) are prevalent causes of acute respiratory disease (ARD) in military and civilian communities. Over the last 20 years, collaborative efforts between US public health, military and academic laboratories have gathered comprehensive data documenting the emergence and re-emerge...
The aim of this study was to investigate the mechanisms of beta-lactam-resistance and the clonal relatedness of carbapenem-nonsusceptible Klebsiella pneumoniae and Escherichia coli isolates, collected consecutively in eight centers in five Bulgarian cities from November 2014 to March 2018. Carbapene...
No abstract available
Adenoviral epidemic keratoconjunctivitis (EKC) presents as severe conjunctival inflammations involving the cornea that can lead to the development of corneal opacities and blurred vision, which can persist for months. EKC is highly contagious and responsible for outbreaks worldwide, therefore accura...
In Australia, vanB vancomycin-resistant Enterococcus faecium (VREfm) has been endemic for over 20 years, but vanA VREfm isolates have rarely been reported. This outbreak report describes an outbreak of vanA VREfm in the intensive care unit (ICU) and cardiothoracic surgery (CTS) wards of a Melbourne...
Serratia marcescens is a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-ba...
Escherichia coli is a leading cause of bloodstream infection (BSI) in hospitals and communities. We conducted a retrospective study in 2015 to evaluate the clinical features and microbiological characteristics of E. coli BSI acquired in the hospital and community. A total of 100 patients with E. col...
Pseudomonas aeruginosa is a Gram-negative bacterium that causes severe infections, especially in hospitalised and immunocompromised patients. Polymyxins are the last therapeutic option to treat infections caused by this micro-organism. Here we describe a polymyxin-resistant P. aeruginosa assigned as...
The aim of this study was to identify and characterise probable extended-spectrum β-lactamase (ESBL)-, AmpC lactamase- and/or metallo-β-lactamase (MBL)-producing Escherichia coli variants circulating in the livestock and poultry environment to establish their epidemiological significance, genetic di...
During 2015-2016 an outbreak of invasive meningococcal disease due to N. meningitidis serogroup C ST-11 (cc11) occurred in Tuscany, Italy. The outbreak affected mainly the age group 20-30 years, men who have sex with men, and the area located between the cities of Firenze, Prato and Empoli, with dis...
Enterobacteriaceae are recognized as leading pathogens of healthcare-associated infections. To report the investigation of a nosocomial outbreak of extended-spectrum β-lactamase-producing Enterobacter cloacae affecting cardiothoracic surgery patients in a Belgian academic hospital. Cases were define...
Whole genome sequencing (WGS) studies can enhance our understanding of the role of patients with asymptomatic Clostridium difficile colonization in transmission. Isolates obtained from patients with Clostridium difficile infection (CDI) and colonization identified in a study conducted during 2006-20...
Dengue virus type 4 (DENV-4) was first reported in Brazil in 1982 and since then no more cases were detected again in Brazil until 2010, when the virus was reintroduced. Over the following years, the virus spread to several Brazilian states and resulted in about 1,400,000 dengue cases, in 2013. The...
No abstract available
The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak,...
No abstract available
Global burden of acute viral gastroenteritis remains high, particularly in developing countries including Bangladesh. Sewage water (SW) is an important node to monitor enteric pathogens both in the environment and among the population. Analysis of SW in Dhaka city deems crucially important because a...
Human treponematosis is caused by various pathogenic subspecies, including subsp. , subsp. , subsp. , and The global prevalence of syphilis has been increasing since the 2000s. Men account for more than 90% of the cases, with the majority being men who have sex with men (MSM). In Japan, the inc...
This study investigated the molecular and phenotypic characteristics of carbapenemase-producing Klebsiella pneumoniae, and identified the risk factors underlying its acquisition. We evaluated K. pneumoniae isolated in Nagasaki University Hospital between January 2009 and June 2015. The presence of c...
We studied the genetic diversity and the population structure of human isolates of Histoplasma capsulatum, the causative agent of histoplasmosis, using a randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) assay to identify associations with the geographic distribution of isolate...
Norovirus, a major cause of gastroenteritis in people of all ages worldwide, was first reported in South Korea in 1999. The most common causal agents of pediatric acute gastroenteritis are norovirus and rotavirus. While vaccination has reduced the pediatric rotavirus infection rate, norovirus vaccin...
Incidence of human yersiniosis in New Zealand has increased between 2013 and 2017. For surveillance and outbreak investigations it is essential that an appropriate level of discrimination between pathogenic Yersinia enterocolitica isolates is provided, in order to support epidemiological linking of...
To characterise the dissemination patterns of uropathogenic Escherichia coli (UPEC) in a community, we conducted a study utilising molecular and fundamental descriptive epidemiology. The subjects, consisted of women having community-acquired acute urinary tract infection (UTI), were enrolled in the...
This article describes the identification and investigation of two extended outbreaks of listeriosis in which crabmeat was identified as the vehicle of infection. Comparing contemporary and retrospective typing data of Listeria monocytogenes isolates from clinical cases and from food and food proces...
In November 2018, yellow fever was diagnosed in a Dutch traveller returning from a bicycle tour in the Gambia-Senegal region. A complete genome sequence of yellow fever virus (YFV) from the case was generated and clustered phylogenetically with YFV from the Gambia and Senegal, ruling out importation...
In Italy, B and C are the predominant serogroups among meningococci causing invasive diseases. Nevertheless, in the period from 2013 to 2016, an increase in serogroup W (MenW) was observed. This study intends to define the main characteristics of 63 MenW isolates responsible of invasive meningococc...
BackgroundMandatory reporting of methicillin-resistant (MRSA) bloodstream infections (BSI) has occurred in England for over 15years. Epidemiological information is recorded, but routine collection of isolates for characterisation has not been routinely undertaken. Ongoing developments in whole-geno...
IntroductionWater supply and air-conditioner cooling towers (ACCT) are potential sources of infection in people. During outbreaks, traditional typing methods cannot sufficiently segregate strains to reliably trace back transmissions to these artificial water systems. Moreover, because multiple st...
The outbreak of carbapenem-resistant Klebsiella pneumoniae is a serious public health problem, especially in the neonatal intensive care unit (NICU).Fifteen K. pneumoniae strains were isolated from 7 neonates during June 3 to 28, 2017 in an NICU. Antimicrobial susceptibility was determined by the Vi...
We report a seasonal increase of enterovirus D68 (EV-D68) cases in France, with 54 cases detected between 19 August and 14 November 2018. Molecular typing revealed that 20 of 32 of the isolates belonged to clade D1, only sporadically detected before in France. Median age of D1-cases was 42 years, 10...
Increasingly, routine surveillance and monitoring of foodborne pathogens using whole-genome sequencing is creating opportunities to study foodborne illness epidemiology beyond routine outbreak investigations and case-control studies. Using a global phylogeny of Salmonella enterica serotype Typhimuri...
To examine the epidemiology of β-lactam resistance in 'clonal group 258' (CG258), a successful KPC clonal group, over 14 years. Isolates were collected from 1999 to 2013 for a study of antibiotic resistance in Enterobacteriaceae in New York City; 515 bloodstream isolates had antibiotic susceptibilit...
Candida auris is a multidrug-resistant yeast associated with hospital outbreaks worldwide. During 2015-2016, multiple outbreaks were reported in Colombia. We aimed to understand the extent of contamination in healthcare settings and to characterize the molecular epidemiology of C. auris in Colombia....
No abstract available
The present study was conducted in order to isolate, identify and characterize fowl aviadenovirus associated with inclusion body hepatitis (IBH) in three poultry farms (two of broiler chickens and one of breeder broiler chickens) in Morocco during 2015. Liver samples collected from affected three po...
, a main causative agent associated with invasive and non-invasive infection in elderly population, is a major global health problem. After pneumococcal conjugate vaccines (PCV) and pneumococcal polysaccharide vaccines (PPV) were introduced, the distribution of serotypes has changed. There was curr...
The rapidly increasing prevalence and spread of antibiotic-resistant worldwide have become a thorny problem that poses a serious threat to human health. It is speculated that antibiotic abuse, frequent traveling, and mass gatherings accelerate this threat. To explore this hypothesis, we investigate...
The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recen...
A number of episodes of nosocomial spp bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation. Cases of spp bacteremias that occurred between August 2011 and February 2017 were investigated employing line...
-induced pyogenic liver abscess (KP-PLA) has emerged as a life-threatening disease worldwide. However, to date, a limited number of scholars have attempted to systematically elucidate the characteristics of KP-PLA. The aim of the present study was to analyze clinical, microbiological, and molecular...
Mycoplasma hyorhinis is one of the causative agents of polyserositis and arthritis in post-weaning pigs. Here we describe the development of a multi-locus sequence typing (MLST) protocol for the characterization of M. hyorhinis field isolates. A total of 104 field isolates from different geographica...
Recurrent tuberculosis (TB) is one of the main challenges in TB control. Genotyping based on Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) has been widely used to differentiate between relapse and reinfection, which are the two main causes of recurrent TB. There is...
We report a recurrent outbreak of postoperative infections with extended-spectrum β-lactamase (ESBL)-producing complex in cardiac surgery patients, describe the outbreak investigation and highlight the infection control measures. Cases were defined as cardiac surgery patients in Ghent University Ho...
Salmonella enterica serovar Enteritidis (S. Enteritidis) is the most common and essential serotype that causes salmonellosis in Guizhou province. This study aimed to investigate the antimicrobial resistance (AMR) and molecular genotyping of 79 S. Enteritidis clinical isolates from 2011 to 2016 in Gu...
is part of the human gastrointestinal flora but may act as opportunistic pathogen. Environmental persistence, high colonization capability and diverse intrinsic and acquired resistance mechanisms make it especially successful in nosocomial high-risk settings. In March 2014, an outbreak of Linezolid...
Preventing the spread of methicillin-resistant (MRSA) and understanding the pathophysiology and transmission is essential. This study describes an MRSA outbreak in a neonatal intensive care unit in Reykjavik, Iceland at a time where no screening procedures were active. After isolating MRSA in the...
Dengue viruses (DENVs), the causative agents of dengue (DEN), are classified into four serotypes and several genotypes. Identifying circulating serotypes and genotypes has clinical and epidemiological importance; however, limited information in this regard is available from Central India. This labor...
Despite the increasing occurrence of and in clinical settings, little is known about their microbiological and clinical properties. Herein, we conducted a national retrospective study (2014-2019) from multiple centers in Iran. Among the 1,770 isolates collected, we identified 600 species complex...
During zika and dengue viruse (ZIKV and DENV) outbreaks, the majority of the infected individuals remain clinically asymptomatic. Such asymptomatic individuals may occasionally acquire both arboviruses, donate blood, and contaminate haemoderivatives. The aim of this study was to characterize a ZIKV/...
is the most common pathogen causing death in children under 5 years old. This retrospective surveillance aimed to analyze serotype distribution, drug resistance, virulence factors, and molecular characteristics of pneumonia isolates from children in Shanghai, China. A total of 287 clinical pneumoco...
To clarify the molecular epidemiology of carbapenem-resistant complex (CREC) and the risk factors for acquisition of carbapenemase-producing complex (CPEC). Using clinical CREC isolates detected in a Japanese university hospital over 4 years, carbapenemase production was screened with phenotypic m...
Human enterovirus D68 (EV-D68) was first isolated in 1962 and has aroused public concern recently because of a nationwide outbreak among children in 2014-2015 in the USA. The symptoms include fever, runny nose, sneezing, cough and muscle pains. It might be associated with severe respiratory illness...
Criniviruses accumulate in the phloem tissue and damage crops by reducing chlorophyll which is essential for plant growth and development. Tomato chlorosis crinivirus (ToCV) is vectored by several whitefly species that damage tomato crops throughout the world. In South Africa, ToCV is a poorly studi...
Hand, foot, and mouth disease (HFMD) is caused by various serotypes of genus. Coxsackievirus A16 (CV-A16) and enterovirus A71 (EV-A71) were known to be the only responsible agents for these epidemics; however, this opinion was challenged after the detection that coxsackievirus A6 (CV-A6) was the re...
Infection with carbapenem-resistant Acinetobacter baumannii (CRAB) is an increasing problem for critically ill patients. The srains are frequently resistant to all antibiotics and disinfectants are often used to block the spread of these bacteria, playing an important role in infection control. The...
Shiga-toxin producing Escherichia coli (STEC) O26:H11 is the second most common cause of severe diarrhea and hemolytic uremic syndrome worldwide. The implementation of whole genome sequencing (WGS) enhances the detection and in-depth characterization of these non-O157 STEC strains. The aim of this s...
Due to the Expanded Program on Immunization (EPI) and supplementary immunization activities (SIAs) in China, the incidence of measles in China has decreased extensively. The incidence reached its lowest levels in contemporary history in 2012 and 2017, with incidence rates of 4.6 and 4.3 per million...
We conducted active surveillance to elucidate the distribution of Streptococcus pneumoniae serotypes causing invasive pneumococcal disease (IPD) and clarified the genetic relatedness among the isolates in Kobe City, Japan. Forty-five IPD-causing S. pneumoniae strains were analyzed from March 2016 to...
Multi-locus sequencing typing (MLST) is widely used to monitor the phylogeny of microbial outbreaks. However, several strains of vancomycin-resistant Enterococcus faecium (VREfm) with a missing MLST locus (pstS) have recently emerged in Australia, with a few cases also reported in England. Here, we...
is a major human pathogen. Panton-Valentine leukocidin (PVL) is a virulence factor produced by some strains that causes leukocyte lysis and tissue necrosis. PVL-associated (PVL-SA) predominantly causes skin and soft-tissue infections (SSTIs) but can also cause invasive infections such as necrotizin...
is an emerging pathogen capable of causing hospital-acquired infections (HAIs). It has the ability to survive on environmental surfaces for months, making transmission difficult to control. Our report describes the investigation and restriction of an outbreak of in the Neonatal Intensive Care Unit...
In 2015-2016, a cross-sectional carriage survey was performed in Tuscany Region, Italy, during an outbreak of invasive meningococcal disease due to Neisseria meningitidis serogroup C clonal complex 11 (MenC:cc11). This study aims to evaluate the genomic profile of meningococcal carriage isolates col...
Bacterial whole-genome sequencing is now increasingly available to researchers, reference laboratories and individual healthcare institutions. It can be possible to predict antimicrobial minimum inhibitory concentrations (MICs) for Neisseria gonorrhoeae using sequencing data, for many antimicrobials...
Porcine circovirus-associated disease encompasses multiple disease syndromes including porcine circovirus 2 systemic diseases, reproductive failure, and porcine dermatitis and nephropathy syndrome. Until recently, porcine circovirus 2 was the only species associated with the porcine circovirus-assoc...
To undertake the first detailed genomic analysis of methicillin-resistant (MRSA) isolated in Sri Lanka. A prospective observational study was performed on 94 MRSA isolates collected over a 4 months period from the Anuradhapura Teaching Hospital, Sri Lanka. Screening for A, C, and the Panton-Valent...
Xanthomonas vasicola pv. musacearum (Xvm) which causes Xanthomonas wilt (XW) on banana (Musa accuminata x balbisiana) and enset (Ensete ventricosum), is closely related to the species Xanthomonas vasicola that contains the pathovars vasculorum (Xvv) and holcicola (Xvh), respectively pathogenic to su...
Since 2013, South African nutrition policy focuses on "the first thousand days," (conception to two years), informed by Developmental Origins of Health and Disease research. Drawing on ethnographic research, we show how policy foregrounds certain categories of persons and casts "the maternal" as a t...
Compare the molecular epidemiology of tuberculosis (TB) between two large Canadian provinces-Ontario and British Columbia (BC)-to identify genotypic clusters within and across both provinces, allowing for an improved understanding of genotype data and providing context to more accurately identify cl...
A consistently decreasing prevalence of MRSA infections in China has been reported, however, the underlying mechanism of molecular processes responsible for this decline in MRSA infections has been poorly understood. We conducted an epidemiologic investigation to determine the dynamic changes of Sta...
Dengue fever, a mosquito-borne disease, is caused by dengue virus (DENV) which includes four major serotypes (DENV-1, -2, -3, and -4). Some serotypes cause more severe diseases than the other; severe dengue is associated with secondary infections by a different serotype. Timely serotyping can provid...
Macrolides such as erythromycin are the empirical treatment of Bordetella pertussis infections. China has experienced an increase in erythromycin-resistant B. pertussis isolates since they were first reported in 2013. Here, we undertook a genomic study on Chinese B. pertussis isolates from 2012 to 2...
The aim of this study was to characterize the bacterial microbiome of hard ticks with affinity to bite humans in La Rioja (North of Spain). A total of 88 adult ticks (22 Rhipicephalus sanguineus sensu lato, 27 Haemaphysalis punctata, 30 Dermacentor marginatus and 9 Ixodes ricinus) and 120 I. ricinus...
Clostridium (Clostridioides) difficile is the main cause of nosocomial diarrhoea. Ribotype 018 (RT018) has been recognized as the predominant strain responsible for C. difficile infection (CDI) in Italy, whereas in most other European countries only sporadic RT018 cases occur. Between August and Oct...
An outbreak with a remarkable Listeria monocytogenes clone causing 163 cases of non-invasive listeriosis occurred in Germany in 2015. Core genome multi locus sequence typing grouped non-invasive outbreak isolates and isolates obtained from related food samples into a single cluster, but clearly sepa...
Molecular typing and whole genome sequencing (WGS) information is used for (inter-) national outbreak investigations. To assist the implementation of these techniques for tuberculosis (TB) surveillance and outbreak investigations at European level there is a need for inter-country collaboration and...
The whitefly Bemisia tabaci MEAM1 is a notorious vector capable of transmitting many plant viruses, resulting in serious crop loss and food shortage around the world. To investigate potential sRNA-mediated regulatory mechanisms in whiteflies that are affected by virus acquisition and transmission, w...
The transmission of tuberculosis may affect the incidence rate of the disease in Poland. Genetic methods are of assistance in tracing the infection transmission, identifying its sources, determining the risk groups, and focusing on the preventive actions. The objectives of this study lie in an asses...
Bovine tuberculosis (bTB) caused by Mycobacterium bovis is a re-emerging problem in both livestock and humans. The association of some M. bovis strains with hyper-virulence, MDR-TB and disseminated disease makes it imperative to understand the biology of the pathogen. Mycobacterium bovis (15) among...
We investigated the molecular characteristics and antimicrobial susceptibility of Clostridium difficile isolated from animals in China. We obtained 538 rectal swabs from pigs, chickens and ducks in 5 provinces during 2015 and 2016. C. difficile isolates were characterized by detection of toxin genes...
Acinetobacter baumannii is considered to be an important nosocomial pathogen responsible for various outbreaks that have resulted in a need for effective epidemiological typing methods. Different typing methods are available for A. baumannii epidemiological studies. Currently, the phenotypic typing...
Molecular typing techniques are useful in understanding tuberculosis epidemiology; yet, they have been under-utilised at the human-animal interface in Nigeria. Sixty-four Mycobacterium tuberculosis complex (MTBC) isolates including 42 M. tuberculosis, 13 M. bovis and nine M. africanum obtained from...
infection (CDI) is known as one of the most important causes of nosocomial infections. The main objective of this study was to evaluate the presence of in the stool of hospitalized patients with diarrhea as well as in their environments. isolates were characterized according to the presence of tox...
Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, larg...
Klebsiella pneumoniae is a common cause of nosocomial infections; however, there is limited information in Iran regarding nosocomial outbreaks due to extended-spectrum β-lactamase (ESBL) producing K pneumoniae strains, particularly using molecular methods. The present study focused on the molecular...
Studying bacterial population diversity is important to understand healthcare associated infections' epidemiology and has a significant impact on dealing with multidrug resistant bacterial outbreaks. We characterised the extended-spectrum beta-lactamase producing K. pneumoniae (ESBLp KPN) population...
Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities with strategies to mitigate pathogen spread. However, no such strategies are in place for ambulances, wh...
Nosocomial infections have become alarming with the increase of multidrug-resistant bacterial strains of . Being the causative agent in ~80% of the cases, these pathogenic gram-negative species could be deadly for hospitalized patients, especially in intensive care units utilizing ventilators, urina...
Colonization with has been identified as a risk for subsequent occurrence of infection. This study investigated the relationship between colonization of patients and healthcare workers (HCWs), and subsequent surgical site infections (SSI). Between December 2014 and September 2015, a total of 930 p...
Methicillin resistant (MRSA) strains were once confined to hospitals however, in the last 20 years MRSA infections have emerged in the community in people with no prior exposure to hospitals. Strains causing such infections were novel and referred to as community-associated MRSA (CA-MRSA). The aim...
The high burden of healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) is partially due to excessive antimicrobial use both in human and animal medicine worldwide. How can technology help to overcome challenges in infection prevention and control (IPC) and to prevent HAI and e...
Urinary tract infections (UTIs) are a highly prevalent infection among children and Escherichia coli is one of the most important pathogens causing pediatric UTIs. Production of extended spectrum b-lactamase (ESBL) enzymes is an important factor in the emergence of antibiotic resistance among these...
We investigated the prevalence and molecular epidemiology of methicillin-resistant (MRSA) among 356 residents of nine long-term care facilities (LTCFs) in Japan during 2015 and 2017. In total, 800 specimens were tested and 39 MRSA isolates were recovered from 31 (8.71%) residents. PCR-based open re...
Clostridium difficile (CD) is the leading cause of infectious health-care associated diarrhea. However, little is known regarding CD carriage and transmission amongst asymptomatic colonizers. We evaluated carriage, characterized strains and examined epidemiologic linkages in asymptomatic colonized C...
aEPEC are associated with persistent diarrhea, and diarrheal outbreaks in both humans and animals worldwide. They are differentiated from typical EPEC by the lack of bundle-forming pili, and from EHEC by the lack of phage-mediated toxins. However, phylogenetic analyses often associate aEPEC with EH...
Onchocerciasis and lymphatic filariasis are targeted for elimination, primarily using mass drug administration at the country and community levels. Elimination of transmission is the onchocerciasis target and global elimination as a public health problem is the end point for lymphatic filariasis. Wh...
Noroviruses are a major cause of viral epidemic gastroenteritis in humans worldwide. The protease (Pro) encoded in open reading frame 1 (ORF1) is an essential enzyme for proteolysis of the viral polyprotein. Although there are some reports regarding the evolutionary analysis of norovirus GII-encodin...
() is a globally distributed bacterial pathogen whose population structure has largely been shaped by the activities of its obligate human host. Oceania was the last major global region to be reached by Europeans and is the last region for which the dispersal and evolution of remains largely unexpl...
Foot-and-mouth disease (FMD) affects the livestock industry in a transboundary manner. It is essential to understand the FMD phylodynamics to assist in the disease-eradication. FMD critically affects the Sri Lankan cattle industry causing substantial economic losses. Even though many studies have co...
The circulation of carbapenem-resistant (CRKP) is a significant problem worldwide. In this work we characterize the isolates and reconstruct the spread of a multi-clone epidemic event that occurred in an Intensive Care Unit in a hospital in Northern Italy. The event took place from August 2015 to M...
Understanding the phylogeographic history of an invasive species may facilitate reconstructing the history and routes of its invasion. The longhorn crazy ant, , is a ubiquitous agricultural and household pest throughout much of the tropics and subtropics, but little is known about the history of its...
Legume plants have colonized almost all terrestrial biotopes. Their ecological success is partly due to the selective advantage provided by their symbiotic association with nitrogen-fixing bacteria called rhizobia, which allow legumes to thrive on marginal lands and nitrogen depleted soils where non...
Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing develop...
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requ...
The human immunodeficiency virus-type 1 (HIV-1) subtype B has probably been circulating on the island of Hispaniola since the 1960s, but information about the early viral history on this Caribbean island is scarce. In this study, we reconstruct the dissemination dynamics of early divergent non-pande...
In this chapter, we focus on the computational challenges associated with statistical phylogenomics and how use of the broad-platform evolutionary analysis general likelihood evaluator (BEAGLE), a high-performance library for likelihood computation, can help to substantially reduce computation time...
Astrovirus species members of the genus (family ) have been increasingly recognized as neuroinvasive pathogens in various mammals, including humans, mink, cattle, sheep, and pigs. While cases of astrovirus-associated encephalitis have been reported in North America, Europe, and Asia, their presence...
Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve AMR surveillance by providing a greater understanding of the transmission of resistant bacteria and AMR genes throughout the food...
The information about the dynamics of the viral population and migration events that affect the epidemic in different parts of the Russia is insufficient. Possibly, the huge size of the country and limited transport accessibility to certain territories may determine unique traits of the HIV-1 evolut...
The current outbreak of yellow fever virus (YFV) that is afflicting Brazil since the end of 2016 probably originated from a re-introduction of YFV from endemic areas into the non-endemic Southeastern Brazil. However, the lack of genomic sequences from endemic regions hinders the tracking of YFV's di...
Packaged raw milk contaminated with mediated a large yersiniosis outbreak in southern Finland in 2014. The outbreak was traced back to a single dairy farm in southern Finland. Here we explore risk factors leading to the outbreak through epidemiologic investigation of the outbreak farm and through g...
Non-O1/O139 is increasingly reported in the clinical settings. However, intestinal infections via the consumption of non-O1/O139 -carrying seafood are rarely documented in China. In this study, we reported a case of mild watery diarrhea in a young male, caused by non-O1/O139 in the downstream of L...
Human immunodeficiency virus type 1 (HIV-1) non-B subtype infections occurred in Belgium since the 1980s, mainly amongst migrants and heterosexuals, whereas subtype B predominated in men-having-sex-with-men (MSM). In the last decade, the diagnosis of F1 sub-subtype in particular has increased substa...
Washington, DC consistently has one of the highest annual rates of new HIV-1 diagnoses in the United States over the last 10 years. To guide intervention and prevention strategies to combat DC HIV infection, it is helpful to understand HIV transmission dynamics in a historical context. Toward this a...
This study analyzes the HIV-1 subtype diversity and its phylodynamics in Moscow region, which is the most densely populated area of Russia characterized by high rates of internal and external migration. The demographic and viral data from 896 HIV-infected individuals collected during 2011-2016 were...
is a Gram-negative bacterium which mainly causes peptic ulcer disease in human, but is also the predominant cause of stomach cancer. It has been coevolving with human since 120,000 years and, according to Multi-locus sequence typing (MLST), can be classified into seven major population types, namel...
The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) is not yet routinely employed to characterize group isolates from fo...
In many parts of the world the damaging potato late blight pathogen, Phytophthora infestans, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and driv...
Human enteroviruses (HEVs) are common causal agents of aseptic meningitis in young children. Laboratory and syndromic surveillance during December 2015 and January 2016 noted an unusually high number of paediatric aseptic meningitis cases at a hospital in Mossel Bay, Western Cape Province, South Afr...
Outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) in the neonatal intensive care unit (NICU) have been reported worldwide. Some outbreaks were caused by USA300, which is a community-associated MRSA clone. In 2011, polymerase chain reaction-based open reading frame typing (POT) for the...
In June 2016, a Streptococcus suis outbreak occurred in Guangxi, China. We determined the genetic characteristics of six clinically isolated strains by serotyping, PCR, and whole-genome sequencing, performing genome epidemiology analysis on these and 961 public available S. suis genomes. We also cla...
In the past years, the carbapenemase (KPC)-producing sequence type 258 (ST258) became an important worldwide spread nosocomial pathogen. Recent evidence shows that the global epidemiology is changing, with the rise of new lineages. In this study we report the microbiological and genomic features o...
Tobacco mosaic virus (TMV) is widespread in China and causes considerable economic losses to tobacco production. The molecular epidemiology of this virus is, however, poorly understood. In this study, we sequenced the genomes of 51 TMV isolates from five tobacco-producing regions in China and invest...
Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation. We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant S...
The aim of this study was to characterize the population structure of 56 OXA-48-like-producing isolates, as well as extended-spectrum β-lactamase (ESBL) and carbapenemase genes, recovered in 2014 and 2015 from 16 hospitals in southern Spain. XbaI pulsed-field gel electrophoresis and multilocus sequ...
Plants of the genus Pleione, originating from hobby growers in the Netherlands and in the Czech Republic, were conspicuous for viral infection, showing symptoms of leaf mosaic or flower breaking. Using Sanger and high throughput sequencing, the full genome sequence of a novel potyvirus was obtained...
Multi-drug resistant Acinetobacter baumannii has emerged as important nosocomial pathogen associated with various infections including lower respiratory tract. Limited therapeutic options contribute to increased morbidity and mortality. Acinetobacter baumannii has the ability to persist in the envir...
Facing multidrug resistant (MDR) bacterial pathogens is one of the most important challenges for our society. The spread of highly virulent and resistant pathogens can be described using molecular typing technologies; in particular, whole genome sequencing (WGS) data can be used for molecular typing...
Aedes aegypti is associated with dengue, yellow fever, chikungunya and Zika viruses. This vector is widespread in tropical and subtropical areas, and can also occur in temperate areas at higher latitudes. The geographical distribution of Ae. aegypti continues to spread due to human activities. This...
The dissemination of multiresistant carbapenemase (KPC)-2-producing isolates belonging to international high-risk clones poses a major health care threat. In this study, 48 nonduplicated, carbapenem-resistant isolated from 2011 to 2014 in a tertiary hospital were investigated. The gene was the o...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious nosocomial pathogen that causes a variety of serious, often life-threatening, infections and outbreaks. This study aimed to investigate the molecular epidemiology of clinical CRAB isolates from an outbreak that occurred in the intensiv...
The pathogen Flavobacterium psychrophilum is a major problem for the expanding salmonid fish farming industry in Sweden as well as worldwide. A better understanding of the phylogeography and infection routes of F. psychrophilum outbreaks could help to improve aquaculture profitability and the welfar...
Escherichia coli is one of the major causative agents of nosocomial infections. Here we report the first draft genome sequence of an E. coli strain (no. 158) isolated in Poland carrying bla, bla, bla, aac(3)-IIa and aac(6')-Ib-cr genes together with mutations in the gyrA and parC genes. Total DNA wa...
Clostridioides difficile is the leading cause of nosocomial diarrhea and antibiotics associated diarrhea, but it is also an increasingly common cause of community diarrhea. In recent years we have observed a progressive increase in the incidence of C. difficile infection (CDI) both at the hospital a...
Despite increasing access to antiretrovirals, HIV incidence in rural KwaZulu-Natal remains among the highest ever reported in Africa. While many epidemiological factors have been invoked to explain such high incidence, widespread human mobility and viral movement suggest that transmission between co...
Feline kobuvirus (FeKoV), a novel picornavirus of the genus kobuvirus, was initially identified in the feces of cats with diarrhea in South Korea in 2013. To date, there is only one report of the circulation of kobuvirus in cats in southern China. To investigate the presence and genetic variability...
Following the alarming outbreak of carbapenem-resistant Klebsiella pneumonia (CRKP) in five intensive care units (ICUs) of a tertiary care hospital in China, a prospective investigation of CRKP colonized/infected patients was conducted. To describe the diffusion and transmission of CRKP among epidem...
Porcine reproductive and respiratory syndrome (PRRS) is one of the most important viral swine diseases, resulting in immense economic losses in Chinese pig industry. Currently, four major lineages: lineage 1 (NADC30-like), 3 (QYYZ-like), 5.1 (VR2332-like) and 8.7 (JXA1-like) of type 2 PRRSV (North A...
Based on molecular data, previous studies have suggested a high overall diversity and co-infection rates of Bartonella bacteria in wild rodents and their fleas. However, partial genetic characterization of uncultured co-infecting bacteria limited sound conclusions concerning intra- and inter-specifi...
Mycobacterium abscessus can cause true infection or be present in the host as a harmless colonist. The ability of M. abscessus to cause disease and develop drug resistance is known to have a genetic basis. We aimed to differentiate between persistent infection and reinfection using multilocus sequen...
Multidrug-resistant Klebsiella pneumoniae strains are regularly involved in hospital outbreaks. This study describes an ESBL-producing K. pneumoniae clone (ST607-K25) responsible for a nosocomial outbreak in a neonatal intensive care unit. Fourteen strains isolated from 13 patients were included. An...
Acinetobacter baumannii is an opportunistic pathogen that has been held responsible for a lot of infections worldwide. Infections caused by this pathogen are difficult to control because of the widespread of antimicrobial resistance mechanisms. The aim of the present study is to assess the prevalenc...
Helicobacter cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a s...
Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a nosocomial pathogen worldwide. The dissemination of VREfm is due to both clonal spread and spread of mobile genetic elements (MGEs) such as transposons. We aimed to combine vanB-carrying transposon data with core-genome MLST (cgMLST)...
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this we...
We summarize and analyze historical and current data regarding the reemergence of St. Louis encephalitis virus (SLEV; genus Flavivirus) in the Americas. Historically, SLEV caused encephalitis outbreaks in the United States; however, it was not considered a public health concern in the rest of the Am...
Host migration and emerging pathogens are strongly associated, especially with regard to zoonotic diseases. West Nile virus (WNV), a mosquitoborne pathogen capable of causing severe, sometimes fatal, neuroinvasive disease in humans, is maintained in highly mobile avian hosts. Using phylogeographic a...
Given globalization and other social phenomena, controlling the spread of infectious diseases has become an imperative public health priority. A plethora of interventions that in theory can mitigate the spread of pathogens have been proposed and applied. Evaluating the effectiveness of such interven...
Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-t...
Few studies describe the molecular characterization of mupirocin resistance in strains. In this study, we evaluated the characteristics of mupirocin resistance in isolates for 1-year period in Tehran, Iran. In a cross-sectional study, we collected 51 unique mupirocin-resistant strains obtained fro...
Oropouche orthobunyavirus (OROV) has significant impact in public health in Amazon region. This arbovirus is one of the most common causes of febrile illness in Brazil, and is responsible for several epidemics since 1960's. In this study, we sequenced and characterized the complete coding sequences...
To identify transmission patterns of Carbapenem-resistant Klebsiella pneumoniae infection during an outbreak at a large, tertiary care hospital and to detect whether the outbreak organisms spread to other facilities in the integrated healthcare network. We analyzed 71 K. pneumoniae whole genome sequ...
Wolbachia endosymbiotic bacteria are widespread throughout insect species and Wolbachia transinfected in Aedes mosquito species has formed the basis for biocontrol programs as Wolbachia strains inhibit arboviral replication and can spread through populations. Resident strains in wild Culicine mosqui...
To characterize extended-spectrum β-lactamase-producing Escherichia coli harboring the colistin resistance gene mcr-1 from human fecal samples collected in 2012 in a rural area of Shandong province, PR China. Whole-genome sequencing and antimicrobial susceptibility testing was performed on 25 mcr-1-...
The H1N1 influenza virus responsible for the most recent pandemic in 2009 (H1N1pdm) has spread to swine populations worldwide while it replaced the previous seasonal H1N1 virus in humans. In France, surveillance of swine influenza A viruses in pig herds with respiratory outbreaks led to the detectio...
Prior to 2010, the lagoviruses that cause rabbit hemorrhagic disease (RHD) in European rabbits (Oryctolagus cuniculus) and European brown hare syndrome (EBHS) in hares (Lepus spp.) were generally genus-specific. However, in 2010, rabbit hemorrhagic disease virus 2 (RHDV2), also known as Lagovirus eu...
No abstract available
Tsetse flies (Diptera: Glossinidae) are solely responsible for the transmission of African trypanosomes, causative agents of sleeping sickness in humans and nagana in livestock. Due to the lack of efficient vaccines and the emergence of drug resistance, vector control approaches such as the sterile...
Avian influenza H5N1 subtype has caused a global public health concern due to its high pathogenicity in poultry and high case fatality rates in humans. The recently emerged H7N9 is a growing pandemic risk due to its sustained high rates of human infections, and recently acquired high pathogenicity i...
Recovery of multidrug-resistant (MDR) Pseudomonas aeruginosa and Klebsiella pneumoniae from a cluster of patients in the medical intensive care unit (MICU) prompted an epidemiologic investigation for a common exposure. Clinical and microbiologic data from MICU patients were retrospectively reviewed,...
In March 2017, a patient became febrile within 4 days after visiting a rustic conference center in Austin, Texas, USA, where Austin Public Health suspected an outbreak of tickborne relapsing fever a month earlier. Evaluation of a patient blood smear and molecular diagnostic assays identified Borreli...
Acinetobacter baumannii is a multidrug resistant nosocomial pathogen that shows an outstanding ability to undergo genetic exchange, thereby acquiring different traits that contribute to its success. In this work, we identified genetic features of an indigo-pigmented A. baumannii strain (Ab33405) tha...
The emergence of carbapenem-resistant Klebsiella pneumoniae (CR-KP) has become a significant problem worldwide and also being a major threat to children and newborns. Here we report an outbreak of NDM-1-producing K. pneumoniae in a neonatal unit. Six CR-KP strains, isolated from neonates with sympto...
Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality...
Carbapenem-resistant Acinetobacter baumannii (CRAB) has become a worldwide issue. This study aimed to characterise the epidemiology and genetic relationships of A. baumannii isolates in Guangdong Province, China. CRAB isolates were collected from five municipal hospitals from June-December 2017. The...
A genome sequence-based analysis of 74 carbapenem-resistant Klebsiella pneumoniae (CRKP) from 12 hospitals in Sichuan, China, revealed that the isolates carried blaKPC-2 (n = 48), blaNDM (n = 22), or blaIMP-4 (n = 4) were identified as K. pneumoniae (n = 67), Klebsiella variicola (n = 5), and Klebsi...
This study was performed to elucidate the changing epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in a Chinese teaching hospital. We performed whole-genome sequencing and phylogenetic analysis on MRSA isolates recovered at Sir Run Run Shaw Hospital (SRRSH) from 2013 to 2015. MRSA...
The global dissemination of carbapenem-resistant Acinetobacter baumannii clonal complex (CC) 92 has become an urgent public health concern. A. baumannii isolates were collected in 5 tertiary hospitals in south China during 2012-2015, and their clinical data were obtained. The clinical characterizati...
Wolbachia is an intracellular bacterium that infects a remarkable range of insect hosts. Insects such as mosquitos act as vectors for many devastating human viruses such as Dengue, West Nile, and Zika. Remarkably, Wolbachia infection provides insect hosts with resistance to many arboviruses thereby...
Molecular epidemiology is one of the most rapidly developing research area. In the light of past and modern technologies it has gained number of typing methods based on molecular biology techniques. In this report, the subspecies differentiation of Francisella tularensis and genotyping of strains is...
The aim of this study was to better understand the molecular epidemiology of Campylobacter coli isolated from multiple sources in Belgium, by studying the genotypic diversity and antimicrobial resistance phenotypes and resistance mechanisms of 59 C. coli isolates. Isolates from broiler carcasses and...
Acinetobacter spp. are opportunistic pathogens being A. baumannii the most frequently identified in nosocomial settings. A. ursingii was mainly described as causing bacteremia and outbreaks in neonatal intensive care units. Ten A. ursingii isolates were recovered from rectal swab screening for carba...
This hospital-based surveillance study was carried out in Novosibirsk, Asian Russia from September 2009 to December 2012. Stool samples from 5486 children with diarrhea and from 339 healthy controls were screened for rotavirus, norovirus, astrovirus, and bocavirus by RT-PCR. At least one enteric vir...
is considered an important pathogen of clinical significance that is responsible for a wide range of nosocomial infections. Carbapenem resistance among isolates has increased dramatically in the Past years because of the emergence and dissemination of specific epidemic clones. We aimed to character...
Two strains of classical swine fever virus (CSFV) (SRB/CSFV/1264/2005 and SRB/CSFV/6168/2006), producing serious clinical signs of disease during outbreaks in 2005 and 2006 in Serbia, were isolated on porcine kidney cells, and their complete genomes were determined by next-generation sequencing. Thi...
Vancomycin-resistant Enterococci (VRE) are a major public health problem worldwide, since they are commonly implicated in nosocomial infections in various regions in the world. The aim of our study was to investigate genetic features and clonal relationship of VRE in the Military hospital of Tunisia...
Over a 35-month period, group B Streptococcus isolates with reduced penicillin susceptibility (PRGBS) were detected from elderly patients at a regional hospital in Japan, accompanying population-level transition of PRGBS serotypes. The genetic relatedness of 77 non-duplicate PRGBS from 73 patients w...
Methicillin-resistant Staphylococcus aureus (MRSA) remains a major challenge for patient care. Community-associated (CA)-MRSA often have a fitness and virulence advantage compared with their nosocomial counterparts. Increased mobility, travel activities and migration accelerate the intercontinental...
In 2017, the World Health Organization categorized carbapenem-resistant Acinetobacter baumannii (CRAB) as a priority 1, critical antibiotic-resistant bacteria. This study analyzed the clinical outcomes and investigated the molecular epidemiology of CRAB bacteremia in a medical center in Northern Tai...
Xylella fastidiosa is an insect-transmitted bacterial plant pathogen which causes a variety of economically important diseases worldwide. Molecular identification of X. fastidiosa is used for quarantine screening, surveillance, and research applications; many of which require subspecies level differ...
Carbapenemase-producing Enterobacteriaceae (CPE) occur only sporadically in Slovenia. To describe the first Slovenian carbapenemase-producing (CP) Klebsiella pneumoniae and Escherichia coli outbreak which occurred at the tertiary teaching hospital University Medical Centre Ljubljana from October 201...
Identifying the animal origins of RNA viruses requires years of field and laboratory studies that stall responses to emerging infectious diseases. Using large genomic and ecological datasets, we demonstrate that animal reservoirs and the existence and identity of arthropod vectors can be predicted d...
No abstract available
Molecular technology to identify relatedness between complex isolates, representative of possible tuberculosis (TB) transmission between individuals, continues to evolve. At the same time, tools to utilise this information for public health action to improve TB control should also be implemented. P...
Current predominant routes of group B Streptococcus (GBS) transmission in preterm neonates admitted to neonatal intensive care unit (NICU) are poorly defined. We report 2 overlapping clusters of GBS late-onset disease (LOD) from June to September 2015 in an Italian NICU. During the outbreak, possibl...
Bill Hanage is an Associate Professor of Epidemiology at Harvard School of Public Health, where he studies fundamental and applied epidemiology using genomic and evolutionary methods. Bill spoke to us about the different types of selection that determine pathogen populations, asking reviewers to hig...
No abstract available
Acinetobacter baumannii causes serious hospital-acquired infections and has been positioned as a priority organism by the World Health Organization. This study includes 36 A. baumannii isolates from a children hospital recovered between March 2014 and May 2015 in Cochabamba. The majority of the isol...
Panton-Valentine leukocidin (PVL) is a virulent cytotoxin and an indicator of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infection. In this study, we evaluated the prevalence and clinical and molecular characteristics of PVL-positive invasive S. aureus (ISA) infection...
Bacterial factors favoring the unprecedented multidrug-resistant tuberculosis (MDR-TB) epidemic in the former Soviet Union remain unclear. We utilized whole genome sequencing and Bayesian statistics to analyze the evolutionary history, temporal emergence of resistance and transmission networks of MD...
Since the Global Polio Eradication Initiative was launched in 1988 (1), the number of polio cases worldwide has declined by >99.99%. Among the three wild poliovirus (WPV) serotypes, only type 1 (WPV1) has been detected since 2012. This decline is attributable primarily to use of the live, attenuated...
Enterococcus faecalis are a major cause of nosocomial infection worldwide, and the spread of vancomycin resistant strains (VRE) limits treatment options. Tigecycline-resistant VRE began to be isolated from inpatients at a Brazilian hospital within months following the addition of tigecycline to the...
Although rare in the U.S., outbreaks due to Neisseria meningitidis do occur. Rapid, early outbreak detection is important for timely public health response. In this study, we characterized U.S. meningococcal isolates (N = 201) from 15 epidemiologically defined outbreaks (2009-2015) along with tempor...
As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter has a significant impact on human health. In the developed world, most campylobacteriosis cases are attributed to the consumption of undercooked, contaminated poultry; however, it has been shown that Campylobacter can b...
Whole-genome sequencing (WGS) via next-generation sequencing (NGS) technologies is a powerful tool for determining the relatedness of bacterial isolates in foodborne illness detection and outbreak investigations. WGS has been applied to national outbreaks (for example, ); however, WGS has rarely bee...
Epidemiological and microbiological data on strains isolated between April 2004 and March 2018 ( = 836) and held at the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome-derived specie...
In order to obtain an insight into genomic changes and associated evolution and adaptation of Infectious Pancreatic Necrosis Virus (IPNV), the complete coding genomes of 57 IPNV isolates collected from Scottish aquafarms from 1982 to 2014 were sequenced and analysed. Phylogenetic analysis of the seq...
Rapid detection of sources and transmission routes by molecular methods provides key data for risk management of methicillin-resistant Staphylococcus aureus-induced infections acquired in both the community and hospitals. This study aimed to determine the clonal relationship of methicillin-resistant...
Estimates of the prevalence of asymptomatically carried Clostridium difficile in elderly patients in long-term care range from 0% to 51%. Asymptomatic carriage is possibly a risk factor for the development of infection, and there is ongoing debate surrounding the role of asymptomatic carriage in tra...
Ural genetic family is a part of the Euro-American lineage of Mycobacterium tuberculosis and is endemic in Northern Eurasia (former Soviet Union [FSU]). These strains were long described as drug susceptible and of low virulence, but recent studies reported an increasing circulation of the multidrug-...
Studies on the microbial communities in non-human primate hosts provide unique insights in both evolution and function of microbes related to human health and diseases. Using 16S rRNA gene amplicon profiling, we examined the oral, anal and vaginal microbiota in a group of non-captive rhesus macaques...
In the context of the pre-elimination of malaria, biological control may provide an alternative or additional tool to current malaria control strategies. During their various stages of development, mosquitoes undergo subsequent changes in their associated microbiota, depending on their environment a...
Hepatitis B virus disease progression in East Asia is most frequently associated with genotype C (HBV/C). The increasing availability of HBV/C genetic sequences and detailed annotations provides an opportunity to investigate the epidemiological factors underlying its evolutionary history. In this st...
The detailed epidemiological and molecular characterization of an outbreak of Burkholderia cepacia at a neurotrauma intensive care unit of a level 1 trauma centre is described. The stringent infection control interventions taken to successfully curb this outbreak are emphasized. The clinical and mic...
Highly pathogenic avian influenza A(H5N8) viruses have been detected in several continents. However, limited viral sequence data are available from countries in the Middle East. We report full-genome analyses of highly pathogenic H5N8 viruses recently detected in different provinces in Saudi Arabia.
Rotavirus species H (RVH) has been detected in pigs, humans and bats. Moreover, porcine RVHs have often been identified in several swine-producing countries in recent years. Despite their zoonotic impact, genome information for RVHs is still limited. This study aimed to establish a tentative complet...
Pandemic O3:K6 Vibrio parahaemolyticus emerged in 1996. Since then, this strain of pathogen and its serovariants (predominantly O1:KUT [untypable], O1:K25 and O4:K68) have caused gastroenteritis worldwide. Owing to the limitation in established K antisera, tracking the sources of KUT for epidemiolog...
In 2015, the influenza virus A/H1N1/pdm09 strain outbreak became prevalent throughout the different provinces of Iran. There are relatively limited complete genetic sequences available for this virus from Asian countries. Diagnosis and virological surveillance of influenza is essential for detecting...
Cyberlindnera fabianii has rarely been reported as a human pathogen. Here, we describe an outbreak of C. fabianii fungaemia involving 10 preterm neonates during a seven-month period in Kuwait and review the published reports. Blood cultures were processed, and yeast isolates were initially identifie...
No abstract available
On April 25, 2017, a cluster of unexplained illnesses and deaths associated with a funeral was reported in Sinoe County, Liberia. Molecular testing identified Neisseria meningitidis serogroup C (NmC) in specimens from patients. We describe the epidemiological investigation of this cluster and metage...
Cryptococcosis is a major opportunistic fungal infection caused by members of the genus Cryptococcus, mainly those belonging to the Cryptococcus neoformans/Cryptococcus gattii species complexes. Here, we report a comprehensive molecular epidemiological study of the environmental distribution of Cryp...
Recently, following import by travel and migration, epidemic community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has caused nosocomial outbreaks in Europe, sometimes with a fatal outcome. We describe clinico-epidemiological characteristics of CA-MRSA detected by the European N...
We aimed to identify the main spreading clones, describe the resistance mechanisms associated with carbapenem- and/or multidrug-resistant P. aeruginosa and characterize patients at risk of acquiring these strains in Estonian hospitals. Ninety-two non-duplicated carbapenem- and/or multidrug-resistant...
Campylobacter is the leading cause of bacterial enteritis in the developed world, and infections with the organism are largely sporadic in nature. Links between sporadic cases have not been established, with the majority of infections thought to be caused by genetically distinct isolates. Using a re...
Nipah virus (NiV), a zoonotic paramyxovirus belonging to the genus Henipavirus, is classified as a Biosafety Level-4 pathogen based on its high pathogenicity in humans and the lack of available vaccines or therapeutics. Since its initial emergence in 1998 in Malaysia, this virus has become a great t...
We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within...
A key issue in infectious disease epidemiology is to identify and predict geographic sites of epidemic establishment that contribute to onward spread, especially in the context of invasion waves of emerging pathogens. Conventional wisdom suggests that these sites are likely to be in densely-populate...
The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately pre...
Potato virus S (PVS) is a major plant pathogen that causes considerable losses in global potato production. Knowledge of the evolutionary history and spatio-temporal dynamics of PVS is vital for developing sustainable management schemes. In this study, we investigated the phylodynamics of the virus...
Transmission of multidrug-resistant Candida auris infection has been reported in the USA. To better understand its emergence and transmission dynamics and to guide clinical and public health responses, we did a molecular epidemiological investigation of C auris cases in the USA. In this molecular ep...
To evaluate whole-genome sequencing (WGS) as a molecular typing tool for MRSA outbreak investigation. Investigation of MRSA colonization/infection in a neonatal intensive care unit (NICU) over 3 years (2014-2017). Single-center level IV NICU.PatientsNICU infants and healthcare workers (HCWs). Infant...
Increasing rate of silent intestinal carriers with extended-spectrum betalactamase (ESBL)-producing (ESBL-KP) has given rise to a serious healthcare problem in clinical settings. Various epidemiological studies are being conducted to determine clonal relatedness among carriers. In this study, we in...
Tuberculosis (TB) is an infectious disease with a higher risk for infection and disease among household contacts (HHC). Here, we report a molecular epidemiology-based approach to study disease transmission and the genetic characteristics of Mycobacterium tuberculosis (Mtb) strains among HHC in the c...
In Japan, Mycoplasma pneumoniae resistance to macrolides is high. To compare sequence types (STs) of susceptible and resistant isolates, we performed multilocus sequence typing for 417 isolates obtained in Japan during 2002-2016. The most prevalent ST overall was ST3, for macrolide-resistant was ST1...
We used whole-genome sequencing to investigate a tuberculosis outbreak involving U.S.-born persons in the prison system and both U.S.- and foreign-born persons in the community in Florida over a 7-year period (2009-2015). Genotyping by spacer oligonucleotide typing and 24-locus mycobacterial intersp...
To analyse VIM/IMP-type MBL-producing Enterobacteriaceae isolates identified in Poland during 2006-12. Isolates were typed by PFGE, followed by MLST. blaVIM/IMP genes were amplified and sequenced within class 1 integrons. Their plasmidic versus chromosomal location was assessed by nuclease S1 and I-...
No abstract available
Three German patients developed nosocomial pneumonia after cardiac surgery and had complex detected in respiratory specimens. Two patients died of septic multi-organ failure. Whole-genome sequencing detected genetically identical complex strains in patient samples, from a batch of octenidine mouth...
The introduction of genotypic tools to analyze isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of . This review integrates two approaches: on t...
We report invasive candidiasis caused by Candida viswanathii over 2 time periods during 2013-2015 in a tertiary care hospital in Chandigarh, India. Molecular typing revealed multiple clusters of the isolates. We detected high MICs for fluconazole in the second time period.
Group B Streptococcus (GBS) is one of the major pathogens in severe materno-neonatal infections. We aimed to describe the clinical and molecular characteristics of GBS isolates causing infections in 45 maternal and 50 neonatal subjects, collected from eight healthcare centres in mainland China over...
This article describes a CDI outbreak in a long-term care (LTC) facility that used molecular typing techniques and whole-genome sequencing to identify widespread dissemination of the clonal strain in the environment which was successfully removed after terminal cleaning. This study was conducted in...
In January 2015, Public Health England and the United Kingdom (UK) Ministry of Defence investigated cases of diarrhoea and fever in military personnel recently returned to the UK after supporting the response to the Ebola epidemic in Sierra Leone. Tests for Ebola virus infection were negative. PCR t...
The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses...
Traditional epidemiological investigation of nosocomial transmission of influenza involves the identification of patients who have the same influenza virus type and who have overlapped in time and place. This method may misidentify transmission where it has not occurred or miss transmission when it...
Time-stamped, trait-annotated phylogenetic trees built from virus genome data are increasingly used for outbreak investigation and monitoring ongoing epidemics. This routinely involves reconstructing the spatial and demographic processes from large data sets to help unveil the patterns and drivers o...
The aim of the study was to investigate cellulitis caused by Escherichia coli which has been responsible for economic and welfare problems in Danish broiler production between 2014 and 2016. The study included 13 flocks with unusually high condemnation rates due to cellulitis during a period of appr...
Mice in buildings are a hygiene hazard because they harbour several zoonoses and animal diseases. The aim of this study was to gather information on specific bacteria in house mice caught in the urban environment. Mice caught in snap traps during pest control activities were collected in and around...
Whole genome sequencing (WGS) helps to better investigate the transmission and characterization of meticillin-resistant Staphylococcus aureus (MRSA) strains. We describe the detection and unfolding of a prolonged and spatially distributed nosocomial outbreak of Panton-Valentine leucocidin (PVL)-posi...
The usefulness of colonization pressure as a working model and proxy for infection transmission is limited due to the inability to grade or quantify the specific risk within environments that are subject to change. To elaborate on the colonization pressure model by comparing the molecular epidemiolo...
Chikungunya virus (CHIKV) and dengue virus (DENV) are important arboviruses transmitted by Aedes mosquitoes. These viruses are known to coexist within the same vector and coinfect the same host. Although information is available on the mechanism of replication of CHIKV and DENV when present independ...
Screening and identification of methicillin-resistant Staphylococcus aureus (MRSA) carriage are helpful for controlling MRSA dissemination in hospitals. The aim of our study was to determine the prevalence of nasal carriages and diversity of MRSA among patients and healthcare workers (HCWs) at two r...
The dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli belonging to high-virulent pandemic lineages has become a global problem with serious consequences for public health worldwide. In this regard, E. coli lineages belonging to the sequence type ST648, which are mostly...
The diffusion of carbapenemase-producing Enterobacteriaceae (CPE) represents a worldwide public health problem. This study revealed that the prevalence of OXA-48-producing enterobacteria was 4.6% (19/414) and 1.6% (7/422) in mothers and newborns, respectively, from 2 maternity units in Algeria. Prev...
(MDMV) is a serious maize pathogen, epidemic worldwide, and one of the most common virus diseases for monocotyledonous plants, causing up to 70% loss in corn yield globally since 1960. MDMV belongs to the genus Potyvirus () and was first identified in 1964 in Illinois in corn and Johnsongrass. MDMV...
Neonatal sepsis is a leading cause of morbidity and mortality in neonatal units worldwide. Meticillin-resistant Staphylococcus aureus (MRSA) has become a leading causative pathogen. Many neonatal units experience endemic colonization and infection of their infants, which is often very challenging to...
, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant (MRS...
Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly ev...
Adenoviruses are significant pathogens for the immunocompromised, arising from primary infection or reinfection. Serotyping is insufficient to support nosocomial transmission investigations. We investigate whether whole-genome sequencing (WGS) provides clinically relevant information on transmission...
Cycloviruses, small ssDNA viruses belonging to the Circoviridae family, have been suggested as possible causes of enteric, respiratory and neurological disorders in human patients. One of these species, cyclovirus-Vietnam (CyCV-VN), initially isolated from cerebrospinal fluid samples of patients wit...
There is an ongoing global pandemic of human respiratory syncytial virus (RSV) infection that results in substantial annual morbidity and mortality. In Australia, RSV is a major cause of acute lower respiratory tract infections (ALRI). Nevertheless, little is known about the extent and origins of th...
Nontyphoidal (NTS), particularly serovar Typhimurium, is among the leading etiologic agents of bacterial enterocolitis globally and a well-characterized cause of invasive disease (iNTS) in sub-Saharan Africa. In contrast, Typhimurium is poorly defined in Southeast Asia, a known hot spot for zoono...
Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the ide...
Recently, mammalian orthoreoviruses (MRVs) were detected for the first time in European bats, and the closely related strain SI-MRV01 was isolated from a child with severe diarrhoea in Slovenia. Genetically similar strains have also been reported from other mammals, which reveals their wide host dis...
Diarrhea is a major source of morbidity and mortality among young children in low-income and middle-income countries. Human adenoviruses (HAdV), particular HAdV species F (40, 41) has been recognized as important causal pathogens, however limited data exist on molecular epidemiology of other HAdV as...
Outbreaks of adenovirus in neonatal intensive care units (NICUs) can lead to widespread transmission and serious adverse outcomes. We describe the investigation, response, and successful containment of an adenovirus outbreak in a NICU associated with contaminated handheld ophthalmologic equipment us...
In early 2017, a United Kingdom (UK)-born person in their 20s presented with a skin ulcer on the foot 3 weeks after returning from Ghana. The patient had last received a diphtheria-containing vaccine in 2013, completing the recommended course. MALDI-TOF of a cutaneous swab identified . Real-time PCR...
In Italy, there are limited studies on the molecular epidemiology of Clostridium difficile, possibly due to insufficient laboratory diagnostic capacity, low awareness and lack of high-quality surveillance systems. The aim of this study was to evaluate the diffusion of C. difficile in a tertiary care...
The increase in infections as a result of MDR strains of Escherichia coli is a global health crisis. The emergence of globally disseminated lineages of E. coli carrying ESBL genes has been well characterized. An increase in strains producing carbapenemase enzymes and mobile colistin resistance is no...
HIV patients form clusters in HIV transmission networks. Accurate identification of these transmission clusters is essential to effectively target public health interventions. One reason for clustering is that the underlying contact network contains many local communities. We present a new maximum-l...
In evolutionary biology and epidemiology, phylodynamic methods are widely used to infer population biological characteristics, such as the rates of replication, death, migration, or, in the epidemiological context, pathogen spread. More recently, these methods have been used to elucidate the dynamic...
Tinea pedis and tinea unguium are common infectious diseases, and many elderly people are reported to contract these infections. In this study, to investigate whether strains of the same origin are spreading inside a long-term care facility, we analyzed Trichophyton rubrum and Trichophyton mentagrop...
The aim of this retrospective study was to investigate the resistance determinants and genetic relatedness of colistin-resistant Klebsiella pneumoniae (Col-Kp) isolates in the National Bone Marrow Transplant Center of Tunis (NBMTC) between 2002 and 2013. Minimum inhibitory concentrations (MICs) for...
Carbapenem antibiotics are one of the last-resort agents against multidrug-resistant (MDR) bacteria. The occurrence of carbapenemase-producing Enterobacteriaceae (CPE) in wastewater and aquatic environments is an indication of MDR bacteria in the community. This study evaluated CPE in aquatic enviro...
Enterohemorrhagic Escherichia coli (EHEC) O26:H11/H, the most common non-O157 serotype causing hemolytic uremic syndrome worldwide, are evolutionarily highly dynamic with new pathogenic clones emerging rapidly. Here, we investigated the population structure of EHEC O26 isolated from patients in seve...
Nontyphoidal Salmonella is the leading cause of bacterial gastroenteritis in the United States. Meal replacement products containing raw and "superfood" ingredients have gained increasing popularity among consumers in recent years. In January 2016, we investigated a multistate outbreak of infections...
Clostridium difficile infection (CDI) is a major cause of morbidity and mortality in North America and Europe. The aim of this study was to identify epidemiologically-confirmed cases of community-acquired (CA)-CDI in a large North American urban center and analyze isolates using multiple genetic and...
Most nursing facilities (NFs) lack methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) surveillance programs due to limited resources and high costs. We investigated the utility of environmental screening of high-touch surfaces in patient rooms as a way to...
Multidrug-resistant organisms (MDROs) are an important cause of morbidity and mortality after solid organ transplantation. We aimed to characterize MDRO colonization dynamics and infection in liver transplant (LT) recipients through innovative use of active surveillance and whole-genome sequencing (...
Human rhinovirus (HRV) can cause severe illnesses in hospitalized patients. However, there are no studies regarding the prevalence of HRV infection, particularly the recently identified HRV-C, in hospitalized patients reported from Taiwan. Respiratory specimens collected from 487 hospitalized patien...
Staphylococcal food poisoning (SFP) is one of the most common food-borne diseases in the world. Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and spa typing methods were used to characterize Staphylococcus aureus isolates from food surveillance during 2013-2015 in southw...
The increasing trend of ceftriaxone resistant non-typhoidal Salmonella (NTS) worldwide is of serious concern, however, data is lacked in southern Taiwan. Salmonella isolates were collected at a regional hospital in Kaohsiung during 2004-2013. Ceftriaxone resistant NTS isolates were further character...
Huanglongbing (HLB), also known as citrus greening disease, is the most serious disease of citrus plants. It is associated with the Gram-negative bacterium ' Candidatus Liberibacter asiaticus' ( CLas), which is transmitted between host plants by the hemipteran insect vector Diaphorina citri in a cir...
Vancomycin resistance increased significantly to 31.3% among Enterococcus faecium in 2006 and remained high thereafter at a university hospital in Taiwan. A longitudinal study was retrospectively conducted to characterize these vancomycin-resistant E. faecium (VRE-fm). A total of 378 non-repetitive...
To investigate the resistance mechanisms of tigecycline-non-susceptible Acinetobacter baumannii and for providing the evidence of the control of nosocomial infection and rational use of antibiotics. The minimum inhibitory concentrations (MICs) of 94 non repetitive tigecycline-non-susceptible A. baum...
Human enteroviruses are a major cause of neurological and other diseases. More than 100 serotypes are known that exhibit unexplained complex patterns of incidence, from regular cycles to more irregular patterns, and new emergences. Using 15 years of surveillance data from Japan (2000-2014) and a sto...
To describe a hospital outbreak of influenza B virus (InfB) infection during season 2015/2016 by combining clinical and epidemiological data with molecular methods. Twenty patients diagnosed with InfB from a hospital outbreak over a four-week-period were included. Nasopharyngeal samples (NPS) positi...
We determined the molecular epidemiology of Bordetella pertussis isolates to evaluate its potential impact on pertussis reemergence in a population of Mexico. Symptomatic and asymptomatic cases were included. Pertussis infection was confirmed by culture and real-time polymerase chain reaction (PCR)....
The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approache...
Bovine mastitis has been a concern for dairy herd for decades. The adaptation capacity of one of the main species responsible for this disease, Staphylococcus aureus (S. aureus), plays a pivotal role in this issue. The aim of this study was to establish a molecular and phenotypic profile of 285 S. a...
Human adenovirus (HAdV) infection is prevalent and has an important clinical impact on children. We aim to investigate the molecular epidemiology of HAdV infection and discover the correlations between clinical features and HAdV species in an HAdV outbreak of 2014. This is a retrospective study, enr...
No abstract available
Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions...
Streptococcus suis (S. suis) is an important emerging zoonotic agent. Here, we report two cases of S. suis infection in pig farmers in Gunma Prefecture, Japan. We conducted a high-resolution molecular epidemiologic analysis on the basis of whole-genome sequencing data of each isolate using next-gene...
A total of 592 people reported gastrointestinal illness following attendance at Street Spice, a food festival held in Newcastle-upon-Tyne, North East England in February/March 2013. Epidemiological, microbiological and environmental investigations were undertaken to identify the source and prevent f...
Cystic fibrosis (CF) is an inherited recessive disease that affects mucocillary clearance in the lung, allowing it to be colonised with bacteria such as Staphylococcus aureus. To survive in the CF lung S. aureus adapts both phenotypically and genotypically, through various mechanisms. In this study,...
Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states. We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG,...
The recent convergence of genetic elements encoding phenotypic carbapenem-resistance and hypervirulence within a single Klebsiella pneumoniae host strain represents a major public concern. To obtain a better understanding of the genetic characteristic of this emerging 'superbug', the complete genome...
Genetic background and molecular characteristics of Staphylococcus aureus collected from patients with skin and soft tissue infections were studied in the North-Central region of Bangladesh from 2015 to 2016. Among 430 clinical isolates, methicillin-resistant S. aureus (MRSA) accounted for 31% havin...
Spotty Liver Disease is an acute infectious disease of layer chickens that was likely first described in the USA and Canada in the 1950s and 1960's. The disease occurs almost exclusively in barn and free-range production systems. Outbreaks usually, but not exclusively occur in young layers (≅25 week...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major multidrug-resistant (MDR) opportunistic pathogen that is responsible for nosocomial infections worldwide. The emergence of MRSA in food-producing animals has heightened concerns regarding the presence of MRSA in foods having an animal ori...
In Canada, tuberculosis disproportionately affects foreign-born and First Nations populations. Within First Nations' peoples, a high proportion of cases occur in association with outbreaks. Tuberculosis transmission in the context of outbreaks is thought to result from the convergence of several fac...
Pepper mild mottle virus (PMMoV) is one of the most destructive pathogens of pepper crops and has major impacts on global crop yields. Some aspects of the molecular biology of PMMoV have been studied intensively, but estimates of its evolutionary rate have shown considerable variation. We investigat...
We aimed to determine the genetic diversity, phylogenetic relationship and transmission dynamics of Mycobacterium tuberculosis complex (MTBC) genotypes in an area with high tuberculosis (TB) incidence. A set of 164 MTBC isolates from new TB patients of Golestan province, Iran, were subjected to geno...
Avian pox is an infectious disease caused by avipoxviruses (APV), resulting in cutaneous and/or tracheal lesions. Poxviruses share large genome sizes (from 130 to 360 kb), featuring repetitions, deletions or insertions as a result of a long-term recombination history. The increasing performances of...
Adolfo Lutz Institute in Sao Paolo State performs mycobacterial identification for many healthcare units, and in 2008 identified a possible outbreak involving patients submitted to bronchoscopy at the same hospital. This study aimed to analyse the clonality of isolates. Mycobacterium abscessus subsp...
sasX is a colonization-virulence factor that potentially underlies the success of methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 239 in Asia. We aimed to study the spread of sasX and the population structure of MRSA in two geographically distinct regions, Europe and India. MRS...
Microsporum canis is a zoophilic dermatophyte, which is very contagious, especially to cats and dogs. Asymptomatic animal carriers of M. canis are regarded a critical factor in the epidemiology of the disease. The aim of this study was to investigate the epidemiological origin of M. canis isolates u...
In 2015 an increased incidence of invasive meningococcal disease due to serogroup-C (MenC) occurred in Tuscany, Italy. This led the Regional Health Authority of Tuscany to implement a reactive immunisation campaign and to launch an epidemiological field investigation aiming to address targeted immun...
Background and aimThe trend in reported case counts of invasive (), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/EEA). We aimed to validate the microbiological and epidemiological aspects...
Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a challenging nosocomial pathogen in the last 50 years. To describe an investigation and containment of an MRSA outbreak in a neonatal intensive care unit (NICU). Our NICU is a 25-bed level III unit. Almost 540 neonates are admitted y...
To investigate the genetic background for the emergence of macrolide resistance, we characterized the genetic features of Mycoplasma pneumoniae using multilocus sequence typing. Of the 146 M. pneumoniae strains collected during the 5 consecutive outbreaks of M. pneumoniae pneumonia during 2000-2016...
On 10 August 2016, the Maricopa County Department of Public Health identified culture-confirmed Salmonella enterica serotype Javiana isolates from two persons who reported eating at a seafood restaurant; seven additional cases were reported by 15 August. We investigated to identify a source and prev...
We conducted a nationwide molecular epidemiological study of Clostridium difficile infection (CDI) in Japan investigated the correlation between the presence of binary toxin genes and CDI severity. This is the first report on molecular epidemiological analyses for CDI in multiple university hospital...
Advances in sequencing techniques, improved computational methods of sequence interrogation and more accurate collection of epidemiological data through Global Positioning System (GPS) technology are improving our ability to monitor rabies outbreaks and better understand the processes that affect vi...
BackgroundRemarkably high carriage prevalence of a community-associated meticillin-resistant (MRSA) strain of sequence type (ST) 22 in the Gaza strip was reported in 2012. This strain is linked to the pandemic hospital-associated EMRSA-15. The origin and evolutionary history of ST22 in Gaza communi...
Hospital-acquired aspergillosis is usually associated with environmental contamination. In 2015, continuous monitoring of airborne fungi and multilocus variable-number tandem-repeat analysis identified the source of Aspergillus fumigatus as the airway of a patient. Therefore, patients colonized with...
The present review summarizes new knowledge about Legionella epidemiology, clinical characteristics, community-associated and hospital-based outbreaks, molecular typing and molecular epidemiology, prevention, and detection in environmental and clinical specimens. The incidence of Legionnaire's disea...
Pseudomonas aeruginosa is a ubiquitous and important opportunistic pathogen in immunocompromised or critically ill patients. Nosocomial P. aeruginosa outbreaks have been associated with hospital water sources. To describe engineering interventions to minimize contamination of water outlets and the s...
An outbreak of enterohemorrhagic Escherichia coli (EHEC) O157:H7 infection occurred in October 2016 in Kanagawa, Japan. A total of 61 patients and 17 asymptomatic cases of EHEC O157:H7 infection were confirmed by laboratory testing. Among them, 24 patients were hospitalized and 4 developed hemolytic...
Leptospirosis is a globally distributed zoonosis. Epidemiological data are scarce and present major challenge because of the varied clinical presentations. Multilocus Sequence Typing has already proven to be a robust molecular typing method providing accurate results for strain characterization. We...
Avian-origin H3N2 canine influenza virus (CIV) transferred to dogs in Asia around 2005, becoming enzootic throughout China and South Korea before reaching the United States in early 2015. To understand the posttransfer evolution and epidemiology of this virus, particularly the cause of recent and on...
There is an increase in the number of Enterobacteriaceae with Extended-spectrum beta-lactamase (ESBL) type of antibiotic resistance in the Kingdom of Bahrain. However, the virulence determinants of the clinical isolates have not been previously assessed. The current study investigates the distributi...
The current paradigm for hospital outbreak detection and investigation is based on methodology first developed over 150 years ago. Daily surveillance to detect patients positive for pathogens of particular importance for nosocomial infection is supported by epidemiological investigation to determine...
Invasive aspergillosis (IA) in immunocompromised patients has been associated with demolition in or adjacent to hospitals. In recent years, azole-resistant clinical isolates of Aspergillus fumigatus, the most common agent of IA, have emerged in Western Europe and are spreading globally. To determine...
Salmonella enterica serovar Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as fruits, vegetables, seeds and spices. Studies have shown that Montevideo also is frequently associated with healthy cattle and can be isolated from ground bee...
Peste des petits ruminants (PPR) is an endemic and highly infectious disease of several tropical countries, including Pakistan. Despite exhaustive vaccination, outbreaks are on the rise annually across different parts of the country. Clinical outcomes are largely employed to diagnose disease, while...
Contact tracing requires reliable identification of closely related bacterial isolates. When we noticed the reporting of artifactual variation between isolates during routine next-generation sequencing of spp., we investigated its basis in 2,018 consecutive isolates. In the routine process used,...
Routine use of whole-genome analysis for infectious diseases can be used to enlighten various scenarios pertaining to public health, including identification of microbial pathogens, relating individual cases to an outbreak of infectious disease, establishing an association between an outbreak of foo...
This study investigated the transmission cycle of methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus pseudintermedius (MRSP) in small companion animal veterinary practice. Sampling was undertaken at two small animal veterinary hospitals in Sydney, Australia. Samples were collected...
Measuring contemporary dispersal in highly mobile terrestrial species is challenging, especially when species are characterized by low levels of population differentiation. Directly transmitted viruses can be used as a surrogate for traditional methods of tracking host movement. Feline immunodeficie...
Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD), which is a commercially important disease of farmed salmonids. Typing by conventional methods provides limited information on the evolution and spread of this pathogen, as there is a low level of standing variation...
Over the last decade, many scientific disciplines have been impacted by the dawn of new sequencing techniques (HTS: high throughput sequencing). Plant pathology and more specifically virology have been greatly transformed by this 'metagenomics' paradigm shift. Such tools significantly facilitate dis...
Africa has the highest incidence of gonorrhea in the world. However, little is known about gonococcal populations in this continent or mechanisms of antimicrobial resistance (AMR). Whole-genome sequence data were analyzed from 103 Neisseria gonorrhoeae isolates from 73 patients, mainly men who have...
Antimicrobial resistance (AMR) is a global public-health emergency, which threatens the advances made by modern medical care over the past century. The World Health Organization has recently published a global priority list of antibiotic-resistant bacteria, which includes extended-spectrum β-lactama...
The aim was to investigate an outbreak of invasive meningococcal disease (IMD) in Southern Sardinia. Epidemiological and microbiological investigations were performed. The latter included antimicrobial susceptibility testing and whole-genome sequencing (WGS). Seven individuals with severe IMD were f...
To investigate the prevalence and evolution of the H6 subtype avian influenza viruses (AIVs) circulating in poultry in China from 2011 to 2016, 11 molecular epidemiological surveys was performed in this study. In total, 893 H6 subtype viral strains were isolated from 67,639 swab samples and 360 envi...
sequence type 410 (ST410) has been reported worldwide as an extraintestinal pathogen associated with resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In the present study, we investigated national epidemiology of ST410 isolates from Danish patients. Furthermore, ST...
While typing methods are increasingly refined, the sampling of bacteria to be typed in healthcare-associated infection context retains less attention. Through 2 emblematic cases of in-hospital transmission of extensively drug-resistant bacteria producing carbapenemases, we demonstrate the impact of...
Tribal individuals presented with fever and uni- or bi-lateral parotitis in Galonda and Silli villages (Dadra and Nagar Haveli, India) between 2 October 2016 and 19 March 2017. Consequently, the magnitude and epidemiological characteristics of the outbreak were investigated. Overall, 139 cases of su...
The biogeographic histories of parasites and pathogens are infrequently compared with those of free-living species, including their hosts. Documenting the frequency with which parasites and pathogens disperse across geographic regions contributes to understanding not only their evolution, but also t...
The Candida parapsilosis complex species has emerged as an important cause of human disease. The molecular identification of C. parapsilosis isolates at the species level can be helpful for epidemiological studies and then for the establishment of appropriate therapies and prophylactic measures. The...
Pseudomonas aeruginosa is one of the most important pathogens worldwide. Population genetics studies have shown that the P. aeruginosa population has an epidemic structure with highly conserved clonal complexes. Nonetheless, epidemiological studies of P. aeruginosa have been historically absent or i...
Mobile genetic elements (MGEs) that frequently transfer within and between bacterial species play a critical role in bacterial evolution, and often carry key accessory genes that associate with a bacteria's ability to cause disease. MGEs carrying antimicrobial resistance (AMR) and/or virulence deter...
Bacillus endophyticus is a soil plant-endophytic bacterium, while B. anthracis is the causative agent of anthrax. The virulence factors of B. anthracis are the plasmid encoded tripartite toxins (pXO1) and poly-γ-glutamic acid (PGA) capsule (pXO2). B. endophyticus isolated alongside B. anthracis from...
Outbreaks of fever of unknown origin start with nonspecific symptoms and case definition is only slowly developed and adapted, therefore, identifying the causative agent is crucial to ensure suitable treatment and control measures. As an alternative method for Polymerase Chain Reaction in molecular...
In September 2015, an outbreak of Escherichia coli Phage Type 32 with an indistinguishable multi locus variable number tandem repeat analysis profile was identified in Scotland. Twelve cases were identified; nine primary cases, two secondary and one asymptomatic case. Extensive food history investig...
In recent years, the wearing of pierced earrings for personal adornment has increased among health care workers in Japan. However, the transmission dynamics between bacteria in pierced earring holes and fingers has not been clearly shown. Earlobes and fingers of 200 nurses (128 nurses with pierced e...
Carbapenem-resistant Klebsiella pneumoniae infections are associated with increased rates of treatment failure and death. Several studies have reported isolates with a combined hypervirulent and antimicrobial-resistant phenotype. In this study, the molecular characteristics of hypervirulent K. pneum...
Trichophyton verrucosum is a zoophilic fungus that is the most frequent aetiological agent of dermatophytosis in cattle. During the last few years, the number of cases of T. verrucosum from humans has been increasing constantly, which is correlated with the presence of cattle-rearing farms. We ident...
New Zealand has a relatively high incidence of human cases of Shiga toxin-producing (STEC), with 8.9 STEC cases per 100,000 people reported in 2016. Previous research showed living near cattle and contact with cattle feces as significant risk factors for STEC infections in humans in New Zealand, bu...
Although pediatric Clostridium difficile infections (CDIs) are increasing, C. difficile transmission patterns among children are poorly understood. We performed whole genome sequencing (WGS) on C. difficile isolates collected from children diagnosed with CDI between December 2012 and December 2013 a...
Marine microbes encounter a myriad of biotic and abiotic factors that can impact fitness by limiting their range and capacity to move between habitats. This is especially true for environmentally transmitted bacteria that cycle between their hosts and the surrounding habitat. As geologic history, bi...
A large outbreak of vancomycin-resistant enterococci (VRE) is affecting four hospitals in the Canton of Bern, Switzerland, since December 2017. Of 89 cases identified as carriers, 77 (86.5%) VRE isolates were virtually indistinguishable using whole genome sequencing, and identified as multilocus seq...
During January 2013-April 2014, we subjected nasopharyngeal specimens collected from patients with acute febrile respiratory illness in a military hospital to PCR testing to detect 12 respiratory viruses and sequence a partial hexon gene for human adenovirus (HAdV) molecular typing. We analyzed the...
Whole-genome sequencing unveiled host and environment-related insights to Shigella sonnei transmission within cyclic epidemics during 2000-2012 in Israel. The Israeli reservoir contains isolates belonging to S. sonnei lineage III but of different origin, shows loss of tetracycline resistance genes,...
Carbapenem-resistant (CRKP) has emerged as a major challenge for global healthcare systems. The objectives of this study were to determine the nosocomial spread of CRKP clones and analyse the molecular characteristics of CRKP in our hospital. Ninety-eight non-duplicated clinical CRKP isolates were...
The aim of this work was to investigate the presence of selected potential virulence factors, susceptibility and clonal relatedness among 63 isolates recovered from patients exposed to invasive devices in a university hospital in Argentina between January 2004 and August 2012. Genetic relatedness w...
Non-typhoidal is the most common foodborne bacterial pathogen in most countries. It is widely present in food animal species, and therefore blocking its transmission through the food supply is a prominent focus of food safety activities worldwide. Antibiotic resistance in non-typhoidal arises in l...
Detecting de novo mutations in viral and bacterial pathogens enables researchers to reconstruct detailed networks of disease transmission and is a key technique in genomic epidemiology. However, these techniques have not yet been applied to the malaria parasite, Plasmodium falciparum, in which a lar...
Desiccation tolerance increases Staphylococcus aureus survival and risk of transmission. A better understanding of factors driving intraoperative transmission of S. aureus pathogens may lead to innovative improvements in intraoperative infection control. To determine whether desiccation tolerance is...
Pseudomonas aeruginosa (PA) is a Gram-negative environmental organism that can cause severe infection in immunosuppressed patients, including preterm neonates. In recent years, it has become common practice to screen neonates for PA colonization. To assess the value of screening neonates for PA in (...
No abstract available
For many years, patient-area wastewater drains (ie, sink and shower drains) have been considered a potential source of bacterial pathogens that can be transmitted to patients. Recently, evolving genomic epidemiology tools combined with new insights into the ecology of wastewater drain (WWD) biofilm...
Avian influenza A viruses (AIVs) pose a threat to global health because of their sporadic zoonotic transmission and potential to cause pandemics. Genomic surveillance of AIVs has become a powerful, cost-effective approach for studying virus transmission, evolution, and dissemination, and has the pot...
Burkholderia pseudomallei, the causative agent for melioidosis, has become a public health problem in India and across the world. Melioidosis can be difficult to diagnose because of the inconsistent clinical presentations of the disease. This study aims to determine the genetic diversity among the c...
In North America, the raccoon-associated variant of rabies virus (RRV) is of special concern, given its relatively rapid spread throughout the eastern USA and its potential public health impact due to high raccoon host densities in urban areas. Northward expansion of this epizootic included an outbr...
Although much focus is placed on cholera epidemics, the greatest burden occurs in settings in which cholera is endemic, including areas of South Asia, Africa and now Haiti. Dhaka, Bangladesh is a megacity that is hyper-endemic for cholera, and experiences two regular seasonal outbreaks of cholera ea...
Enterovirus A71 (EV-A71) is an important nonpolio enterovirus that causes severe neurological complications. In 1998, Taiwan experienced an EV-A71 outbreak that caused 78 deaths. Since then, periodic epidemics of EV-A71 associated with newly emerging strains have occurred. Several of these strains a...
The review uses the , the gastric bacterium that colonizes the human stomach, to address how to obtain information from bacterial genomes about prophage biology. In a time of continuous growing number of genomes available, this review provides tools to explore genomes for prophage presence, or other...
'Candidatus Liberibacter solanacearum' (CLso) haplotype C is associated with disease in carrots and transmitted by the carrot psyllid Trioza apicalis. To identify possible other sources and vectors of this pathogen in Finland, samples were taken of wild plants within and near the carrot fields, the...
Enterococcus faecalis is commonly found as a commensal gut bacteria, but some linages have caused increasing extra-gastrointestinal infections. In particular, strains with high-level virulence or antimicrobial resistance are prevalent in healthcare settings as nosocomial pathogens. This study was pe...
Carbapenem-resistant Acinetobacter baumannii (CRAB) infections are an increasing concern in intensive care units (ICUs) worldwide. The combination of carbapenemases and 16S rRNA-methyltransferases (16S-RMTases) further reduces the therapeutic options. OXA-carbapenemase/A. baumannii clone tandems in...
Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographi...
A foodborne outbreak of VIM carbapenemase-expressing Citrobacter freundii (CPC) occurred between February 2016 and June 2016 at a major university hospital in Germany. An explosive increase in CPC isolated from rectal swabs of patients during weekly routine screening led to the declaration of an out...
Since 2012-2016 an increased number of listeriosis cases, especially from one region of the Czech Republic, were observed. Most of them were caused by strains of serotype 1/2a, clonal complex 8, indistinguishable by pulsed-field gel electrophoresis. Twenty-six human cases were reported, including tw...
Carbapenem resistance in Gram-negative bacteria constitutes a major clinical problem. We characterized molecular features among carbapenem-resistant Gram-negative clinical isolates collected from Southeastern Tunisian Island Hospital. Eighteen carbapenem-resistant clinical isolates (13 Klebsiella pn...
Severe infections due to methicillin-resistant Staphylococcus aureus (MRSA) have been increasingly recognized in virtually all fields of veterinary medicine. Our objective was to study the occurrence, phylogenetic relationships and antimicrobial resistance properties of MRSA isolated from ocular sur...
The aim of this study was to characterize the fluoroquinolone (FQ) resistance mechanism of serovar Typhi and Paratyphi A in Bangladesh. Typhi isolates were classified into sequence type (ST) 1, ST2, and ST2209 and Paratyphi A isolates were classified into ST85 and ST129. The most common STs of th...
The spread of Panton-Valentine leukocidin (PVL)-carrying strains in both hospital and the community is a significant worldwide problem. The aim of the study was to investigate the clonal dissemination pattern of PVL-producing strains isolated from hospitalized patients in Tehran, Iran. In this cro...
Multidrug-resistant Candida auris has emerged as a cause of insidious hospital outbreaks and complicated infections. We present the analysis of an ongoing C. auris outbreak including the largest published series of C. auris bloodstream infection. All C. auris-positive patients from April-2016 to Jan...
Nosocomial infections caused by methicillin resistant (MRSA) and emergence of vancomycin resistant (VRSA) have led to great concern in healthcare settings worldwide. A total of 100 clinical isolates from hospitalized patients were investigated for antimicrobial susceptibility, the presence of re...
Foodborne non-typhoidal salmonellosis causes approximately 1 million illnesses annually in the USA. In April 2015, we investigated a multistate outbreak of 65 Salmonella Paratyphi B variant L(+) tartrate(+) infections associated with frozen raw tuna imported from Indonesia, which was consumed raw in...
High-level resistance and treatment failures with ceftriaxone and azithromycin, the first-line agents for gonorrhoea treatment are reported and antimicrobial-resistant Neisseria gonorrhoeae is an urgent public health threat. Our aims were to determine antimicrobial resistance rates, resistance deter...
A matched 1:2 case-control study was conducted among critically ill patients in order to identify the risk factors of colistin or tigecycline-resistant carbapenemase-producing Klebsiella pneumoniae (ColR-Kp, TigR-Kp) bacteraemia. MIC to colistin and tigecycline were determined by Etest. From 224 bac...
Infections with Neisseria gonorrhoeae, a sexually transmitted pathogen that causes urethritis, cervicitis, and more severe complications, are increasing. Gonorrhea is typically treated with antibiotics; however, N. gonorrhoeae has rapidly acquired resistance to many antibiotic classes, and lineages...
H5 and H7 subtypes of low pathogenicity avian influenza viruses (LPAIVs) have the potential to evolve into highly pathogenic avian influenza viruses (HPAIVs), causing high mortality in galliforme poultry with substantial economic losses for the poultry industry. This study provides direct evidence o...
International Health Regulations controls international travel including human movement, disease vector, and imported items to prevent the spread of dengue, especially in seaports, airports, and border crossing posts. This study aimed to determine dengue Transovarial Transmission Index (TTI) and dis...
HIV is notorious for its rapid evolution since its transmissions from monkey to human. Currently, HIV contains multiple subtypes, circulating recombinant forms (CRFs) and unique recombinant forms (URFs). Here, from an HIV-positive mother and her child in Tianjin, China, we identified a novel HIV-1 s...
The genus Dichorhavirus includes plant-infecting rhabdoviruses with bisegmented genomes that are horizontally transmitted by false spider mites of the genus Brevipalpus. The complete genome sequences of three isolates of the putative dichorhavirus clerodendrum chlorotic spot virus were determined us...
For almost 50 years sub-Saharan Africa, including Uganda, has experienced several outbreaks due to Vibrio cholerae. Our aim was to determine the genetic relatedness and spread of strains responsible for cholera outbreaks in Uganda. Sixty-three V. cholerae isolates collected from outbreaks in Uganda...
Because the epidemiology of Clostridium difficile infection (CDI) is region-specific, the present study was undertaken to examine the epidemiology of C difficile outbreaks in Beijing, China.Eighty nonduplicate isolates were collected from March, 2016 to December, 2016. The molecular type and phyloge...
VRE are prevalent among patients in ICUs. Non-typeable vanA VRE, due to loss of one of the genes used for MLST (pstS), have increased in Australia, suggestive of a new, hospital-acquired lineage. To understand the significance of this lineage and its transmission using WGS of strains isolated from p...
No abstract available
We describe an outbreak that contributed to a near doubling of the incidence of tuberculosis in Southampton, UK. We examine the importance of 24 locus mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU-VNTR) genotyping in its identification and management and the role of...
Correction to: Emerging Microbes & Infections (2018) 7,43 https://doi.org/10.1038/s41426-018-0045-x ; published online 29 March 2018.
The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expans...
Benzalkonium chlorides (BAC) are commonly used biocides in broad-spectrum disinfectant solutions. How microorganisms cope with BAC exposure remains poorly understood, despite its importance for disinfection and disinfectant-induced antibiotic resistance. To provide insights into these issues, we exp...
New Delhi metallo-β-lactamase (NDM)-producing Acinetobacter baumannii have been described in several countries worldwide, and studies have suggested that Acinetobacter spp. could play the role of intermediate progenitor of the bla gene between environmental progenitor and Enterobacteriaceae. In tota...
To assess the impact of the incidental relocation of an intensive care unit (ICU) on the risk of colonizations/infections with Pseudomonas aeruginosa exhibiting OprD-mediated resistance to imipenem (PA-OprD). The primary aim was to compare the proportion of PA-OprD among P. aeruginosa samples before...
Recent reports have established the escalating threat of carbapenem-resistant complex (CREC). Here, we demonstrate that CREC has evolved as a highly antibiotic-resistant rather than highly virulent nosocomial pathogen. Applying genomics and Bayesian phylogenetic analyses to a 7-year collection of C...
Despite the high reported rates of surgical site infections (SSIs) caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (EPE) in low-income countries, including Tanzania, the role of EPE carriage in subsequent occurrence of SSIs is not known. This study investigated the rat...
The spread of carbapenemase-producing Enterobacteriaceae in the Southwest Indian Ocean islands is poorly known. Here we describe an outbreak of colistin-resistant Enterobacter cloacae harbouring bla in the French overseas department of Mayotte. Between October 2015 and January 2017, all isolates of...
The prevalence of C. difficile infection (CDI) and severe CDI are influenced by the prevalence of specific C. difficile strains, which are themselves influenced by antimicrobial susceptibility determinants as well as antimicrobial usage patterns. Restriction endonuclease analysis (REA) typing and an...
Ocular infections caused by human adenovirus (HAdV) are highly contagious. The most severe are usually caused by members of species HAdV-D (types HAdV8, 19, 37, 53, 54, and 56) and can manifest as epidemic keratoconjunctivitis (EKC), often resulting in prolonged impairment of vision. During the earl...
As whole-genome sequencing becomes an established component of the microbiologist's toolbox, it is imperative that researchers, clinical microbiologists, and public health professionals have access to genomic analysis tools for the rapid extraction of epidemiologically and clinically relevant inform...
A carbapenem-resistant isolate was recovered from human blood. Its whole-genome sequence was obtained using Illumina and long-read MinION sequencing. The strain belongs to sequence type 273 (ST273), which was found recently and caused an outbreak in Southeast Asia. It has two carbapenemase genes,...
The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZI...
Sexually transmissible enteric infections (STEIs) are commonly associated with transmission among men who have sex with men (MSM). In the past decade, the UK has experienced multiple parallel STEI emergences in MSM caused by a range of bacterial species of the genus Shigella, and an outbreak of an u...
Multiple invasive group A Streptococcus (GAS) infections were reported to public health by a skilled nursing facility (facility A) in Illinois between May 2014 and August 2016. Cases continued despite interventions including antibiotic prophylaxis for all residents and staff. Two other geographicall...
Aedes vittatus is currently found in Africa, Asia and Europe, where it acts as a vector of pathogens causing animal and human diseases (e.g. chikungunya, Zika and dengue). Like other Aedes species, Ae. vittatus is able to breed in artificial containers. The ECDC has recently highlighted the need for...
The American dog tick, Dermacentor variabilis, is an important vector of pathogens to humans, wildlife and domestic animals in North America. Although this tick species is widely distributed in the USA and Canada, knowledge of its range-wide phylogeographic patterns remains incomplete. We carried ou...
Extended spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) create a therapeutic challenge and have high potential for dissemination. The purpose of our study was to investigate the epidemiology of these infections in hematopoietic stem cell transplant (HSCT) recipients and to determine the...
Three cases of cholera occurred in South Korea during a period of three weeks in August 2016. All the cases were associated with the consumption of raw seafood in southern coastal area of South Korea. Epidemiologic investigations were performed to track the spread of cholera, including persons in co...
Porcine epidemic diarrhoea virus (PEDV) is a globally emerging and re-emerging enteric coronavirus in pigs causing serious economic threats to the world swine industry. Since the re-emergence of massive PEDV outbreaks in South Korea in 2013-2014, domestic pig farms have continued to experience PED e...
Pseudomonas aeruginosa is one of the most important causes of infection in intensive care units (ICUs). It is intrinsically resistant to many antimicrobials and easily acquires additional resistance genes via horizontal gene transfer of mobile genetic elements. In this study, 1528 P. aeruginosa isol...
Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and to predict and infer transmission of antimicrobial resistance, and can enhance infection control through linkage with epid...
No abstract available
Enterobacter cloacae complex is a common cause of hospital outbreaks. A retrospective and prospective molecular analysis of carbapenem-resistant clinical isolates in a tertiary care center demonstrated an outbreak of a German-imipenemase-1 (GIM-1) metallo-beta-lactamase-producing Enterobacter hormae...
Brucella canis is one of zoonotic pathogens causing infection in human. In this study, we isolated and sequenced 38 B. canis strains from 11 cases. Core genome multilocus sequence typing analysis classified all B. canis isolates into two genogroups, GI and GII. All 38 isolates cluster together formi...
No abstract available
The global spread of carbapenem-resistant Klebsiella pneumoniae (CR-Kp) has become a massive threat to human health. We investigated the clonal relatedness of CR-Kp strains in central Taiwan. CR-Kp strains were prospectively collected from inpatients referred to Chung Shan Medical University Hospita...
Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with tradi...
Mycobacterium tuberculosis is a major health burden worldwide. The disease may present as an individual case, community outbreak, or more rarely as a nosocomial outbreak. Even in countries with a low prevalence such as the UK, tuberculosis (TB) presents a risk to healthcare workers (HCWs). To report...
OBJECTIVETo determine the incidence and risk factors associated with Clostridium difficile colonization among residents of nursing homes and to identify the ribotypes of circulating C. difficile strains.DESIGNA prospective cohort study with a follow-up duration of 22 months.SETTINGNursing homes.PART...
Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. To increase the number of complete sapovirus g...
An innovative metaomics approach integrating metatranscriptomics and metaproteomics was used to characterize bacterial communities in the microbiota of the Lyme borreliosis spirochete vector, Ixodes ricinus (Acari: Ixodidae). Whole internal tissues and salivary glands from unfed larvae and female ti...
The HCV evolutionary dynamics play a key role in the infection onset, maintenance of chronicity, pathogenicity, and drug resistance variants fixation, and are thought to be one of the main caveats in the development of an effective vaccine. Previous studies in HCV/HIV co-infected patients suggest th...
Okinawa Island, located in Southern Japan, has a higher prevalence rate of hepatitis C virus subtype 1a (HCV-1a) infection than that in mainland Japan. Okinawa has a history of US military occupation after World War II. To elucidate the transmission history of HCV-1a in Okinawa, 26 whole-genome sequ...
We characterised Lancefield group B streptococcal (GBS) isolates causing invasive disease among non-pregnant adults in Portugal between 2009 and 2015. All isolates (n = 555) were serotyped, assigned to clonal complexes (CCs) by multilocus sequence typing and characterised by surface protein and pilu...
Invasive meningococcal disease surveillance in Europe combines isolate characterisation and epidemiological data to support public health intervention. A representative European Meningococcal Strain Collection (EMSC) of IMD isolates was obtained, and whole genome sequenced to characterise 799 EMSC i...
We investigated a large outbreak of O157 in the United Kingdom (UK) with 165 cases between 31 May and 29 July 2016. No linked cases were reported in other countries. Cases were predominately female (n = 128) and adult (n = 150), 66 attended hospital and nine had features of haemorrhagic uraemic syn...
HPIVs are serologically and genetically grouped into four species that account for up to 10% of all hospitalizations due to acute respiratory infection in children under the age of five. Genetic and epidemiological data for the four HPIVs derived from two pediatric cohorts in Viet Nam are presented....
Identify the cause of outbreaks of diarrhoea during winter that are not attributable to gastrointestinal nematodes in weaned Merino sheep in the high rainfall regions of south-eastern Australia and determine the efficacy of antimicrobials used to treat this syndrome. We investigated 45 outbreaks on...
Staphylococcus aureus is a common causative agent of bovine mastitis in dairy cows and commonly associated with foodborne disease outbreaks. The aim of this study was to evaluate the presence of enterotoxin genes, agr typing, antimicrobial resistance, and genetic diversity of S. aureus isolated from...
Streptococcus gallolyticus ssp. gallolyticus (Sgg) is a commensal bacterium and an opportunistic pathogen. In humans it has been clinically associated with the incidence of colorectal cancer (CRC) and epidemiologically recognized as an emerging cause of infective endocarditis (IE). The standard ther...
Linezolid-resistant Staphylococcus epidermidis (LRSE) and linezolid-dependent ST22 strains have been shown to predominate in tertiary care facilities all over Greece. We report herein the dissemination of ST22 but also ST2, ST5 and ST168 linezolid-dependent LRSE clones in four unrelated German hospi...
Clostridium difficile strain DH/NAP11/106, a relatively antibiotic-susceptible strain, is now the most common cause of C. difficile infection (CDI) among adults in the USA. To identify mechanisms underlying the evolution and transmission of an MDR DH/NAP11/106 clone. WGS (Illumina MiSeq), restrictio...
This study was conducted to investigate the phenotypic and genotypic characteristics of vancomycin-resistant Enterococcus faecalis and Enterococcus faecium. Antibiotic resistance and virulence genes in the aforementioned resistant isolates were studied using the epsilometer (E)-test and polymerase c...
The spread and establishment of Chandipura virus (CHPV) infection in India has raised serious epidemiological concerns. The virus interface with the vertebrate hosts (including humans) and vector competence are the important parameters of disease prevalence. Interestingly, in the present study, a hi...
Contact tracing is a key part of tuberculosis prevention and care, aiming to hasten diagnosis and prevent transmission. The proportion of case-contact pairs for which recent transmission occurred and the typical timespans between the index case and their contact accessing care are not known; we aime...
Clostridium difficile is the leading cause of health care-associated infections. Previous studies suggest that C. difficile MLST clade 4 strains with higher drug resistance rates constitute the major clone spreading in China. Thus development of a rapid and accurate typing method for these strains i...
Prospective universal genotyping of tuberculosis (TB) isolates is used by many laboratories to detect clusters of cases and inform contact investigations. Prior to universal genotyping, most TB prevention programs genotyped isolates on request only, relying on requests from public health professiona...
A total of 12 isolates belonging to different serovars, , serovar Enteritidis ( = 4), serovar Weltevreden ( = 4), serovar Newport ( = 1), serovar Litchifield ( = 1), and untypeable strains ( = 2) were isolated from 332 diarrheic fecal samples collected from animals, birds, and humans. Of the tw...
colonizes the nasopharyngeal mucus in healthy individuals and can cause otitis media, pneumonia, and invasive pneumococcal diseases. In this study, we analyzed strains that caused 19 pneumonia episodes in long-term inpatients with severe underlying disease in a hospital during a period of 14 months...
Clostridioides difficile (CD), previously known as Clostridium difficile, is an anaerobic Gram-positive rod-shaped bacterium that causes mild to severe diarrhea mainly in hospitalized patients. The bacteria are easily spread between patients and can persist in hospital wards due to its ability to fo...
Mucorales are ubiquitous environmental molds responsible for mucormycosis in diabetic, immunocompromised, and severely burned patients. Small outbreaks of invasive wound mucormycosis (IWM) have already been reported in burn units without extensive microbiological investigations. We faced an outbreak...
Human adenoviruses (HAdVs) can cause respiratory tract infections, conjunctivitis, diarrhoea and outbreaks have been reported. However, little is known about the disease burden and the molecular epidemiology of HAdV. To retrospectively perform a molecular characterization of HAdV positive samples re...
A major difference between infectious and non-communicable diseases is that infectious diseases typically have unique necessary causes whereas noncommunicable diseases have multiple causes which by themselves are usually neither necessary nor sufficient. Epidemiology seems to have reached a limit in...
New human polyomaviruses have been described in the last years, including the Merkel-cell polyomavirus (MCPyV; Human polyomavirus 5) and the Human polyomavirus 6 (HPyV6). Although their infection is usually asymptomatic, in immunocompromised host can cause life-threatening pathologies, such as the M...
Legionella is the causative agent of Legionnaires' disease (LD). In Spain, Catalonia is the region with the highest incidence of LD cases. The characterisation of clinical and environmental isolates using molecular epidemiology techniques provides epidemiological data for a specific geographic regio...
Diagnostic tools for the identification and confirmation of animal diseases have been evolving rapidly over the last decade, with diseases of aquatic animals being no exception. Hence, case definitions used in surveillance may now include molecular and genomic components and ultimately be based on t...
Biodiversity analysis of the foodborne pathogen recently revealed four serotype 4b major hypervirulent clonal complexes (CCs), i.e., CC1, CC2, CC4, and CC6. Hypervirulence was indicated by overrepresentation of these clones, and serotype 4b as a whole, among human clinical isolates in comparison to...
Cannulated surgical instruments may retain biologic debris after routine cleaning and sterilization. Residual debris after cleaning is assumed to be sterile; however, there is no experimental basis for this assumption. The purpose of this study was to determine the sterility of retained biodebris fo...
Foot-and-mouth disease virus (FMDV) causes a highly contagious disease of cloven-hooved animals that poses a constant burden on farmers in endemic regions and threatens the livestock industries in disease-free countries. Despite the increased number of publicly available whole genome sequences, FMDV...
No abstract available
The use of generalized linear models in Bayesian phylogeography has enabled researchers to simultaneously reconstruct the spatiotemporal history of a virus and quantify the contribution of predictor variables to that process. However, little is known about the sensitivity of this method to the choic...
Here we present the characteristics of a large outbreak caused by a clonal Klebsiella pneumoniae strain producing both KPC-2 and VIM-1 carbapenemases in a tertiary teaching hospital. Between January 2013 and January 2015, 45 carbapenem-resistant K. pneumoniae isolates that gave a positive modified H...
To describe clinical characteristics and outcome of Clostridium difficile infection (CDI) patients in Internal Medicine, to identify ribotypes (RTs); to evaluate the association between RT and patient clinical characteristics and report outcome. One year prospective cohort study. Clinical data, Bart...
Campylobacter is the most common cause of bacterial food-borne diarrhoeal disease worldwide. Chicken meat is considered the main source of human infection; however, C. jejuni and C. coli have also been reported in a range of livestock and wildlife species, including pheasants. Wild pheasant meat rea...
The aim of this study is to describe the molecular epidemiology of Neisseria meningitidis invasive disease before the introduction of serogroup C conjugate vaccine in Amazonas State in 2010. Meningococcal disease reported cases were investigated in Amazonas State during the period 2000-2010. N. meni...
Recently, the dissemination of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) into hospitals has frequently been reported worldwide. Hospital-acquired MRSA (HA-MRSA) strains exhibit high-level resistance to multiple antimicrobial agents, whereas CA-MRSA strains are usually...
Kadipiro virus (KDV) belongs to the Reoviridae family, which consists of segmented, non-enveloped, double-stranded RNA viruses. It has previously been isolated from Culex, Anopheles, Armigeres and Aedes mosquitoes in Indonesia and China. Here, we describe the isolation and characterization of SDKL16...
To analyses the antimicrobial resistance and molecular characterization of 21 MRSA isolates cultured from retail foods from different provinces in China, and evaluate the molecular typing methods. Twenty-one MRSA isolates were obtained from national foodborne pathogen surveillance network in 2012 (...
The incidence of Clostridium difficile infections (CDI) in the Clinical Center of Serbia (CCS) and the entire Serbia has been constantly rising in the previous 5 years. We aimed to study C. difficile PCR-ribotypes isolated from patients hospitalized at two healthcare institutions: CCS and Specialize...
Antimicrobial-resistant isolates of Pseudomonas aeruginosa collected from 2005 to 2014 in a university hospital in Kyoto, Japan, were retrospectively analyzed by multilocus sequence typing (MLST), exoenzyme genotype determination, integron characterization, and clinical associations. During the stud...
Staphylococcus aureus strains can be disseminated during dental treatments and occasionally lead to the contamination and infection of patients and dentists, which is an important public health problem. The dynamics of the airborne propagation and the genetic diversity of S. aureus isolated in an ac...
Ceftriaxone is the drug of choice for typhoid fever and the emergence of resistant Salmonella Typhi raises major concerns for treatment. There are an increasing number of sporadic reports of ceftriaxone-resistant S. Typhi and limiting the risk of treatment failure in the patient and outbreaks in the...
Campylobacter jejuni is a zoonotic pathogen commonly associated with human gastroenteritis. Retail poultry meat is a major food-related transmission source of C. jejuni to humans. The present study investigated the genetic diversity, clonal relationship, and strain risk-analysis of 403 representativ...
Culex mosquitoes can act as vectors of several important diseases, including Japanese encephalitis, West Nile virus, St. Louis encephalitis and equine encephalitis. Besides the neurological sequelae caused in humans, Japanese encephalitis can lead to abortion in sows and encephalitis in horses. Effe...
To describe the phenotypic and genotypic profiles of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) strains isolated from patients with invasive infections at an Italian university hospital in order to assess the epidemiological trend. An observational prospective study was und...
No abstract available
BackgroundSince mumps vaccination was introduced in 1981 in Spain, the incidence of the disease has dropped significantly. However, cyclic epidemic waves and outbreaks still occur, despite high vaccination coverage. The World Health Organization (WHO) recommends genotyping to trace the pattern of mu...
DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reser...
Extraintestinal pathogenic (ExPEC) are important pathogens in humans and certain animals. Molecular epidemiological analyses of ExPEC are based on structured observations of strains as they occur in the wild. By assessing real-world phenomena as they occur in authentic contexts and hosts, they pro...
A patient transferred from South Africa to Israel acquired a Candida auris infection. Phylogenetic analysis showed resemblance of C. auris to isolates from South Africa but not Israel, suggesting travel-associated infection. C. auris infection occurred weeks later in another patient at the same hosp...
The emergence and spread of antibiotic-resistant Gram-negative bacteria (rGNB) across global healthcare networks presents a significant threat to public health. As the number of effective antibiotics available to treat these resistant organisms dwindles, it is essential that we devise more effective...
A rapidly increasing number of HIV-1 infections have been identified among men who have sex with men (MSM) in Fujian province of China since 2010. We aimed to investigate the causative factors underlying this surging epidemic. Using immunoassays for HIV-1 diagnosis and phylogenetic analysis for vira...
Repeated outbreaks of salmonellosis caused by Salmonella enterica serovar Infantis at a rehabilitation clinic in Germany were investigated microbiologically from August 2002 to August 2009. To identify the sources of transmission and characterize the S. enterica serovar Infantis isolates. Associated...
Plague, caused by Yersinia pestis, was classified as a reemerging infectious disease by the World Health Organization. The five human pneumonic plague cases in Yulong County in 2005 gave rise to the discovery of a Yulong plague focus in Yunnan province, China. Thereafter, continuous wild rodent plag...
The transmission dynamics of human metapneumovirus (HMPV) in tropical countries remain unclear. Further understanding of the genetic diversity of the virus could aid in HMPV vaccine design and improve our understanding of respiratory virus transmission dynamics in low- and middle-income countries. W...
Candida auris was first described in 2009, and it has since caused nosocomial outbreaks, invasive infections, and fungaemia across at least 19 countries on five continents. An outbreak of C. auris occurred in a specialized cardiothoracic London hospital between April 2015 and November 2016, which to...
CRF31_BC is an HIVs-1 recombinant form very prevalent in the southernmost capital city of Brazil, Porto Alegre. Recent studies have been describing a growing number of cases of infection by CRF31_BC in other Brazilian cities and countries, suggesting a process of expansion of this strain. Aiming to...
The epidemiology of Clostridium difficile infections (CDI) is changing rapidly worldwide; knowledge on the genotypes of C. difficile circulating in specialized geriatric hospitals and their resistance to antibiotics is scarce or non-existent. Prospective study of the molecular epidemiology of CDI, c...
Virulent footrot is an economically significant disease in most sheep-rearing countries. The disease can be controlled with vaccine targeting the fimbriae of virulent strains of the essential causative agent, However, the bacterium is immunologically heterogeneous, and 10 distinct fimbrial serogrou...
The serotype O113:H21 is considered one of the relevant non-O157 STEC serotypes associated with severe human infections. Due to the increased detection of O113 strains and their relationship with clinical cases, which emphasizes the importance of this serogroup as an emerging pathogen, our aim was t...
To investigate the usefulness of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) typing as a first-line epidemiological tool in a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VREfm). Fifty-five VREfm isolates, previously characterized...
Staphylococcus aureus is known to be a predominant pathogen causing bloodstream infection (BSI) from burn units. Our study aimed to perform the clinical epidemiological analysis and virulence features of S. aureus strains isolated from the burn patients with BSI from a burn center in southeastern Ch...
Mycobacterium bovis is a neglected zoonotic organism that epidemiological studies are of crucial importance in identifying its source, control it and prevent it from spreading. The aim of this study was to investigate the most common spoligotypes of Mycobacterium bovis circulating around the world a...
Parvoviruses (family ) are small, single-stranded DNA viruses. Many parvoviral pathogens of medical, veterinary and ecological importance have been identified. In this study, we used high-throughput sequencing (HTS) to investigate the diversity of parvoviruses infecting wild and domestic animals in...
No abstract available
Mycoplasma synoviae (MS) is a poultry pathogen with reported increased prevalence and virulence in recent years. MS strain identification is essential for prevention, control efforts and epidemiological outbreak investigations. Multiple multilocus based sequence typing schemes have been developed fo...
Novel surveillance strategies are needed to detect the rapid and continuous emergence of infectious disease agents. Ideally, new sampling strategies should be simple to implement, technologically uncomplicated, and applicable to areas where emergence events are known to occur. To this end, xenosurve...
Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease, which results in severe economic losses to the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many sero/genotypes are described around the wo...
Salmonella Typhimurium is a common cause of foodborne illness in Australia. We report on seven outbreaks of Salmonella Typhimurium multilocus variable-number tandem-repeat analysis (MLVA) 03-26-13-08-523 (European convention 2-24-12-7-0212) in three Australian states and territories investigated bet...
Although severe infections caused by hypervirulent Klebsiella pneumoniae isolates, such as K1 isolates belonging to sequence type (ST) 23, have been a significant problem in Asian countries, epidemiology of these isolates in Japan remains unclear. We performed a nationwide molecular epidemiological...
Tuberculosis (TB) remains a major health problem within the Community of Portuguese Language Speaking Countries (CPLP). Despite the marked variation in TB incidence across its member-states and continued human migratory flux between countries, a considerable gap in the knowledge on the Mycobacterium...
Tuberculosis (TB) is considered one of the most serious infectious diseases worldwide. Effective control of tuberculosis infection involves multiple steps, such as reliable detection, treatment, an epidemiological control as a part of case management, and further surveillance and monitoring of TB sp...
There is growing concern about the spreading of human microorganisms in relatively untouched ecosystems such as the Antarctic region. For this reason, three pinniped species (Leptonychotes weddellii, Mirounga leonina and Arctocephalus gazella) from the west coast of the Antartic Peninsula were analy...
Pseudomonas aeruginosa chronic infections of cystic fibrosis (CF) airways are a paradigm for within-host evolution with abundant evidence for rapid evolutionary adaptation and diversification. Recently emerged transmissible strains have spread globally, with the Liverpool Epidemic Strain (LES) the m...
Acinetobacter baumannii is one of the antibiotic-resistant superbugs that threatens hospitalized patients. Emergence and spread of the multidrug-resistant (MDR) and extensively drug-resistant (XDR) clones cause erratic outbreaks following environmental contamination of hospital settings. The present...
Single outbreaks have often been reported in health care settings, but the frequency of outbreaks at a hospital over time has not been described. We examined epidemiologic features of all health care-associated outbreak investigations at an academic hospital during a 5-year period. Health care-assoc...
Methicillin resistant Staphylococcus aureus (MRSA) constitutes a major global health concern causing hospital and community acquired infections. A wide diversity of MRSA genotypes are circulating in geographically related regions. Therefore understanding the molecular epidemiology of MRSA is fundame...
The Zika virus (ZIKV) outbreak in the island nation of Cabo Verde was of unprecedented magnitude in Africa and the first to be associated with microcephaly in the continent. Using a simple mathematical framework we present a first epidemiological assessment of attack and observation rates from 7,580...
No abstract available
Methicillin-resistant Staphylococcus aureus (MRSA) can survive for long periods on inanimate objects, and therefore, environmental surfaces constitute an important reservoir for dissemination. However, there is no standardized method for the detection of MRSA from environmental surfaces. The aim of...
Variola virus (VARV), the causative agent of smallpox, is an exclusively human virus belonging to the genus Orthopoxvirus, which includes many other viral species covering a wide range of mammal hosts, such as vaccinia, cowpox, camelpox, taterapox, ectromelia, and monkeypox virus. The tempo and mode...
To understand the epidemiological and molecular characteristics of typhoid and paratyphoid in China from 2009 to 2013, and provide evidence for the prevention and control of typhoid and paratyphoid, the development and improvement of surveillance strategies. Epidemiological analysis was conducted o...
Corynebacterium diphtheriae is a re-emerging pathogen in Europe causing invasive infections in vaccinated persons and classical diphtheria in unvaccinated persons. In the presented study we analysed genetic changes in C. diphtheriae isolates collected in Poland from the period before the introductio...
No abstract available
The emergence and spread of Zika virus in the Americas continues to challenge our disease surveillance systems. Virus genome sequencing during the epidemic uncovered the timescale of Zika virus transmission and spread. Yet, we are only beginning to explore how genomics can enhance our responses to e...
No abstract available
This study reports the molecular characterization of foot-and-mouth disease virus (FMDV) in the provinces of Punjab and Sindh, Pakistan during 2014-17. FMDV genome was detected in 42 and 41 out of 46 samples (epithelial tissue and saliva) by reverse transcriptase loop-mediated isothermal amplificati...
The worldwide dissemination of Mycobacterium tuberculosis strains has led to the study of their genetic diversity. One of the most used genotyping methods is spoligotyping, based on the detection of spacers in the clustered regularly interspaced short palindromic repeats (CRISPR) locus. This study a...
There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used geno...
Vast viruses are thought to be associated with mosquitoes. Anopheles sinensis, Armigeres subalbatus, Culex quinquefasciatus, and Culex tritaeniorhynchus are very common mosquito species in China, and whether the virome structure in each species is species-specific has not been evaluated. In this stu...
Outbreaks of gastrointestinal illness, linked to the consumption of fruits, vegetables, and sprouts, continue to capture the attention of the general public and scientists. The recurrence of these outbreaks, despite heightened producer and consumer awareness, combined with improved sanitation protoc...
An increase in the prevalence of commensal carrying genes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126 -positive and 126 -negative isolates for determinations of the multilocus sequence types (MLSTs)...
In May 2015, following a 30-year diphtheria-free interval in Catalonia, an unvaccinated 6-year-old child was diagnosed with diphtheria caused by toxigenic . After a difficult search for equine-derived diphtheria antitoxin (DAT), the child received the DAT 4 days later but died at the end of June. Tw...
On 11 May 2015, the Dubréka prefecture, Guinea, reported nine laboratory-confirmed cases of Ebola virus disease (EVD). None could be epidemiologically linked to cases previously reported in the prefecture. We describe the epidemiological and molecular investigations of this event. We used the Dubrék...
In May 2016, two separate clusters of febrile gastroenteritis caused by were detected by the local health authority in Piedmont, in northern Italy. We carried out epidemiological, microbiological and traceback investigations to identify the source. The people affected were students and staff member...
Dengue is endemic in the Western Pacific and Oceania and the region reports more than 200,000 cases annually. Outbreaks of dengue and severe dengue occur regularly and movement of virus throughout the region has been reported. Disease surveillance systems, however, in many areas are not fully establ...
Adequacy of the current clinical definition of institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic analysis of institutional influenza outbreaks that occurred during the 2014-15 influenza season in Toronto, Canada. We sequenced the 2 earlies...
Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase blaNDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010-15, including a neonatal NDM-1 S. marcescens outbreak. Isolate...
Pseudomonas aeruginosa is a major cause of severe healthcare-associated infections and often shows MDR phenotypes. Ceftolozane/tazobactam is a new cephalosporin/β-lactamase inhibitor combination with potent activity against P. aeruginosa. This survey was carried out to evaluate the susceptibility of...
Listeriosis caused by Listeria monocytogenes has a high case-fatality rate (CFR) of approximately 20% to 30%. An increasing incidence of listeriosis has been reported in many countries recently. We investigated the annual incidence, clinical characteristics, and outcomes of listeriosis at three diff...
Trichophyton tonsurans, a major pathogen causing tinea capitis and tinea corporis, has been isolated from contact sports-players in Japan. The molecular types of 208 strains isolated between 2011 and 2015 were determined to understand the contemporary Japanese epidemic. Of these, 142 were isolated f...
Two molecular epidemiologic methods, IS restriction fragment length polymorphism (IS-RFLP) and 24-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR), are used worldwide in studies of (MTB). Conversely, because of its poor resolution, pulsed-field gel electrop...
Stenotrophomonas maltophilia (Sm) is an archetypal environmental opportunistic bacterium responsible for health care-associated infections. The role of animals in human Sm infections is unknown. This study aims to reveal the genetic and phylogenetic relationships between pathogenic strains of Sm, bo...
Culicoides biting midges (Diptera: Ceratopogonidae) are responsible for the biological transmission of internationally important arboviruses of livestock. In 2011, a novel Orthobunyavirus was discovered in northern Europe causing congenital malformations and abortions in ruminants. From field studie...
Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Western Australia (WA). Unlike isolates from the major Australian population centres, the remo...
Infections due to multidrug-resistant (MDR) organisms in long-term care facilities (LTCFs) residents constitute a public health concern. This multicenter study investigated the frequency of ESBL-producing pathogens and MDR Clostridium difficile in clinical specimens from LTCF residents in Italy. Dur...
Salmonella Gallinarum biovar Pullorum (S. Pullorum) is a poultry pathogen associated with significant economic losses and animal suffering. Strict eradication programmes have eliminated S. Pullorum from the commercial poultry sector in most regions, but occasional outbreaks still occur in the non-co...
Clostridium difficile is the causative pathogen for antibiotic-related nosocomial diarrhea. For epidemiological study and identification of virulent clones, a new binary typing method was developed for C. difficile in this study. The usefulness of this newly developed optimized 10-loci binary typing...
Although KPC enzymes are most common among carbapenemases produced by complex globally, the epidemiology varies from one country to another. While previous studies have suggested that IMP enzymes are most common in Japan, detailed analysis has been scarce thus far. Here, we carried out a molecular...
Sulbactam is a plausible option for treating infections because of its intrinsic antibacterial activity against the members of the genus, but the mechanisms of sulbactam resistance have not been fully studied in In this study, a total of 2,197 clinical isolates were collected from 27 provinces i...
Culicoides biting midges (Diptera:Ceratopogonidae) cause a significant biting nuisance to humans, livestock, which are the biological vectors of a range of risky pathogens. Accurate illustration of vector play a key role in arthropod borne diseases surveillance. However, few studies have focused on...
Whole-genome sequencing (WGS) is rapidly becoming the method of choice for outbreak investigations and public health surveillance of microbial pathogens. The combination of improved cluster resolution and prediction of resistance and virulence phenotypes provided by a single tool is extremely advant...
The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) was up to 30% between 2014 and 2016 in the study hospital. Of these 77 CRKP isolates, 22 isolates with sequence type ST11 carried the new pKPC_P16 plasmid, a pKPC_LK30 variant, and were widely disseminated between 2014 and 2015 in n...
Southeastern Brazil has been suffering a rapid expansion of a severe sylvatic yellow fever virus (YFV) outbreak since late 2016, which has reached one of the most populated zones in Brazil and South America, heretofore a yellow fever-free zone for more than 70 years. In the current study, we describ...
Influenza A/H3N2 viruses are characterized by highly mutated RNA genomes. In this study, we focused on tracing the phylodynamics of Taiwanese strains over the past four decades. All Taiwanese H3N2 HA1 sequences and references were downloaded from public database. A Bayesian skyline plot (BSP) and ph...
Twenty-seven (0.51%) USA300 isolates were identified from a pool of 5308 meticillin-resistant Staphylococcus aureus (MRSA) isolates collected in Taiwan between 1995 and October 2015, including 12 infecting isolates from 10 patients. The first two isolates were identified in 2005, and 23 isolates hav...
Drug resistant Tuberculosis (TB) is considered a global public health threat. Whole-genome sequencing (WGS) is a new technology for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles and genotypes for epidemiologic surveillance. Therefore, we used WGS to determi...
Emergence and spread of extended spectrum beta-lactamase (ESBL)-producing gram-negative bacteria, mainly due to CTX-M, is a major global public health problem. Patients infected with ESBL-producing gram-negative bacteria have an increased risk of treatment failure and death. We investigated the prev...
causes human sickness throughout the world via the consumption of undercooked seafood or exposure to contaminated water. Previous attempts at phylogenetic analyses of have proven unsuccessful, mainly due to the poorly understood impact of factors on its divergence. In this study, we used advanced s...
Drug resistant HIV is a major threat to the long-term efficacy of antiretroviral treatment. Around 10% of ART-naïve patients in Europe are infected with drug-resistant HIV type 1. Hence it is important to understand the dynamics of transmitted drug resistance evolution. Thanks to routinely performed...
Extended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producing was increasingly described as an important cause of community-acq...
Panton-Valentine leukocidin (PVL) gene (lukS/F-PV)-positive community-acquired methicillin-resistant Staphylococcus aureus (MRSA), particularly the USA300 clone, is a health concern worldwide. Recently, community-acquired MRSA clones have been found to spread and persist in hospital settings. We aim...
In the present study, the potential of serological methods, the repetitive extragenic palindromic PCR (REP-PCR) and the enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) for the typing of the species Tenacibaculum maritimum, Tenacibaculum soleae and Tenacibaculum discolor was e...
Candida albicans is an emerging multidrug-resistant fungal pathogen representing an important source of invasive disease in humans and generating high healthcare costs worldwide. This fungus is frequently found in different anatomical sites of healthy persons and could induce systemic and superficia...
All State TB control programmes in Nigeria were requested to submit 25-50 smear-positive Ziehl-Neelsen (ZN) stained slides for screening during 2013-2014. DNA was extracted from 929 slides for spoligotyping and drug-resistance analysis using microbead-based flow-cytometry suspension arrays. Spoligot...
Carbapenem-resistant Gram-negative bacilli (GNB) have become an important cause of nosocomial infections of hospitalized patients. To investigate the microbial infection patterns and molecular epidemiology characteristics of the carbapenem-resistant GNB isolates from a long-term hospitalized patient...
Vibrio cholerae O1 El Tor, the pathogen responsible for the current cholera pandemic, became pathogenic by acquiring virulent factors including Vibrio seventh pandemic islands (VSP)-I and -II. Diversity of VSP-II is well recognized; however, studies addressing attachment sequence left (attL) sequenc...
Isolates of tick-borne encephalitis virus (TBEV) from arthropod vectors (ticks and mosquitoes) in the Amur, the Jewish Autonomous and the Sakhalin regions as well as on the Khabarovsk territory of the Far East of Russia were studied. Different proportions of four main tick species of the family Ixod...
In 2013, there was an outbreak of acute respiratory disease in racehorses in Turkey. The clinical signs were consistent with equine influenza (EI). The aim was to confirm the cause of the outbreak and characterise the causal virus. A pan-reactive influenza type A real-time RT-PCR and a rapid antigen...
Salmonella enterica serovar I 4,[5],12:i:- has emerged as a common nontyphoidal Salmonella serovar to cause human foodborne illness. An interesting trait of serovar I 4,[5],12:i:- is that it only expresses the fliC gene for bacterial motility (i.e., monophasic), while most Salmonella strains alterna...
Chlamydia trachomatis ompA genotypes A and B, primarily associated with trachoma, were unexpectedly detected in urogenital samples of patients in Spain, a trachoma-free country. In this study, we aimed to explain this finding using analysis of organotropism-related genes and a multilocus sequence ty...
Since 2015, an emerging infectious disease of inclusion body hepatitis and hydropericardium syndrome (IBH-HPS) has been occurred in China, which caused economic loss in poultry farming. In this study, we isolated four fowl adenovirus strains from flocks with an outbreak of HPS. The complete nucleoti...
Ticks are well known to be important vectors for a wide range of bacteria, viruses and protozoa affecting human and animal health. Ixodid ticks are widely distributed in Sardinia, and an increasing number of tick-borne bacteria have been documented in the island. A growing number of evidence are sup...
Mycoplasma bovis infections are responsible for substantial economic losses in the cattle industry, have significant welfare effects and increase antibiotic use. The pathogen is often introduced into naive herds through healthy carrier animals. In countries with a low prevalence of M. bovis, transmi...
To investigate the distribution of molecular types of methicillin-resistant Staphylococcus aureus (MRSA) in a paediatric intensive care unit (PICU) according to their community-associated (CA) and hospital-associated (HA) source of acquisition, and thus assess the degree to which CA-MRSA has been in...
The impacts of hedgehog (Erinaceus europaeus) Salmonella infection on public health and on animal welfare and conservation are unknown. We isolated Salmonella Enteritidis multi-locus sequence-type (ST)183 from 46/170 (27%) hedgehog carcasses (27 S. Enteritidis phage type (PT)11, 18 of a novel PT66 b...
This study was performed to analyze the Canadian invasive serogroup W Neisseria meningitidis (MenW) sequence type 11 (ST-11) clonal complex (CC) isolates by whole genome typing and to compare Canadian isolates with similar isolates from elsewhere. Whole genome typing of 30 MenW ST-11 CC, 20 meningoc...
Clostridium difficile infection (CDI) is a major healthcare-associated infection. The aim of this study was to investigate the genetic relatedness of the endemic C. difficile PCR ribotype 018 strains in an institution and changes to their characteristics during a five-year period. A total of 207 iso...
The decline in methicillin-resistant Staphylococcus aureus (MRSA) isolation rates has become a general observation worldwide, including Japan. We hypothesized that some genetic shift in MRSA might cause this phenomenon, and therefore we investigated the genetic profiles among MRSA clinical isolates...
To determine the predominant strains of Bordetella pertussis in Greece during 2010-2015. Infants and children (n=1150) (15 days to 14 years) of Greek, Roma and immigrant origin with different vaccination statuses were hospitalized in Athens, Greece with suspected pertussis infection. IS481/IS1001 re...
Whole-genome sequencing (WGS) has emerged as a powerful molecular typing method for outbreak analysis enabling the rapid discrimination between outbreak and non-outbreak isolates. However, such analysis can be challenging in the absence of closely related reference genomes. In this study, we assesse...
OBJECTIVE To describe an outbreak of multidrug-resistant Pseudomonas aeruginosa in which the hospital waste-pipe system was the likely source of contamination and to report the bundle of measures that facilitated the long-term control of the outbreak. DESIGN Outbreak investigation. SETTING The hemat...
Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health. No studies to date have examined the genomic epidemiology of gonorrhoea in the Western Pacific Region, where the incidence of gonorrhoea is particularly high. A population-level study of N. gonorrhoeae in New Zealand (...
The prevalence and incidence of human immunodeficiency virus type 1 (HIV-1) among men who have sex with men (MSM) are on the rise throughout China. With a large population of MSM, Jiangsu Province is facing an escalating HIV-1 epidemic.The aim of this study was to explore the phylogenetic and tempor...
Compositional variation of the gut microbiota across host allopatric populations can reflect both adaptation and stochasticity since the time of separation. Major factors shaping this variation include the host phylogeographic and demographic history, the microbiota inheritance, environmental inputs...
Bovine tuberculosis is a chronic contagious disease responsible for major agricultural economic losses. Abattoir monitoring and trace-back systems are an appropriate method to control bovine tuberculosis, particularly in beef cattle. In the present study, a trace-back system was applied to bovine tu...
This study applied High-Performance Computing to explore the high-resolution phylodynamics and the evolutionary dynamics of Influenza viruses (IVs) A and B and their subtypes in-depth to identify peptide-based candidates for broad-spectrum vaccine targets. For this purpose, we collected all the avai...
Campylobacter concisus is an emerging pathogen associated with inflammatory bowel disease (IBD), yet little is known about the genetic diversity of C. concisus in relation to host niches and disease. We isolated 104 C. concisus isolates from saliva, mucosal biopsies and faecal samples from 41 indivi...
In the United Kingdom, rising levels of disease due to Neisseria meningitidis serogroup W clonal complex (cc) sequence type (ST) 11 (MenW:cc11) strains led to introduction of meningococcal conjugate vaccine (MenACWY) for teenagers. We investigated the impact of immunization on carriage of meningococ...
Landscape heterogeneity plays an important role in disease spread and persistence, but quantifying landscape influences and their scale dependence is challenging. Studies have focused on how environmental features or global transport networks influence pathogen invasion and spread, but their influen...
An alarming increase of vancomycin-resistant Enterococcus faecium (VREfm) isolates was detected in an Italian referral hospital subjected to policies of infection control validated by the Joint Commission International. Analysis of the population structure of 122 consecutive, nonreplicate VREfm isol...
Increasing rates of gonorrhoea have been observed among women within the Australian state of New South Wales. Here, we applied whole genome sequencing (WGS) to better understand the associated networks and transmission dynamics. Ninety-four isolates of a particular N. gonorrhoeae genotype (G122) ass...
No abstract available
A genomic epidemiologic investigation of a putative carbapenem-resistant Enterobacter cloacae outbreak revealed few plausible instances of nosocomial transmission, highlighting instead the frequent importation of E. cloacae into our hospital. Searching for genetic determinants of carbapenem resistan...
Bovine tuberculosis is a zoonotic disease with largely unknown impact in Africa, with risk factors such as HIV and direct contact with animals or consumption of Mycobacterium bovis infected animal products. In order to understand and quantify this risk and design intervention strategies, good epidem...
Mycobacterium xenopi is responsible for pulmonary disease (PD) in Europe and Canada. Despite its high prevalence and increasing clinical importance, little is known about the genetic diversity of M. xenopi. Through a prospective study for M. xenopi strain type and the relation to clinical phenotype,...
Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determin...
The current increase in nosocomial infections caused by vancomycin-resistant enterococci (VRE) warrants improvement of detection methods and hygiene measures. Knowledge of the local epidemiology is important for monitoring compliance of medical personnel with hygiene measures. To evaluate semi-autom...
From 2013 to 2014, bacterial leaf spot epidemics incited by Pseudomonas syringae pv. syringae affected an estimated 3,000 ha of watermelon and squash in Florida, and caused foliar blighting and transplant losses in severely affected fields. To investigate the diversity of the causal agent, we isolat...
In Australia, the incidence of Salmonella Typhimurium has increased dramatically over the past decade. Whole-genome sequencing (WGS) is transforming public health microbiology, but poses challenges for surveillance. To compare WGS-based approaches with conventional typing for Salmonella surveillance...
Ukraine has one of the largest HIV epidemics in Europe, historically driven by people who inject drugs (PWID). The epidemic showed signs of stabilization in 2012, but the recent war in eastern Ukraine may be reigniting virus spread. We investigated the movement of HIV-infected people within Ukraine...
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus from camels causing significant mortality and morbidity in humans in the Arabian Peninsula. The epidemiology of the virus remains poorly understood, and while case-based and seroepidemiological studies have been employed ext...
Newcastle disease viruses (NDV) are highly contagious and cause disease in both wild birds and poultry. A pigeon-adapted variant of genotype VI NDV, often termed pigeon paramyxovirus 1, is commonly isolated from columbids in the United States and worldwide. Complete genomic characterization of these...
Tuberculosis (TB) has remained an ongoing concern in China. The national scale-up of the Directly Observed Treatment, Short Course (DOTS) program has accelerated the fight against TB in China. Nevertheless, many challenges still remain, including the spread of drug-resistant strains, high disease bu...
Preterm infants are at high risk for extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) sepsis and neonatal intensive care unit (NICU) outbreaks. Maternal colonization with ESBL-E may be precursory to mother-to-child transmission. However, there is no consensus regarding surveill...
No abstract available
Brucellosis incidence in China is divided into three stages: high incidence (1950s-1960s), decline (1970s-1980s), and re-emergence (1990s-2010s). At the re-emergence stage, Brucellosis incidence grew exponentially and spread to all 32 provinces. We describe the magnitude and the etiological distribu...
Direct and indirect contact among animals and holdings are important in the spread of Brachyspira hyodysenteriae. The objective of this study was to investigate the role of slaughterhouse vehicles in spreading B. hyodysenteriae between unconnected farms. Multilocus sequence typing (MLST) and Multipl...
MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data...
The prevalence and genetic diversity of bovine viral diarrhea virus (BVDV) in a geographic area are largely influenced by live animal trade and management practices. Despite control and eradication programs currently underway in several European countries, the risk of BVDV spread within and among co...
Outbreaks of health care-associated infections (HAIs) caused by Burkholderia cepacia complex (Bcc) have been associated with medical devices and water-based products. Water is the most common raw ingredient in nonsterile liquid drugs, and the significance of organisms recovered from microbiologic te...
Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing te...
To analyse Klebsiella pneumoniae (KP) isolates from an outbreak of extended-spectrum β-lactamase (ESBL)-producing KP and Escherichia coli (EC) among infants admitted to neonatal intensive care units and to determine the duration of the intestinal colonization. We performed a prospective cohort study...
Hypervirulent K. pneumoniae (hvKp) causes severe community acquired infections, predominantly in Asia. Though initially isolated from liver abscesses, they are now prevalent among invasive infections such as bacteraemia. There have been no studies reported till date on the prevalence and characteris...
Mutations that accumulate in the genome of cells or viruses can be used to infer their evolutionary history. In the case of rapidly evolving organisms, genomes can reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidl...
Propionibacteria are important members of the human skin microbiota, but are also opportunistic pathogens associated with periprosthetic joint infection (PJI). While the role of Propionibacterium acnes in PJI has been widely described, insight into the capacity of Propionibacterium avidum to cause P...
Control of gonorrhea in resource-limited countries, such as Indonesia, is mostly unsuccessful. Examining Neisseria gonorrhoeae (Ng) transmission networks using strain typing might help prioritizing public health interventions. In 2014, urogenital Ng strains were isolated from clients of sexually tra...
Presently, the bottleneck in the deployment of high-throughput sequencing technology is the ability to analyse the increasing amount of data produced in a fit-for-purpose manner. The field of microbial bioinformatics is thriving and quickly adapting to technological changes, which creates difficulti...
Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogenic S aureus strain characteristic associated with increased patient morbidity and mortality. The health care system needs to understand MRSA transmissibility in all settings to improve basic preventive measures to generate sustained red...
On 1 December 2017, an outbreak of Agona infections among infants was identified in France. To date, 37 cases (median age: 4 months) and two further international cases have been confirmed. Five different infant milk products manufactured at one facility were implicated. On 2 and 10 December, the c...
In January 2017, an increase in reported serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case-control study to identify the source, including all cases after December 2016. Adjusted odds ratios were calculated using logistic regression analysis....
Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks for inference of transmission history from viral genomic data often do not consider intra-host diversity of pathogens and heavily rely on additional epidemiological data...
Molecular-based diagnostic methods for the detection of gastrointestinal pathogens are becoming increasingly commonplace in microbiology laboratories. This review aims to summarize recent developments in this field and discuss the clinical application and limitations of implementing these techniques...
The often-noted and persistent increased incidence of Escherichia coli O157:H7 infections in rural areas is not well understood. We used a cohort of E. coli O157:H7 cases reported in Washington, USA, during 2005-2014, along with phylogenomic characterization of the infecting isolates, to identify ge...
is a common nosocomial pathogen known for its high transmission potential. A high rate of carbapenem-susceptible (ACB)-complex in clinical specimens led to the implementation of a pathogen-based surveillance on a 32-bed surgical intensive care unit (SICU) in a German tertiary care centre. Between A...
To understand the molecular epidemiology and antibiotic resistance of air and clinical isolates of Acinetobacter baumannii , the intensive care unit settings of a hospital in Northern China were surveyed in 2014. Twenty non-duplicate A. baumannii isolates were obtained from patients and five isolate...
Pseudomonas aeruginosa is one of the most common opportunistic pathogens that cause severe infections in humans. The burden of carbapenem resistance is particularly high and is on the rise. Very little information is available on the molecular mechanisms and its clonal types of carbapenem-resistant...
We collected 8,700 mosquitoes in three sites in China, which belonged to seven species. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The abundant viral sequences were detected and annotated belonging to more than 50 viral taxonomic families. The results were ver...
More than 6,000 mosquitoes of six species from six sites were collected and tested for their virome using metagenomics sequencing and bioinformatic analysis. The identified viral sequences belonged to more than 50 viral families. The results were verified by PCR of selected viruses in all mosquitoes...
Methicillin-resistant Staphylococcus aureus (MRSA) USA300 isolates have been recognized globally, not only in community but also in healthcare settings. USA300 isolates were initially resistant only to methicillin, but resistance to non-β-lactams has emerged with time. To evaluate the prevalence and...
As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated '33F-1'). We investigated the...
The objective was to describe and validate a new and alternative software procedure for 24-locus mycobacterial interspersed repetitive unit-variable number-tandem repeat (MIRU-VNTR) typing of Mycobacterium tuberculosis (Mtb) based on the multipurpose BioNumerics software. DNA from randomly selected...
Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations a...
The way of treating different types of infectious diseases is really important. Using genotyping method, we can determine the genetic relatedness between the organisms with different resistance profile from different sources. The aim of this study was to determine antibiotic resistance and genotypin...
Previous studies suggest the burden of pulmonary tuberculosis (PTB) in Ethiopia may be greater in university students relative to the overall population. However, little is known about the transmission dynamics of PTB among students and members of the communities surrounding university campuses in E...
To identify risk factors and clinical outcomes in patients with bacteremia due to extended-spectrum beta-lactamase (ESBL) or carbapenemase-producing Escherichia coli, as well as to determine the prevalence and genetic background of such isolates. Case control study was performed with patients with E...
serovar Mbandaka is an infrequent cause of salmonellosis in New South Wales (NSW) with an average of 17 cases reported annually. This study examined the added value of whole genome sequencing (WGS) for investigating a non-point source outbreak of ser. Mbandaka with limited geographical spread. In F...
In 2015, a dengue outbreak with 1,067 reported cases occurred in Xishuangbanna, a city in China that borders Burma and Laos. To characterize the virus, the complete genome sequence was obtained and phylogenetic, mutation, substitution and recombinant analyses were performed. DENV-NS1 positive serum...
Being able to track bacterial pathogens is essential for epidemiological purposes as well as monitoring in-house production facilities. Common bacterial pathogens, such as Salmonella serovars, are already been well defined, and their detection methods are very advanced. However, this will not be the...
Carbapenem-resistant (CRKP) is a major cause of nosocomial infections worldwide. The transmission route of CRKP isolates within an outbreak is rarely described. This study aimed to reveal the molecular characteristics and transmission route of CRKP isolates within an outbreak of nosocomial infectio...
A dengue outbreak abruptly occurred at the border of China, Myanmar, and Laos in June 2017. By November 3rd 2017, 1184 infected individuals were confirmed as NS1-positivein Xishuangbanna, a city located at the border. To verify the causative agent, complete genome information was obtained through PC...
Sepsis is a significant cause of morbidity and mortality amongst neonates. Klebsiella pneumoniae is a common cause of nosocomial outbreaks causing bacteraemia and having potential of acquiring plasmids enhancing antimicrobial resistance. In the present study, we investigate K. pneumoniae outbreak ca...
Dengue is one of the most prevalent arboviral diseases in the world with 390 million dengue infections per year. In this study, we report the molecular characterisation of dengue outbreak in Pasighat, Arunachal Pradesh, Northeast India during 2015. : A total of 613 dengue-suspected cases were screen...
Staphylococcus aureus is one of the top six most common etiologic agents of nosocomial, community and livestock acquired bacterial infections. These infections although initially were described as a major problem in hospitals have now also become a serious threat in community not only in India but a...
USA500 isolates are clonal complex 8 (CC8) strains closely related to the prominent community- and hospital-associated USA300 group. Despite being relatively understudied, USA500 strains cause a significant burden of disease and are the third most common methicillin-resistant (MRSA) strains identi...
Strains of in clonal complex 8 (CC8), including USA300, USA500, and the Iberian clone, are prevalent pathogens in the United States, both inside and outside health care settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify, and whole-genome sequencing ha...
Staphylococcus aureus has strong association with anthropogenic environments. This association has not been well supported by use of genetic tools. The aim of this study was to phylogenetically relate numerous isolates from three environments - NCBI samples from hospitals, a community, and a previou...
Klebsiella pneumoniae is an important nosocomial pathogen that can lead to high morbidity and mortality. ESBL and carbapenamase producing strains may cause epidemic situations. The aim of our study was to investigate the molecular epidemiology and clonal relationship between carbapenem resistant K....
Escherichia coli O104:H4, a hybrid pathotype reported in a large 2011 foodborne outbreak in Germany, has not been detected in cattle feces. However, cattle harbor and shed in the feces other O104 serotypes, particularly O104:H7, which has been associated with sporadic cases of diarrhea in humans. Th...
Suppression of gastric acid by proton pump inhibitors is associated with the increase of in human gut microbiota. Gastric acid secretion is also suppressed by infection and following atrophic gastritis. However, few studies have examined the association between infection and species in gut micro...
Whole genome sequencing (WGS) methods provide new possibilities in the field of molecular epidemiology. This is particularly true for monomorphic organisms where the discriminatory power of traditional methods (e.g., restriction enzyme length polymorphism typing, multi locus sequence typing etc.) is...
Vancomycin-resistant (VRE) is a leading cause of hospital-acquired infections. New, presumably better-adapted strains of VRE appear unpredictably; it is uncertain how they spread despite improved infection control. We aimed to investigate the relatedness of a novel sequence type (ST) of - ST796 -...
Foot and mouth disease (FMD) has devastated the cattle industry in Sri Lanka many times in the past. Despite its seriousness, limited attempts have been made to understand the disease to ameliorate its effects-current recommendation for vaccines being based solely on immunological assessments rather...
To determine the prevalence of intestinal colonization of patients at a large teaching hospital and determine the molecular characteristics of the identified strains. The second objective of this research was to determine risk factors associated with intestinal colonization. A cross-sectional stud...
Infection by carbapenem-resistant Klebsiella pneumoniae (CR-KP) is a public health challenge worldwide, in particular among children, which was associated with high morbidity and mortality rates. There was limited data in pediatric populations, thus this study aimed to investigate molecular epidemio...
The plasmid-encoded multidrug efflux pump confers bacterial resistance primarily to olaquindox, quinolones, and chloramphenicol. The aims of this study were to investigate the prevalence of among isolates from dogs, cats, and humans in Henan, China and the susceptibilities of isolates to common...
Carbapenem-nonsusceptible complex have emerged worldwide, but the epidemiology in Indonesian hospitals has not been studied. A prospective observational study was performed on the intensive care units (ICUs) of the national referral hospital in Jakarta-Indonesia, in 2013 and 2014. All consecutive a...
Zika is a re-emerging infection that has been considered a major threat to global public health. Currently at least 100 countries are at risk of Zika virus (ZIKV) transmission. Aedes aegypti is the main mosquito vector in the Americas. This vector is exposed to, and interacts symbiotically with a va...
Acinetobacter baumannii is a major threat to public health due to the emergence and dissemination of antibiotic-resistant strains. The purpose of this study was to determine the molecular epidemiology of antibiotic-resistant A. baumannii isolates collected from four tertiary hospitals in Thailand du...
The global success of multidrug-resistant Acinetobacter baumannii has been associated with the dissemination of a high-risk clone designated clonal complex (CC) 92 (Bartual scheme)/CC2 (Pasteur scheme), which is the most frequent genetic lineage in European, Asian, and North American carbapenem-resi...
We report nosocomial transmission of multi-resistant serotype 15A (MRSP) that resulted in two lower respiratory tract infections in a centre for chronic pulmonary diseases. This outbreak highlights the potential for transmission of MRSP among vulnerable patients when laboratory turnaround time is l...
Staphylococcus aureus is an important human pathogen that causes serious antibiotic-resistant infections. Its population structure is marked by the appearance and dissemination of successful lineages across different settings. To begin understanding the population structure of S. aureus causing ocul...
Surfaces with regular contact with the human body are typically contaminated with microorganisms and might be considered as fomites. Despite spectacles being widespread across populations, little is known about their microbial contamination. Therefore, we swab-sampled 11 worn spectacles within a uni...
A group of related bacilliform, nuclear viruses with a bisegmented negative-sense RNA genome that are transmitted by Brevipalpus mites likely in a circulative-propagative manner were recently classified in the new genus Dichorhavirus, family Rhabdoviridae. These viruses cause localized lesions on le...
Nontyphoidal Salmonella serotypes are the main cause of human food-borne infection, including several hospitalization cases in the developing countries. To detect the main serotypes and to characterize the antibiotic resistance of human non-enteric and enteric nontyphoidal Salmonella from clinical i...
Vancomycin is still one of the most commonly used drug for treatment of severe methicillin-resistant (MRSA) infections. Vancomycin-resistant (VRSA) strains are a serious danger for public health. This study aimed to characterize healthcare-associated MRSA (HA-MRSA) strains, resistant to at least o...
Vancomycin resistant enterococci (VRE) occur with enhanced frequency in hospitalised patients. This study elucidates the prevalence of VRE on admission among surgical intensive care unit (SICU) patients, whether these patients are at special risk for VRE acquisition and which risk factors support th...
No abstract available
Aerobactin is a critical factor for the hypervirulent (hvKp), but data for the aerobactin-positive genotype of hvKp in elderly persons with ventilator-associated pneumonia (VAP) is limited. The purpose of this study is to understand the risk factors and characteristics of the hvKp genotype for elde...
The number of plant viruses that are known likely remains only a vanishingly small fraction of all extant plant virus species. Consequently, the distribution and population dynamics of plant viruses within even the best-studied ecosystems have only ever been studied for small groups of virus species...
Bacillus cereus is the 2nd most frequent bacterial agent responsible for food-borne outbreaks in France and the 3rd in Europe. In addition, local and systemic infections have been reported, mainly describing individual cases or single hospital setting. The real incidence of such infection is unknown...
Intracranial abscess caused by methicillin-resistant Staphylococcus aureus (MRSA) is rare and unexplored. The aim of the present study is to examine the prevalence, clinical and molecular characteristics, treatment options and outcome of MRSA intracranial abscess over a period of 6 years. A total of...
Acinetobacter baumannii has emerged as an important nosocomial pathogen, its ability to acquire resistance to carbapenems and aminoglycosides, has complicated their treatment regimen. The present study investigates the prevalence and diversity of aminoglycoside-modifying enzymes and 16S methyltransf...
Frequent changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) occurring worldwide demand regular surveillance to study their composition and distribution in healthcare facilities. We investigated the genotypic characteristics of MRSA obtained in Kuwait hospitals to bette...
Outbreaks of healthcare-associated fungal infections have repeatedly been described over recent years, often caused by new or uncommon species. , a recently described multidrug-resistant yeast species, is certainly the most worrisome species having caused several severe healthcare outbreaks of invas...
Catheter-related bloodstream infections (CRBSI) constitute an important cause of hospital-acquired infection associated with morbidity, mortality, and cost. The aim of these guidelines is to provide updated recommendations for the diagnosis and management of CRBSI in adults. Prevention of CRBSI is e...
Noroviruses are the leading cause of viral gastroenteritis in humans across the world. RNA-dependent RNA polymerase (RdRp) plays a critical role in the replication of the viral genome. Although there have been some reports on a limited number of genotypes with respect to the norovirus evolution of t...
serotype is primarily a poultry adapted serotype of Salmonella that can also colonize other hosts and cause human disease. In this study, we compared the genomes of outbreak associated non-outbreak causing ser. strains from diverse hosts and geographical regions. Human outbreak associated strains...
The HIV-1 subtype B epidemic in French Guiana and Suriname is characterized by the co-circulation of the globally disseminated "B" lineage and of non-pandemic subtype B lineages of Caribbean origin (B). To reconstruct the spatiotemporal pattern of spread of those viral lineages circulating in these...
Whole-genome sequence (WGS) analysis has revolutionized the food safety industry by enabling high-resolution typing of foodborne bacteria. Higher resolving power allows investigators to identify origins of contamination during illness outbreaks and regulatory activities quickly and accurately. Gover...
Over the years, the emergence of novel H5 and H7 highly pathogenic avian influenza viruses (HPAI) has been taking place through two main mechanisms: first, the conversion of a low pathogenic into a highly pathogenic virus, and second, the reassortment between different genetic segments of low and hi...
The Campylobacter genus is a large and diverse group of Gram-negative bacteria that are known to colonize humans and other mammals, birds, reptiles, and shellfish. While it is now recognized that several emerging Campylobacter species can be associated with human disease, two species, C. jejuni and...
Bacterial meningitis remains an important cause of global morbidity and mortality. Although effective vaccinations exist and are being increasingly used worldwide, bacterial diversity threatens their impact and the ultimate goal of eliminating the disease. Through genomic epidemiology, we can apprec...
African swine fever (ASF) is a complex infectious disease of swine that constitutes devastating impacts on animal health and the world economy. Here, we investigated the evolutionary epidemiology of ASF virus (ASFV) in Eurasia and Africa using the concatenated gene sequences of the viral protein 72...
Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of mul...
Codon adaptation index (CAI) is a measure of synonymous codon usage biases given a usage reference. Through mutation, selection, and drift, viruses can optimize their replication efficiency and produce more offspring, which could increase the chance of secondary transmission. To evaluate how higher...
The leishmaniases are a group of diseases caused by protozoans of the genus Leishmania, which are transmitted by the bite of phlebotomine sand flies. In the New World, Lutzomyia longipalpis is the most important vector of visceral leishmaniasis and is a proven vector for Leishmania infantum chagasi...
There has been a marked increase in the incidence of meticillin-resistant Staphylococcus aureus (MRSA) during the past decade in Norway; a country with one of the lowest prevalence rates and an active 'search-and-destroy' policy applied to hospital settings. To characterize the trends of notificatio...
The aim of this study was to investigate the characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP) collected during an outbreak in a Chinese teaching hospital and to provide insights into the prevention and control of nosocomial infection. We collected unique CRKP clinical isolates fr...
Carbapenem resistance is a critical healthcare challenge worldwide. Particularly concerning is the widespread dissemination of Klebsiella pneumoniae carbapenemase (KPC). Klebsiella pneumoniae harboring blaKPC (KPC-Kpn) is endemic in many areas including the United States, where the epidemic was prim...
is the most virulent and economically important species for poultry worldwide. Currently, strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome sequences (WGS) of many human and animal pathogens have been succes...
Strain genotyping based on the variable-number tandem repeat (VNTR) is widely applied for identifying the transmission of A consensus set of four hypervariable loci (1982, 3232, 3820, and 4120) has been proposed to improve the discrimination of Beijing lineage strains. Herein, we evaluated the util...
The pneumococcal conjugate vaccine (PCV) was introduced in 2001. Widespread PCV use nearly eradicated pneumococcal colonization by vaccine serotypes. Since 2008, however, colonization by PCV-serotype 19F has increased in Alaska residents. We describe the epidemiology of re-emerging serotype 19F colo...
Mycoplasma pneumoniae (MP) is particularly prevalent in low-immunity school-age children. Few data have been reported on MP prevalence in Yunnan, China. This study was designed to investigate the prevalence and characterize genomic DNA of MP in a small outbreak in 2016, Southwest China. RepMP4 and R...
In a German pediatric oncology unit, the attending physicians diagnosed 27 cases of Clostridium difficile-associated disease (CDI) from January 01, 2010 to October 31, 2013. This refers to a CDI incidence density of 2.0/1000 inpatient days. According to the hospital hygiene standard, symptomatic pat...
The incidence of multidrug-resistant bacteria in wildlife animals has been investigated to improve our knowledge of the spread of clinically relevant antimicrobial resistance genes. The aim of this study was to report the first draft genome sequence of an extensively drug-resistant (XDR) Pseudomonas...
Colistin resistance causes substantial problems in the treatment of serious infections with carbapenem-resistant (CR) gram-negative bacteria. In this study, we report a fatal hospital outbreak from the spread of a pandrug-resistant Klebsiella pneumoniae clone. An outbreak investigation was conducted...
No abstract available
Streptococcus pyogenes (group A Streptococcus [GAS]) is a major human pathogen that causes a wide spectrum of clinical manifestations. Although invasive GAS (iGAS) infections are relatively uncommon, emm3/ST15 GAS is a highly virulent, invasive, and pathogenic strain. Global molecular epidemiology a...
Foot-and-mouth disease (FMD) is, arguably, the animal disease with the most devastating global economic impact owing in part, to the severe trade restrictions imposed upon affected countries and regions. South Asia is one of the regions where widespread lineages of the FMDV virus (FMDV) have emerged...
Pseudomonas aeruginosan has emerged as an important pathogen elated to serious infections and nosocomial outbreaks worldwide. This study was conducted to understand the prevalence of aminoglycoside (AMG)-resistant P. aeruginosa in our hospital and to provide a scientific basis for control measures a...
The Tuberculosis (TB) notification rates are 5 to 81 times higher in prisons worldwide when compared to the general population. The state of Santa Catarina (SC) has few epidemiological data regarding TB in prisons. The aim of this study was to evaluate the molecular epidemiology of circulating strai...
Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial com...
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The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Pakistan is known to be high, but very few studies have described the molecular epidemiology of the different MRSA clones circulating in the country. Forty-four MRSA isolates were collected from two tertiary care hospitals of th...
The prevalence of hypervirulent Klebsiella pneumoniae (hvKP) is high in China, but clinical characteristics and outcomes of hvKP induced bloodstream infections (BSIs) are not clear. The purpose of the present study was to determine the risk factors and clinical outcomes of hvKP-BSIs in populations a...
Resistant and virulent Staphylococcus aureus is a global public health challenge. Staphylococcal Bi-component leukotoxins are cytolytic to immune cells and evolve to disarm the innate immunity during infections, hence the severity of the disease. We studied drug resistance profile and the occurrence...
Foot-and-mouth disease (FMD) is highly infectious, but despite the large quantities of FMD virus released into the environment and the extreme susceptibility of host species to infection, transmission is not always predictable. Whereas virus spread in endemic settings is characterised by frequent di...
Pseudomonas aeruginosa healthcare outbreaks can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical for decision-making. To explore the usefulness of whole-genome sequencing (WGS) in the investigation of a P. aeruginosa outbreak, describ...
Senecavirus A (SVA) is an emerging non-enveloped virus with a single-stranded, positive-sense RNA genome that belongs to the Senecavirus genus in the Picornaviridae family. Senecavirus A-associated swine idiopathic vesicular disease and epidemic transient neonatal losses have caused substantial econ...
OBJECTIVE Candida auris (CA) is an emerging multidrug-resistant pathogen associated with increased mortality. The environment may play a role, but transmission dynamics remain poorly understood. We sought to limit environmental and patient CA contamination following a sustained unsuspected exposure....
The objective of this prospective study was to verify the effectiveness of a multidisciplinary surveillance program that was implemented in a teaching hospital in southern Brazil, to prevent and control the spread of multidrug-resistant organisms. The program implemented involved establishment of pr...
Chlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens. Demonstration of C. gallinacea in human atypical pneumonia suggests its zoonotic potential. Its prevalence in chickens exceeds that of C. psittaci, but genetic and genomic research on C. gallinacea is...
No abstract available
Emerging fungal diseases represent a threat to food security, animal and human health worldwide. Amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has been associated with catastrophic and well-documented amphibian population declines and extinctions. For the firs...
No abstract available
Bovine tuberculosis (bTB) is an important zoonosis, which has been re-emerging in different ecological scenarios. In Sicily, Italy, from 2004 to 2014, an anatomopathological survey for tuberculosis-like lesions both in farmed and wild animals was performed. The isolates were genotyped using spoligot...
No abstract available
Highly pathogenic avian influenza virus (HPAIV) is a multihost pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs, and wild birds were the likely sources of a Eurasian (EA) lineage H...
In August 2017, an outbreak of six listeriosis cases in Denmark was traced to cold-smoked salmon, using epidemiological investigations and whole-genome sequencing (WGS) analyses. Exchange of genome sequences allowed identification in France of a food isolate from a salmon-derived product and a human...
Following notification of a serovar Typhimurium gastroenteritis outbreak, we identified 82 cases linked to a restaurant with symptom onset from 12 February 2015 to 8 March 2016. Seventy-two cases had an isolate matching the nationally unique whole genome sequencing profile (single nucleotide polymo...
We describe an outbreak of associated with contaminated washing gloves, a commercially available Class I medical device. Triggered by an increase in complex (BCC) bacteremias and the detection of BCC in unopened packages of washing gloves, an ad hoc national outbreak committee comprising represent...
Recent disease outbreaks caused by (re-)emerging plant pathogens have been associated with expansions in pathogen geographic distribution and increased virulence. For example, in the past two decades' wheat yellow (stripe) rust, Puccinia striiformis f. sp. tritici, has seen the emergence of new race...
In 2016, an epidemic of highly pathogenic avian influenza A virus subtype H5N8 in the Netherlands caused mass deaths among wild birds, and several commercial poultry farms and captive bird holdings were affected. We performed complete genome sequencing to study the relationship between the wild bird...
Two cases of Crimean-Congo hemorrhagic fever were reported in Spain during 2016. We obtained the virus from a patient sample and characterized its full genomic sequence. Phylogenetic analysis indicated that the virus corresponds to the African genotype III, which includes viruses previously found in...
There is little information about carbapenemase-producing (CP) Citrobacter spp. We studied the molecular epidemiology and microbiological features of CP Citrobacter spp. isolates collected in Spain (2013-15). In total, 119 isolates suspected of being CP by the EUCAST screening cut-off values were an...
Linezolid is often the drug of last resort to treat infections caused by Gram-positive cocci. Linezolid resistance can be mutational (23S rRNA or L-protein) or, less commonly, acquired [predominantly cfr, conferring resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins and streptogra...
To investigate the molecular epidemiology, antimicrobial susceptibility and carbapenem resistance determinants of Acinetobacter baumannii isolates from respiratory tract samples of patients diagnosed with ventilator-associated pneumonia (VAP) who were enrolled in the MagicBullet clinical trial. A. b...
Clostridium difficile is the main pathogen related to healthcare-associated diarrhea and it is the cause of 20 to 30% of diarrhea cases caused by antibiotics. In Colombia and Latin America, the knowledge about the epidemiological behavior of this infection is limited. To describe the characteristics...
Pseudomonas aeruginosa (P. aeruginosa) is one of the most common nosocomial pathogens worldwide. Although the emergence of multidrug-resistant (MDR) P. aeruginosa is a critical problem in medical practice, the key features involved in the emergence and spread of MDR P. aeruginosa remain unknown. Thi...
This study investigated the trend in antimicrobial resistance among group B Streptococcus (GBS) from a national surveillance programme in Taiwan and delineated characteristics of and factors associated with levofloxacin-resistant isolates. Clinical isolates of all sample types and patient groups wer...
To investigate the epidemiology of infection in Romanian hospitals. A survey was conducted at nine hospitals throughout Romania between November 2013 and February 2014. The survey identified 393 patients with infection. The median age was 67 years (range: 2-94 years); 56% of patients were aged >65...
Methicillin-resistant Staphylococcus aureus (MRSA) colonization in cystic fibrosis (CF) patients is an increasing problem in many countries. In our Respiratory Center at the Hospital de Niños "Dr. Ricardo Gutiérrez", Buenos Aires, Argentina, the prevalence has climbed from 23% in 1995 up to 32% in 2...
In Japan, indigenous tick-borne phleboviruses (TBPVs) and their associated diseases first became evident in 2013 by reported human cases of severe fever with thrombocytopenia syndrome (SFTS). In this study, we report a novel member of the genus Phlebovirus designated as Kabuto Mountain virus (KAMV),...
Animal brucellosis is a re-emerging disease in China with high prevalence in the northwest region. A total of 66 isolates of Brucella were recovered from sheep and yaks in the Inner Mongolia, Xinjiang, Qinghai and Gansu provinces of northwest China in 2015 and 2016. Using classical biotyping and the...
Whole-genome sequencing (WGS) has typically been used to confirm or refute hospital/ward outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) identified through routine practice. However, appropriately targeted WGS strategies that identify routinely "undetectable" transmission remain the...
In the past twenty years, numerous novel zoonotic viral agents with pandemic potential have emerged in China, such as the severe acute respiratory syndrome (SARS) coronavirus and, more recently, the avian-origin influenza A/H7N9 virus, which have caused outbreaks among humans with high morbidity and...
Several outbreaks of serogroup B meningococcal disease have occurred among university students in recent years. In the setting of high coverage of the quadrivalent meningococcal conjugate vaccine and prior to widespread use of serogroup B meningococcal vaccines among adolescents, we conducted survey...
This study evaluated the occurrence of enterococci resistant to clinically relevant antibiotics in long-term care facility (LTCF) residents in Porto, Portugal, a region with high rates of multidrug-resistant enterococci in infected patients and healthy carriers. Faecal samples from 48 residents in t...
Of 250 clinical isolates of obtained in Nepal, 38 were carbapenem resistant, with MICs of imipenem or meropenem of ≥4 μg/ml. All 38 isolates harbored the following s: , , , , , , and Most of these isolates also harbored the 16S rRNA methylase gene(s) , , and/or .
Most multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa strains belonged to epidemic high-risk (EHR) clones that succeeded worldwide in the context of hospital outbreaks. In order to study the intraclonal diversity in EHR P. aeruginosa, we selected clinical and environmenta...
No abstract available
In rabbit, P. multocida is considered a predominant pathogenic agent; despite this, few data on the molecular epidemiology are available so far. The aim of this work was to characterize P. multocida isolates from rabbit affected by various diseases in Italy. Comparison was made to reference strains...
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an increasingly prevalent pathogen in veterinary medicine. This study examined the molecular epidemiology of clinical MRSP isolated from Australian animals. Clinical staphylococci submitted to all Australian veterinary diagnostic labora...
This report describes an outbreak of gentamicin-resistant, meticillin-resistant Staphylococcus aureus (GR MSSA) which occurred on a 21-bed neonatal unit (NNU) in Ninewells Hospital, Dundee, UK. An outbreak investigation was triggered by two new GR MSSA isolates from babies admitted directly to the N...
Dengue is one of the most important arthropod-borne viral diseases. It is endemic in > 125 countries including Pakistan, with a global incidence of 50-200 million. We determined the frequency of different serotypes of dengue virus to highlight its hyperendemicity in Rawalpindi, Pakistan. Between May...
Acinetobacter baumannii is a nosocomial pathogen which is establishing as a major cause of morbidity and mortality within the healthcare community. The success of this pathogen is largely due to its ability to rapidly gain resistance to antimicrobial therapies and its capability to persist in an abi...
The central variable region (CVR) within the B602L gene of the African swine fever virus (ASFV) is highly polymorphic within the 23 ASFV genotypes defined by sequencing of the C-terminal end of the p72 locus. Sequencing the p54 gene further discriminates ASFV genotypes that are conserved at the p72...
Sequencing pathogen samples during a communicable disease outbreak is becoming an increasingly common procedure in epidemiologic investigations. Identifying who infected whom sheds considerable light on transmission patterns, high-risk settings and subpopulations, and the effectiveness of infection...
Whole genome sequencing (WGS) is being adopted in public health for improved surveillance and outbreak analysis. In public health, subtyping has been used to infer phenotypes and distinguish bacterial strain groups. In silico tools that predict subtypes from sequences data are needed to transition h...
Methicillin resistant Staphylococcus aureus (MRSA) is a versatile pathogen capable of causing multitude of human diseases. It is one of the most important nosocomial pathogen that implicated in community and healthcare associated infections. Therefore, this study aims to characterize different SCCme...
Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole-genome sequencing...
A thorough understanding of the role of human immunodeficiency virus (HIV) intrahost evolution in AIDS pathogenesis has been limited by the need for longitudinally sampled viral sequences from the vast target space within the host, which are often difficult to obtain from human subjects. CD8 lymphoc...
The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes - now a staple of the public health microbiology laboratory in well-resourced settings - c...
Neisseria meningitidis group W (NmW) belonging to the clonal complex ST-11 (NmW/cc11) spread in Europe and in France in 2000 and declined thereafter. In France, invasive meningococcal disease (IMD) due to NmW increased again in 2012 and thereafter since 2015. Several sub-lineages of NmW/cc11 are cir...
The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded...
Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi-host and/or multi-parasite interactions to understand and predict current and future disease thre...
Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the...
Zoonotic tuberculosis is a risk for human health, especially when animals are in close contact with humans. Mycobacterium tuberculosis was cultured from several organs, including lung tissue and gastric mucosa, of three captive elephants euthanized in a Swiss zoo. The elephants presented weight loss...
Salmonella Typhimurium is the most dominant Salmonella serovar around the world. It is associated with foodborne gastroenteritis outbreaks but has recently been associated with invasive illness and deaths. Characterization of S. Typhimurium is therefore very crucial for epidemiological surveillance....
Staphylococcus aureus is an important cause of infections in hospitalized neonates. Preterm or low birthweight infants are especially at risk to develop a S. aureus infection due to the immaturity of the immune system, length of hospital stay and invasive procedures. Exfoliative toxin (ET)-producing...
The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS d...
The humoral immune responses against 46 different staphylococcal antigens in 27 bacteremia patients infected by clonally related methicillin-resistant Staphylococcus aureus (MRSA) strains of a single sequence type (ST) 239 were investigated. A group of non-infected patients (n = 31) hospitalized for...
Nearly two decades after completion of the genome sequence of Mycobacterium tuberculosis (MTB), and with the advent of next generation sequencing technologies (NGS), whole-genome sequencing (WGS) has been applied to a wide range of clinical scenarios. Starting in 2017, England is the first country i...
In 1988, the World Health Assembly launched the Global Polio Eradication Initiative (GPEI) (1). Among the three wild poliovirus (WPV) serotypes, only type 1 (WPV1) has been detected since 2012. Since 2014, detection of WPV1 has been limited to three countries, with 37 cases in 2016 and 11 cases in 2...
IntroductionAt the beginning of 2016, an increase in paediatric haemolytic uremic syndrome (HUS) cases was observed in Romania. The microbiological investigations allowed isolation of Shiga toxin-producing (STEC) O26 as the causative agent from most cases. An enhanced national surveillance of HUS...
IntroductionWhole genome sequencing (WGS) is increasingly used in Legionnaires' disease (LD) outbreak investigations, owing to its higher resolution than sequence-based typing, the gold standard typing method for in the analysis of endemic strains. Recently, a gene-by-gene typing approach based on...
Currently, surveillance of livestock-associated meticillin-resistant (LA-MRSA) in humans in Europe is not systematic but mainly event-based. In September 2014, the European Centre for Disease Prevention and Control (ECDC) initiated a questionnaire to collect data on the number of LA-MRSA from human...
During the summer of 2015, New York, New York, USA, had one of the largest and deadliest outbreaks of Legionnaires' disease in the history of the United States. A total of 138 cases and 16 deaths were linked to a single cooling tower in the South Bronx. Analysis of environmental samples and clinical...
Carbapenemase-producing Enterobacteriaceae (CPE), including KPC-producing Klebsiella pneumoniae (KPC-Kpn), are an increasing threat to patient safety. To use WGS to investigate the extent and complexity of carbapenemase gene dissemination in a controlled KPC outbreak. Enterobacteriaceae with reduced...
Containing the recent West African outbreak of Ebola virus (EBOV) required the deployment of substantial global resources. Despite recent progress in analysing and modelling EBOV epidemiological data, a complete characterization of the spatio-temporal spread of Ebola cases remains a challenge. In th...
Urban expansion has widespread impacts on wildlife species globally, including the transmission and emergence of infectious diseases. However, there is almost no information about how urban landscapes shape transmission dynamics in wildlife. Using an innovative phylodynamic approach combining host a...
Heterogeneity in individual-level transmissibility can be quantified by the dispersion parameter k of the offspring distribution. Quantifying heterogeneity is important as it affects other parameter estimates, it modulates the degree of unpredictability of an epidemic, and it needs to be accounted f...
Phylogeographic methods can help reveal the movement of genes between populations of organisms. This has been widely done to quantify pathogen movement between different host populations, the migration history of humans, and the geographic spread of languages or gene flow between species using the l...
Aedes aegypti and Aedes albopictus are the primary and secondary vectors, respectively, of dengue, the most important arboviral disease in the world. The aim of this study was to detect and serotype dengue viruses (DENV) in the vectors Ae. aegypti and Ae. albopictus in Surabaya, Indonesia. Between 2...
Pneumonia is a major healthcare problem. Rapid pathogen identification is critical, but often delayed due to the duration of culturing. Early, broad antibacterial therapy might lead to false-negative culture findings and eventually to the development of antibiotic resistances. We aimed to assess the...
The ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified. We analysed the whole genome sequences of S. Typhimurium isolates from UK pati...
Multiple-locus variable-number tandem-repeat analysis (MLVA) typing was performed for Mycoplasma pneumoniae strains isolated between 2004 and 2014 in Yamagata, Japan. The results were examined by considering the combination of the P1 type and prevalence of macrolide resistance-associated mutations....
Data regarding the incidence and molecular epidemiology of Clostridium difficile infections (CDIs) in Greece are limited. A retrospective study of all laboratory-confirmed CDI cases in a university hospital during a 9-month period. Stool samples from inpatients with diarrhoea were tested with a comb...
The H9N2 influenza viruses are extensively circulating in the poultry population, and variable genotypes can be generated through mutation, recombination and reassortment, which may be better adapted to infect a new host, resist drug treatment or escape immune pressure. The LPAI H9N2 viruses have th...
The protein composition of an Outer Membrane Vesicle (OMV) preparation that constitutes the active pharmaceutical ingredient of VA-MENGOC-BC®, an effective vaccine against Neisseria meningitidis serogroups B, and C is presented. This preparation has a high lipid content and five abundant membrane pr...
Acinetobacter baumannii has often been associated with colonization and/or infection in neonatal intensive care units (NICU). This study describes a clonal spread of carbapenem-resistant A. baumannii (CRAB) isolates in an NICU. In total, 21 CRAB isolates were collected from premature newborns. Only...
Difficulties in distinguishing species of the Elizabethkingia genus by MALDI-TOF prompted use of rpoB sequencing to investigate species distribution among 44 isolates from cystic fibrosis (CF) patients. Forty-three isolates from 38 patients formed a cluster comprising E. miricola and proposed novel...
Genome sequencing has provided snapshots of the transmission of methicillin-resistant (MRSA) during suspected outbreaks in isolated hospital wards. Scale-up to populations is now required to establish the full potential of this technology for surveillance. We prospectively identified all individual...
To retrospectively investigate the epidemiology of cryptococcosis in Ljubljana, Slovenia. Forty-six sequentially obtained isolates from 19 patients were subjected to amplified fragment length polymorphism (AFLP) genotyping, microsatellite typing, mating- and serotype PCRs and antifungal susceptibili...
sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL...
Carbapenem antibiotics are among the mainstays for treating infections caused by , especially in the Northwest United States, where carbapenem-resistant remains relatively rare. However, between June 2012 and October 2014, an outbreak of carbapenem-resistant occurred in 16 patients from five healt...
Swine are a key reservoir host for influenza A viruses (IAVs), with the potential to cause global pandemics in humans. Gaps in surveillance in many of the world's largest swine populations impede our understanding of how novel viruses emerge and expand their spatial range in pigs. Although US swine...
Staphylococcal food poisoning (SFP) is caused by staphylococcal enterotoxins (SEs) preformed in food materials. SE genes are encoded on mobile genetic elements and are widely found across Staphylococcus species including S. argenteus, although most SFP cases are caused by S. aureus. S. argenteus, re...
Until the introduction of fidaxomicin, antimicrobial treatment for Clostridium difficile infection (CDI) was limited to metronidazole and vancomycin. The changing epidemiology of CDI and the emergence of epidemic C. difficile PCR ribotype 027 necessitate continued surveillance to identify shifts in...
Vancomycin-resistant enterococci (VRE) are an important agent of colonization and infection in haematology patients. However, the role of virulence on VRE colonization and infection is controversial. To characterize the lineage, virulence and resistance profile of VRE infection and colonization isol...
This study aimed to evaluate MALDI-TOF MS for species discrimination of Listeria in the context of routine surveillance. MALDI-TOF MS yielded 100% accuracy for the identification of L. monocytogenes, L. innocua, L. ivanovii, L. fleischmannii, L. grayi, L. seeligeri, L. weihenstephanensis and L. wels...
Recent studies support a change of Clostridium difficile infections (CDIs) epidemiology in pediatric patients. Since limited information is available about C. difficile in this population, we investigated the epidemiology of CDI in a large pediatric hospital that acts as reference centre in Italy an...
Rabbit hemorrhagic disease (RHD) is a veterinary disease that affects the European rabbit and has a significant economic and ecological negative impact. In Portugal, rabbit hemorrhagic disease virus (RHDV) was reported in 1989 and still causes enzootic outbreaks. Several recombination events have be...
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium () has an unusual population structure, with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused...
No abstract available
Helicobacter pylori infection is common in Algeria, but there are few data on the characterization of isolated strains. The aim of this study was to update data on the prevalence of H. pylori in patients submitted to endoscopy, antibiotic resistance, and phylogeography of H. pylori strains isolated...
To compare the epidemiology of tuberculosis (TB) in Denmark, Sweden and Finland, by focusing on the native population in order to identify epidemiologic differences and thus indirectly possible differences in TB control. TB incidence trends from 1990 through 2015 were compared among the countries. I...
The primary objective of this work was to examine the acquisition and spread of multi-drug resistant (MDR) tuberculosis (TB) in Ireland. All available Mycobacterium tuberculosis complex (MTBC) isolates (n = 42), from MDR-TB cases diagnosed in Ireland between 2001 and 2014, were analysed using phenot...
Citrus tristeza virus (CTV) is a major pathogen affecting citrus trees worldwide. However, few studies have focused on CTV's evolutionary history and geographic behavior. CTV is locally dispersed by an aphid vector and long distance dispersion due to transportation of contaminated material. With the...
Spatio-temporal patterns of the spread of infectious diseases are commonly driven by environmental and ecological factors. This is particularly true for vector-borne diseases because vector populations can be strongly affected by host distribution as well as by climatic and landscape variables. Here...
Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli have disseminated worldwide. This study investigated bla-positive E. coli on a large-scale Vietnamese chicken farm and analysed whether there was any difference in prevalence and molecular characteristics of bla-positive E. coli between...
Despite tight biosecurity measures, an outbreak of respiratory disease rapidly spread across the Icelandic equine population in 2010. Horse transportation was brought to a halt in order to contain the spread of the infectious agent. In a recent article, Björnsdóttir and colleagues (S. Björnsdóttir e...
Clostridium difficile is an emerging cause of healthcare-associated infections. The increasing frequency and severity is attributed to highly virulent ribotypes such as 027. The aim of this study was to retrospectively analyze the prevalence of CDI and ribotype 027 in 481 clinical samples collected...
Klebsiella pneumoniae is among the most important pathogens found in hospitals. The emergence of multiple antibiotic resistant K. pneumoniae associated with its virulence factors is a worldwide concern and its early identification is crucial, especially for controlling the spread of emerging clones....
The natural habitats and potential reservoirs of the nosocomial pathogen Acinetobacter baumannii are poorly defined. Here, we put forth and tested the hypothesis of avian reservoirs of A. baumannii. We screened tracheal and rectal swab samples from livestock (chicken, geese) and wild birds (white st...
To reveal the molecular epidemiological characteristics of Carbapenem-Resistant (CRKP) isolated from a three level teaching hospital in Beijing. Pulsed field gel electrophoresis (PFGE) was carried out to subtyping 375 CRKP isolated in that hospital between May 2010 and October 2015. Fifteen strain...
Due to the limitations of serotyping, to differentiate closely related microbial isolates and to investigate disease outbreaks, molecular genotyping methods including multiple loci variable number of tandem repeats (VNTR) analysis (MLVA) has been developed. The usefulness of MLVA was recently demons...
Carbapenemase-producing Enterobacteriaceae (CPE) are emerging worldwide, limiting therapeutic options. Mutational and plasmid-mediated mechanisms of colistin resistance have both been reported. The emergence and clonal spread of colistin resistance was analysed in 40 epidemiologically-related NDM-1...
Clostridium difficile is a Gram-positive spore forming anaerobic bacterium and the main cause of healthcare-associated diarrhea. This study aimed to perform the phenotypic characterization and molecular typing of Clostridium difficile isolates among patients at a cancer hospital in Brazil. During 18...
No abstract available
The emergence of carbapenem resistance among Escherichia coli is a serious threat to public health. The objective of this study was to investigate resistance genes and clonality of carbapenem resistant E. coli in Iran. Between February 2015 and July 2016, a total of 32 non-duplicate E. coli isolates...
Little is known about the phylogeography of norovirus (NoV) in China. In norovirus, a clear understanding for the characteristics of tree topology, migration patterns and its demographic dynamics in viral circulation are needed to identify its prevalence trends, which can help us better prepare for...
To describe the clinical characteristics, outcomes, and factors associated with Clostridium difficile infection (CDI) due to ribotype 027 (RT027) and recurrence, including an outbreak period, with transition to endemicity. A case-control study was performed. Clinical and demographic data were collec...
Regarded as one of the most expensive production diseases of dairy sheep and goats, contagious agalactia (CA) is caused by any of four agents: Mycoplasma agalactiae, M. mycoides subspecies capri (Mmc), M. capricolum subspecies capricolum (Mcc) and M. putrefaciens. Although CA is worldwide in distrib...
During a large outbreak of Shiga toxin-producing Escherichia coli illness associated with an agricultural show in Australia, we used whole-genome sequencing to detect an IS1203v insertion in the Shiga toxin 2c subunit A gene of Shiga toxin-producing E. coli. Our study showed that clinical illness wa...
We investigated 543 Listeria monocytogenes isolates from food having a temporal and spatial distribution compatible with that of the invasive listeriosis outbreak occurring 2012-2016 in southern Germany. Using forensic microbiology, we identified several products from 1 manufacturer contaminated wit...
Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for healthcare facilities worldwide. A continuous monitoring of ST distribution and its association with resistance and virulence genes is required for early detection of successful K. pneumoniae lineages. In this study, we used W...
Infectious hematopoietic necrosis virus (IHNV) is among the most important pathogens affecting the salmonid industry. Here, we investigated the molecular evolution and circulation of isolates from 11 countries or regions all over the world, with a special focus on the epidemiological situation in Fr...
Rabies is an important zoonotic disease distributed worldwide. A key question in rabies epidemiology is the identification of factors that impact virus dispersion. Here we apply new analytical methods, based on phylogeographic reconstructions of viral lineage movement, to undertake a comparative evo...
Invasive meningococcal disease (IMD) is a major public health problem worldwide. An epidemic of serogroup C (NmC) IMD occurred in 2010 in the city of Salvador. In this study, we describe the antigenic and genetic characterization of meningococcal isolates collected from meningitis cases in Salvador...
Two nationwide Mycoplasma pneumoniae epidemics occurred in Slovenia between 2006 and 2016. The aim of this study was to assess which M. pneumoniae genotypes were present in our area during the selected timeframe, whether the origin of the epidemics was monoclonal or polyclonal and whether the propor...
Non-fermentative Gram-negative bacilli are now one of the most important causes of severe infections in Polish hospitals. Acinetobacter species are serious concern because of the high prevalence of multi-drug resistance among strains. Resistance profiles for 53 Gram-negative non-fermentative blood i...
Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in p...
is an important pathogen causing a spectrum of diseases ranging from mild skin and soft tissue infections to life-threatening conditions. Bloodstream infections are particularly important, and the treatment approach is complicated by the presence of methicillin-resistant (MRSA) isolates. The emerge...
Outbreaks of Kingella kingae infection are an emerging public health concern among daycare attendees carrying epidemic clones in the oropharynx. However, genotyping of such epidemic clones from affected cases is limited by the low performance of current methods to detect K. kingae from blood samples...
Thanks to recent advances in random amplification technologies, metagenomic surveillance expanded the number of novel, often unclassified viruses within the family Rhabdoviridae. Using a vector-enabled metagenomic (VEM) tool, we identified a novel rhabdovirus in Aedes cantans mosquitoes collected fr...
Coxsackievirus A4 (CV-A4) has been reported frequently in association with many infectious diseases and cases of hand, foot, and mouth disease potentially associated with CV-A4 infection are also identified. This study summarized the Shandong CV-A4 strains isolated from 25years acute flaccid paralys...
Burkholderia cepacia is intrinsically resistant to certain antiseptics. The authors noted a sudden increase in the frequency of isolation of B. cepacia from blood cultures in a neonatal intensive care unit (NICU) of a university-affiliated hospital. To identify the source and intervene in the ongoin...
Recent history has provided us with one pandemic (Influenza A/H1N1) and two severe viral outbreaks (Ebola and Zika). In all three cases, post-hoc analyses have given us deep insights into what triggered these outbreaks, their timing, evolutionary dynamics, and phylogeography, but the genomic charact...
Shiga toxin-producing Escherichia coli (STEC) is a significant cause of gastrointestinal infection and the haemolytic-uremic syndrome (HUS). STEC outbreaks are commonly associated with food but animal contact is increasingly being implicated in its transmission. We report an outbreak of STEC affecti...
Burkholderia cepacia is an important opportunistic organism in hospitalized and immunocompromised patients, particularly in cystic fibrosis. To describe the epidemiological investigation of an outbreak of B. cepacia bacteraemia. The study examined 14 patients during their admission to three intensiv...
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation...
There is increasing interest in the heritable bacteria of invertebrate vectors of disease as they present novel targets for control initiatives. Previous studies on biting midges (Culicoides spp.), known to transmit several RNA viruses of veterinary importance, have revealed infections with the endo...
is a Gram-negative intestinal pathogen of humans and has been responsible for several nationwide gastrointestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenic species of the genus and allowing a high-resolution understanding of the ecology, ev...
During 2015-2016, we evaluated the performance of whole-genome sequencing (WGS) as a routine typing tool. Its added value for microbiological and epidemiologic surveillance of listeriosis was compared with that for pulsed-field gel electrophoresis (PFGE), the current standard method. A total of 2,74...
No abstract available
The objective of this study was to determine the prevalence, serotypes, antimicrobial resistance phenotypes, and pulsed-field gel electrophoresis (PFGE) patterns of Salmonella recovered in feces and mesenteric and prefemoral lymph nodes (LNs) from cohorts of calves with and without a confirmed outbr...
Group B Streptococcus or Streptococcus agalactiae continue to be challenging for milk quality programs in countries with emerging dairy industries, such as Colombia, where high prevalence has been reported. Molecular typing of isolates is needed to understand the variability and epidemiology of this...
The anaerobic Gram-positive coccus is a rare cause of infections of bone and joints. The aim of this study was to describe the microbiological and clinical characteristics of orthopedic implant-associated infections caused by We retrospectively analyzed samples consisting of anaerobic Gram-positiv...
Although there has been a decrease in the number of cases of salmonellosis in the European Union, it still represents the primary cause of foodborne outbreaks. In Calabria region, data are lacking for the incidence of human non-typhoid salmonellosis as active surveillance has never been carried out....
Little is known about Clostridium difficile infection (CDI) in Asia. The aims of our study were to explore (i) the prevalence, risk factors and molecular epidemiology of CDI and colonization in a tertiary academic hospital in North-Eastern Peninsular Malaysia; (ii) the rate of carriage of C. diffici...
Twelve nonreplicate carbapenemase-negative ertapenem (ETP)-nonsusceptible (CNENS) Escherichia coli isolates obtained at a Thai university hospital between 2010 and 2014 were characterized and compared with 2 carbapenemase-producing E. coli isolates from the same hospital. Eight unique pulsed-field g...
Pseudomonas aeruginosa is the predominant opportunistic pathogen leading to nosocomial infection and outbreak in hospitals. Hospitalized patients may be infected with this bacterium through close contact with contaminated environmental media. However, the molecular epidemiology, resistance, and viru...
The objectives of this study were (i) to determine the genetic basis for carbapenem resistance in multidrug-resistant (MDR) Acinetobacter baumannii strains isolated from patients affected by a sudden increase in the incidence of infections by such organisms in a tertiary care hospital in Virginia, U...
In recent years, Klebsiella pneumoniae has emerged as a leading cause of nosocomial infection owing to the rising prevalence of multidrug-resistant strains, particularly carbapenem-resistant isolates. In this study, the complete genome sequence of carbapenem-resistant K. pneumoniae SWU01 was determi...
RNA viruses are abundant infectious agents and present in all domains of life. Arthropods, including ticks, are well known as vectors of many viruses of concern for human and animal health. Despite their obvious importance, the extent and structure of viral diversity in ticks is still poorly underst...
Methicillin-resistant Staphylococcus aureus (MRSA) is a public health problem worldwide. This study aimed to investigate the antimicrobial susceptibility and molecular epidemiological characteristics of MRSA strains in Xiangyang, China, during 2012-2014. Eighty non-duplicate S. aureus isolates from...
New Delhi MBL (NDM) carbapenemase-producing Klebsiella pneumoniae has become one of the most concerning multidrug-resistant pathogens. The Balkan counties are considered a reservoir for the spread of such strains based on several reports documenting NDM infections after hospitalization in this regio...
The polymyxins have become one of the last resorts to treat serious infections caused by KPC-2-producing Klebsiella pneumoniae worldwide. However, the increase of polymyxin consumption has favored the emergence of resistance to these compounds. In this study, we observed an increase in polymyxin B r...
OBJECTIVE To determine the scope, source, and mode of transmission of a multifacility outbreak of extensively drug-resistant (XDR) Acinetobacter baumannii. DESIGN Outbreak investigation. SETTING AND PARTICIPANTS Residents and patients in skilled nursing facilities, long-term acute-care hospital, and...
In recent years, two of the crinivirus, Tomato chlorosis virus (ToCV) and Cucurbit chlorotic yellows virus (CCYV) have gained increasing attention due to their rapid spread and devastating impacts on vegetable production worldwide. Both of these viruses are transmitted by the sweet potato whitefly,...
is a major cause of infections. Toxic shock syndrome toxin (TSST-1) and Panton-Valentine leukocidin (PVL) are associated with severe clinical syndromes. colonizing isolates recovered from healthcare workers and patients in the intensive care unit (ICU) of a university hospital comprising Group A we...
This study aimed at determining the prevalence, antibiotic resistance patterns, and genetic linkage of Vancomycin Resistant Enterococcus faecium (VREfm) from different sources in the southwest of Iran. A total of 51 VREfm isolates were obtained and subjected to antibiotic susceptibility testing, car...
SasX is a known virulence factor of Staphylococcus aureus involved in colonisation and immune evasion of the bacterium. The sasX gene, which is located on the ϕSPβ prophage, is frequently found in the sequence type (ST) 239 S. aureus lineage, which is the predominant healthcare-associated clone in A...
In 2015, an outbreak involving a highly virulent zoonotic outbreak strain of Streptococcus agalactiae serotype III, multilocus sequence type 283 occurred in Singapore with increased neurologic complications, septic arthritis, and spinal infections in healthier patients. We report a case of a success...
The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. However, the ana...
Neisseria gonorrhoeae antimicrobial resistance (AMR) is a globally recognized health threat; new strategies are needed to enhance AMR surveillance. The Northern Territory of Australia is unique in that 2 different first-line therapies, based primarily on geographic location, are used for gonorrhea t...
Carriage of S. aureus in the anterior nares seems to play a significant role in the pathogenesis of infection. This study aimed to determine the molecular characteristics and antibiotic susceptibility pattern of S. aureus isolates obtained from the nasal carriage of health care workers (HCWs). This...
Disease control programs aim to constrain and reduce the spread of infection. Human disease interventions such as wildlife vaccination play a major role in determining the limits of a pathogen's spatial distribution. Over the past few decades, a raccoon-specific variant of rabies virus (RRV) has inv...
Hand foot and mouth disease (HFMD) is a relatively unreported disease in India. This study was undertaken to characterize the enterovirus type/s associated with two unexpectedly-massive epidemics that occurred in Bangalore, India in 2013 and 2015. Stool samples of 229 children with HFMD living in No...
Spread of methicillin-resistant Staphylococcus aureus (MRSA) isolates is a worldwide problem. Molecular typing is a useful tool to understand MRSA epidemiology. Herein, we determined vancomycin-resistant, SCCmec and spa types among MRSA isolates recovered from healthcare and community-acquired infec...
Hypervirulent Klebsiella pneumoniae strains often cause life-threatening community-acquired infections in young and healthy hosts, but are usually sensitive to antibiotics. In this study, we investigated a fatal outbreak of ventilator-associated pneumonia caused by a new emerging hypervirulent K pne...
Clostridium difficile infection (CDI) is increasingly recognized globally as a cause of significant morbidity and mortality. This study aimed to provide insight into the various dynamics of C. difficile transmission and infection in the hospital. We monitored the toxin and resistance profiles as wel...
Clostridium difficile infection (CDI) is associated with risk for severe disease and high mortality. Little is known about the extent of hospital-acquired CDI in Mainland China. In this study, we aimed to investigate the annual CDI incidence, bacterial genotypes, risk factors for severe CDI and surv...
We compared the proportion of cases of community-associated and healthcare-associated methicillin-resistant Staphylococcus aureus (CA-MRSA and HA-MRSA, respectively) bacteraemia among patients at five hospitals in the Gauteng and Western Cape provinces in South Africa and described the molecular cha...
This retrospective study investigated clinical manifestations of candidemia caused by uncommon Candida species and antifungal susceptibility of the isolates in a regional hospital in Taiwan. The uncommon Candida species was initially defined as Candida species other than C. albicans, C. tropicalis,...
Coxsackievirus A16 (CV-A16; ) is an enterovirus (EV) type associated with hand, foot, and mouth disease (HFMD) in children. To investigate the spatial spread of CV-A16, we used viral sequence data sampled during a prospective sentinel surveillance of HFMD in France (2010 to 2014) and phylogenetic re...
No abstract available
Burkholderia sp. infections are extremely complex in cystic fibrosis (CF) patients, especially considering the lack of knowledge regarding its behavior, its relationship with prognosis, as well as its transmissibility and multidrug resistance features. This study evaluated the frequency of chronic i...
Acute hepatopancreatic necrosis disease (AHPND) (formerly, early mortality syndrome) is a high-mortality-rate shrimp disease prevalent in shrimp farming areas. Although AHPND is known to be caused by pathogenic Vibrio parahaemolyticus hosting the plasmid-related PirAB toxin gene, the effects of dist...
Salmonella enterica subspecies enterica serovar Typhimurium is the most common zoonotic pathogen in Bulgaria. To allow efficient outbreak investigations and surveillance in the food chain, accurate and discriminatory methods for typing are needed. This study evaluated the use of multiple-locus varia...
H4Nx viruses were reported in swine in Canada and China, but had not been recognized in swine in the USA. In late 2015, an avian-origin H4N6 influenza A virus was isolated from pigs in the United States during a routine diagnostic investigation of clinical respiratory disease in the herd. Serologica...
The aim of this study was to evaluate the risk factors for pneumonia due to extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) and to analyse the molecular epidemiology of ESBL-KP in Xiamen, China. A case-control study was conducted at Zhongshan Hospital from January 2014 to Aug...
Macrolides are among the most widely prescribed antibiotics worldwide. However, their impact on the gut's bacterial microbiota remains uncertain. We characterised the intestinal microbiota in 6-11 month-old infants in India who received a 3-day course of azithromycin or placebo during a randomised t...
In recent years, New Delhi metallo-beta-lactamases 1 (bla ) has been reported with increasing frequency and become prevalent. The present study was undertaken to investigate the epidemiological dissemination of the bla gene in Enterobacter cloacae isolates at a teaching hospital in Yunnan, China. A...
Japan has an aging population and an increasing number of patients who reside in long-term care and mental health facilities. Both pneumococcal pneumonia and influenza B infection outbreaks have been observed in these populations, although no reports have described concurrent outbreaks of pneumococc...
Angiostrongylus cantonensis is of increasing public health importance as the main zoonotic pathogen causing eosinophilic meningitis or meningoencephalitis, which has been documented all over the world. However, there are very limited studies about its phylogeography and spread pattern. In the presen...
To investigate an unusual outbreak of five patients with a total of eight episodes of a Clostridium difficile infection on a gastrointestinal surgical ward of a Dutch tertiary-care, university-affiliated hospital. Clinical case investigations and laboratory analyses were performed. Laboratory analys...
The multi-drug resistant (MDR) Acinetobacter baumannii as an important nosocomial pathogen has emerged a global health concern in recent years. In this study, we applied three easier, faster, and cost-effective methods including PCR-based open reading frames (ORFs) typing, sequence typing of bla and...
This study was undertaken to determine the genotypic distribution of Chinese M. bovis strains and their similarity to isolates from other countries. Two multilocus sequence typing (MLST) schemes (MLST-1 and MLST-2) and pulsed field gel electrophoresis (PFGE) were used to compare 44 Chinese strains a...
Cholera, caused by , remains a global threat to public health. In Myanmar, the availability of published information on the occurrence of the disease is scarce. We report here that cholera incidence in Mandalay generally exhibited a single annual peak, with an annual average of 312 patients with sev...
Aeromonas spp. are gram-negative bacteria that can cause a variety of infections in both humans and animals and play a controversial role in diarrhea outbreaks. Our aim was to identify clinical and environmental Aeromonas isolates associated with a cholera outbreak in a northeast county of Brazil at...
Mayaro virus (MAYV), causative agent of Mayaro Fever, is an arbovirus transmitted by Haemagogus mosquitoes. Despite recent attention due to the identification of several cases in South and Central America and the Caribbean, limited information on MAYV evolution and epidemiology exists and represents...
One imported and five secondary cases of measles were detected in Finland between June and August 2017. The measles sequences available for five laboratory-confirmed cases were identical and belonged to serotype D8. The large number of potentially exposed Finnish and foreign individuals called for c...
Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this ques...
Hypervirulent strain of Klebsiella pneumoniae genotype K1 isolates have recently emerged, causing severe pyogenic liver abscess complicated by devastating metastatic infections in humans. We describe a short outbreak of the non-human primate (NHP) research center, associated with a hypervirulent K....
Automation of laboratory tests, bioinformatic analysis of biological sequences, and professional data management are used routinely in a modern university hospital-based infectious diseases institute. This dates back to at least the 1980s. However, the scientific methods of this 21st century are cha...
Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relat...
Twelve strains of meticillin-resistant Staphylococcus aureus (MRSA) isolated during a suspected outbreak in a paediatric intensive care unit were analysed by whole-genome sequencing (WGS). To define the clonality of MRSA strains to a high discriminative power, and to evaluate the presence of genetic...
MLVA analysis of 103 PCR ribotype 027 strains showed a regional specificity and the persistence of the same clone within a hospital several years apart. Capillary electrophoresis PCR ribotyping led to the identification of seven 027 variant strains and five 176 strains, four of them being implicated...
We report the first outbreak caused by Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae sequence type 258 (ST 258) clone that occurred in Croatia from May to December 2012. 23 carbapenem-resistant K. pneumoniae isolates were recovered from clinical and screening specimens of 12 pati...
Acinetobacter baumannii infections in neonates are not uncommon but rarely studied. Clinical and molecular epidemiology of 40 patients with A. baumannii bacteremia in the neonatal intensive care units (NICUs) of a medical center from 2004 to 2014 was analyzed. Multi-drug resistance was found in only...
The global spread of carbapenem-resistant Acinetobacter baumannii (CRAB) is now a public health problem. In Taiwan, the relationship of the CRAB circulation between long-term care facilities (LTCFs) and acute care hospitals remains unclear. Here, we use molecular epidemiologic methods to describe th...
Increasing incidence rates of invasive Streptococcus dysgalactiae subspecies equisimilis (SDSE) infections have been reported worldwide, but the evolutionary mechanisms underlying this development remain elusive. Through prospective surveillance of invasive SDSE infections in western Norway, we obse...
Of great concern is the increased frequency of carbapenem-resistant Acinetobacter baumannii (CRAB) causing healthcare-associated infections. Different classes of β-lactamases are involved in this resistance through hydrolyzing carbapenems. Multilocus sequence typing (MLST) has been applied successfu...
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an emerging problem in many parts of the world. LA-MRSA has been isolated previously from animals and humans in the United Kingdom (UK), but the prevalence is unknown. The aim of this study was to determine the prevalence...
Yellow fever virus (YFV) strains circulating in the Americas belong to two distinct genotypes (I and II) that have diversified into several concurrent enzootic lineages. Since 1999, YFV genotype I has spread outside endemic regions and its recent (2017) reemergence in non-endemic Southeastern Brazil...
Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) bacterial population. However, MSSA also colonise asymptomat...
A frequent complication of Clostridium difficile infection (CDI) is recurrent disease. The aim of this study was to determine whether early recurrence risk was higher after infection with ribotype 027 (outbreak strain) compared with infection with endemic strain types of C. difficile. Consecutive pa...
Phylogenetic methods are being increasingly used to help understand the transmission dynamics of measurably evolving viruses, including HIV. Clusters of highly similar sequences are often observed, which appear to follow a 'power law' behaviour, with a small number of very large clusters. These clus...
Porcine reproductive and respiratory syndrome (PRRS) has caused huge economic losses to Chinese swine industry and remains a major threat since it was first reported in 1996. However, investigations of molecular epidemiological and genetic diversity of PRRS viruses (PRRSVs) in China were limited to...
In 2015, a cluster of respiratory diphtheria cases was reported from KwaZulu-Natal Province in South Africa. By using whole-genome analysis, we characterized 21 Corynebacterium diphtheriae isolates collected from 20 patients and contacts during the outbreak (1 patient was infected with 2 variants of...
Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approa...
Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were first seen in the UK in 2003 and have been increasingly reported since 2010, largely owing to an ongoing outbreak in North-West England. We examined the role of clonal spread and plasmid transmission in their emergence. Isol...
The KPC-producing Klebsiella pneumoniae (KPC-KP) clonal group (CG) 258 has disseminated throughout Israeli post-acute care hospitals (PACHs). The objectives of the study were (i) to describe the evolution and (ii) to understand the dissemination modes of CG 258 in the PACH system in Israel. KPC-KP s...
This study was performed to investigate the concordance in terms of molecular characteristics and antimicrobial susceptibility between colonizing and clinical Staphylococcus aureus isolates obtained from children in Korea, where ST72 is the major genotype.This was a prospective observational descrip...
Variation in Clostridium difficile infection (CDI) rates between healthcare institutions suggests overall incidence could be reduced if the lowest rates could be achieved more widely. We used whole-genome sequencing (WGS) of consecutive C. difficile isolates from 6 English hospitals over 1 year (201...
Effective control and monitoring of foot-and-mouth disease (FMD) relies upon rapid and accurate disease confirmation. Currently, clinical samples are usually tested in reference laboratories using standardized assays recommended by The World Organisation for Animal Health (OIE). However, the require...
We report an outbreak of Burkholderia cenocepacia bacteremia and infection in 11 patients predominately in intensive care units caused by contaminated ultrasound gel used in central line insertion and sterile procedures within 4 hospitals across Australia. Burkholderia cenocepacia was first identifi...
Enterobacter cloacae has recently emerged as an important agent of nosocomial infections owing to the dissemination of extended-spectrum β-lactamases and carbapenemases in this species. In this context, a rise in the therapeutic use of aminoglycosides was noticed, followed by the accelerated develop...
Meticillin-resistant Staphylococcus aureus (MRSA) is a frequently encountered pathogen in burn units. Burn patients are especially susceptible to MRSA acquisition and MRSA spread may cause outbreaks in burn units. To report the characteristics and successful control of an MRSA outbreak and to demons...
Multidrug-resistant Acinetobacter baumannii (MR-AB) can cause outbreaks in a burns unit. To study the incidence, risk factors and outcome of MR-AB colonization during an outbreak. A prospective study was conducted from April to November 2014 in a burns unit in Paris. Weekly surveillance cultures of...
A temporal increase in non-B subtypes has earlier been described in Sweden by us and we hypothesized that this increased viral heterogeneity may become a hotspot for the development of more complex and unique recombinant forms (URFs) if the epidemics converge. In the present study, we performed subt...
Echovirus 6 (E6) infections are associated with aseptic meningitis and acute flaccid paralysis (AFP). But some infections, sometimes most of them, are asymptomatic. The mechanism of E6 virulence is unknown. Analyses of the molecular evolution of asymptomatic E6 may help understand why the infections...
Staphylococcus aureus remains the most important cause of infections in hospitals and long-term care facilities. The aim of this study was to analyse the resistance, virulence, and epidemiological and genetic relationships of S. aureus from bloodstream infections (BSIs) and pneumonia from patients i...
An Enterococcus faecium isolate (Efa-125) carrying both the vanA and vanB genes was recovered from a patient with bacteraemia treated in a Greek hospital. Since this is the first description in Europe of E. faecium carrying both vanA and vanB genes, the isolate was further studied. Susceptibility to...
sequence type 131 (ST131) predominates globally among multidrug-resistant (MDR) strains. We used whole-genome sequencing (WGS) to investigate 63 MDR isolates from 7 North Carolina community hospitals (2010 to 2015). Of these, 39 (62%) represented ST131, including 37 (95%) from the ST131-30R subclo...
Colonizations due to carbapenem-resistant (CRE) are a source of antimicrobial resistance transmission in health care settings. Eleven strains producing KPC-3 carbapenemase were isolated from rectal swabs during a 3-year surveillance program. -carrying plasmids were found to belong to the IncX3 gro...
This study sought to determine the genotypes of circulating Bordetella pertussis, the causative agent of pertussis, in Cambodia by direct molecular typing of clinical specimens. DNA extracts from nasopharyngeal swabs obtained from 82 pertussis patients in 2008-2016 were analyzed by multilocus variab...
Colonization of methicillin resistant Staphylococccus aureus (MRSA) can occur more commonly in healthy people who live in close together or are in close physical contact with each other. Having knowledge about the molecular characteristics of these strains provides considerable discernment into the...
Ticks are considered the second vector of human and animal diseases after mosquitoes. Therefore, identification of ticks and associated pathogens is an important step in the management of these vectors. In recent years, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MA...
Multidrug resistant (MDR) Klebsiella pneumoniae is a common cause of nosocomial infections worldwide. Recent years have seen an explosion of resistance to extended-spectrum β-lactamases (ESBLs) and emergence of carbapenem resistance. Here, we examine 198 invasive K. pneumoniae isolates collected fro...
All VIM-producing Enterobacteriaceae (six Enterobacter cloacae) submitted to the Argentinian Reference Laboratory in Antimicrobial Resistance in the period 2008-13 were characterized. The isolates were referred from 6 nosocomial institutions located in 5 different cities across the country. All isol...
Clostridium difficile is a Gram-positive, spore-forming obligate anaerobe responsible for antibiotic-associated diarrhoea. Its virulence is associated with the production of endotoxins A and B and endospores, which can cause symptoms, such as diarrhoea, toxic megacolon, and pseudomembranous colitis....
The first Spanish multi-centre study on the microbiology of cystic fibrosis (CF) was conducted from 2013 to 2014. The study involved 24 CF units from 17 hospitals, and recruited 341 patients. The aim of this study was to characterise Pseudomonas aeruginosa isolates, 79 of which were recovered from 7...
The purpose of the study was to investigate the molecular characteristics of meticillin-resistant Staphylococcus aureus (MRSA) isolated from clinical sources in Tripoli, Libya. A total of 95 MRSA strains collected at the Tripoli medical Centre were investigated by spa typing and identification of th...
The aim of this study is to characterize the molecular support of antibiotic resistance in MDR Klebsiella pneumoniae recovered from inanimate surfaces between March 2012 to February 2014 in three teaching hospitals (Setif, Bejaia and Constantine) in Algeria. Forty-four K. pneumoniae producing ESBL w...
The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common infections. bla , encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific trans...
Molecular epidemiological investigations of the highly clonal Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) are important in outbreak detection and in tracking disease transmission. In this study, we developed and evaluated a multiple-locus variable-number tandem-repeats (VNTR) an...
To describe an outbreak of Salmonella enteritidis phage type (PT) 14b in people who had eaten at a restaurant, and the investigation and subsequent prosecution of the food business operator (FBO). The local health protection team and environmental health department formed an outbreak control team to...
The aim of this study was to characterize 32 MRSA isolates recovered from wound specimens of patients in a Hospital in Tripoli, Libya, during 2013. MRSA isolates were characterized by determining their antibiotic susceptibilities, genes encoding antibiotic resistance and virulence factors, the SCCme...
The aim of this study was to investigate the prevalence and molecular characteristics of clinical oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA) isolates in China from July 2009 to June 2014. A total of 2068 non-duplicate S. aureus isolates were collected from 21 hospitals. Anti...
Klebsiella pneumoniae is an opportunistic pathogen and leading cause of hospital-associated infections. Intensive care unit (ICU) patients are particularly at risk. Klebsiella pneumoniae is part of the healthy human microbiome, providing a potential reservoir for infection. However, the frequency of...
H5N1 highly pathogenic avian influenza virus (HPAIV) was first observed in Nigeria in early 2006 and has now spread to more than 17 African countries having severe economic and public health implications. Here, we explore the spatiotemporal patterns of viral dispersal both among West African countri...
The use of PCV7 for children immunization was gradually implemented in the Italian regions starting from 2006 and was replaced by PCV13 in 2010-2011. In this study we aimed to assess the PCV impact on invasive pneumococcal diseases (IPD) incidence, serotype distribution and antibiotic resistance in...
Between February and May 2017, two cases of invasive meningococcal disease caused by a new, rapidly expanding serogroup W meningococci variant were reported among students of an international university in Paris. Bacteriological investigations showed that isolates shared identical genotypic formula...
Resistant Gram-negative bacterial (GNB) infections, apart from tremendously escalating the cost of treatment, are a cause for substantial morbidity and mortality among hospitalized patients. Such bacteria are rapidly acquiring resistance to many antimicrobial agents, especially the beta-lactams whic...
Mechanisms of colistin and carbapenem resistance among a collection of Klebsiella pneumoniae isolates recovered in a university hospital in Tunisia were studied. In vitro antimicrobial susceptibility testing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blotting and PCR-based rep...
Acinetobacter baumannii is an important opportunistic and multidrug-resistant pathogen responsible for nosocomial infections in health facilities. The aim of this study was to characterize the molecular mechanisms of carbapenem resistance in A. baumannii isolates isolated from Mohamed Kassab Orthope...
Thanks to the significant advent of high throughput sequencing in the last ten years, it is now possible via metagenomics to define the spectrum of the microbial sequences present in human blood samples. Therefore, metagenomics sequencing appears as a promising approach for the identification and gl...
Acinetobacter pittii is a nosocomial pathogen rarely involved in community-acquired infections. We report for the first time that A. pittii can be responsible for cavitary community-acquired pneumonia and study its virulence, and discuss its pathogenesis and treatment options. A 45-year-old woman wi...
Listeria monocytogenes (Lm) is a bacterium widely distributed in nature and able to contaminate food processing environments, including those of dairy products. Lm is a primary public health issue, due to the very low infectious dose and the ability to produce severe outcomes, in particular in elder...
var. is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically human immunodeficiency virus/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global...
The aim of the study was to provide an update on the epidemiology of C. difficile infection (CDI) in a representative number of hospitals within the Czech Republic in 2015. In 2015, twenty-eight Czech hospitals were invited to participate in a CDI study. Laboratories sent the first 20 consecutive C....
We describe the largest molecular epidemiological study of Bovine Tuberculosis (bTB) in a sub-Saharan African country with higher spatial resolution providing new insights into bTB. Four hundred and ninety-nine samples were collected for culture from 201 and 179 cattle with and without bTB-like lesi...
is a newly named species previously described as a divergent lineage of that has recently been shown to have a global distribution. Despite growing evidence of the clinical importance of this species, knowledge about its population epidemiology and genomic architecture is limited. We used whole-gen...
The large outbreak of cholera reported during July to September 2014 in the Narla block of Kalahandi district, India, was investigated to determine the causative organism. Rectal swabs collected from patients with diarrhea and environmental water samples were cultured following standard techniques....
Intraspecies polymorphisms of Microsporum canis strains isolated from human lesions and domesticated cats in Japan were examined by multilocus microsatellite (MS) analysis. Using 9 MS markers, 70 strains were classified into 20 genotypes (genotypes A to T). Of the 9 MS markers used, 5 were considere...
Outbreaks of infection due to Salmonella enterica servovar Typhi (S. Typhi) are a great threat to public health. A rapid molecular typing method to characterize strains implicated in an outbreak is critical in implementing appropriate control measures. This study was done to demonstrate the power of...
In May 2016, an outbreak of Shiga toxin-producing Escherichia coli O157 infections occurred among children who had played in a stream flowing through a park. Analysis of E. coli isolates from the patients, stream water, and deer and coyote scat showed that feces from deer were the most likely source...
The molecular epidemiology and the antifungal susceptibility profiles of Candida albicans are scarce in Cameroon. Authors studied the genetic diversity and the antifungal susceptibility of C. albicans isolates from Yaoundé HIV-infected patients. Clinical isolates were obtained by mycological diagnos...
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminator...
To investigate the occurrence and characteristics of ESBL/AmpC-producing Escherichia coli in faecal samples from horses at one equine clinic in the Netherlands. A total of 91 horses, including residents and patients, were sampled. ESBL/AmpC-producing E. coli were identified by a combination disc dif...
Transmissibility is the defining characteristic of infectious diseases. Quantifying transmission matters for understanding infectious disease epidemiology and designing evidence-based disease control programs. Tracing individual transmission events can be achieved by epidemiological investigation co...
Community-acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) isolates belonging to clonal complex 80 (CC80) are recognized as the European CA-MRSA. The prevailing European CA-MRSA clone carries a type IVc staphylococcal cassette chromosome mec (SCCmec) and expresses Panton-Valentine le...
In Europe, enterovirus A71 (EV-A71) has primarily been associated with sporadic cases of neurological disease. The recent emergence of new genotypes and larger outbreaks with severely ill patients demonstrates a potential for the spread of new, highly pathogenic EV-A71 strains. Detection and charact...
Epidemiology of fosfomycin susceptibility and the plasmid-mediated fosfomycinase genes of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Taiwan remain unclear. 642 CRKP clinical isolates were collected from a nation-wide surveillance study (16 hospitals) in Taiwan in 2012-2013. Antimi...
Whether chromosomal and transmissible mechanisms contribute simultaneously to colistin resistance in Klebsiella pneumoniae and Escherichia coli remains unknown. This study aims to identify the underlying mechanisms of colistin resistance in inpatient and avian K. pneumoniae and E. coli in China. We...
Real-time reverse-transcription polymerase chain reaction (rRT-PCR) to detect enterovirus 71 (EV-A71) and coxsackievirus A16 (CV-A16) has facilitated the rapid and accurate identification of the two most common etiological agents underlying hand, foot, and mouth disease (HFMD). However, the worldwid...
Community-acquired Clostridium difficile infection (CA-CDI) is a growing concern. CA-CDI differs from hospital-acquired C. difficile infection (HA-CDI) in its epidemiology, risk factors, severity, and outcomes. In this study, we investigated C. difficile infections in a tertiary care hospital in Seo...
Despite the non-clonal epidemic population structure of Pseudomonas aeruginosa, several multi-locus sequence types are distributed worldwide and are frequently associated with epidemics where multidrug resistance confounds treatment. ST235 is the most prevalent of these widespread clones. In this st...
In the past few decades, dengue has spread rapidly and is an emerging disease in China. An unexpected dengue outbreak occurred in Xishuangbanna, Yunnan, China, resulting in 1331 patients in 2013. In order to obtain the complete genome information and perform mutation and evolutionary analysis of cau...
Between July and November 2014, 15 community-acquired cases of Legionnaires´ disease (LD), including four with Legionella pneumophila serogroup 1 sequence type (ST) 82, were diagnosed in Northern Zealand, Denmark. An outbreak was suspected. No ST82 isolates were found in environmental samples and no...
Studies are conflicting regarding the association of the North American pulsed-field gel electrophoresis type 1 (NAP1) strain in Clostridium difficile infection (CDI) and outcomes. We evaluated the association of NAP1 with healthcare-associated CDI disease severity, mortality, and recurrence at our...
Repeated Listeria outbreaks particularly associated with Ready-To-Eat (RTE) delicatessen meat products have been reported annually at global level. The most frequent scenario that led to foodborne outbreaks was the post-thermal treatment cross-contamination of deli meat products during slicing and m...
In 2015, New Delhi witnessed a massive outbreak of Dengue virus (DENV) resulting in high morbidity and mortality. We report the molecular characterisation of the dominant circulating DENV strain to understand its evolution and dispersal. DENV infections were diagnosed by detection of IgM/NS1 antigen...
To explore the epidemiological, phylogeographic, and migration characteristics of human rabies in Shaanxi province, China from 2009 to 2015. The collected data were described and the sequenced glycoprotein (G) and nucleoprotein (N) genes were implemented to estimate the evolutionary rates and phylog...
Vancomycin-resistant enterococci (VRE) are a challenge to the health-care system regarding transmission rate and treatment of infections. VRE outbreaks have to be controlled from the first cases which means that appropriate and sensitive genotyping methods are needed. The aim of this study was to in...
Dissemination of carbapenem-resistant Acinetobacter baumannii (CRAB) is mainly due to the spread of clonal lineages, particularly those included into the clonal complexes (CC) CC1, CC2, CC15, CC25, and CC79. We evaluated the usefulness of a recently modified PCR-based trilocus sequence-based typing...
Leptospirosis is caused by pathogenic spirochetes of the genus Leptospira spp. This zoonotic disease is distributed globally and affects domestic animals, including cattle. Leptospira interrogans serogroup Sejroe serovar Hardjo and Leptospira borgpetersenii serogroup Sejroe serovar Hardjo remain imp...
Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-dr...
Melioidosis is a tropical disease caused by the bacterium . Outbreaks are uncommon and can generally be attributed to a single point source and strain. We used whole-genome sequencing to analyse isolates collected from an historical 2-year long case cluster that occurred in a remote northern Austra...
Quinolone antimicrobials are frequently misused due to self-medication and suboptimal dose administration, leading to the development of resistance as well as treatment failure. The present study aimed to characterise plasmid-mediated quinolone resistance (PMQR) determinants and their genetic select...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is endemic in Greece. CRAB initially emerged in 2000 and since then, carbapenemases still have a crucial role in CRAB appearance, except for a few cases resulting from efflux pump or outer-membrane protein mechanisms. OXA-type carbapenemases presen...
This study aimed to determine the frequency and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) from Australian animals and whether animal-derived MRSA was similar to that from Australian veterinarians. A total of 1,080 clinical coagulase positive Staphylococcus isolates...
The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Trans...
PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The Pul...
Methicillin-resistant Staphylococcus aureus (MRSA) colonizes the skin of hospitalized patients and is associated with high morbidity and mortality. To prevent colonization and infection by S. aureus, better disinfection practices are required. Therefore, we evaluated the effect of chlorhexidine whol...
OBJECTIVE Distinguishing recurrent Clostridium difficile infection (CDI), defined as CDI caused by the same genotype, from reinfection with a different genotype, has important implications for surveillance and clinical trials investigating treatment effectiveness. We validated the proposed 8-week pe...
The aim of this study was to investigate the patterns of antimicrobial resistance and molecular features of methicillin-resistant Staphylococcus aureus (MRSA) isolates in Russia. Isolates recovered from hospital patients (n=480), healthy medical personnel (n=25), and healthy carriers (n=13) were inc...
Public health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. He...
Skin and soft tissue infections (SSTIs) caused by mupirocin-resistant strains have recently increased in number in our settings. We sought to evaluate the characteristics of these cases over a 43-month period. Data for all community-acquired staphylococcal infections caused by mupirocin-resistant s...
Influenza A(H1N1)pdm09 was responsible for the first global flu pandemic in 21st century affecting all the world. In Brazil, A(H1N1)pdm09 is still circulating as a seasonal virus, causing deaths every year. Nevertheless, the viral diffusion process that yearly seeds new influenza strains in the coun...
Rabies is an important but underestimated threat to public health, with most cases reported in Asia. Since 2000, a new epidemic wave of rabies has emerged in Yunnan Province, southwestern China, which borders three countries in Southeast Asia. We estimated gene-specific evolutionary rates for rabies...
Species of the genus Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) are mainly known as vectors of arboviruses such as bluetongue (BTV) and Schmallenberg (SBV). Among the known vectors, few species within the subgenus Culicoides Latreille, 1809 have been implicated in the transmission of BTV...
The purpose of this investigation was to evaluate the epidemiology of hypervirulent Clostridium difficile ribotypes from January 2013 to February 2017 in the Marseille area of southern France. By using the Xpert Clostridium difficile Epi polymerase chain reaction (PCR) assay and sequencing the tcdC...
An outbreak of febrile respiratory illness associated with human adenovirus (HAdV) occurred in the South Korea military during the 2014-15 influenza season and thereafter. Molecular typing and phylogenetic analysis of patient samples identified HAdV type 55 as the causative agent. Emergence of this...
During March-July 2014, rotavirus G8P[8] emerged as the predominant cause of rotavirus gastroenteritis among children in Hokkaido Prefecture, Japan. Clinical characteristics were similar for infections caused by G8 and non-G8 strains. Sequence and phylogenetic analyses suggest the strains were gener...
Vaccinia virus (VACV) is a zoonotic agent that causes a disease called bovine vaccinia, which is detected mainly in milking cattle and humans in close contact with these animals. Even though many aspects of VACV infection have been described, much is still unknown about its circulation in the enviro...
Metagenomic next-generation sequencing (mNGS) has been used to uncover unusual causes of infectious diseases but has not been used routinely for the investigation of putative nosocomial outbreaks. Here, we describe the use of mNGS during investigation of a cluster of human rhinovirus (HRV)-positive...
In 2008-09, the KPC carbapenemase epidemiology in Poland was dominated by a Klebsiella pneumoniae ST258 KPC-2 outbreak in Warsaw and its administrative region. The aim of this study was to analyse the situation in 2010-14, with a focus on new outbreaks in other parts of the country. KPCs were detect...
Enterococcus faecalis is one of the most important causative agents of nosocomial infections. Control and prevention of these infections require appropriate epidemiological knowledge. This study investigated the correlation between molecular characteristics and drug resistance of E. faecalis isolate...
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We examined whether disparities existed in hospital-onset (HO) Staphylococcus aureus bloodstream infections (BSIs) and used whole-genome sequencing (WGS) to identify factors associated with USA300 transmission networks. We evaluated HO methicillin-susceptible S. aureus (MSSA) and HO methicillin-resi...
The development of resistance of Neisseria gonorrhoeae to available first-line antibiotics, including penicillins, tetracyclines, fluoroquinolones and cephalosporins, has led to the circulation of multidrug-resistant gonorrhea at a global scale. Advancements in high-throughput whole-genome sequencin...
Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is b...
Phylodynamics is a recent field that aims at using genetic sequence data to estimate epidemiological parameters such as the viral population growth rate, the number of infections in the population or even their duration. Its main underlying assumption is that the way viruses spread leaves marks in t...
The molecular epidemiology of equine group A rotaviruses (RVAs) in Ireland from 2011 to 2015 was investigated. Of 438 diagnostic specimens submitted from foals with enteric disease, 102 (23.3%) were positive for RVA using an immunochromatographic assay. G genotypes were determined for 76 equine RVAs...
Enterococcus spp. is the common of intestinal micro flora in humans but nowadays this gram-positive bacterium causes the variety of nosocomial infections. Resistance to antibiotic and also, presence of different virulence genes in the enterococcus spp. can change it to problematic microorganisms in...
Staphylococcal food poisoning is the result of consumption of food contaminated with staphylococcal enterotoxins (SEs) produced by Staphylococcus aureus. To date, 23 SEs and SE-like enterotoxins (SEls) have been described in the literature. They are divided into classical SEs (SEA-SEE) and new SE/SE...
The clonal spread of multiple drug-resistant Acinetobacter baumannii is an emerging problem in China. We analysed the molecular epidemiology of Acinetobacter baumanni isolates at three teaching hospitals and investigated the risk factors, clinical features, and outcomes of hospital-acquired pneumoni...
No abstract available
A multidrug-resistant, methicillin-resistant Staphylococcus aureus (MRSA) clone, PVL-positive ST772-MRSA-V, named the Bengal Bay clone, is emerging worldwide. In Norway, where MRSA prevalence is low, a sudden increase in ST772-MRSA-V initiated a nationwide molecular epidemiological study. Clinical d...
Multidrug-resistant (MDR) O25b-ST131 clone of Escherichia coli is well established as a significant cause of extra-intestinal infections worldwide. However, there have been no studies about the prevalence of ST131 and its H30/H30Rx subclones from Iran. The prevalence of ST131 was 29.8% among phylogr...
Zika virus (ZIKV) is an emerging arbovirus belonging to the genus of the family During replication processes, flavivirus manipulates host cell systems to facilitate its replication, while the host cells activate antiviral responses. Identification of host proteins involved in the flavivirus replic...
The prevalence of Panton-Valentine leukocidin gene (pvl)-positive community-acquired methicillin-resistant Staphylococcus aureus USA300 clone, which is designated as the ST8-staphylococcal cassette chromosome (SCC) mec type IV (ST8-IV) lineage, is a major public health concern worldwide. Thus, to el...
We report an ongoing, protracted and geographically dispersed outbreak of haemolytic uraemic syndrome (HUS) and gastroenteritis in Germany, involving 30 cases since December 2016. The outbreak was caused by the sorbitol-fermenting immotile variant of Shiga toxin-producing (STEC) Escherichia coli O15...
To characterise and compare twenty-eight Finnish Clostridium difficile RT027-like isolates, selected based on the presence of 18 bp deletion in the tcdC gene and toxin gene profile (A, B, binary), with eleven RT027 isolates from different Finnish geographical areas and time periods. Twenty-eight C....
Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the...
isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. T...
Outbreaks of invasive infections have recently been reported in day care centers. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) revealed that although the invasive strains had widespread dissemination in the day care population, less virulent strains were also circul...
The Rangipo strain of Mycobacterium tuberculosis achieved notoriety in New Zealand due to its role in several tuberculosis (TB) outbreaks. Why this strain should be the source of relatively large clusters of the disease is unknown. In this work, we performed an in-depth analysis of the genome of the...
This study describes an outbreak caused by imipenem-resistant Acinetobacter baumannii (IRAB) involving 2 general wards at the Penghu branch of Tri-Service General Hospital. Clinical data obtained from the patients with IRAB during an outbreak from May 2014-October 2014 were reviewed. Microbiologic s...
Klebsiella pneumoniae is a frequent nosocomial pathogen causing difficult-to-treat infections worldwide. The prevalence of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-KP) is increasing in China. The aim of this study was to investigate the molecular epidemiology of...
Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an "accidental pathogen"; however, the transition from carriage to disease phenotype remains poorly understood. This study examined the...
As rabies in carnivores is increasingly controlled throughout much of the Americas, bats are emerging as a significant source of rabies virus infection of humans and domestic animals. Knowledge of the bat species that maintain rabies is a crucial first step in reducing this public health problem. In...
Early detection of Acinetobacter baumannii, an emerging pathogen in hospital settings, is of interest. The bla family had been used as a marker to detect A. baumannii. During an infection outbreak, 14 isolates produced a 1.7-kb PCR band instead of 353 bp for this marker. This work sought the reasons...
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characte...
Streptococcus pneumoniae (pneumococcus) is a leading cause of death and disease in children and elderly. Genetic variability among isolates from this species is high. These differences, often the product of gene loss or gene acquisition via horizontal gene transfer, can endow strains with new molecu...
Porcine epidemic diarrhea (PED) re-emerged in China in late 2010 and has now become widespread. Accumulated evidence indicates that this large-scale outbreak of diarrhea was caused by variants of the highly virulent porcine epidemic diarrhea virus (PEDV). A pandemic PEDV YC2014 strain (YC2014) was i...
As a part of strategy to control diarrheal diseases, World Health Organization (WHO) recommends to include rotavirus vaccines in national immunization programs. Sentinel surveillance networks have been established to monitor rotavirus disease burden and genotype distribution in both pre and post vac...
Comorbid diabetes mellitus (DM) increases tuberculosis (TB) risk and adverse outcomes but the pathological interactions between DM and TB remain incompletely understood. We performed an integrative analysis of whole blood gene expression and plasma analytes, comparing South Indian TB patients with a...
Enteroviruses are among the most common human viruses around the world. More than 100 different serotypes that can cause a range of clinical pathologies have been identified, although the most frequent are those that affect the central nervous system, such as aseptic meningitis, encephalitis or para...
In the Netherlands, the number of cases of infection with New Delhi metallo-beta-lactamase (NDM)-positive is low. Here, we report an outbreak of NDM-1-producing infection in a Dutch hospital with interspecies transfer of the resistance plasmid and unexpected occurrence in other unrelated health ca...
is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for , it is imperative to understand...
Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernize vector surveillance. When combined with DNA barcoding, it is termed 'metabar...
Over the last 20 years there have been 32 reports of carbapenem-resistant organisms in the hospital water environment, with half of these occurring since 2010. The majority of these reports have described associated clinical outbreaks in the intensive care setting, affecting the critically ill and t...
Staphylococcus aureus can cause minor to severe life-threatening infections. The changing epidemiology of S. aureus is of public health concern due to the emergence of multi-drug resistant (MDR) strains. Environmental surfaces play a crucial role in the transmission of S. aureus. The objective of th...
An outbreak of Clostridium difficile infection (CDI) caused by ribotype 027 (B1/NAP1) began in our hospital in November 2014, and produced 141 episodes in the following months. The aim of this study is to describe this outbreak, assess risk factors for recurrence of CDI-027 and to analyze the implem...
Although canine respiratory coronavirus (CRCoV) is an important respiratory pathogen that is prevalent in many countries, only one complete genome sequence of CRCoV (South Korea strain K37) has been obtained to date. Genome-wide analyses and recombination have rarely been conducted, as small numbers...
Molecular subtyping and enhanced surveillance in Lombardy region identified a cluster of possibly related listeriosis cases from 2006 to 2010. This cluster grouped 31 isolates that belonged to serotype 1/2a and Sequence Type 38 (ST38) as defined by Multilocus Sequence Typing (MLST). Our study expand...
In November 2016, sheep located in the south of Corsica island exhibited clinical signs suggestive of bluetongue virus (BTV) infection. Laboratory analyses allowed to isolate and identify a BTV strain of serotype 4. The analysis of the full viral genome showed that all the 10 genomic segments were c...
Acinetobacter baumannii is known for nosocomial outbreaks worldwide. In this study, we aimed to investigate the antibiotic susceptibility patterns and the clonal relationship of A. baumannii isolates from the intensive care unit (ICU) of an Egyptian hospital. In the present study, 50 clinical isolat...
Multidrug-resistant Klebsiella pneumoniae is a common nosocomial pathogen that plays an important role in ventilator-associated pneumonia (VAP). This study aimed to define the clonal relatedness of K. pneumoniae strains isolated from paediatric VAP in addition to those isolated from environmental sa...
Staphylococcus aureus is one of the most common causes of skin and soft tissue infections in health-care and community settings, but transmission of S. aureus in community-based populations is incompletely understood. S. aureus carriage phenotypes (persistent, intermittent, and non-carriers) were de...
Spoligotyping is a valuable genotyping tool to study the genetic diversity and molecular epidemiology of Mycobacterium tuberculosis (M. tb). The aim of this study was to analyse different spoligotype patterns of M. tb strains isolated from patients with tuberculosis from different parts of India. A...
The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) isolated in horse infections is not well documented, especially in France. The aim of the study was to evaluate the prevalence of MRSA isolates in horse infections from 2007 to 2013 in France and to characterize phenotypically an...
An epidemic of post-surgical wound infections, caused by a non-tuberculous mycobacterium, has been on-going in Brazil. It has been unclear whether one or multiple lineages are responsible and whether their wide geographical distribution across Brazil is due to spread from a single point source or is...
Whole-genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at a high resolution, thereby helping to characterize outbreaks. However, for , the accumulation of within-host diversity during carriage might limit the interpretation of sequencing data. In this stud...
Brucellosis was a common human and livestock disease caused by Brucella strains, the category B priority pathogens by the US Center for Disease Control (CDC). Identified as a priority disease in human and livestock populations, the increasing incidence in recent years in China needs urgent control m...
Antimicrobial resistance in non-typhoidal Salmonella is a critical problem globally, with the emergence of resistance to third-generation cephalosporins (3GCs) a particular concern. The aim of this study was to use whole-genome sequencing (WGS) to characterise recently identified human and non-human...
Four cases of infection with serogroup X meningococci (MenX) (1 in 2015 and 3 in 2016) occurred in migrants living in refugee camps or reception centers in Italy. All MenX isolates were identified as clonal complex 181. Our report suggests that serogroup X represents an emerging health threat for pe...
Legionnaires' disease is an important cause of hospital-acquired pneumonia and is caused by infection with the bacterium Legionella. Because current typing methods often fail to resolve the infection source in possible nosocomial cases, we aimed to determine whether whole-genome sequencing (WGS) cou...
The role of symptomatic patients who are toxigenic strain positive (TS+) but fecal toxin negative (FT-) in transmission of Clostridium difficile is currently unknown. We investigated the contribution of symptomatic TS+/FT- and TS+/FT+ patients in C. difficile transmission in 2 UK regions. From 2-ste...
No abstract available
Within-host genetic diversity and large transmission bottlenecks confound phylodynamic inference of epidemiological dynamics. Conventional phylodynamic approaches assume that nodes in a time-scaled pathogen phylogeny correspond closely to the time of transmission between hosts that are ancestral to...
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context...
Skin ulcer development in sea-reared salmonids, commonly associated with Tenacibaculum spp., is a significant fish welfare- and economical problem in Norwegian aquaculture. A collection of 89 Tenacibaculum isolates was subjected to multilocus sequence analysis (MLSA). The isolates were retrieved fro...
Neisseria meningitidis serogroups B and C have been responsible for the majority of invasive meningococcal disease in Australia, with serogroup B strains causing an increasing proportion of cases in recent years. Serogroup Y has typically caused sporadic disease in Australia. In 2002, a cluster of 4...
Acinetobacter baumannii (A. baumannii) is one of the leading pathogens in hospital infections. To characterize the epidemiology of A. baumannii in a burn ward, we collected all A. baumannii isolates though 18 months. Antibiotic susceptibility and antibiotic resistant genes were tested. Multilocus se...
The epidemiological and clinical aspects of human immunodeficiency virus subtypes are of great interest worldwide. These subtypes are rarely studied in North African countries. Libya is a large country with the longest coast on the Mediterranean Sea, facing the Southern European countries. Studies o...
Carbapenem-resistant Enterobacteriaceae (CRE) are identified as a major global health concern. The success of CRE is facilitated by the emergence, acquisition and spread of successful clones carrying plasmid-encoded resistance genes. In this study, an outbreak of carbapenem-resistant Klebsiella pneu...
Acquisition of Legionnaires' disease is a serious complication of hospitalization. Rapid determination of whether or not the infection is caused by strains of Legionella pneumophila in the hospital environment is crucial to avoid further cases. This study investigated the use of whole-genome sequenc...
No abstract available
Multidrug-resistant (MDR) and extensively drug resistant (XDR) strains of pose major problems for global health. The GeneXpert MTB/RIF (Xpert) assay rapidly detects resistance to rifampin (RIF), but for detection of the additional resistance that defines MDR-TB (MDR tuberculosis) and XDR-TB, and fo...
Human campylobacteriosis, caused by and , remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. Whole-ge...
Salmonella enterica subspecies enterica serovar Enteritidis (SE) is one of the most common causes of human salmonellosis and in Canada currently accounts for over 40% of human cases. Reliable subtyping of isolates is required for outbreak detection and source attribution. However, Pulsed-Field Gel E...
The global spread of producing carbapenemase (KPC) has been mainly associated with the dissemination of high-risk clones. In the last decade, hospital outbreaks involving KPC-producing have been predominantly attributed to isolates belonging to clonal group (CG) 258. However, results of recent ep...
To characterise populations during chronic lung infections of non-cystic fibrosis bronchiectasis patients, we used whole-genome sequencing to 1) assess the diversity of and the prevalence of multilineage infections; 2) seek evidence for cross-infection or common source acquisition; and 3) characte...
Recent studies in addition to studies based on whole genome sequencing (WGS) of clinical isolates of Mycobacterium tuberculosis (MTB) from diverse geographical regions have provided useful insights into the mechanisms of drug resistance. Of importance, are some of the findings pertaining to mechanis...
Clostridium difficile is a spore-forming anaerobic intestinal pathogen that causes Clostridium difficile infection (CDI). C. difficile is the leading cause of toxin-mediated nosocomial antibiotic-associated diarrhea. The pathogenesis of CDI is attributed to two major virulence factors, TcdA and TcdB...
To establish risk factors for Clostridium difficile colonization among hospitalized patients in England. Patients admitted to elderly medicine wards at three acute hospitals in England were recruited to a prospective observational study. Participants were asked to provide a stool sample as soon as p...
Mycobacterium tuberculosis (M. tuberculosis) genotyping has dramatically improved the understanding of the epidemiology of tuberculosis (TB). In this study, 187 M. tuberculosis isolates from Xinjiang Uygur Autonomous Region (Xinjiang) and Gansu province in China were genotyped using large sequence p...
Methicillin resistant Staphylococcus aureus (MRSA) has become as a nosocomial pathogen worldwide. Considering the importance of MRSA typing for understanding the evolution and dissemination of these strains, we studied the molecular characteristics of MRSA colonized healthcare workers (HCWs). All MR...
Lasiodiplodia theobromae is a plant pathogen with a worldwide distribution, with low host specificity, causing stem cankers, dieback diseases, and fruit rot in several species of plants. In coconut, this pathogen is reported as the etiological agent of "coconut leaf blight" (CLB) disease, causing se...
Analysis of whole genome sequencing data uncovered a previously undetected outbreak of Salmonella Enteritidis that had been on-going for four years. Cases were resident in all countries of the United Kingdom and 40% of the cases were aged less than 11 years old. Initial investigations revealed that...
In a previous nationwide study in Greece, OXA-58 was the sole carbapenemase present among carbapenem-resistant Acinetobacter baumannii (CRAB) isolated between 2000 and 2009. In this study, the antibiotic resistances, carbapenemase gene content and clonal relatedness of 194 single-patient CRAB clinic...
The spread of Extended Spectrum β-lactamases (ESBLs) among Enterobacteriaceae and other Gram-Negative pathogens in the community and hospitals represents a major challenge to combat infections. We conducted a study to assess the prevalence and genetic makeup of ESBL-type resistance in bacterial isol...
Although there have been many epidemiological reports of the inter-country transmission of measles, systematic analysis of the global transmission dynamics of the measles virus (MV) is limited. In this study, we applied phylogeographic analysis to characterize the global transmission dynamics of the...
Staphylococcus aureus is recognized as a typical food-born pathogen in food safety, and its rapid detection and typing methods are in desperate need. To study their evolution characteristics and drug resistance condition, Staphylococci isolates were subject to the investigation. Strain identificatio...
Methicillin-resistant Staphylococcus aureus (MRSA) is an established pathogen that causes hospital- and community-acquired infections worldwide. The prevalence rate of MRSA infections were reported to be the highest in Asia. As there is limited epidemiological study being done in Malaysia, this stud...
Foot-and-mouth disease virus (FMDV) is endemic in Vietnam, a country that plays an important role in livestock trade within Southeast Asia. The large populations of FMDV-susceptible species in Vietnam are important components of food production and of the national livelihood. In this study, we inves...
We described Klebsiella pneumoniae producing carbapenemase (CPKP) spread from 01/01/2015 to 13/09/16 in a tertiary level hospital. The first positive surveillance rectal swab (SRS) or clinical sample (CS) collected in the medical department (MD), surgical department (SD) and intensive care departmen...
Whole-genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the...
Acinetobacter baumannii is a leading emerging pathogen that is frequently recovered from patients during hospital outbreaks. The role of environmental A. baumannii reservoirs is therefore of great concern worldwide. To investigate the connection between A. baumannii causing hospital outbreaks and en...
Whereas Klebsiella species are the most frequently occurring agents in nosocomial outbreaks due to multidrug-resistant Gram-negative organisms, very few outbreaks have been reported from rehabilitation wards. To describe a long-lasting outbreak due to extended-spectrum β-lactamase-producing (ESBL) K...
The adaptation of pathogens to either their hosts or to environmental conditions is the focus of many current ecological studies. In this work we compared the ability of six spatially-distant Lymantria dispar (gypsy moth) multiple nucleopolyhedrovirus (LdMNPV) strains (three from eastern North Ameri...
Stenotrophomona maltophilia has emerged as an important opportunistic pathogen that is highly antibiotic resistant. Analysis of antibiotic susceptibilities, drug-resistant gene profiles and molecular typing of S. maltophilia was undertaken in a university hospital of traditional Chinese medicine in...
Shigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed...
Emergence and spread of Klebsiella pneumoniae isolates producing extended-spectrum β-lactamases (ESBLs) present a major threat to public health. In this study, we characterized β-lactam-resistant K. pneumoniae isolates from six wastewater samples obtained from two pharmaceutical industries located i...
Whole-genome sequencing (WGS) is an emerging and powerful technique by which to perform epidemiological studies in outbreak situations. WGS was used to identify and evaluate an outbreak of OXA-232-expressing carbapenem-resistant Klebsiella pneumoniae (CRKP) transmitted to 16 patients over the course...
Genomic data are increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic tree...
To define the population structure of extraintestinal pathogenic Escherichia coli (ExPEC) in Japan and its relationship with antimicrobial resistance and the major resistance mechanisms for fluoroquinolones and β-lactams, we designed a multicentre prospective study. A total of 329 ExPEC isolates wer...
Nontuberculous mycobacteria (NTM) commonly colonize municipal water supplies and cause healthcare-associated outbreaks. We investigated a biphasic outbreak of Mycobacterium abscessus at a tertiary care hospital. Case patients had recent hospital exposure and laboratory-confirmed colonization or infe...
To investigate antimicrobial susceptibility in Staphylococcus pseudintermedius and the occurrence of methicillin-resistant S. pseudintermedius (MRSP), to explore the molecular structure of the MRSP population and to analyse risk factors for MRSP. Susceptibility data for clinical S. pseudintermedius...
We investigated the epidemiological, clinical, microbiological and genetic characteristics of linezolid-resistant (LZR) Staphylococcus capitis isolates from French ICUs, and compared them with LZR S. capitis isolates from other European countries. All LZR isolates were subjected to antimicrobial sus...
Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit acros...
Whole genome sequencing (WGS) is a laboratory method that has emerged as a promising tool for epidemiologic investigations. Genomic epidemiology approaches have been utilized in outbreak settings, community settings, within acute care hospitals, and across healthcare facilities to better understand...
Cystic fibrosis (CF) patients in the Czech Republic suffered in the late 1990s from an epidemic with ST32 strain of Burkholderia cepacia complex (Bcc). Cohort segregation of Bcc and of ST32 positive patients was introduced in 1999 and 2002, respectively. We performed a study to evaluate the molecula...
The current study was conducted to shed light on the role of imported camels as a transboundary vector for emerging exotic Salmonella serovars. Fecal samples were collected from 206 camels directly after slaughtering including 25 local camels and 181 imported ones as well as stool specimens were obt...
Several Escherichia coli pathotypes have been reported in Thailand; however, information on enteroaggregative heat-stable enterotoxin 1 (EAST1)-carrying E. coli (EAST1-EC) is insufficient. Previous reports show that consumption of raw meats causes diarrheagenic E. coli infections. In this study, we...
Tetracycline resistance (Tet) is a phenotypic marker of the livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) CC398 clone. The aim of this study was to analyse the prevalence of MRSA CC398 in patients in contact with healthcare facilities and differences between patients with M...
There is a high incidence and prevalence of dengue in the department of Cundinamarca, and recently Aedes aegypti, the main vector of dengue virus (DENV), was detected in some of its rural areas. To evaluate viral transovarial transmission in larvae and pupae collected in rural areas of the municipal...
Aedes aegypti and Ae. albopictus are recognized vectors of dengue, yellow fever, chikungunya and Zika arboviruses in several countries worldwide. In Colombia, Ae. albopictus geographical distribution has increased to include highly populated cities such as Cali and Medellín. Although this species ha...
The Leishmania developmental life cycle within its sand fly vector occurs exclusively in the lumen of the insect's digestive tract in the presence of symbiotic bacteria. The composition of the gut microbiota and the factors that influence its composition are currently poorly understood. A set of fac...
An 32.2 invasive group A streptococcus (iGAS) outbreak occurred in Liverpool from January 2010 to September 2012. This genotype had not previously been identified in Liverpool, but was responsible for 32% (14/44) of all iGAS cases reported during this time period. We performed a case-case comparison...
We aimed to describe the molecular epidemiological characteristics and clinical treatment outcome of typhoid fever in Ningbo, China during 2005-2014. Eighty-eight Salmonella Typhi isolates were obtained from 307 hospitalized patients. Three prevalent pulsed-field gel electrophoresis (PFGE) patterns...
Phylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations. However, these models generally assume that individual hosts contact one another at random, ignoring the fact that many pathogens spread through highly structured conta...
Species of the genus Culicoides (Diptera: Ceratopogonidae) are well known for their importance in the field of medical and veterinary entomology. Culicoides spp. transmit a wide variety of pathogens, primarily viruses that affect animals and humans. In Europe, the most economically important disease...
is an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood, with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database for was created in 2008, and a large number of clones have b...
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of whi...
Nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA) is poorly described for surgeons, despite the increased exposure to nosocomial pathogens and at-risk patients. This study investigated the molecular epidemiology and antimicrobial resistance of 26 MRSA isolates cultured from...
Sexually transmitted infections are frequently related to outbreaks in high-risk populations due to the dense sexual networks. We wanted to determine the dissemination of a Chlamydia trachomatis variant characterized by the pmpH-recombinant gene between L and G genotypes, which was previously descri...
This study investigated the cause of recent outbreaks of septicaemia in neonatal pigs in Australia (Victoria and Queensland). Septicaemia in neonatal pigs is commonly caused by enterotoxigenic E. coli, extraintestinal pathogenic E. coli and beta-haemolytic streptococci. Infrequent causes of septicae...
Molecular epidemiologic studies have shown that the dynamics of tuberculosis transmission varies geographically. We sought to determine which strains of Mycobacterium tuberculosis (MTB) were infecting household contacts (HHC), and which were causing clusters of tuberculosis (TB) disease in Vitoria-E...
Carbapenem-resistant Klebsiella pneumoniae infections are reported with increasing frequency elsewhere in the world, representing a worrying phenomenon for global health. In Italy, there are hotspot data on the diffusion and type of carbapenemase-producing Enterobacteriaceae and K. pneumoniae in par...
The purpose of this study was to evaluate Streptococcus mutans genotypes (GT) between mother and child (M-C) in a high caries risk cohort to explore the association with early childhood caries (ECC). Sixty-nine infants (each approximately one year old) had periodic oral examinations (dmfs) and micro...
Hantaviruses (family Bunyaviridae) are enveloped negative-sense tripartite RNA viruses. The natural hosts of hantaviruses include rodents, shrews, moles, and bats. Imjin virus (MJNV) is a shrew-borne hantavirus identified from the Ussuri white-toothed shrews (Crocidura lasiura) in the Republic of Ko...
Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen in hospitals and the community. As the rapid spread and wide distribution of antimicrobial resistance (such as MRSA), treatment for infectious diseases caused by microorganisms has become a vital threat. Thus, early identificati...
Carbapenemase-producing Enterobacteriaceae (CPE), particularly carbapenemase-producing Klebsiella pneumoniae isolates, are important causative agents of nosocomial infections associated with significant mortality rates mostly in critical wards. The rapid detection and typing of these strains is crit...
Healthcare-associated infections caused by Klebsiella pneumoniae isolates are increasing and few effective antibiotics are currently available to treat patients. To assess the epidemiology, molecular basis, clinical features, and outcomes in the acquisition and dissemination of OXA-48-producing K. p...
Multilocus variable-number tandem repeat analysis (MLVA) is a rapid and reproducible typing method that is an important tool for investigation, as well as detection, of national and multinational outbreaks of a range of food-borne pathogens. Salmonella enterica serovar Enteritidis is the most common...
This review describes the current state of knowledge regarding the application of whole-genome sequencing (WGS) in the epidemiology of , the leading cause of bacterial gastroenteritis worldwide. We describe how WGS has increased our understanding of the evolutionary and epidemiological dynamics of t...
The molecular epidemiology of Pseudomonas aeruginosa bloodstream infection (BSI) isolates has received limited attention. This study aims to characterize the molecular relationship of P. aeruginosa BSI isolates in the non-outbreak setting at a single tertiary healthcare facility. P. aeruginosa BSI...
We have found clusters of Klebsiella pneumoniae with OXA48-carbepenemase cases in some hospital rooms, and decided to investigate whether bathroom siphons could be a reservoir for OXA48 bacteria, as occurs with K. oxytoca with other types of carbepenemases. We evaluated the microbial competition bet...
The in-hospital infections are one of the most serious problems of medicine, especially if patients have a background immunosuppression of various genesis conditioned by both disease itself and corresponding therapy. The detection of presence of infection and identification of agent and detection of...
Methicillin-resistant Staphylococcus aureus (MRSA) strains are responsible for high rates of mortality and thus pose a substantial burden to public health worldwide. Here, we investigated the antimicrobial susceptibility and molecular characteristics of MRSA isolated from child patients at Shenzhen...
is a well-known foodborne pathogen causing gastrointestinal infections worldwide. The strain FORC_002 was isolated from the gill of flatfish (plaice) and its genome was sequenced. The genomic DNA consists of 4,837,317 bp with a GC content of 47.1%, and is predicted to contain 4,221 open reading fra...
Campylobacteriosis is the most common cause of bacterial gastroenteritis worldwide. Consumption of poultry, especially chicken's meat is considered the most common route for human infection. The aim of this study was to determine if Campylobacter spp. might persist in the poultry plant environment b...
The metallo-beta-lactamase GIM-1 has been found in various bacterial host species nearly exclusively in western Germany. However, not much is known about the epidemiology of GIM-1-positive Here we report on a surprisingly protracted regional dissemination. In-hospital transmission was investigated...
Clostridium difficile infection (CDI) has risen in prominence in Australia recently. We conducted laboratory-based surveillance of CDI to examine C. difficile circulating in Australia in October/November 2012. We collected 542 isolates from all States and Territories of Australia except the Northern...
colonisation is common in pregnant women, and it has been claimed that mother-to-child transmission may occur in 10%-70% of deliveries. infections are nevertheless rarely encountered in infants in clinical practice. In order to evaluate the reason for this discrepancy, we designed a nationwide stud...
Carbapenem-nonsusceptible (Carba-NS) Acinetobacter baumannii has emerged as an important cause of nosocomial infections. In the present study, we characterized 91 Carba-NS A. baumannii isolates collected from patients of surgical departments and intensive care units at three hospitals in Moscow in 2...
Pertussis is a worldwide acute respiratory disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, the bacterium continues to circulate in populations and is still one of the most common vaccine-preventable diseases. In Brazil, pertussis incidence has presented a signifi...
is a human commensal and opportunistic pathogen that has become a leading causative agent of hospital-based infections over the past few decades. The emergence and global expansion of hypervirulent and multidrug-resistant (MDR) clones of have been increasingly reported in community-acquired and nos...
Characterizing HIV-1 transmission networks can be important in understanding the evolutionary patterns and geospatial spread of the epidemic. We reconstructed the broad molecular epidemiology of HIV from individuals with primary HIV-1 infection (PHI) enrolled in France in the ANRS PRIMO C06 cohort o...
High-resolution screening methodologies which enable the differentiation of Chlamydia trachomatis at the strain level, directly from clinical samples, can provide the detailed information required for epidemiological questions such as the dynamics of treatment failure. In addition, they give a detai...
This study investigated the prevalence of multidrug-resistant organisms (MDROs) in the residents and environments of long-term care facilities (LTCFs) in Taiwan. We prospectively investigated the distribution of MDROs in residents of six LTCFs and their environments from January 2015 to December 201...
Between 2014 and 2015, the European Centre for Disease Prevention and Control was informed of an increase in numbers of Salmonella enterica serotype Chester cases with travel to Morocco occurring in six European countries. Epidemiological and microbiological investigations were conducted. In additio...
In January and February 2016, five cases of confirmed and two cases of probable infection due to Listeria monocytogenes serotype 4b, sequence type (ST) 6 belonging to a single pulsed-field gel electrophoresis pulsotype pattern were registered in a region of southern Switzerland. L. monocytogenes was...
A fundamental assumption in the use and interpretation of microbial subtyping results for public health investigations is that isolates that appear to be related based on molecular subtyping data are expected to share commonalities with respect to their origin, history, and distribution. Critically,...
Within 1 week in April 2013, three cases of pulmonary tuberculosis (TB) were reported among students attending training sessions at an educational institution in Oslo, Norway. By the end of October 2013, a total of nine epidemiologically linked cases had been reported. The outbreak encompassed a tot...
Bacterial wilt caused by the species complex (RSSC) is considered one of the most harmful plant diseases in the world. Special attention should be paid to phylotype I due to its large host range, its worldwide distribution, and its high evolutionary potential. So far, the molecular epidemiology an...
Klebsiella pneumoniae poses a major challenge to healthcare worldwide as an important cause of multidrug-resistant infections. Nosocomial clones, including epidemic sequence type 258 (ST258), have shown an affinity for acquiring and disseminating resistance plasmids, particularly variants of the K....
Contact precautions are recommended by health authorities in Europe and the United States for patients with Clostridium difficile infection (CDI). Recently, the significance of nosocomial transmission has been challenged by screening on admission studies and whole-genome sequencing, providing eviden...
Pseudomonas aeruginosa is one of the most common pathogens causing nosocomial pneumonia. The aim of this study was to investigate the epidemiology and resistance of P. aeruginosa isolated from hospitalised patients in the respiratory department of a hospital in China. Clinical isolates were collecte...
Clostridium difficile is an important healthcare-associated pathogen, responsible for a broad spectrum of diarrheal diseases. The aim of this prospective study was to determine the occurrence of C. difficile infection (CDI), to characterize cultured C. difficile strains and to investigate the associ...
Stenotrophomonas maltophilia is an opportunistic multi-drug-resistant bacterium responsible for healthcare-associated infections. Strategies for in-hospital infection control and management of carriers and environmental reservoirs remain controversial. To determine the population structure of S. mal...
The aim of this study is to determine the frequency of quaternary ammonium compound-resistant genes, including qacA/B, qacC/D, qacE, qacΔE1, qacG, qacJ, and β-lactamase genes, including blaCTX-M, blaTEM, blaSHV, blaOXA-23, blaVIM, blaIMP, blaNDM and blaGIM in 51 isolates of carbapenem-resistant Acin...
Enterobacter aerogenes and Enterobacter cloacae complex are the two species of this genus most involved in healthcare-associated infections that are ESBL and carbapenemase producers. This study characterized, phenotypically and genotypically, 51 isolates of E. aerogenes and E. cloacae complex origin...
This study investigated several cleaning and disinfection protocols for their ability to eliminate Salmonella and to reduce levels of Enterobacteriaceae, within the lairage pens of a commercial pig abattoir. Eight protocols were evaluated in each of 12 lairage pens at the end of the slaughtering day...
Methicillin-resistant Staphylococcus aureus (MRSA) as a major cause of infection in health care, hospital and community settings is a global health concern. The purpose of this study was to determine the antibiotic susceptibility pattern and distribution of circulating molecular types of MRSA in a b...
The widespread emergence of methicillin resistant Staphylococcus aureus, as a common cause of nosocomial infections, is becoming a serious concern in global public health. The objective of the present study was to investigate antimicrobial susceptibility pattern, frequency of virulence genes and mol...
In Japan, hot springs and public baths are the major sources of legionellosis. In 2015, an outbreak of Legionnaires' disease occurred among 7 patients who had visited a spa house. Laboratory investigation indicated that L. pneumophila serogroup 1 and 13 strains caused the outbreak and that these str...
Methicillin-resistant Staphylococcus aureus (MRSA) has caused a series of public health problems since it was first found in 1961. However, there are few research studies on the MRSA environmental contamination in railway stations and coach stations. Therefore, the aim of this study was to determine...
With the growing importance of infectious diseases in health care and communicable disease outbreaks garnering increasing attention, new technologies are playing a greater role in helping us prevent health care-associated infections and provide optimal public health. The microbiology laboratory has...
Recently, carbapenemase-producing Enterobacteriaceae (CPE) have been spreading worldwide and have become a threat in healthcare systems. We investigated the isolation frequency and molecular epidemiological characteristics of CPE isolated from clinical samples collected at a primary care hospital ov...
Salmonella is one of the most common enteric pathogens related to foodborne illness. Alberta's Provincial Laboratory for Public Health (ProvLab) provides Outbreak and Surveillance support by performing serotyping. The Check&Trace Salmonella™ (CTS) assay (Check-Points, Netherlands), a commercial DNA...
Foodborne illnesses can be due to a wide range of bacteria, one of the most common being Salmonella. In this study, PulseNet International was implemented in Lebanon to identify circulating pathogens at the species and strain levels, determine antimicrobial resistance, and link food sources and clin...
Identifying transmission route of antimicrobial-resistant pathogen is essential for appropriate infection control strategy in healthcare facilities. We report the utility of single-nucleotide variation analysis in tracing nosocomial transmission of antimicrobial-resistant pathogens by describing a p...
Whole-genome sequencing (WGS) is a promising tool for identifying transmission pathways in outbreaks caused by multidrug-resistant bacteria. However, it is uncertain how the data produced by WGS can be best integrated into epidemiologic investigations. We tested various genomic analyses to identify...
Undetected pathogen clusters can often be a source of spreading in-hospital infections. Unfortunately, detection of clusters can be problematic because epidemiological connection is not always easily established. Infection prevention and control (IPC) measures, however, are most effective when appli...
Outbreaks of Streptococcus pyogenes hypervirulent clones are constant public health threats. In western Switzerland, an increase of severe cases of S. pyogenes invasive infections was observed between December 2015 and March 2016. Our aim was (i) to investigate these cases by the use of Whole Genome...
Since 2010 the WHO has held a series of informal consultations to explore ways of improving the currently highly complex and time-pressured influenza vaccine virus selection and development process. In November 2015 experts from around the world met to review the current status of efforts in this fi...
Klebsiella pneumoniae is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recently become a major causative agent of clinical infections worldwide. Despite growing knowledge about the highly divers...
Culex quinquefasciatus (Diptera: Culicidae) is a vector of many pathogens and parasites of humans, as well as domestic and wild animals. In urban and semi-urban Asian countries, Cx. quinquefasciatus is a main vector of nematodes causing lymphatic filariasis. In the African region, it vectors the Rif...
In 2012, an elderly immunocompromised man died from legionellosis at a hospital in Uppsala, Sweden. The patient had visited a dental ward at the hospital during the incubation period. Legionella spp. at a concentration of 2000 colony-forming units/L were isolated from the cupfiller outlet providing...
Antimicrobial-resistant Escherichia coli are a concern for military health services. We studied 100 extended-spectrum beta-lactamase (ESBL)-producing and non-producing E. coli clinical and surveillance isolates from military personnel and civilians at Brooke Army Medical Center (2007-2011). Major E....
Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a lar...
Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antig...
The objective of this study was to compare the genetic features of heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) and vancomycin-sensitive methicillin-resistant S. aureus (VS-MRSA) isolates. The presence of staphylococcal cassette chromosome mec (SCCmec) types, Panton-Valentine...
The aim of this study was to characterise carbapenem-resistant Klebsiella pneumoniae isolates recovered from neonatal clinical specimens over a 4-month period. Seven carbapenem-resistant K. pneumoniae isolates were analysed. Antibiotic susceptibilities of the isolates were determined by the agar dil...
Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic-resistant strains throughout the 2000s. However, diseases caused by resistant nonvaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) th...
Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based culture-independent approaches, s...
Hepatitis C virus (HCV) infection is a major health burden worldwide. A patient with no history of HCV infection while on a renal unit was found to seroconvert to HCV. To report the use of sequencing to postulate how transmission of HCV occurred in a healthcare setting, and how this guided our outbr...
It has been suggested that zoonotic transmission of Staphylococcus aureus (SA) and methicillin-resistant S. aureus (MRSA) can occur between owners and their pets within the same household. However, the influence that pet-ownership could have in the biodiversity of SA/MRSA strains circulating among o...
AbstractThe incidence of hepatitis E in Singapore appears to be increasing. A retrospective case-series study of patients diagnosed with hepatitis E in a tertiary hospital from 2009 to 2013 was conducted. Of 16 cases, eight (50%) were solid-organ transplant recipients (SOTRs), and 14 (88%) were foun...
The German infectious disease surveillance system revealed an increase of epidemic keratoconjunctivitis (EKC) from an average of 320 cases/year (2001 to 2010) up to 2146 and 1986 cases in 2012 and 2013, respectively. From November 2011 until December 2013 (epidemic period) 85% of typed isolates were...
Avian influenza virus (AIV) causes both severe outbreaks and endemic disease among poultry and has caused sporadic human infections in Asia, furthermore the routes of transmission in avian species between geographic regions can be numerous and complex. Using nucleotide sequences from the internal pr...
Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are spreading worldwide in both hospital and community settings. In this study, the molecular epidemiology and the transmission modalities of ESBL-E in intensive care- and bone marrow transplant were investigated. All patients inclu...
Rift Valley Fever is an acute zoonotic viral disease caused by Rift Valley Fever virus (RVFV) that affects ruminants and humans in Sub-Saharan Africa and the Arabian Peninsula. We used phylogenetic analyses to understand the demographic history of RVFV populations, using sequence data from the three...
Whole apples have not been previously implicated in outbreaks of foodborne bacterial illness. We investigated a nationwide listeriosis outbreak associated with caramel apples. We defined an outbreak-associated case as an infection with one or both of two outbreak strains of Listeria monocytogenes hi...
One case of hospital-acquired listeriosis was linked to milkshakes produced in a commercial-grade shake freezer machine. This machine was found to be contaminated with a strain of Listeria monocytogenes epidemiologically and molecularly linked to a contaminated pasteurized, dairy-based ice cream pro...
The molecular epidemiology of HIV-1 in Iceland has not been described so far. Detailed analyses of the dynamics of HIV-1 can give insights for prevention of virus spread. The objective of the current study was to characterize the genetic diversity and transmission dynamics of HIV-1 in Iceland. Parti...
To identify the spread of nosocomial infections and halt outbreak development caused by Escherichia coli that carry multiple antibiotic resistance factors, such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases, is becoming demanding challenges due to the rapid global increase and cons...
Carbapenem-resistant Acinetobacter baumannii poses a significant threat to hospitalized patients, as few therapeutic options remain. Thus, we investigated the molecular epidemiology and mechanism of resistance of carbapenem-resistant A.baumannii isolates in Beijing, China. Carbapenem-resistant A.bau...
Extended-spectrum β-lactamase (ESBL)-producing bacteria are resistant to several types of antibiotics excluding carbapenems. A transmissibility of ESBL-producing Enterobacteriaceae would be depending on each bacterial property, however, that has not been elucidated in clinical setting. In this study...
Escherichia coli (E. coli) comprise part of the normal vaginal microflora. Transfer from mother to neonate can occur during delivery resulting, sometimes, in neonatal bacterial disease. Here, we aim to report the first outbreak of CTX-M ESBL-producing E. coli with evidence of mother-to-neonate trans...
Vibrio parahaemolyticus has been the most common food-borne pathogen in southern China, especially the O3:K6 pandemic clone and its serovariants. Recently, the serotype O4:K8 became more and more prevalent in southern China, which was different from the O3:K6 pandemic clone. Thus, the aim of the pre...
Today, next-generation whole-genome sequencing (WGS) is increasingly used to determine the genetic relationships of bacteria on a nearly whole-genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring trial comprising five laboratories to determine...
We described a health care-associated Serratia marcescens outbreak of wound and soft tissue infection lasting approximately 11 months at Ankara University Ibni Sina Hospital. After identification of S marcescens strains from the clinical and environmental samples, and their susceptibility testing to...
No abstract available
Multidrug resistance in the nosocomial pathogen Acinetobacter baumannii limits therapeutic options and impacts on clinical care. Resistance against carbapenems, a group of last-resort antimicrobials for treating multidrug-resistant (MDR) A. baumannii infections, is associated with the expression (an...
Determine features of epidemic process (EP) of Sonnei dysentery in Khabarovsk Region in 2012 - 2014 due to atypical causative agent. Detailed characteristics of 161 cultures of Shigella sonnei isolated from 81 patients from epidemic focus in children boarding school in Bikin as well as from 22 patie...
Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlyin...
Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 62...
To apply a multiplex real-time polymerase chain reaction (PCR) technique to detect Salmonella spp., Listeria monocytogenes, and Yersinia enterocolitica as a diagnostic support tool for the surveillance of foodborne disease outbreaks. Molecular methodology was applied on clinical samples taken from i...
Melioidosis has recently gained importance as an emerging disease in India. Recurrent melioidosis has been reported from different parts of the world and can be due to relapse or reinfection. Distinction between relapse and reinfection is important for epidemiology, investigation and management. Her...
Reported literature on invasive group A streptococcal isolates in India is very scanty. This study was undertaken to determine the molecular heterogeneity of such isolates as seen in a tertiary care center. Thirty two blood culture isolates and 18 from other sterile body fluids were characterized by...
The changing epidemiology of methicillin-resistant (MRSA) from a hospital-associated pathogen to an organism commonly found in the community and in livestock reflects an organism well-equipped to survive in diverse environments and adjust to different environmental conditions including antimicrobia...
Tick-borne diseases (TBDs) cause significant losses among livestock and impact the livelihoods of resource-poor farming communities worldwide. In Ethiopia, detailed studies on the epidemiology of tick-borne pathogens (TBPs) in cattle using sensitive molecular detection methods are scarce. The object...
American foulbrood (AFB), caused by Paenibacillus larvae, is a devastating disease in honeybees. In most countries, the disease is controlled through compulsory burning of symptomatic colonies causing major economic losses in apiculture. The pathogen is endemic to honeybees world-wide and is readily...
Hand, foot, and mouth disease (HFMD) has caused a substantial burden of disease in China, especially in Guangdong Province. Based on notifiable cases, we use the time series Susceptible-Infected-Recovered model to estimate the basic reproduction rate (R0) and the herd immunity threshold, understandi...
Burkholderia cepacia complex (Bcc) has emerged as a serious nosocomial pathogen worldwide especially in patients with indwelling catheters and cystic fibrosis. Bcc is a common contaminant of pharmaceutical products. We describe an outbreak of Bcc bacteraemia amongst children admitted in Paediatric I...
Shiga toxin (Stx)-producing Escherichia coli (STEC) infections are implicated in the development of the life-threatening hemolytic-uremic syndrome (HUS). Despite the magnitude of the social and economic problems caused by HUS, no licensed vaccine or effective therapy is currently available for human...
To characterize the microbiological, molecular and epidemiological data of an outbreak of carbapenem-resistant Enterobacteriaceae (CRE) in a tertiary-care hospital in Mexico. From September 2014 to July 2015, all CRE clinical isolates recovered during an outbreak in the Hospital Civil "Fray Antonio...
Huanglongbing, or citrus greening disease, is an economically devastating bacterial disease of citrus. It is associated with infection by the gram-negative bacterium Candidatus Liberibacter asiaticus (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid (ACP). For insect transmis...
In recent years, foot-and-mouth disease virus (FMDV) serotype O, topotype Middle East-South Asia (ME-SA), lineage Ind-2001d has spread from the Indian subcontinent to the Middle East, North Africa, and Southeast Asia. In the current report, we describe the first detection of this lineage in Vietnam...
Shiga toxin-producing Escherichia coli (STEC) causes an estimated 265 000 infections in the United States annually. Of emerging non-O157:H7 STEC serotypes, O26 is the most commonly recognized. During an outbreak of STEC O26 in Oregon in 2015, we used syndromic surveillance data to supplement case fi...
Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB) is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome...
In China, has been a leading cause of foodborne outbreaks and bacterial infectious diarrhea since the 1990s, and most infections have been associated with the pandemic O3:K6 and its serovariants. However, a comprehensive overview of the sero-prevalence and genetic diversity of the pandemic clone...
Hypervirulent and multidrug resistant strains pose a significant threat to the public health. In the present study, 21 carbapenem-resistant isolates (CRKP) were determined by the string test as hypermucoviscous (HMKP), with the prevalence of 15.0% (21/140) among CRKP, and 1.1% (21/1838) among all...
Peste-des-petits ruminants (PPR) is one of the most important infectious diseases of domesticated small ruminants. From the initial identification in 1942 in West Africa, PPR virus (PPRV) has spread throughout much of the developing world. PPRV is now considered endemic throughout Africa, with the n...
Although the nares represent the most common carriage site for traditional hospital-associated strains of Staphylococcus aureus (SA), the predominant site of carriage of SA in the community is less certain. We conducted a cross-sectional study in 285 patients attending sexually transmitted diseases...
Carbapenemase-producing (KPC) has emerged and spread throughout the world. A retrospective analysis was performed on carbapenem-resistant isolated at our teaching hospital during the period 2009-2010, when the initial outbreak occurred. To determine the mechanism(s) that underlies the increased in...
is highly pathogenic and can cause diseases in both humans and domestic animals. In animal species, including ruminants, may cause severe or sub-clinical mastitis. This study aimed to investigate the molecular profile, antimicrobial resistance, and genotype/phenotype correlation of 212 isolates re...
Corynebacterium pseudotuberculosis is a Gram-positive, pleomorphic, facultative intracellular pathogen that causes Oedematous Skin Disease (OSD) in buffalo. To better understand the pathogenic mechanisms of OSD, we performed a comparative genomic analysis of 11 strains of C. pseudotuberculosis isola...
Methicillin-resistant (MRSA), is one of the most prevalent clinical pathogens isolated from hospital settings, and has increasingly identified in community settings. In China, the SCCIII-ST239 strains are disseminated in different geographic regions, accounting for >75% of all MRSA isolates in some...
In developed countries, pregnancy-related listeriosis accounts for 20-43% of total invasive listeriosis. This work describes the first pregnancy-related listeriosis survey in Italy based on two data sources, that is, mandatory notification system and regional laboratory-based network. Out of 610 lis...
Clostridium difficile is one of the main etiological agents causing antibiotic-associated diarrhea. This study investigated the genetic diversity of 70 toxigenic C. difficile isolates from two Korean hospitals by employing toxinotyping, ribotyping, multilocus sequence typing (MLST), and pulsed-field...
Despite being the most prevalent arboviral disease worldwide, dengue has been neglected lately. However, recent epidemics of arboviruses such as Zika and chikungunya in locations throughout the world have alerted health authorities to these diseases. This study evaluated the incidence pattern of den...
This study aims to understand trends in spoligotype patterns of Mycobacterium tuberculosis (MTB) in Central India. Elucidation of these trends may provide baseline information to understand the transmission dynamics of strains of MTB in the region. Spoligotyping was carried out on 340 MTB strains is...
Streptococcus agalactiae is one of the most common pathogens leading to mastitis in dairy herds worldwide; consequently, the pathogen causes major economic losses for affected farmers. In this study, multilocus sequence typing (MLST), genotypic capsular typing by multiplex polymerase chain reaction...
The tuberculosis (TB) incidence rate in Brussels-Capital Region is 3-fold higher than in Belgium as a whole. Eight years after the realization of initial prospective population-based molecular epidemiology investigations in this Region, a similar study over the period 2010-2013 was conducted. TB str...
After 15 years of absence, in 2013 bovine tuberculosis (bTB), caused by Mycobacterium (M.) bovis and M. caprae, reemerged in the Swiss dairy cattle population. In order to identify the sources of infection as well as the spread of the agents, molecular-epidemiologic tracing by MIRU-VNTR analysis in...
Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and g...
Vibrio parahaemolyticus is an important human pathogen that has been isolated worldwide from clinical cases, most of which have been associated with seafood consumption. Environmental and clinical toxigenic strains of V. parahaemolyticus that were isolated in Mexico from 1998 to 2012, including thos...
The objectives of this study were to determine the frequency of methicillin-resistant Staphylococcus aureus (MRSA) colonization or infection while on admission to the intensive care unit (ICU), and examine the genetic backgrounds of the MRSA isolates to establish transmission among the patients. Thi...
The aim of the present study was to assess and compare the antimicrobial susceptibility pattern against a panel of antibiotics and molecular and methicillin resistance-associated genotypes of 120 carriage S. aureus isolates previously isolated from a student population at two isolation events within...
Chryseobacterium species are rarely reported as aetiological agents of nosocomial urinary tract infection. Here, we evaluated the clinical significance of 19 isolates of Chryseobacterium species (15 Chryseobacterium indologenes and 4 Chryseobacterium gleum; identified by matrix-assisted laser desorp...
Cephalosporin resistance in clinical isolates is increasing internationally. The increase has been caused by virulent and often multidrug-resistant clones, especially the extended spectrum β-lactamase (ESBL) producing clone O25b-ST131. In Norway, recommended empirical treatment of sepsis consists...
West Africa is the only region in the world where six out of seven mycobacterial lineages of human importance are endemic. In particular, two evolutionary ancient lineages, Mycobacterium africanum West Africa 1 (MTBC Lineage 5) and M. africanum West Africa 2 (MTBC Lineage 6) are of interest as they...
The application of next generation sequencing technologies has opened the door to a new molecular epidemiology of tuberculosis, in which we can now look at transmission at a resolution not possible before. At the same time, new technical and analytical challenges have appeared, and we are still expl...
The purpose of this study was to evaluate the discriminatory power of two DNA-based technique and a protein-based technique for the typing of nosocomial isolates of Klebsiella pneumoniae. A second objective was to determine the antimicrobial susceptibility pattern and characterise the presence of ge...
Group B streptococcus (GBS) is a leading cause of neonatal mortality and morbidity in the United States and Europe. It is part of the vaginal microbiota in up to 30% of pregnant women and can be passed on to the newborn through perinatal transmission. GBS has the ability to survive in multiple diffe...
Emergence of vancomycin-intermediate Staphylococcus aureus (VISA) and vancomycin-resistant S. aureus (VRSA) strains has led to great concern in global public health in both developing and developed countries. This study investigated distribution and molecular characterization of VRSA strains in Tehr...
Pulmonary emphysema is an important radiological finding in chronic obstructive pulmonary disease patients, but bacteriological differences in pneumonia patients according to the severity of emphysematous changes have not been reported. Therefore, we evaluated the bacteriological incidence in the br...
Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as an important global nosocomial pathogen, and this trend is associated with the spread of high-risk clones. Here, we determined the genetic and phenotypic features of 93 VREfm isolates that were obtained from patients in 13 hospitals in...
In developing countries, hospitalized burn victims are at high risk of nosocomial infections caused by Staphylococcus aureus. Risk factors include poor infection control practices, prolonged hospitalisation and limited capacity for laboratory microbiological analyses. These problems are compounded b...
Vibrio parahaemolyticus is recognized as major cause of foodborne illness of global public health concern. This study collected 107 strains of V. parahaemolyticus during active surveillance of diarrheal diseases in hospitals in Zhoushan during 2013 to 2014 and investigated their serotypes, virulence...
Urogenital infection due to Chlamydia trachomatis (CT) is one of the most common bacterial sexually transmitted infections (STIs) and is a major public health problem worldwide. Molecular characterisation of CT is important for understanding the pathophysiological mechanisms of chlamydial disease an...
No abstract available
Multidrug resistant (MDR) Enterococcus faecium is a nosocomial pathogen and clonal complex 17 (CC17) is the main genetic subpopulation of E. faecium in hospitals worldwide. There has thus far been no report of major E. faecium clones in Iranian hospitals. The present study analyzed strains of MDR E....
Whole-genome sequencing (WGS) has become an essential tool for public health surveillance and molecular epidemiology of infectious diseases and antimicrobial drug resistance. It provides precise geographical delineation of spread and enables incidence monitoring of pathogens at genotype level. Coupl...
The increased presence of clinically relevant multidrug resistant bacteria in natural environments is an emerging challenge for global health care. Little is known regarding the occurrence of extended-spectrum beta-lactamase producing (ESBL-) from environmental sentinels in Pakistan. The goal of th...
Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the e...
Genome sequencing has been useful to gain an understanding of bacterial evolution. It has been used for studying the phylogeography and/or the impact of mutation and recombination on bacterial populations. However, it has rarely been used to study gene turnover at microevolutionary scales. Here, we...
The field of phylogeography allows researchers to model the spread and evolution of viral genetic sequences. Phylogeography plays a major role in infectious disease surveillance, viral epidemiology and vaccine design. When conducting viral phylogeographic studies, researchers require the location of...
Globalization of food networks increases opportunities for the spread of foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping of pathogens promises to vastly improve our ability to track and control foodborne disease, but to do so it must be c...
West Nile virus lineage 2 (WNV-2) was mainly confined to sub-Saharan Africa until the early 2000s, when it was identified for the first time in Central Europe causing outbreaks of human and animal infection. The aim of this study was to reconstruct the origin and dispersion of WNV-2 in Central Europ...
Emerging infectious diseases pose a serious threat to public health security; this is especially true in the underdeveloped world because of limited resources to combat them. These emerging pathogens are characterized by a novel mode of pathogenesis and, in some cases, a broad host range. Over the p...
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the req...
Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling techniques such as pulsed-field gel electrophoresis, WGS requires a variety of computational methods. Since 2013, United States ag...
In the recent years, the data on the molecular epidemiology of influenza viruses have expanded enormously because of the availability of cutting-edge sequencing technologies. However, much of the information is from the temperate regions with few studies from tropical regions such as South-east Asia...
The economic impact of Clostridium difficile infection (CDI) on the healthcare system is significant. From May 2013 to May 2014, an outbreak of C. difficile ribotype 027 occurred in a Dutch tertiary care hospital, involving 72 patients. The primary aim of this study was to provide insight into the f...
With increasing reports about Corynebacterium striatum, its potential pathogenicity and clinical significance are drawing more attention in recent years. During a 14-month period, Corynebacterium striatum strains were routinely isolated in lower respiratory tract samples of the inpatients in a terti...
Infections caused by multidrug-resistant bacteria are increasingly common and represent a serious problem for public health. Staphylococcus aureus is one of the major agents of infections, and methicillin-resistant S. aureus (MRSA) has spread worldwide. The aim of this study was to phenotypically an...
Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, informatio...
The diarrheal pathogen consists of at least six distinct evolutionary lineages. The RT017 lineage is anomalous, as strains only express toxin B, compared to strains from other lineages that produce toxins A and B and, occasionally, binary toxin. Historically, RT017 initially was reported in Asia bu...
Clostridium difficile infection (CDI) is becoming less exclusively a health care-associated CDI (HA-CDI). The incidence of community-associated CDI (CA-CDI) has increased over the past few decades. It has been postulated that asymptomatic toxigenic C. difficile (TCD)-colonized patients may play a ro...
Metagenomic next-generation sequencing (mNGS) is increasingly used for the unbiased detection of viruses, bacteria, fungi, and eukaryotic parasites in clinical samples. Whole-genome sequencing (WGS) of clinical bacterial isolates has been shown to inform hospital infection prevention practices, but...
Both early localized and late disseminated forms of Lyme borreliosis are caused by Borrelia burgdorferi senso lato. Differentiating between the spirochetes that only cause localized skin infection from those that cause disseminated infection, and tracing the group of medically-important spirochetes...
Over a 5-month period between the end of June and the beginning of November in 2015, a KPC-producing Enterobacteriaceae outbreak occurred in a general hospital in Busan, South Korea, being associated with a total of 50 clinical isolates from 47 patients. Multilocus sequence typing and pulsed-field g...
Molecular epidemiology analysis of tuberculosis transmission is based mostly on the application of MIRU-VNTR. In certain isolates a complete 24-loci genotype is not obtained and these incompletely genotyped isolates can not be used in the definition of clusters. In a population-based molecular epide...
Prompt genotyping of Mycobacterium tuberculosis (M. tuberculosis) is crucial for improving molecular epidemiological investigation of tuberculosis (TB). We performed a retrospective study to evaluate the use of 24 loci MIRU-VNTR (mycobacterial interspersed repetitive unit-variable number of tandem-r...
It is still unclear whether different HHV-8 genotypes may have different pathogenic and tumorigenic properties associated with a diverse rate of disease progression. In some areas where genotype C was found to be prominent among classic KS patients, genotype A was shown to be more frequent among AID...
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying t...
No abstract available
No abstract available
We evaluated the epidemiological and molecular features of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) and methicillin-sensitive S. aureus (MSSA) from children and adult patients with skin and soft-tissue infections (SSTIs) in China. Prospective community-acquired S. a...
Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focu...
The aim of this study was to investigate the molecular epidemiology and the genetic support of carbapenem-resistant Enterobacteriaceae and Acinetobacter spp. isolates collected in the University Hospital of Ouargla, southern Algeria. A total of 99 Gram-negative bacteria (GNB) were collected from sto...
Ovine herpesvirus 2 (OvHV-2) was responsible for two outbreaks of malignant catarrhal fever (MCF) on two water buffalo farms in Southern Italy. In this study, the presence of this virus in the nasal swabs from sick animals as well as in the organs of dead buffaloes was ascertained by a Real-time PCR...
Previous studies comparing Clostridium difficile infection (CDI) due to different ribotypes have been conflicting, and many have only compared small numbers of cases or few ribotypes. To compare patient and episode characteristics for CDI due to different ribotypes. The ribotyping results from 3333...
No abstract available
Few studies on risk factors for and transmission of infection (CDI) in China have been reported. A cross-sectional study was conducted for 3 years in eastern China. Consecutive stool specimens from hospitalized patients with diarrhea were cultured for isolates from these patients then were analyze...
In October 2014, Public Health England (PHE) identified cases of Shiga toxin-producing Escherichia coli (STEC) serogroup O157 sharing a multiple locus variable-number tandem repeat analysis (MLVA) profile. We conducted a case-control study using multivariable logistic regression to calculate adjuste...
The Bengal Bay clone, ST772-MRSA-V, associated with multi-drug resistance, Panton-Valentine leukocidin (PVL) and skin and soft tissue infections, is emerging worldwide. In Norway, a country with low prevalence of meticillin-resistant Staphylococcus aureus (MRSA), increased occurrence of ST772-MRSA-V...
Corynebacterium pseudotuberculosis biovar Equi is an important pathogen of horses. It is increasing in frequency in the United States, and is responsible for various clinical forms of infection, including external abscesses, internal abscesses of the abdominal or thoracic cavities, and ulcerative ly...
Acinetobacter baumannii is an opportunistic pathogen that has become a major cause of concern, since it is a frequent cause of healthcare-associated infections (HAIs). The aim of the study was to describe the occurrence, the management and the control of an outbreak that occurred in an intensive car...
We report two cases of severe pneumonia due to clone ST93 methicillin-resistant (MRSA) presenting from a remote Australian Indigenous community within a 2-week period, and the utilization of whole genome sequences to determine whether these were part of an outbreak. was isolated from 12 of 92 nasa...
is a growing cause of healthcare-associated infections for which multi-drug resistance is a concern. Its polysaccharide capsule is a major virulence determinant and epidemiological marker. However, little is known about capsule epidemiology since serological typing is not widely accessible and many...
The present study aimed to screen for the presence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in wild boars and Barbary macaques in Béjaïa and Jijel, Algeria. A total of 216 faecal samples collected between September 2014 and August 2015 were cultured on MacConkey agar supp...
The coagulase enzyme, encoded by the coa gene, is an important virulence factor of Staphylococcus aureus and can be used for typing of S. aureus isolates. In this study, coa gene typing was used to study the epidemiology of S. aureus at a university hospital in Hamadān (Iran). A total of 200 S. aure...
The resurgence of invasive meningococcal disease caused by Neisseria meningitidis serogroup W with sequence type ST-11 (cc11) was observed in Madagascar in 2015-2016. Three cases were investigated in this study. Molecular characterization of the strains suggests the local transmission of a single ge...
During the last decades, healthcare-associated genotypes of methicillin-resistant Staphylococcus epidermidis (HA-MRSE) have been established as important opportunistic pathogens. However, data on potential reservoirs on HA-MRSE is limited. The aim of the present study was to investigate the dynamics...
Bacteriophages (phages) are widely distributed in the biosphere and play a key role in modulating microbial ecology in the soil, ocean, and humans. Although the role of DNA bacteriophages is well described, the biology of RNA bacteriophages is poorly understood. More than 1900 phage genomes are curr...
The greater white-toothed shrew (Crocidura russula) is an invasive mammalian species that was first recorded in Ireland in 2007. It currently occupies an area of approximately 7,600 km2 on the island. C. russula is normally distributed in Northern Africa and Western Europe, and was previously absent...
The green peach aphid, , is a vector of the (PLRV, Luteoviridae), transmitted exclusively by aphids in a circulative manner. PLRV transmission efficiency was significantly reduced when a clonal lineage of was reared on turnip as compared with the weed physalis, and this was a transient effect caus...
Fusarium is a rapidly emerging, multidrug-resistant genus of fungal opportunists that was first identified in 1958 and is presently recognized in numerous cases of fusariosis each year. The authors examined trends in global Fusarium distribution, clinical presentation and prevalence since 1958 with...
Infections caused by multidrug resistant microorganisms are a global health problem, and Pseudomonas aeruginosa is an important nosocomial pathogen, easily disseminated in the hospital environment. The aim of this study was to determine SPM-1 in P. aeruginosa strains in 30 Brazilian hospitals and th...
Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of...
In 2014, a sustained outbreak of yersiniosis due to Yersinia pseudotuberculosis occurred across all major cities in New Zealand (NZ), with a total of 220 laboratory-confirmed cases, representing one of the largest ever reported outbreaks of Y. pseudotuberculosis. Here, we performed whole genome sequ...
The aim of this study was to identify and characterise Bacillus cereus from a unique national collection of 564 strains associated with 140 strong-evidence food-borne outbreaks (FBOs) occurring in France during 2007 to 2014. Starchy food and vegetables were the most frequent food vehicles identified...
In August 2015, plague was diagnosed for 2 persons who had visited Yosemite National Park in California, USA. One case was septicemic and the other bubonic. Subsequent environmental investigation identified probable locations of exposure for each patient and evidence of epizootic plague in other are...
Between March and May 2012, three neonates born at a regional maternity hospital developed Elizabethkingia meningoseptica (previously Chryseobacterium meningosepticum) sepsis with meningitis aged <10 days, and were treated successfully with intravenous ciprofloxacin plus vancomycin or piperacillin-t...
This prospective cohort study evaluates colonization dynamics and molecular characteristics of methicillin-susceptible and - resistant Staphylococcus aureus (MSSA/MRSA) in a German general population. Nasal swabs of 1878 non-hospitalized adults were screened for S. aureus. Participants were screened...
Shigella sonnei is a major cause of diarrhea especially in children. Molecular study can help to determine the outbreak of this bacterium. Multiple-Locus Variable number tandem repeat Analysis (MLVA) will largely influence the public health field by introducing newer, faster, safer, and effective pr...
No abstract available
In 2013, an unusual increase in the number of serotype Paratyphi A ( Paratyphi A) infections was reported in patients in Phnom Penh, Cambodia, and in European, American and Japanese travellers returning from Cambodia. Epidemiological investigations did not identify a common source of exposure. To a...
Clostridium difficile is an anaerobic Gram-positive, spore-forming, toxin-producing bacillus transmitted among humans through the faecal-oral route. Despite increasing carriage rates and the presence of C. difficile toxin in stool, patients with CF rarely appear to develop typical manifestations of...
Foot-and-mouth disease virus (FMDV) is one of the highest risk factors that affects the animal industry of the country. The virus causes production loss and high ratio mortality in young cloven-hoofed animals in Vietnam. The VP1 coding gene of 80 FMDV samples (66 samples of the serotype O and 14 sam...
OBJECTIVE To determine the origin of grouped cases of Pneumocystis pneumonia in solid-organ transplant recipients at our institution. DESIGN A case series with clinical examinations, genotyping, and an epidemiological survey. SETTING A university hospital in France. PATIENTS We report 12 solid-organ...
The use of MALDI-TOF MS (matrix-assisted laser desorption/ ionization-time of flight mass spectrometry) and WGS (whole genome sequencing) has been described for identification and strain relatedness determination. We describe the complementary use of MALDI-TOF MS and WGS in a VRE (vancomycin-resista...
Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), remains an unresolved public health problem in India. Emergence of antimicrobial resistant strains poses a great concern for typhoid treatment and influences reshaping of current S. Typhi population. We included representative S....
This work set out to shed light on the phylogeography of the SAR11 clade of Alphaproteobacteria, which is probably the most abundant group of heterotrophic bacteria on Earth. In particular, we assessed the degree to which empirical evidence (environmental DNA sequences) supports the concept that SAR...
Comparing genotype results of tuberculosis (TB) isolates from individuals diagnosed with TB can support or refute transmission; however, these conclusions are based upon the criteria used to define a genotype match. We used a genotype-match definition which allowed for variation in IS6110 restrictio...
A total of 431 Pseudomonas aeruginosa clinical isolates were collected from 29 general hospitals in South Korea in 2015. Antimicrobial susceptibility was tested by the disk diffusion method, and MICs of carbapenems were determined by the agar dilution method. Carbapenemase genes were amplified by PC...
A total of 2,201 nonduplicate enterococcal isolates collected from 29 hospitals in 23 cities in China between 2004 and 2014 were screened for the oxazolidinone resistance gene optrA; 45 isolates (2.0%) were optrA positive with 11 OptrA variants identified. The positive rate of optrA increased from 0...
The distinct epidemiology of original hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) and early community-associated MRSA (CA-MRSA) is largely unexplained. S. aureus carries either five or six rRNA operon copies. Evidence is provided for a scenario in which MRSA has adapted...
Among 504 clinical lineage II isolates of Listeria monocytogenes isolated during 1958-2010 in Sweden, 119 pulsed-field gel electrophoresis (PFGE) types (AscI) have been identified based on the number and distribution of all banding patterns in each DNA profile. In this study, these types were furthe...
This study was conducted to investigate the molecular epidemiology of resistance in Acinetobacter baumannii isolates collected at a hospital in Riyadh, Saudi Arabia, from January through December 2010. Twenty-seven A. baumannii were highly resistant (MIC > 256 μg/ml) to ceftazidime, cefepime, and az...
Multidrug-resistant (MDR) Acinetobacter baumannii has increasingly emerged as an important nosocomial pathogen. The aim of this study was to determine the resistance profiles and genetic diversity in A. baumannii clinical isolates in a tertiary medical center in Malaysia. The minimum inhibitory conc...
Acinetobacter baumannii is recognised as a major pathogen of nosocomial infections that frequently show resistance to last-resort antimicrobials. To investigate whether A. baumannii from companion animals harbour carbapenem resistance mechanisms, 223 clinical isolates obtained from veterinary clinic...
Late-onset sepsis (LOS) in preterm neonates is increasingly reported to be associated with gut-colonizing Staphylococcus epidermidis. We aimed to describe the molecular epidemiology of S. epidermidis colonizing the gut of neonates hospitalized in two neonatal intensive care units. S. epidermidis fro...
Non-clonal, carbapenem- and multidrug-resistant Citrobacter freundii isolates were collected from unrelated outpatients admitted to a Portuguese hospital emergency department. One patient lived in a nursing home and was never hospitalised, whereas the other patient was repeatedly hospitalised in thi...
Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease with high morbidity and mortality that predominantly affects preterm neonates during outbreaks. In a previous study, the present authors identified 15 Clostridium butyricum isolates from stool samples during a series of NEC ca...
Increasing incidences of non-typeable Haemophilus influenzae (NTHi) with β-lactam resistance mediated through mutations in penicillin-binding protein 3 (BLNAR or rPBP3) have been observed in the past decades. Recently, an rPBP3 NTHi sequence type (ST) 14 with PBP3 type IIb/A caused a disease outbrea...
The aim of this study was to determine whether the route of extended-spectrum β-lactamase (ESBL) transmission to hospitalized newborns was from their mothers during delivery. Neonatal intensive care unit (NICU) hospitalized newborns were sampled for ESBL presence by stool cultures on the first and f...
Mongolia has a high incidence of brucellosis in human and animals due to livestock husbandry. To investigate the genetic characteristics of Mongolian B. melitensis, an MLVA (multi-locus variable-number tandem-repeat analysis)-16 assay was performed with 94 B. melitensis isolates. They were identifie...
The 23rd World Scout Jamboree in 2015 took place in Japan and included over 33,000 scouts from 162 countries. Within nine days of the meeting ending, six cases of laboratory-confirmed invasive serogroup W meningococcal disease occurred among scouts and their close contacts in Scotland and Sweden. Th...
OBJECTIVE To measure transmission frequencies and risk factors for household acquisition of community-associated and healthcare-associated (HA-) methicillin-resistant Staphylococcus aureus (MRSA). DESIGN Prospective cohort study from October 4, 2008, through December 3, 2012. SETTING Seven acute car...
To investigate the feature of antimicrobial resistance, homology and other molecular epidemiology of methicillin-resistant staphylococcus aureus(MRSA) in Department of Critical Care Medicine(ICU). From October 2010 to December 2011, 149 strains of MRSA were collected and identified through sputum c...
Noroviruses (NoVs) are the most frequent cause of acute gastroenteritis worldwide among people of all ages and the leading cause of gastrointestinal disease outbreaks in various settings. To clarify the differences in epidemic situations among different settings, we investigated epidemiological tren...
The annual prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Malaysia has been estimated to be 30 % to 40 % of all S. aureus infections. Nevertheless, data on the antimicrobial resistance and genetic diversity of Malaysian MRSAs remain few. In 2009, we collected 318 MRSA strains fr...
Accumulated data indicate that meticillin-resistant Staphylococcus aureus (MRSA) infections are associated with a worse prognosis than methicillin-susceptible S. aureus infections. To assess the epidemiological profile of S. aureus infections and the genetic diversity of clinical strains of MRSA in...
Sequence type 131 (ST131) is a predominant lineage among extraintestinal pathogenic Escherichia coli. It plays a major role in the worldwide dissemination of E. coli producing extended-spectrum β-lactamases (ESBLs). Here we describe the long-term epidemiology of this clonal group in a French univers...
Genome sequence analysis of Middle East respiratory syndrome coronavirus (MERS-CoV) variants from patient specimens has revealed the evolutionary dynamics and mechanisms of pathogenesis of the virus. However, most studies have analyzed the consensus sequences of MERS-CoVs, precluding an investigatio...
The clinical impact of enteroviruses associated with hand, foot and mouth disease (HFMD) is unknown outside Asia, and the prevalence of enterovirus A71 (EV-A71) in particular might be underestimated. To investigate the prevalence of enterovirus serotypes and the clinical presentations associated wit...
Bacterial pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) represent a well-known public health problem affecting both healthcare-associated and community populations. Past studies have clearly shown the value of characterizing problem organisms including MRSA through the use of...
Tomato spotted wilt virus (TSWV) is mainly vectored by Frankliniella occidentalis Pergande, and it potentially activates the vector's immune response. However, molecular background of the altered immune response is not clearly understood. Therefore, using a proteomic approach, we investigated the im...
No abstract available
Uropathogenic virulence factors have been identified by comparing the prevalence of these among urinary tract isolates and environmental strains. The uropathogenic-specific protein (USP) gene is present on the pathogenicity island (PAI) of uropathogenic Escherichia coli (UPEC) and, depending on its...
Models of the spread of disease in a population often make the simplifying assumption that the population is homogeneously mixed, or is divided into homogeneously mixed compartments. However, human populations have complex structures formed by social contacts, which can have a significant influence...
To date, only a few sporadic cases of infections due to Klebsiella pneumoniae carbapenemase (KPC) producers have been reported in Portugal. Here, we report for the first time an outbreak of K. pneumoniae KPC-3 producers in a tertiary-care hospital during 2013. Twenty-seven ertapenem-resistant K. pne...
The Pennsylvania Egg Quality Assurance Program (EQAP) provided the framework for Salmonella Enteritidis (SE) control programs, including the Food and Drug Administration (FDA) mandated Final Egg Rule, for commercial layer facilities throughout the United States. Although flocks with ≥3000 birds must...
Vibrio cholerae is ubiquitous in aquatic environments, with environmental toxigenic V. cholerae O1 strains serving as a source for recurrent cholera epidemics and pandemic disease. However, a number of questions remain about long-term survival and evolution of V. cholerae strains within these aquati...
Klebsiella pneumoniae is a prominent nosocomial pathogen that accounts for up to 10 % of all hospital-acquired infections. It is a frequent cause of ventilator-associated pneumonia (VAP). The purpose of this study was to investigate the clinical characteristics of K. pneumoniae-associated VAP and th...
Clostridium difficile is the main cause of nosocomial antibiotic-associated diarrhea in adults in Europe and North America. Infections with C. difficile typically occur in elderly patients with comorbidities and prior antibiotic therapy. Other risk factors are proton pump inhibitors, which are taken...
Whole genome sequencing (WGS) can help to relate Mycobacterium tuberculosis genomes to one another to assess genetic relatedness and infer the likelihood of transmission between cases. The same sequence data are now increasingly being used to predict drug resistance and susceptibility. Controlling t...
Acinetobacter baumannii is a major hospital-acquired pathogen in Thailand that has a negative effect on patient survival. The nature of its transmission is poorly understood. To investigate the genotypic and spatiotemporal pattern of A. baumannii infection at a hospital in Thailand. The medical reco...
Terminal disinfection and daily cleaning have been performed in hospitals in Taiwan for many years to reduce the risks of healthcare-associated infections. However, the effectiveness of these cleaning approaches and dynamic changes of surface microbiota upon cleaning remain unclear. Here, we report...
Klebsiella pneumoniae is a bacterial pathogen that has developed resistance to multiple antibiotics and is a major cause of nosocomial infections worldwide. Carbapenemase-producing Klebsiella pneumoniae have been isolated in many hospitals in Venezuela, but they have not been well-studied. The aim o...
A subtyping methodology for Campylobacter, Comparative Genomic Fingerprinting (CGF40), has been described recently. The objective of this study was to assess the utility of CGF40 as a tool to enhance routine public health surveillance of campylobacteriosis. Isolates of Campylobacter from across the...
Emerging public health challenges of Shiga toxin (stx)-producing Escherichia coli (STEC) include the occurrence of more frequent or severe disease and risk factors shifts associated with changes, often interconnected, in the pathogen, the population, and the environment. In 3 outbreaks with heighten...
Following its immergence in December 2013, the recent Zaire Ebola virus (EBOV) outbreak in West Africa has spread and persisted for more than two years, making it the largest EBOV epidemic in both scale and geographical region to date. In this study, a total of 726 glycoprotein (GP) gene sequences o...
Quinupristin/dalfopristin (Q/D) is a valuable alternative antibiotic to vancomycin for the treatment of multi-drug resistant Enterococcus faecium infections. However, resistance to Q/D in E. faecium clinical isolates and nosocomial dissemination of Q/D-resistant E. faecium have been reported in seve...
Carbapenemase-producing Enterobacteriaceae (CPE) are increasing globally; here we report on the investigation of CPE in Canada over a 5-year period. Participating acute care facilities across Canada submitted carbapenem-nonsusceptible Enterobacteriaceae from 1 January 2010 to 31 December 2014 to the...
An outbreak of Legionnaires' disease occurred in an inner city district in Calgary, Canada. This outbreak spanned a 3-week period in November-December 2012, and a total of eight cases were identified. Four of these cases were critically ill requiring intensive care admission but there was no associa...
The increasing threat of antimicrobial resistance poses one of the greatest challenges to modern medicine. The collection of all antimicrobial resistance genes carried by various microorganisms in the human body is called the human resistome and represents the source of resistance in pathogens that...
For infectious diseases, a genetic cluster is a group of closely related infections that is usually interpreted as representing a recent outbreak of transmission. Genetic clustering methods are becoming increasingly popular for molecular epidemiology, especially in the context of HIV where there is...
This study compared the antimicrobial susceptibility and genotypes of strains of Neisseria gonorrhoeae isolated from men who have sex with men (MSM) and from heterosexuals. One hundred and eleven strains were characterized from 107 patients, comprising 57 strains from 54 heterosexuals and 54 strains...
Surveillance and monitoring of viral pathogens circulating in humans and wildlife, together with the identification of emerging infectious diseases (EIDs), are critical for the prediction of future disease outbreaks and epidemics at an early stage. It is advisable to sample a broad range of vertebra...
Clostridium botulinum is the bacterial agent of botulism, a rare but severe neuro-paralytic disease. Because of its high impact, in Italy botulism is monitored by an ad hoc surveillance system. The National Reference Centre for Botulism, as part of this system, collects and analyzes all demographic,...
Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for ∼40% of staphylococcal infections in China. However, the molecular characterization of MSSA is not well described. In this study, 124 MSSA strains collected in 2013 from a comprehensive teaching hospital in Chongqing, Southwestern Chi...
Salmonella is an important cause of food-borne infection worldwide. Detection of outbreaks caused by Salmonella spp. relies on suitable and robust methods for genotyping. Little is known about the genetic diversity of the Salmonella enterica subspecies enterica serotype Infantis strains isolated fro...
MRSA is a therapeutic concern worldwide, and a major agent of community-acquired skin and soft tissue infections (CA-SSTIs). While the US epidemiology of MRSA in CA-SSTIs is well described and reports the high prevalence of the USA300 clone, data on the European situation are lacking. To determine t...
This study was designed to investigate environmental colonisation in Algerian hospitals by carbapenem-resistant Gram-negative bacilli (GNB), including molecular characterisation of their resistance, and to perform a comparative molecular analysis between clinical and environmental strains. GNB isola...
Equine influenza virus (EIV) is considered the most important respiratory pathogen of horses as outbreaks of the disease lead to substantial economic losses. The H3N8 EIV has caused respiratory disease in horses across the world, including South American countries. Nucleotide and deduced amino acid...
While Clostridium difficile epidemiology is well documented in many European countries, data are largely missing for South Eastern European region. Here we report the PCR ribotype distribution of 249 C. difficile isolates received for typing from six hospital settings from Croatia, Bosnia and Herzeg...
Trypanosoma vivax has been associated with asymptomatic infections in African and South American buffalo. In this study, T. vivax was analyzed in water buffalo (Bubalus bubalis) from Venezuela in a molecular survey involving 293 blood samples collected from 2006 to 2015 across the Llanos region. Res...
Pseudomonas aeruginosa (Pa) is one of the major bacterial pathogens causing nosocomial infections. During the past few decades, multidrug-resistant (MDR) and extensively drug-resistant (XDR) lineages of Pa have emerged in hospital settings with increasing numbers. However, it remains unclear which d...
The spread of resistance to carbapenems among Enterobacteriaceae has become a major public health problem in recent years. In this study, we describe an outbreak of Klebsiella pneumoniae in the neonatal ward. First, we aimed to study the drug resistance, genetic relatedness, and transmission mechani...
The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunit...
Mycoplasma bovis is the most frequent etiologic agent of bovine mycoplasmosis. It causes various diseases in bovines and considerable economic loss due to the lack of effective treatment or preventive measures such as vaccination. In contrast to the US, where M. bovis-mastitis has been reported for...
Antimicrobial-resistant Klebsiella pneumoniae (Kp) has emerged as a major global public health problem. While resistance can occur across a broad range of Kp clones, a small number have become globally distributed and commonly cause outbreaks in hospital settings. Here we describe recent comparative...
During 2010-14 surveys in the major sesame growing areas of Fars, Yazd and Isfahan provinces (Iran), genetic diversity and vector transmission of phytoplasmas associated with sesame phyllody were studied. Virtual RFLP, phylogenetic, and DNA homology analyses of partial 16S ribosomal sequences of phy...
Coagulase-negative staphylococci (CNS) represent one of the most prevalent microorganisms in nosocomial infections worldwide, nevertheless little is known about their pathogenicity features. Thus, our aim was to characterize virulence aspects of CNS isolated from patients with bloodstream infections...
Enterobacter spp. have emerged as an important group of pathogens linked to outbreaks in neonatal intensive care units (NICUs), usually involving strains expressing extended-spectrum β-lactamases (ESBLs). The aim of this study was to describe the first nosocomial bloodstream infection outbreak cause...
Recent surveys indicate that the majority of toxigenic Clostridium difficile strains isolated in European hospitals belonged to PCR-ribotypes (RTs) different from RT 027 or RT 078. Among these types, RT 018 has been reported in Italy and, more recently, in Korea and Japan. In Italy, strains RT 018 h...
A prolonged outbreak of Salmonella enterica serotype Enteritidis occurred in northern France between December 2014 and April 2015. Epidemiological investigations following the initial notification on 30 December 2014 of five cases of salmonellosis (two confirmed S. Enteritidis) in young children res...
Genomic data generated from clinical Vibrio cholerae O1 isolates collected over a five year period in an area of Kolkata, India with seasonal cholera outbreaks allowed a detailed genetic analysis of serotype switching that occurred from Ogawa to Inaba and back to Ogawa. The change from Ogawa to Inab...
Many countries worldwide have reported increasing numbers of emm89 group A Streptococcus (GAS) infections during last decade. Pathogen genetic factors linked to this increase need assessment. We investigated epidemiological characteristics of emm89 GAS bacteremic infections, including 7-day and 30-...
Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant Staphylococcus aureus (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology a...
In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we p...
While obligate primary (P-) endosymbionts usually cospeciate with their insect hosts, less is known about codiversification of secondary (S-) endosymbionts that are generally considered facultative. Typically, insects of the superfamily Psylloidea harbour one P- (Carsonella) and at least one S-endos...
Enterovirus (EV) has over 100 serotypes of species A-D, which can cause various symptoms in infants. Enterovirus encephalitis (EVE) is serve disease with high morbidity and mortality in children. To well define the epidemiology of EVE, we wanted to know more about EV and EV molecular typing by condu...
In 2015, Niger reported the largest epidemic of Neisseria meningitidis serogroup C (NmC) meningitis in sub-Saharan Africa. The NmC epidemic coincided with serogroup W (NmW) cases during the epidemic season, resulting in a total of 9,367 meningococcal cases through June 2015. To clarify the phylogene...
The molecular epidemiology of C. difficile strains causing disease in South Africa is currently unknown. Previously, multidrug resistant ribotype (RT)017 strains were those most commonly isolated from patients with diarrhoea attending Groote Schuur Hospital in Cape Town, South Africa. This larger st...
No abstract available
Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We h...
Although fosfomycin is a treatment option for infections caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, fosfomycin resistance has been documented. To our knowledge, fosfomycin resistance mechanisms in Klebsiella pneumoniae have not been systematically investigated. A to...
Further knowledge about the clinical and microbiological characteristics of prosthetic joint infections (PJIs) caused by different coagulase-negative staphylococci (CoNS) may facilitate interpretation of microbiological findings and improve treatment algorithms. Staphylococcus capitis is a CoNS with...
To estimate UK prevalence and incidence of clinically significant carbapenemase-producing Enterobacteriaceae (CPE), and to determine epidemiological characteristics, laboratory methods and infection prevention and control (IPC) measures in acute care facilities. A 6 month survey was undertaken in No...
VIRO-TypeNed is a collaborative molecular surveillance platform facilitated through a web-based database. Genetic data in combination with epidemiological, clinical and patient data are shared between clinical and public health laboratories, as part of the surveillance underpinning poliovirus eradic...
Epidemic (PA) plays an important role in cystic fibrosis (CF) lung disease. A novel strain, the 'Prairie Epidemic Strain' (PES), has been identified in up to 30% of patients in Prairie-based Canadian CF centres. To determine the incidence, prevalence and long-term clinical impact of PES infection....
The aims of this study were to characterize the molecular epidemiological profiles of CTX-M-producing uropathogenic Escherichia coli isolates from a tertiary hospital in Daejeon, Korea, and to investigate the genetic diversity and compare the prevalence of sequence types (STs) in different areas. Ex...
No abstract available
Molecular subtyping of pathogens is critical for foodborne disease outbreak detection and investigation. Many clusters initially identified by pulsed-field gel electrophoresis (PFGE) are not confirmed as point-source outbreaks. We evaluated characteristics of clusters that can help prioritize invest...
Coagulase-negative staphylococci (CoNS) have become the leading cause of bloodstream infections (BSIs) in intensive care units (ICUs), particularly in premature neonates. Vancomycin-intermediate heteroresistant CoNS (hVICoNS) have been identified as sources of BSIs worldwide, and their potential to...
The extreme variability and rapid evolution of Infectious bronchitis virus (IBV) has always represented the key challenge for its control because of the limited cross-protection among different strains. Several experimental trials have proven a broadening of the protection spectrum when animals are...
No abstract available
In summer 2013, an excess of paediatric cases of haemolytic uraemic syndrome (HUS) in a southern region of Italy prompted the investigation of a community-wide outbreak of Shiga toxin 2-producing Escherichia coli (STEC) O26:H11 infections. Case finding was based on testing patients with HUS or blood...
To investigate the population structure of Enterococcus faecium causing bloodstream infections (BSIs) in a tertiary Spanish hospital with low glycopeptide resistance, and to enhance our knowledge of the dynamics of emergence and spread of high-risk clonal complexes. All available E. faecium causing...
Management of invasive Staphylococcus aureus infections is complex. Dramatic improvements in bacterial whole genome sequencing (WGS) offer new opportunities for personalising the treatment of S. aureus infections. Areas covered: We address recent achievements in S. aureus genomics, describe genetic...
We unexpectedly identified MRSA isolates carrying mecC (mecC-MRSA) from a Danish swine farm located in eastern Zealand. The objective of the present study was to investigate the origin of these isolates and their genetic relatedness to other mecC-MRSA isolates from Zealand. WGS was used to infer the...
Staphylococcus aureus (S. aureus) has established itself over the years as a major cause of morbidity and mortality both within the community and in healthcare settings. Methicillin resistant S. aureus (MRSA) in particular has been a major cause of nosocomial infections resulting in significant incr...
To investigate the molecular epidemiology of Acinetobacter baumannii strains isolated from different hospitals in Lebanon. A total of 119 non-duplicate Acinetobacter strains were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and partial...
No abstract available
Poliomyelitis associated with circulating vaccine-derived polioviruses (cVDPVs) is a serious public health issue in the post-eradication era, and the occurrence of recombinant cVDPVs emphasizes the need to elucidate enterovirus C (EV-C) epidemiology. Stool samples were collected from 826 healthy chi...
After 20 years of successfully tracking and preventing outbreaks of foodborne diseases, PulseNet, a US surveillance program, is implementing new diagnostic technologies and expanding its international cooperation with public health agencies. [Image: see text]
Carbapenemase-producing Enterobacteriaceae are increasingly reported worldwide. The aim of the study was to determine the incidence and molecular epidemiology of carbapenemase-producing (CP) Escherichia coli and Klebsiella pneumoniae (CP-E/K) in Belgium. Eleven hospital-based laboratories collected...
Anopheles gambiae are a major vector of malaria in sub-Saharan Africa. Viruses that naturally infect these mosquitoes may impact their physiology and ability to transmit pathogens. We therefore used metagenomics sequencing to search for viruses in adult Anopheles mosquitoes collected from Liberia, S...
Tomato yellow leaf curl virus (TYLCV) seriously impacts tomato production throughout tropical and sub-tropical regions of the world. It has a broad geographical distribution and continues to spread to new regions in the Indian and Pacific Oceans including Australia, New Caledonia and Mauritius. We u...
Vancomycin-resistant Enterococcus raffinosus has rarely been associated with nosocomial infection and outbreaks. To report the successful control of a nosocomial outbreak of vanA-type vancomycin-resistant E. raffinosus in a surgical intensive care unit. The investigation of the outbreak is reported...
Most antigenically novel and evolutionarily successful strains of seasonal influenza A (H3N2) originate in East, South and Southeast Asia. To understand this pattern, we simulated the ecological and evolutionary dynamics of influenza in a host metapopulation representing the temperate north, tropics...
Multidrug-resistant bacteria are responsible for substantial morbidity and mortality worldwide. Tracking the nosocomial spread of resistant bacteria is critical to infection control. Mellmann et al. (J. Clin. Microbiol. 54:2874-2881, 2016, http://dx.doi.org/10.1128/JCM.00790-16) have described prosp...
A carriage study was undertaken (n = 112) to ascertain the prevalence of Neisseria spp. following the eighth case of invasive meningococcal disease in young children (5 to 46 months) and members of a large extended indigenous ethnic minority Traveller family (n = 123), typically associated with high...
No abstract available
Anticipating how epidemics will spread across landscapes requires understanding host dispersal events that are notoriously difficult to measure. Here, we contrast host and virus genetic signatures to resolve the spatiotemporal dynamics underlying geographic expansions of vampire bat rabies virus (VB...
Bacteria resistant to colistin, a last resort antibiotic reflect the pre-antibiotic era. In this study, colistin resistance carbapenem-resistant K. pneumoniae (COL- CRKP) strains from neonate's intensive care unit were evaluated. Molecular analysis showed that all the four colistin resistant K. pneu...
Enteroaggregative (EAEC) and Shiga-toxin producing Escherichia coli (STEC) are a major cause of diarrhea worldwide. E. coli carrying both virulence factors characteristic for EAEC and STEC and producing extended-spectrum beta-lactamase caused severe and protracted disease during an outbreak of E. co...
Clostridium difficile is recognised worldwide as the main cause of infectious bacterial antibiotic-associated diarrhoea in hospitals and other healthcare settings. The aim of this study was to first survey C. difficile prevalence during the summer of 2014 at the Central University Hospital of Asturi...
Bovine viral diarrhea virus (BVDV) type 1 in Italy is characterized by high genetic diversity, with at least 20 subtypes. Subtype 1f is endemic in a restricted geographic area, meaning that it has local distribution. We investigated the population dynamics of BVDV-1f in Northern Italy and characteri...
The incidence of Campylobacter infection in Israel, particularly among children <2 years of age, has risen over the last decade and became one of the highest among industrialized countries. This study explored the molecular epidemiology of Campylobacter jejuni in Israel over a decade (2003-2012) usi...
The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illus...
From 2012 to 2014, there has been a huge increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) in Copenhagen, Denmark, with 602 patients infected or colonized with VREfm in 2014 compared with just 22 in 2012. The objective of this study was to describe the genetic epidemiology of VREf...
Acinetobacter baumannii infection is a serious threat to burn patients. Bacteremia due to A. baumannii is becoming the most common cause of mortality following burn. However, the epidemiology of A. baumannii causing burn-related bloodstream infections has rarely been reported. We retrospectively col...
Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67 Fusarium strains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, a...
Population-based studies on Staphylococcus aureus nasal colonization are scarce. We examined the prevalence, resistance, and molecular diversity of S. aureus in the general population in Northeast Germany. Nasal swabs were obtained from 3,891 adults in the large-scale population-based Study of Healt...
Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexi...
Mycobacterium avium subsp. hominissuis (MAH) causes disease in both humans and swine; however, the genetic variations in MAH isolates are unclear. The aim of this study was to elucidate the genetic variations in MAH isolates from humans and swine in Japan. We analysed the 16S-23S rDNA internal trans...
Copy number variants (CNVs) are a class of structural variants (SVs) and are defined as fragments of DNA that are present at variable copy number in comparison with a reference genome. Recent advances in bioinformatics methodologies and sequencing technologies have enabled the high-resolution quanti...
In 2010, the 10-valent pneumococcal conjugate vaccine (PCV10) was introduced into the Brazilian childhood vaccination programme. Concerns have been raised that non-vaccine serotypes could increase in prevalence and reduce the benefits of vaccination; therefore, we examined non-PCV10 isolates recover...
Gram-negative bacilli are a cause of serious infections in the pediatric population. Carbapenem are the treatment of choice for infections caused by multidrug-resistant Gram-negative bacilli, but the emergence of carbapenem resistance has substantially reduced access to effective antimicrobial regim...
We describe the epidemiology, clinical features, and molecular characterization of enterohemorrhagic Escherichia coli (EHEC) infections caused by the singular hybrid pathotype O80:H2, and we examine the influence of antibiotics on Shiga toxin production. In France, during 2005-2014, a total of 54 pa...
Shigellae are sensitive indicator species for studying trends in the international transmission of antimicrobial-resistant Enterobacteriaceae. Orthodox Jewish communities (OJCs) are a known risk group for shigellosis; Shigella sonnei is cyclically epidemic in OJCs in Israel, and sporadic outbreaks o...
In 2014, sepsis-like illness affected 9 full-term newborns in 1 hospital in Austria. Although results of initial microbiological testing were negative, electron microscopy identified picornavirus. Archived serum samples and feces obtained after discharge were positive by PCR for human parechovirus 3...
No abstract available
The spread of carbapenem-resistant Enterobacteriaceae (CRE) represents one of the most worrisome problems for clinical medicine worldwide. In Italy, the Antibiotic-Resistance-Istituto Superiore di Sanità surveillance network, in collaboration with the Committee for Antimicrobial Agents of the Italia...
Extended-spectrum-beta-lactamase-producing and carbapenemase-producing Klebsiella pneumoniae strains have rapidly spread through clinical units worldwide. This study investigated the epidemiology and resistance profiles of K. pneumoniae strains isolated in central China between 2009 and 2014. Antimi...
Bacillus anthracis is the causative agent of anthrax, a disease endemic in regions of Northern Cape Province and Kruger National Park of South Africa. Accurate identification of virulent B. anthracis is essential but challenging due to its close relationship with other members of B. cereus group. Th...
The role of the hospital environment as a reservoir of resistant bacteria in Tunisia has been poorly investigated; however, it could be responsible for the transmission of multidrug-resistant bacteria. The objective was to study the prevalence of Enterococcus in the environment of a Tunisian hospita...
Toxigenic Corynebacterium diphtheriae is an important and potentially fatal threat to patients and public health. During the current dramatic influx of refugees into Europe, our objective was to use whole genome sequencing for the characterization of a suspected outbreak of C. diphtheriae wound infe...
The objectives of this study were to undertake the microbiological and molecular characterization of Corynebacterium diphtheriae isolates collected in Algeria during epidemic and post-epidemic periods between 1992 and 2015. Microbiological characterization includes the determination of biotype and t...
Acinetobacter baumannii has emerged as an important cause of healthcare-associated infections causing great morbidity and mortality. Despite its clinical importance, it is still unknown which molecular typing method is the best to determine or confirm institutional outbreaks as well as to identify e...
The high incidence of AIDS cases and the dominance of HIV-1 subtype C infections are two features that distinguish the HIV-1 epidemic in the two southernmost Brazilian states (Rio Grande do Sul [RS] and Santa Catarina [SC]) from the epidemic in other parts of the country. Nevertheless, previous stud...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious threat for hospitalized patients and it can survive for long periods in hospital settings, particularly on inanimate surfaces. The environment occupied by these resistant and resilient isolates may act as a reservoir for cross-coloniza...
Carbapenem-resistant Enterobacteriaceae (CRE), especially those that produce Klebsiella pneumoniae carbapenemase (KPC) and are associated with colistin resistance, pose a severe health threat due to the limited treatment options. To describe two outbreaks of KPC-producing K. pneumoniae in an adult i...
Dengue virus is circulating in Pakistan since 1994, which causes major and minor outbreaks in many areas of the country. The incidence of dengue in Pakistan in past years mainly restricted to parts of Sindh and Punjab provinces. As such, a severe dengue outbreak appeared in Pakistan in 2011, particu...
Outbreaks of Enteritidis have long been associated with contaminated poultry and eggs. In the summer of 2014 a large multi-national outbreak of Enteritidis phage type 14b occurred with over 350 cases reported in the United Kingdom, Germany, Austria, France and Luxembourg. Egg supply network invest...
Two outbreaks of gastroenteritis occurred in South Korea, affecting a middle school in the Jeollanam-do province in 2013 (Outbreak 1) and 10 schools in the Incheon province in 2014 (Outbreak 2). We investigated the outbreaks to identify the pathogen and mode of transmission. A retrospective cohort s...
While there is an abundance of data on the epidemiology and molecular typing of Staphylococcus aureus, especially those carrying Panton-Valentine leucocidin (PVL) genes or mecA from Western Europe, Northern America and Australia, comparably few studies target African strains. In this study, we chara...
Understanding the dynamics of aerial spread of Acinetobacter may provide useful information for production of effective control measurements. We investigated genetic relationships between air and clinical isolates of Acinetobacter baumannii in an intensive care unit (ICU) setting. We conducted a pro...
Between January and December 2013, swab samples were taken for the throat and external ear canals of 1037 newborns for screening of Group B Streptococcus (GBS or S. agalactiae). Isolates were analyzed form Multilocus sequence typing (MLST), capsular type, virulence genes and antibiotic susceptibilit...
Candidemia is an increasing problem in tertiary care hospitals worldwide. Here, we report the first outbreak of candidemia caused by fluconazole-resistant C. parapsilosis (FRCP) strains in Brazil. This was a cross-sectional study of clinical and microbiological data of all candidemic episodes diagno...
Carbapenemase-producing Enterobacteriaceae (CPE) may cause healthcare-associated infections with high mortality rates. New Delhi metallo-β-lactamase-1 (NDM-1) is among the most recently discovered carbapenemases. To report the first outbreak of NDM-1 CPE in Ireland, including microbiological and epi...
The relationships between plant viruses and their vectors have evolved over the millennia, and yet, studies on viruses began <150 years ago and investigations into the virus and vector interactions even more recently. The advent of next generation sequencing, including rapid genome and transcriptome...
The prevalence of carbapenem-resistant Acinetobacter baumannii in Saudi Arabia and their resistance genetic mechanisms are yet to be identified. We studied the prevalence and genetic diversity of extended-spectrum beta-lactamase genes, particularly the PER-1 gene, among carbapenem-resistant A. bauma...
Vector-borne diseases (VBDs) present a major threat to human and animal health, as well as place a substantial burden on livestock production. As a way of sustainable VBD control, focus is set on vaccine development. Advances in genomics and other "omics" over the past two decades have given rise to...
Vancomycin-resistant Enterococcus faecium (VREfm) have been increasingly reported since the 1980s. Despite the high number of published studies about VRE epidemiology, the dynamics and evolvability of these microorganisms are still not fully understood. A multilevel population genetic analysis of VR...
We analysed the microbiological traits and population structure of KPC-producing Enterobacteriaceae isolates collected in Spain between 2012 and 2014. We also performed a comparative WGS analysis of the three major KPC-producing Klebsiella pneumoniae clones detected. Carbapenemase and ESBL genes wer...
Enterococcus faecium is a major nosocomial pathogen causing significant morbidity and mortality worldwide. Assessment of E. faecium using MLST to understand the spread of this organism is an important component of hospital infection control measures. Recent studies, however, suggest that MLST might...
The ongoing Ebola virus (also known as Zaire ebolavirus, a member of the Ebolavirus family) outbreak in West Africa has so far resulted in >28000 confirmed cases compared with previous Ebolavirus outbreaks that affected a maximum of a few hundred individuals. Hence, Ebolaviruses impose a much greate...
The nontuberculous mycobacteria (NTM) are widely spread. In Brazil, 2,520 cases of rapidly growing mycobacteria (RGM) infections after medical procedures were reported, with 5.4% of cases related to nonsurgical invasive procedures and with an occurrence of 1 clone (BRA100) of Mycobacterium abscessus...
One hundred and twenty-six epidemiologically sequential, unrelated, carbapenem-resistant Acinetobacter baumannii isolates from nine hospitals in six countries of South America were collected between July 2013 and June 2014. Genes coding for Ambler class D and B carbapenemases were sought by PCR. All...
Clostridium difficile is a leading nosocomial pathogen and molecular typing is a crucial part of monitoring its occurrence and spread. Over a three-year period (2013-2015), clinical C. difficile isolates from 32 Czech hospitals were collected for molecular characterisation. Of 2201 C. difficile isol...
In 1988, the World Health Assembly resolved to eradicate poliomyelitis worldwide (1). One of the main tools used in polio eradication efforts has been the live, attenuated, oral poliovirus vaccine (OPV) (2), an inexpensive vaccine easily administered by trained volunteers. OPV might require several...
Bacterial contamination of platelet concentrates (PCs) remains a serious problem in transfusion. We have been conducting sterility tests on all PCs rejected by blood centers or hospitals due to abnormal appearances. We recently experienced a case in which discrepant results were obtained between the...
An outbreak of Serratia marcescens infections outbreak is described, as well as the epidemiological study that linked the outbreak to the use of 2% aqueous chlorhexidine antiseptic. In late November 2014 an increasing incidence of S. marcescens isolates was detected in patients treated in the emerge...
The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostic...
The aim of the study was to investigate the prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase production among clinical isolates of Enterobacteriaceae recovered from Tunisian and Libyan hospitals. Bacterial isolates were recovered from patients in intensive care units and identifi...
Within the past few years identification of bacteria by MALDI-TOF MS has become a standard technique in bacteriological laboratories for good reasons. MALDI-TOF MS identification is rapid, robust, automatable, and the per-sample costs are low. Yet, the spectra are very informative and the reliable i...
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of health care-associated infections, and the role that the hospital environment might play in the transmission cycle remains undefined. We determined the distribution of environmental MRSA isolates, studied contamination patterns...
Molecular epidemiology of 100 consecutive gonococcal isolates collected between April 2010 and October 2013 from New Delhi was investigated using Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) along with its association with antimicrobial resistance profiles. Neisseria gonorrhoeae isol...
With the advent of next-generation sequencing technology, the genotyping of clinical Mycobacterium tuberculosis strains went through a major breakup that dramatically improved the field of molecular epidemiology but also revolutionized our deep understanding of the M. tuberculosis complex evolutiona...
Objective To investigate the genotype of klebsiella pneumonia strains isolated from eldly inpatients by multiple-locus variable-number tandem-repeat analysis. Methods Totally 184 klebsiella pneumonia strains,isolated from eldly inpatients,were collected,and their genome DNA were extracted. The polym...
The incidence of MRSP has been increasing, and treatment options in veterinary medicine are limited. Few previous studies of MRSP have described the relationships between the genotypes, phenotypes, and clinical backgrounds of the isolates. To gain insight into the associations between the microbiolo...
No abstract available
Cholera is a water-borne, severe enteric infection essentially caused by toxigenic strains of Vibrio cholera O1 and O139 serogroups. An outbreak of cholera was registered during May-July 2011 in Mariupol, Ukraine, with 33 cholera cases and 25 carriers of cholera. Following this outbreak, the toxigen...
No abstract available
Knowledge of risk factors and clinical characteristics of bacteraemia caused by plasmid-mediated AmpC β-lactamase (pAmpC)-producing Klebsiella pneumoniae (pAmpC-Kp) is not well described. This was a retrospective cohort study of patients with K. pneumoniae bacteraemia in three Hong Kong regional hos...
Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central...
Mongolia has high and rising rates of multi-drug resistant tuberculosis (MDR-TB). Spatio-temporal and programmatic evidence suggests a major contribution from MDR-TB transmission, but genotypic evidence has not been assessed. All MDR-TB cases identified during 2012 were examined. Demographic and bac...
Dermatophytosis is a very common skin disorder and the most frequent infection encountered by practicing dermatologists. The identification, pathogenicity, biology, and epidemiology of dermatophytes, the causative agents of dermatophytosis, are of interest for both dermatologists and medical mycolog...
Campylobacter spp. is the most common gastrointestinal pathogen worldwide with a very low reported incidence in Italy. In November of 2013, local and national public health authorities investigated an outbreak caused by Campylobacter jejuni among children in a kindergarten in Northern Italy. A case...
Vibrio parahaemolyticus causes foodborne gastroenteritis, which is often associated with the consumption of raw or undercooked shellfish. Molecular typing can provide critical information for detecting outbreaks and for source attribution. In this study, we describe the development and evaluation of...
The first Virus Genomics and Evolution Conference was held at the Wellcome Genome Campus in Hinxton, UK, 8-10 June 2016.
The aim of the study was to investigate the resistant mechanisms and homology of imipenem-resistant Acinetobacter baumannii (A. baumannii). A total of 46 non-duplicate imipenem‑resistant A. baumannii clinical isolates were collected from three tertiary hospitals between July, 2011 and June, 2012. Th...
Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a serious hospital and community-acquired infection and some strains are associated with greater severity. We investigated the clinical variability and molecular characteristics of MRSA infections in Shenzhen, China through a study at...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of both hospital and community infections globally. It's important to illuminate the differences between community-acquired MRSA (CA-MRSA) and hospital-acquired MRSA (HA-MRSA), but there have been confusions on the definition, espec...
The rising incidence of Clostridium difficile infections (CDIs) in adults is partly related to the global spread of fluoroquinolone-resistant strains, namely, BI/NAP1/027. Although CDIs are also increasingly diagnosed in children, BI/NAP1/027 is relatively uncommon in children. Little is known about...
Carbapenemase-producing organisms have spread worldwide, and infections with these bacteria cause significant morbidity. Horizontal transfer of plasmids carrying genes that encode carbapenemases plays an important role in the spread of multidrug-resistant Gram-negative bacteria. Here we investigate...
The study of the gastric pathogen Helicobacter pylori brought us interesting data on the history of mankind. Based on multi-locus sequence typing, it was possible to trace the migration of Homo sapiens all around the world, and to infer the time when he went Out of Africa. Beside these phylogeograph...
To develop a European surveillance protocol for Clostridium difficile infection (CDI), existing national CDI surveillance systems were assessed in 2011. A web-based electronic form was provided for all national coordinators of the European CDI Surveillance Network (ECDIS-Net). Of 35 national coordin...
There are limited national epidemiological data for community-associated (CA)-Clostridium difficile infections (CDIs). Between March 2011 and March 2013, laboratories in England submitted to the Clostridium difficile Ribotyping Network (CDRN) up to 10 diarrhoeal faecal samples from successive patien...
Cholera is an infectious disease of major concern in Vietnam and other Asian countries. In 2009, there was a large outbreak of cholera in northern Vietnam. To investigate relationships among isolates of the causative pathogen Vibrio cholerae in this region since 2007, we carried out a multilocus var...
In April 2014, pulmonary Pseudomonas aeruginosa and Stenotrophomonas maltophilia co-infections potentially related to bronchoscopic procedures were identified in the intensive care units of a university hospital in Lyon, France. A retrospective cohort of 157 patients exposed to bronchoscopes from 1...
Enteropathogenic Escherichia coli (EPEC) are important agents of diarrhoea in industrialized as well as developing countries, such as Brazil. The hallmark of EPEC pathogenesis is the establishment of attaching and effacing lesions in enterocytes, in which pedestal-like structures are formed undernea...
Kenema Government Hospital (KGH) has developed an advanced clinical and laboratory research capacity to manage the threat of Lassa fever, a viral hemorrhagic fever (VHF). The 2013-2016 Ebola virus (EBOV) disease (EVD) outbreak is the first to have occurred in an area close to a facility with establi...
The opportunistic Propionibacterium acnes recovered frequently from failed endodontic treatments might be the result of nosocomial endodontic infections. The study was aimed to determine if gloves worn by dentists could be one of the sources of these nosocomial infections and to investigate the P. a...
Staphylococcus aureus remains a major cause of nosocomial infection worldwide. Characterization of S. aureus isolates circulating in the southwest of Iran will contribute to understand and control the spread of the strains in this area. spa and SCCmec typing methods were used for genotyping of 125 S...
In October and November 2010, six children and one woman were presented with symptoms of aseptic meningitis in Jena, Thuringia, Germany. Enterovirus RNA was detected in the cerebrospinal fluid of all patients by RT-PCR, and preliminary molecular typing revealed echovirus 18 (E-18) as causative agent...
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman's coalescent process enables inference of past population dynamics directly from molecular sequence data, and researcher...
In 2009, an outbreak of Vibrio parahaemolyticus occurred in Piura, Cajamarca, Lambayeque, and Lima, Peru. Whole-genome sequencing of clinical and environmental samples from the outbreak revealed a new V. parahaemolyticus clone. All the isolates identified belonged to a single clonal complex describe...
Bartonella spp. are endemic in wild rodents in many parts of the world. A study conducted in two northern California counties (Sonoma and Yolo) sampling California ground squirrels (Otospermophilus beecheyi) and four other rodent species (Peromyscus maniculatus, P. boylii, P. truei and Neotoma fusci...
No abstract available
Campylobacteriosis is one of the most important foodborne diseases worldwide and a significant health burden in New Zealand. Campylobacter jejuni is the predominant species worldwide, accounting for approximately 90% of human cases, followed by Campylobacter coli Most studies in New Zealand have foc...
We characterized two epidemiologically similar Acinetobacter baumannii clusters from two separate intensive care units (ICU) using core genome multilocus sequence typing. Clonal spread was confirmed in ICU-1 (12 of 14 isolates shared genotypes); in ICU-2, all genotypes (13 isolates) were diverse, th...
Vancomycin-resistant enterococci are among the major causes of nosocomial infections and represent a growing problem in many European countries. Among the most common enterococcal isolates, Enterococcus faecium is considered to be the reservoir of VanA and VanB-mediated resistance to glycopeptides....
Gonorrhea is a sexually transmitted disease causing growing concern, with a substantial increase in reported incidence over the past few years in the United Kingdom and rising levels of resistance to a wide range of antibiotics. Understanding its epidemiology is therefore of major biomedical importa...
Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is...
Tuberculosis (TB) has had a recrudescence in the last few decades in Italy as a result of many factors, among which migration from countries where TB is endemic is one of them. In Sardinia, a major island of Italy, there was no knowledge of the mechanisms of transmission of TB in the immigrant subpo...
Staphylococcus aureus is a well-known organism which is responsible for a variety of human infectious diseases including skin infections, pneumonia, bacteremia, and endocarditis. Few of the microorganisms can be transmitted from mother to the newborn or infant by milk breastfeeding. This study aims...
The early detection of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak is decisive to control its spread and rapidly initiate adequate infection control measures. Therefore, prompt determination of epidemiologic relatedness of clinical MRSA isolates is essential. Genetic typing methods...
Acinetobacter baumannii is regarded as one of the most important pathogens in hospital outbreaks. To obtain an efficient and simple epidemiologic method of surveillance during outbreaks, we assessed the applicability of the polymerase chain reaction-based open reading frames typing (POT) method and...
Clostridium difficile is the most common infectious etiology of nosocomial diarrhea. Fecal calprotectin (fc) is a sensitive marker of intestinal inflammation, found to be associated with enteric bacterial infections and inflammatory bowel disease. We evaluated fc levels using a Chemiluminescent immu...
Global dissemination of KPC-type carbapenemases is mainly associated with the spread of high-risk clones of Klebsiella pneumoniae and of KPC-encoding plasmids. In this study, we explored the population structure of KPC-encoding plasmids from the recent epidemics of KPC-producing K. pneumoniae (KPC-K...
We report complete genome sequences of four blaNDM-1-harboring Gram-negative multidrug-resistant (MDR) isolates from Colombia. The blaNDM-1 genes were located on 193-kb Inc FIA, 178-kb Inc A/C2, and 47-kb (unknown Inc type) plasmids. Multilocus sequence typing (MLST) revealed that these isolates bel...
We characterized extended-spectrum beta-lactamases (ESBLs) and plasmid-mediated quinolone resistance (PMQR) in 32 Escherichia coli extended spectrum cephalosporin (ESC)-resistant clinical isolates from UK companion animals from several clinics. In addition, to investigate the possible dissemination...
Macroautophagy/autophagy plays an important role against pathogen infection in mammals and plants. However, little has been known about the role of autophagy in the interactions of insect vectors with the plant viruses, which they transmit. Begomoviruses are a group of single-stranded DNA viruses an...
Extended-Spectrum Beta-Lactamases (ESBL)-producing Escherichia coli have disseminated in both humans and animals worldwide. However, the ESBL epidemiology in these two reservoirs differs markedly, with CTX-M-15 frequently found in humans and CTX-M-1 preferentially found in animals. Our goal was to e...
The aetiology and epidemiology of outbreaks of clinical mastitis in sheep under extensive pastoral conditions are incompletely understood. The objective of this study was to conduct a detailed investigation of a clinical mastitis outbreak that affected more than 10% of 230 at-risk ewes on a sheep an...
New Delhi metallo-β-lactamase (bla NDM), a plasmid-borne carbapenemase gene associated with significant mortality and severely limited treatment options, is of global public health concern as it is found in extremely diverse Gram-negative bacterial strains. This study thus aims to genetically charac...
Escherichia coli O26 is the second most important enterohemorrhagic E. coli (EHEC) serogroup worldwide. Serogroup O26 strains are categorized mainly into two groups: enteropathogenic (EPEC) O26, carrying a locus of enterocyte effacement (LEE) and mostly causing mild diarrhea, and Shiga-toxigenic (ST...
Diphtheria is a debilitating disease caused by toxigenic Corynebacterium diphtheriae strains and has been effectively controlled by the toxoid vaccine, yet several recent outbreaks have been reported across the globe. Moreover, non-toxigenic C. diphtheriae strains are emerging as a major global heal...
Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current "gold standard" typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila However, as common sequence types (STs) cause many infections, some investigations remain unresolved...
The limited influenza A(H3N2) genetic data available from the Southern Hemisphere (particularly from Africa and Latin America), constrains the accurate reconstruction of viral dissemination dynamics within those regions. Our objective was to describe the spatial dissemination dynamics of influenza A...
Shigella sonnei is an important causative agent of bacillary dysentery worldwide that has recently emerged in developing countries. However, there are few studies that have characterized strains ofS. sonnei isolated in Brazil. The aims of this study were to assess the presence of 12 virulence genes,...
Epidemic clones of Acinetobacter baumannii, described as European clones I, II, and III, are associated with hospital epidemics throughout the world. We aimed to determine the molecular characteristics and genetic diversity between European clones I, II, and III from Turkey and Azerbaijan. In this s...
No abstract available
Temporal variabilities in the genetic patterns and antibiotic resistance profiles of enterococci were monitored over a 7-month period. Enterococcus faecalis isolates (103 strains) collected from feces showed only one genetic pattern and antibiotic resistance profile within 0 d and 30 d. In contrast,...
No abstract available
Roseomonas spp. are increasingly involved in human infectious diseases. The environmental source for infection is generally admitted in published cases owing to the origin of most Roseomonas species and to their affiliation to the family Acetobacteraceae in Rhodospirillales, which mainly groups envi...
A data analysis of yeast collections from the National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) programme in 2013 revealed a sudden increase in the proportion of Candida parapsilosis complex isolates (n = 98) in one participating hospital (Hospital H). Out of 443 yeast isolates sub...
Human immunodeficiency virus type 1 (HIV-1) was discovered in the early 1980s when the virus had already established a pandemic. For at least three decades the epidemic in the Western World has been dominated by subtype B infections, as part of a sub-epidemic that traveled from Africa through Haiti...
Methicillin resistant Staphylococcus aureus is one of the most common causes of a variety of infections ranging from wound infections to urinary tract infections (UTI) in hospital and community. In this study during 3 years we characterized the antibiotic resistance patterns of 491 hospital acquired...
Carbapenems are considered the last-resort antibiotics to treat infections caused by multidrug-resistant Gram-negative bacilli. The Klebsiella pneumoniae carbapenemase (KPC) enzyme hydrolyses β-lactam antibiotics including the carbapenems. KPC has been detected worldwide in Enterobacteriaceae and Ps...
In July 2002, an outbreak of cholera occurred in north India with two separate geographical foci. Pulsed field gel electrophoresis (PFGE) was previously used in typing a representative sample of these isolates. This study evaluates the usefulness of MALDI-TOF as an epidemiological tool for typing Vi...
The aim of this study was to assess the genetic diversity of Vibrio cholerae isolated from 2012 and 2013 outbreaks in Iran, with regard to their virulence properties. A total of 20 V. cholerae strains were collected from Sistan-Baluchestan province of Iran during 2012 and 2013 outbreaks. Hybridizati...
Population genomics, an interdiscipline of genomics and population genetics, is booming in recent years with the rapid growth number of deciphered genomes and revolutionizes the understanding of bacterial population diversity and evolution dynamics. It also largely improves the prevention and contro...
Staphylococcus epidermidis is one of the major concerns with respect to hospital-acquired infections. Therefore, a rapid and easy method to identify at species level S. epidermidis isolates out of a broad range of bacteria is necessary. Based on earlier studies, the sesC gene encoding a S. epidermid...
We report an updated method for inferring the time at which an infectious disease was transmitted between persons from a time-labelled pathogen genome phylogeny. We applied the method to 48 genomes as part of a real-time public health outbreak investigation, demonstrating that although active tuber...
USA300 represents the dominant community-associated methicillin-resistant lineage in the USA, where it is a major cause of skin and soft tissue infections. Previous comparative genomic studies have described the population structure and evolution of USA300 based on geographically restricted isolate...
A total of 30 Legionella pneumophila serogroup 1 isolates representing 10 separate legionellosis laboratory investigations ("outbreaks") that occurred in New York State between 2004 and 2012 were selected for evaluation of whole-genome sequencing (WGS) approaches for molecular subtyping of this orga...
Staphylococcus aureus by producing biofilm and facilitating chronic infection is a common cause of mastitis in cows and thereby can cause food poisoning by production of enterotoxins in milk. The agr typing method is an important tool for epidemiological investigation about S. aureus. The aims of th...
Vancomycin-resistant enterococci (VRE) are a major cause of nosocomial infections with high mortality and morbidity. There is limited data on the molecular characterization of VRE in Saudi Arabia. This study was carried out to investigate the premise that a shift in VRE epidemiology is occurring in...
Cholera remains to be an international threat, with high rates of illness and death. In 2012 and 2013, two cholera outbreak happened in Iran, affecting lots of people. Vibrio cholerae O1 was confirmed as the etiological agent. Source identification and controlling the spread of the cholera disease a...
Coxsackievirus B3 (CV-B3) has frequently been associated with aseptic meningitis outbreaks in China. To identify sequence motifs related to aseptic meningitis and to construct an infectious clone, the genome sequence of 08TC170, a representative strain isolated from cerebrospinal fluid (CSF) samples...
We aim to study the disease burden, risk factors and severity of Clostridium difficile infection (CDI) in Hong Kong. We conducted a prospective, case-control study in three acute-care hospitals in Hong Kong. Adult inpatients who developed CDI diarrhoea confirmed by PCR (n = 139) were compared with t...
Ghana is affected by regular cholera epidemics and an annual average of 3,066 cases since 2000. In 2014, Ghana experienced one of its largest cholera outbreaks within a decade with more than 20,000 notified infections. In order to attribute this rise in cases to a newly emerging strain or to multipl...
Vibrio cholerae O1 biotype El Tor, the causative agent of the seventh pandemic, has recently been replaced by strains carrying classical and Haitian ctxB in India, Haiti and other parts of the world. We conducted phenotypic and genetic tests to characterize V. cholerae O1 isolated between 2012 and 2...
Pseudomonas aeruginosa is a leading cause of healthcare-associated infections in the intensive care unit (ICU). To investigate an unexplained increase in the incidence of P. aeruginosa recovered from clinical samples in the ICU over a two-year period. After unsuccessful epidemiological investigation...
The rapid spread of Clostridium difficile NAP1/BI/027 (C. difficile 027) has become one of the leading threats of healthcare-associated infections worldwide. However, C. difficile 027 infections have been rarely reported in Asia, particularly in China. In this study, we identified a rare C. difficil...
Coxiella burnetii, the causative agent of Q fever, was first discovered in Australia in 1937. However, little is known about the strains of C. burnetii present in this country. In this study, six published genotyping methods were applied to 42 isolates from Australian patients with acute (n=39) and...
Staphylococcus lugdunensis is a major cause of aggressive endocarditis, but it is also responsible for a broad spectrum of infections. The differences in clinical and molecular characteristics between community-associated (CA) and health care-associated (HA) S. lugdunensis infections have remained u...
This is the first report to show an insidious outbreak of armA- and blaOXA-72-carrying Acinetobacter baumannii sequence type 512 (ST512) at a study hospital in northern Taiwan. Multilocus sequence typing revealed that this was a ST512 clone. All of the isolates with ST512 carried a novel 12,056-bp r...
To describe a spatio-temporal cluster of invasive meningococcal disease (IMD) due to serogroup C meningococci, occurred in a restricted area of Tuscany between January and October 2015, and the results of whole genome sequencing (WGS). Surveillance activities and public health measures were implemen...
The multidrug-resistant sequence type 131 (ST131) Escherichia coli is a spreading epidemiological burden particularly among isolates resistant to fluoroquinolones. We aimed to evaluate the commonality of ST131-O25b and ST131-O16 among fluoroquinolone-resistant E. coli isolates causing community-acqu...
Dengue is hyperendemic in Indonesia. In 2015, reported cases of dengue fever doubled those of 2014 in the Jambi municipality of Sumatra. We examined viral aetiology and its relationship with disease outcome in Jambi. Dengue-suspected patients' sera were collected and NS1 detection and IgM/IgG serolo...
The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are a therapy of last resort against this family of common bacterial pathogens. Resistance genes can mobilize via various mechanisms, including conjugation and transpositio...
The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput g...
Extensively drug-resistant Acinetobacter baumannii (XDRAB) is a great threat in intensive care units (ICUs). The aim of this study was to describe an XDRAB outbreak which was cross-transmitted in the ICU and respiratory intensive care unit (RICU) in a tertiary care hospital from January-March 2013....
For a better understanding of the multidrug resistant Pseudomonas aeruginosa (MDR-PA) epidemiology in mainland China, a nationwide surveillance network of 27 tertiary hospitals was established. Non-duplicate MDR-PA isolates from 254 cases of nosocomial infections, were collected during the period Au...
To compare the discriminatory power of pulsed-field gel electrophoresis (PFGE) and sequence-based typing (SBT) in Legionella outbreaks for determining the infection source. Twenty-five investigations of Legionnaires' disease were analyzed by PFGE, SBT and Dresden monoclonal antibody. The results sug...
Epidemic keratoconjunctivitis (EKC) is a highly contagious infectious disease of the ocular surface and is caused mainly due to adenoviruses species D, B, and E. The present study was carried out to identify and characterize the viral etiological agents associated with the keratoconjunctivitis cases...
Dengue virus type 1 (DENV-1) was the first serotype introduced in Brazil, during in the 1980s. Since then, this virus has spread in the Brazilian territory, causing several outbreaks. In 2013 the highest number of dengue cases was notified, when compared to the previous years in Brazil, and the stat...
Most Escherichia coli strains are nonpathogenic. However, for clinical diagnosis and food safety analysis, current identification methods for pathogenic E. coli either are time-consuming and/or provide limited information. Here, we utilized a custom DNA microarray with informative genetic features e...
In the summer of 2010, Vibrio parahaemolyticus caused an outbreak in Maryland linked to the consumption of oysters. Strains isolated from both stool and oyster samples were indistinguishable by pulsed-field gel electrophoresis (PFGE). However, the oysters contained other potentially pathogenic V. pa...
Pseudomonas aeruginosa is an important nosocomial pathogen, colonizing hospital water supplies including taps and sinks. We report a cluster of P. aeruginosa acquisitions during a period of five months from tap water to patients occupying the same burns single room in a critical care unit. Pseudomon...
Aim of this study was to determine the incidence and molecular epidemiology of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in Germany. E. coli and K. pneumoniae isolates from clinical samples which were non-susceptible to carbapenems were collected in laboratories serving 20 h...
Identifying Bacillus cereus as the causative agent of a foodborne outbreak still poses a challenge. We report on the epidemiological and microbiological investigation of three outbreaks of food poisoning (A, B, and C) in Austria in 2013. A total of 44% among 32 hotel guests (A), 22% among 63 employe...
Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by exchange of resistance genes between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public hea...
Multidrug-resistant Escherichia coli encoding CTX-M-type extended-spectrum β-lactamases (ESBLs) are isolated in increasing numbers from humans, companion animals and livestock, raising concern regarding the exchange and spread of isolates in these populations. In this study, whole-genome sequencing...
Clostridium difficile is the major causative agent of nosocomial antibiotic-associated diarrhea. In a 2009 outbreak of C. difficile-associated diarrhea that was recorded in a major Costa Rican hospital, the hypervirulent NAP1 strain (45%) predominated together with a local genotype variant (NAPCR1,...
Compared to classical epidemiologic methods, genomics can be used to precisely monitor virus evolution and transmission in real time across large, diverse populations. Integration of pathogen genomics with data about host genetics and global transcriptional responses to infection allows for comprehe...
Aspiration pneumonia has been a growing interest in an aging population. Anaerobes are important pathogens, however, the etiology of aspiration pneumonia is not fully understood. In addition, the relationship between the patient clinical characteristics and the causative pathogens in pneumonia patie...
Domestic animals and animal products are the source of pathogenic Campylobacter jejuni and C. coli in industrialized countries, yet little is known about the transmission of these bacteria in developing countries. Guinea pigs (Cavia porcellus) are commonly raised for food in the Andean region of Sou...
Herein, we report a case of fatal melioidosis in a newborn. The newborn died of serious melioidosis with respiratory and multiorgan failure at 16 days of age despite extensive treatment with antibiotics and methylprednisolone. Burkholderia pseudomallei was isolated from the infant's blood and cerebr...
In Europe, the Ixodes ricinus tick is the most important vector of the etiological agents of Lyme borreliosis and several other emerging tick-borne diseases. Because tick-borne pathogens are dependent on their vectors for transmission, understanding the vector population structure is crucial to info...
No abstract available
Almost 20 % of all infectious human diseases are vector borne and, together, are responsible for over one million deaths per annum. Over the past decade, the decreasing costs of massively parallel sequencing technologies have facilitated the agnostic interrogation of insect vector genomes, giving me...
Escherichia coli is the most common agent of bacteraemia, bacterial gastroenteritis and urinary tract infections (UTIs). Lineages causing UTIs and gastrointestinal disease are well defined, but less is known about those causing bacteraemia. We therefore investigated the population structure of E. co...
A multischool outbreak of salmonellosis caused by Salmonella enterica serovar Napoli was investigated in the province of Milan from October to November 2014, following an increase in school absenteeism coinciding with two positive cases. Epidemiological studies detected 47 cases in four primary scho...
In 2013 in Myanmar, dengue epidemic occurred with 20,255 cases including 84 deaths. This study aimed to determine the serological and molecular characteristics of dengue virus (DENV) infection among children with clinical diagnosis of dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS) dur...
Epidemic Escherichia coli clones have been recovered in marine sediment along the coast of Marche, an Adriatic region in central Italy. In the present study, E. coli strains from the clam Chamelea gallina, sampled from seven natural beds in the same area, were detected. Selected E. coli isolates fro...
Antibiotic resistant strains of Acinetobacter baumannii have been responsible for an increasing number of nosocomial infections including bacteremia and ventilator-associated pneumonia. In this study, we analyzed 38 isolates of A. baumannii obtained from two hospital outbreaks in Los Angeles County...
The objective of this study was to analyse the microbiological traits and the population structure of carbapenemase-producing (CP) Escherichia coli isolates collected in Spain between 2012 and 2014. Two-hundred-and-thirty-nine E. coli isolates non-susceptible to carbapenems were studied. The carbape...
The objective of this survey was to determine the incidence of Clostridium difficile infections (CDI) at the Department of Infectious Diseases, Bulovka Hospital, and to evaluate clinical and epidemiological data on CDI patients together with a detailed molecular characterisation of C. difficile isol...
Human respiratory syncytial virus (HRSV) is the main viral cause of acute lower respiratory tract infections (LRTI) in children worldwide. In recent years, several preclinical trials with vaccine candidates have been reported. It is in this sense that molecular epidemiological studies become importa...
Onychomycosis refers to fungal infection of the nail and is commonly caused by dermatophytes, while yeasts and non-dermatophytic molds (NDM) are increasingly recognized as pathogens in nail infections. The present study was done to delineate molecular epidemiology of Fusarium onychomycosis in India....
To study the genotype and genomic and molecular organization of a GI norovirus isolate from Huzhou, China, the genomic sequence of 2008/Huzhou/N11 was amplified by RT-PCR, then the PCR product was purified,sequenced, and input into phylogenetic and Simplot analyses. The complete genomic sequence of...
Nontypeable Haemophilus influenzae is a particularly important cause of acute otitis media (AOM). There is a high prevalence of β-lactamase-nonproducing ampicillin-resistant (BLNAR) strains in Japanese children, which is associated with recurrent AOM and prolonged treatment. The aim of this study wa...
Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the...
In the first seven weeks of 2016, five serotype 1/2a Listeria monocytogenes isolates were collected from patients with invasive listeriosis in Ancona province in Italy. These strains and six 1/2a isolates identified in 2015 in the same area were typed by ERIC-PCR and PFGE. A clonal relationship, doc...
No abstract available
Any microorganism is capable of causing urinary tract infections (UTI). However, Uropathogenic Escherichia coli (UPEC) is responsible for the majority of UTI. A variety of virulence genes have been identified in UPEC. Diverse epidemiological studies support that specific subsets of genes are charact...
Listeria monocytogenes is an important foodborne pathogen commonly isolated from food processing environments and food products. This organism can multiply at refrigeration temperatures, form biofilms on different materials and under various conditions, resist a range of environmental stresses, and...
A total of 72 consecutive and nonduplicate clinical extended-spectrum β-lactamase (ESBL)-producing Enterobacter cloacae isolates were collected from our hospital from 2012 to 2014 for analyzing the prevalence of plasmid-mediated quinolone resistance (PMQR) genes, 16S rRNA methyltransferase (16S-RMTa...
We conducted a surveillance study to investigate the epidemiology of Staphylococcus aureus infections in Iowa, using a convenience sample. Diagnostic laboratories submitted 20 S. aureus isolates per month for a 20-month period between 2011 and 2013. Of the 2226 isolates analyzed, 73.6% were methicil...
China is one of ten countries with the highest prevalence rate of pneumococcal infections. However, there is limited serotype surveillance data for Streptococcus pneumoniae, especially from the community or rural regions, partly due to limited serotyping capacity because Quellung serotyping is only...
Escherichia coli ST131 is the most frequently isolated fluoroquinolone-resistant (FQR) E. coli clone worldwide and a major cause of urinary tract and bloodstream infections. Although originally identified through its association with the CTX-M-15 extended-spectrum β-lactamase resistance gene, global...
This study investigated the clinical epidemiology and resistance mechanisms of Acinetobacter baumannii and characterised the clonal diversity of carbapenem-resistant A. baumannii (CRAB) during an ICU-associated outbreak at Cayenne Hospital, French Guiana. All non-duplicate A. baumannii isolates from...
Methicillin-resistant Staphylococcus aureus (MRSA) infections cause significant morbidity and mortality in neonatal intensive care units (NICUs). We characterized the clinical and molecular epidemiology of MRSA strains colonizing NICU patients. Nasal MRSA isolates (n = 250, from 96 NICU patients) re...
A collection of 163 Acinetobacter baumannii isolates detected in a large Brazilian hospital, was potentially related with the dissemination of four clonal complexes (CC): 113/79, 103/15, 109/1 and 110/25, defined by University of Oxford/Institut Pasteur multilocus sequence typing (MLST) schemes. The...
In this study we used typing based on the eight multilocus sequence typing scheme housekeeping genes (MLST) and 5S-23S rDNA intergenic spacer (IGS) to explore the population structure of Borrelia burgdorferi sensu lato isolates from patients with Lyme borreliosis (LB) and to test the association bet...
Zika virus (ZIKV), first isolated in Uganda in 1947, is currently spreading rapidly through South America and the Caribbean. In Brazil, infection has been linked with microcephaly and other serious complications, leading to declaration of a public health emergency of international concern; however,...
Since the first description of Porcine circovirus type 2 (PCV2), four genotypes (PCV2a, PCV2b, PCV2c and PCV2d) have been recognized and three of them have been shown to exhibit worldwide distribution. Here, the population dynamics of PCV2 has been reconstructed over time and the factors that have s...
The incidence of syphilis in the Tuva Republic (geographical centre of Asia), Russia has been exceedingly high historically. No detailed examinations and no molecular investigations of Treponema pallidum strains transmitted in the Tuva Republic, or in general, in Russia, were published international...
We investigated the molecular epidemiology and microbiological characteristics of 51 Escherichia coli isolates causing hospital-acquired pneumonia (HAP) in eight Asian areas. Sequence type 131 (ST131) was the most prevalent among E. coli isolates causing HAP, especially in South Korea, Thailand, and...
Acinetobacter baumannii has been prevalent in nosocomial infections, often causing outbreaks in intensive care units. ISAba1 is an insertion sequence that has been identified only in A. baumannii and its copy number varies among strains. It has been reported that ISAba1 provides a promoter for bla(O...
Emergence of carbapenem-resistant Acinetobacter spp., especially Acinetobacter baumannii, in hospitals has been increasingly detected worldwide. In the present study, we analyzed carbapenem-resistant isolates (70 A. baumannii and one Acinetobacter pittii) collected in a period of 4 years (February 2...
A high proportion of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli are of the ST131 lineage, but there are few estimates of ST131 prevalence among ESBL-negative E. coli. Without this information, it is difficult to evaluate the contribution of the ST131 lineage to the emergence...
The H6N1 avian influenza virus has circulated in Taiwan for more than 40 years. The sporadic activity of low pathogenic H5N2 virus has been noted since 2003, and highly pathogenic H5N2 avian influenza virus has been detected since 2008. Ressortant viruses between H6N1 and H5N2 viruses have become es...
Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resol...
To determine the source and extent of a locally acquired hepatitis E virus (HEV) infection outbreak. A cluster of notified cases of HEV infection linked to a single restaurant (X) was identified in May 2014. People with laboratory-confirmed HEV infection in New South Wales between January 2013 and D...
Meticillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of hospital-associated infections. This study investigated the potential use of whole-genome sequencing (WGS) for surveillance purposes by re-examining MRSA strains related to past outbreaks among hospitalized paediatric...
Acinetobacter calcoaceticus-A. baumannii complex (ACB complex) is a nosocomial pathogen. Due to its high ability to develop antibiotic resistance, it has become a problematic challenge in the modern healthcare system. The molecular and genetic mechanisms of gaining multidrug resistance in ACB comple...
Foot-and-mouth disease (FMD) is a highly transmissible disease of hooved livestock. Although FMD has been eradicated from many countries, economic and social consequences of FMD reintroductions are devastating. After achieving disease eradication, Argentina was affected by a major epidemic in 2000-2...
A comprehensive monitoring strategy is vital for tracking the spread of mosquito-borne Japanese encephalitis virus (JEV), the leading cause of viral encephalitis in Asia. Virus detection consists of passive surveillance of primarily humans and swine, and/or active surveillance in mosquitoes, which m...
When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing t...
Clostridium difficile-isolates associated with CDI in different healthcare facilities in Hesse were analysed. The most common ribotypes were 001 (31.1%) and 027 (27.0%). The proportion of ribotype 027 among regional C. difficile-isolates was 10.8% in North Hesse, 17.2% in Middle Hesse, and 33.5% in...
Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study...
HIV-1 circulating recombinant forms (CRFs) represent viral recombinant lineages that play a significant role in the global epidemic. Two of them dominate the epidemic in Burkina Faso: CRF06_cpx (first described in this country) and CRF02_AG. We reconstructed the phylodynamics of both recombinant vir...
Legionella pneumophila is the leading cause of Legionnaires' disease, a severe pneumonia that can occur as sporadic cases or point-source outbreaks affecting multiple patients. The infection is acquired by inhalation of aerosols from contaminated water systems. In order to identify the probable sour...
Methicillin-resistant Staphylococcus aureus (MRSA) carrying SCCmec type IV has emerged in hospitals worldwide. The aim of this study was to evaluate phenotypic and molecular characteristics of antimicrobial resistance in MRSA SCCmec IV isolates, presenting different genetic backgrounds, isolated fro...
Different reports of Pneumocystis jirovecii pneumonia (PcP) outbreaks on oncology and transplant units suggest the possibility of a person-to-person transmission. Based on these reports, we searched retrospectively for possible PcP clusters in UZ Leuven in 2013. A movement and transmission map was e...
The species Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis are the causal agents, respectively, of tuberculosis and paratuberculosis in animals. Both mycobacteria, especially M. bovis, are also important to public health because they can infect humans. In recent years, this...
INTRODUCTION Characterization of Mycobacterium tuberculosis (MTB) isolates by DNA fingerprinting has contributed to tuberculosis (TB) control. The aim of this study was to determine the genetic diversity of MTB isolates from Tehran province in Iran. METHODS MTB isolates from 60 Iranian and 10 Afghan...
To detect and analyze the distribution of virulence factors, antimicrobial resistance and pulsed field gel electrophoresis (PFGE) patterns of Shigella sonnei, isolated in Henan province from 2011 to 2014. Samples of diarrhea patients were collected and isolated with SS selective culture medium in 37...
Denmark has a high incidence of invasive listeriosis (0.9 cases/100,000 population in 2012). We analyzed patient data, clinical outcome, and trends in pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) of Listeria monocytogenes strains isolated in Denmark during 2002-2012....
Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success. To determine microevolution associated with monophasic Salmonella Typhimurium during an epidemic, we performed comparative whole-genome sequencing and phylogen...
The hyper-virulent emm59 genotype of invasive group A Streptococcus was identified in northern Arizona in 2015. Eighteen isolates belonging to a genomic cluster grouped most closely with recently identified isolates in New Mexico. The continued transmission of emm59 in the southwestern United States...
We evaluated clinical Shiga toxin-producing Escherichia coli O157 infections in England and Wales during 1983-2012 to describe changes in microbiological and surveillance methods. A strain replacement event was captured; phage type (PT) 2 decreased to account for just 3% of cases by 2012, whereas PT...
Foot and mouth disease virus (FMDV) is an animal pathogen of global economic significance. Identifying the sources of outbreaks plays an important role in disease control; however, this can be confounded by the ease with which FMDV can spread via movement of infected livestock and animal products, a...
Small colony variants (SCVs) were first described more than 100 years ago for Staphylococcus aureus and various coagulase-negative staphylococci. Two decades ago, an association between chronic staphylococcal infections and the presence of SCVs was observed. Since then, many clinical studies and obs...
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited,...
We sought to determine the epidemiology of carbapenem-resistant Enterobacteriaceae and to investigate the emergence of carbapenem-resistant Klebsiella pneumoniae in two teaching hospitals in Manila, Philippines. We screened 364 Enterobacteriaceae for carbapenem resistance between 2012 and 2013 and d...
Dengue virus infection is a major cause of morbidity within the endemic tropical and subtropical regions of the world. Dengue virus has four distinct serotypes with specific clinical manifestations. In this study, we observed the changing pattern of dengue serotypes, age-wise dengue infection and us...
No abstract available
Over an approximately 50-day period in 2015, an outbreak of CTX-M-15 extended spectrum β-lactamase-(ESBL)-possessing Salmonella Isangi occurred among 19 adult surgical patients and one healthcare worker (HCW) at a large urban tertiary care hospital in the United States. A total of 45 S. Isangi isola...
Sequence type 72 meticillin-resistant Staphylococcus aureus (ST72 MRSA) was recently detected in our hospital. Although in Europe this clone is rarely isolated, it is the leading cause of community-associated MRSA infections in Korea, spreading also into hospitals, where it has also emerged as the m...
The population structure of 71 carbapenem-resistantAcinetobacter baumanniiclinical isolates from several hospitals in Brazil was investigated by ApaI pulsed-field gel electrophoresis,blaOXA-51-like subtyping, and multilocus sequence typing (Institute Pasteur scheme). In addition to the predominance...
Swine pseudorabies (PR) re-emerged in Bartha-vaccinated pig herds and caused death of millions of piglets in China since the later part of 2011. We isolated a novel pseudorabies virus (PRV), named HNX strain, from the brain of abortion fetuses to diagnose the disease. To reveal the genomic organizat...
Stenotrophomonas maltophilia is an emerging nosocomial pathogen responsible for several infections in immunocompromised patients. To characterize the antimicrobial resistance and virulence potential of this microorganism in a Brazilian hospital, a total of 936 samples were collected from a nosocomia...
In addition to intrinsic resistance in Acinetobacter baumannii, many different types of acquired resistance mechanisms have been reported, including the presence of VIM and IMP metallo β-lactamases and also of bla and bla enzymes. In the Kurdistan region of Iraq, the multiresistant A. baumannii-calc...
Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with...
Earthworms carry species-specific Verminephrobacter symbionts in their nephridia (excretory organs). The symbionts are vertically transmitted via the cocoon, can only colonize the host during early embryonic development, and have co-speciated with their host for about 100 million years. Although sev...
Currently, Mycobacterium tuberculosis isolates of Latin-American Mediterranean (LAM) family may be detected far beyond the geographic areas that coined its name 15years ago. Here, we established the framework phylogeny of this geographically intriguing and pathobiologically important mycobacterial l...
Streptococcus dysgalactiae subsp. equisimilis (SDSE) isolates with β-hemolysis and carbohydrate groups G or C are increasingly recovered from invasive infections in Japan. The aim of this study was to determine the epidemiological characteristics of SDSE isolates circulating locally among patients w...
This study describes the dissemination of a carbapenem-resistant Acinetobacter baumannii (CRAB) strain in a university hospital in Northeast Italy. Characterization of the outbreak strain was combined with a retrospective analysis of all CRAB isolates collected in the same hospital during the 5 year...
Characterisation of human-associated viral communities is essential for epidemiological surveillance and to be able to anticipate new potential threats for blood transfusion safety. In high-resource countries, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV)...
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most important pathogens in the hospital environment. Monitoring of this pathogen by molecular characterization and phenotypic methods is important for the development of suitable infection control measures and proper therapy design. I...
The aim of the study was to investigate the molecular epidemiology of Staphylococcus epidermidis in Iranian hospitals and to compare the genotypes with a previously characterized collection of >1,300 S. epidermidis isolates of nosocomial and community origin from Northern Europe, Australia, and USA....
Many giant dsDNA algal viruses share a common ancestor with Mimivirus--one of the largest viruses, in terms of genetic content. Together, these viruses form the proposed 'Megaviridae' clade of nucleocytoplasmic large DNA viruses. To gauge Megaviridae diversity, we designed degenerate primers targeti...
Globally, there are an estimated 22 million cases of Salmonella enterica serovar Typhi infection each year. However, this figure is likely to be an underestimate due to the low sensitivity of blood culture in S. Typhi diagnosis. The aim of this study was to diagnose S. Typhi by conventional polymera...
Aedes aegypti (Diptera: Culicidae) (L.), Ae. albopictus (Skuse), and Ae. scutellaris (Walker) are important mosquito vectors of dengue and chikungunya viruses. They are morphologically similar and sympatric in some parts of their distribution; therefore, there is a risk of incorrect morphological id...
In The Netherlands, efforts to control meticillin-resistant Staphylococcus aureus (MRSA) in hospitals have been largely successful due to stringent screening of patients on admission and isolation of those that fall into defined risk categories. However, Dutch hospitals are not free of MRSA, and a c...
Banana genomes harbour numerous copies of viral sequences derived from banana streak viruses (BSVs) - dsDNA viruses belonging to the family Caulimoviridae.These viral integrants (eBSVs) are mostly defective, probably as a result of 'pseudogenization' driven by host genome evolution. However, some ca...
Methicillin-resistant Staphylococcus aureus (MRSA) is a public health problem worldwide. The aim of the present study was to investigate the molecular epidemiology and antimicrobial susceptibilities of MRSA strains in Stockholm, Sweden in 2014. Pulsed-field gel electrophoresis (PFGE) was used to cha...
We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical carbapenem-resistant Klebsiella pneumoniae strains (TGH1-TGH12). All strains were screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII) (OpGen, USA). WGS (Illumina) was performed on TGH8 and...
A hospitalized 73-year-old woman was infected with a Proteus mirabilis strain, 12 B-r, isolated from the place of injection of a blood catheter. Another strain, 12 B-k, recognized as Proteus genomospecies 5 or 6, was isolated from the patient's faeces, which was an example of a nosocomial infection...
The origin and population structure of Borrelia burgdorferi sensu stricto (s.s.), the agent of Lyme disease, remain obscure. This tick-transmitted bacterial species occurs in both North America and Europe. We sequenced 17 European isolates (representing the most frequently found sequence types in Eu...
Bovine coronaviruses (BCoVs) are widespread around the world and cause enteric or respiratory infections among cattle. The current study includes 13 samples from BCoVs collected in Normandy during an 11-year period (from 2003 to 2014), 16 French HCoV-OC43s, and 113 BCoVs or BCoVs-like sequence data...
Clostridium difficile infection (CDI) continues to affect patients in hospitals and communities worldwide. The spectrum of clinical disease ranges from mild diarrhoea to toxic megacolon, colonic perforation and death. However, this bacterium might also be carried asymptomatically in the gut, potenti...
Dengue is a major problem in Brazil. Epidemiological and clinical aspects were characterized in patients from two epidemics which occurred in Mato Grosso do Sul, Brazil. Dengue cases were classified according to the 2009 WHO criteria, tested by serological and molecular biology tests and analysed fo...
The aim of this study was to investigate human invasive isolates of enterococci, obtained through prospective surveillance in Poland. The consecutive enterococcal isolates were collected in 30 hospitals between May 2010 and June 2011, and studied by species identification, antimicrobial susceptibili...
Staphylococcus aureus (S. aureus) infections range in severity due to expression of certain virulence factors encoded on mobile genetic elements (MGE). As such, characterization of these MGE, as well as single nucleotide polymorphisms, is of high clinical and microbiological importance. To understan...
Outbreaks of infections with multidrug-resistant bacteria in neonatal intensive care units (NICUs) pose a major threat, especially to extremely preterm infants. This study describes a 35-day outbreak of multidrug-resistant Escherichia coli (E. coli) in a tertiary-level NICU in Germany. To underline...
This study describes an outbreak of tuberculosis (TB) in a nursing home for men with mental disorders where residency is lengthy or permanent. This type of setting can provide a model of transmission as contact with the rest of society is extremely limited. To determine if cases of TB, diagnosed aro...
The objective of this study was to investigate the evolution of resistance to antimicrobials, corresponding mechanisms and molecular characteristics of Staphylococcus spp., between 1999 and 2014. Susceptibility to 38 antimicrobials was determined for 632 clinical staphylococcal isolates obtained fro...
Over a 5-month period, four liver transplant patients at a single hospital were diagnosed with Pneumocystis jirovecii pneumonia (PCP). This unusually high incidence was investigated using molecular genotyping. Bronchoalveolar lavage fluids (BALF) obtained from the four liver recipients diagnosed wit...
The incidence and geographic range of dengue have increased dramatically in recent decades. Climate change, rapid urbanization and increased global travel have facilitated the spread of both efficient mosquito vectors and the four dengue virus serotypes between population centers. At the same time,...
We recently reported a dramatic increase in the prevalence of carbapenem-resistant infections in the intensive care unit (ICU) of a Vietnamese hospital. This upsurge was associated with a specific -positive clone that was identified by multilocus VNTR analysis. Here, we used whole-genome sequence a...
The ongoing large-scale increase in the total amount of genetic data for viruses and other pathogens has led to a situation in which it is often not possible to include every available sequence in a phylogenetic analysis and expect the procedure to complete in reasonable computational time. This rai...
No abstract available
Clostridium difficile rose in prominence in the early 2000s with large-scale outbreaks of a particular binary toxin-positive strain, ribotype 027, in North America and Europe. In Australia outbreaks of the same scale had not and have not been seen. A survey of C. difficile across Australia was perfo...
Salmonella is an important cause of bacterial foodborne infections in Denmark. To identify the main animal-food sources of human salmonellosis, risk managers have relied on a routine application of a microbial subtyping-based source attribution model since 1995. In 2013, multiple locus variable numb...
Clinical infections caused by Acinetobacter spp. have increasing public health concerns because of their global occurrence and ability to acquire multidrug resistance. Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex encompasses A. calcoaceticus, A. baumannii, A. pittii (formerly ge...
Leptospirosis is an emerging infectious disease of global significance, and is endemic in tropical countries, including Malaysia. Over the last decade, a dramatic increase of human cases was reported; however, information on the primary vector, the rat, and the Leptospira serovars circulating among...
In countries with established Haemophilus influenzae type b (Hib) immunization programs, nontypeable H. influenzae (NTHi) is now responsible for nearly all invasive H. influenzae cases across all age groups. Public Health England (PHE) conducts enhanced national surveillance of invasive H. influenza...
A collection of forty halophilic actinomycetes isolated from water and mud samples of the saline lake at Kalar Kahar, salt range, Pakistan, was screened to investigate their antimicrobial potential against multi drug resistant (MDR) ventilator associated pneumonia causing bacterial pathogens. The is...
Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g., ferrets, skunks, ermines, and raccoons), but the disease in these hosts has been studied less. In 2007, a mink plasma...
Among 127 Stenotrophomonas maltophilia isolates causing bacteremia, 41 (32.3%) were nonsusceptible to levofloxacin, in which four sequence types and 24 diverse allelic profiles were detected. The most prevalent ST was ST77 (n = 8, 19.5%), followed by ST28 (n = 3, 7.3%). Amino acid substitutions were...
Cholera is potentially a life threatening disease caused by toxigenic Vibrio cholerae. Here we report the identification and characterisation of 76 non-7th pandemic clone O1 V. cholerae isolates including 65 clinical isolates from diarrhoeal patients from 2005 to 2014 in Zhejiang Province, China. We...
No abstract available
During an investigation for potential arboviruses present in mosquitoes in Hungary (Central Europe) three highly similar virus strains of a novel rhabdovirus (family Rhabdoviridae) called Riverside virus (RISV, KU248085-KU248087) were detected and genetically characterized from Ochlerotatus sp. mosq...
Following an outbreak in Mecca Saudi Arabia in 2000, meningococcal strains expressing capsular group W (W) emerged as a major cause of invasive meningococcal disease (IMD) worldwide. The Saudi Arabian outbreak strain (Hajj clone) belonging to the ST-11 clonal complex (cc11) is similar to W cc11 caus...
The study describes the transmission of a CTX-M-15-producing ST15 Klebsiella pneumoniae between patients treated in a single center and the subsequent inter-institutional spread by patient referral occurring between May 2012 and September 2013. A suspected epidemiological link between clinical K. pn...
Plague is a life-threatening disease caused by the bacterium, Yersinia pestis. Since the 1990s, Africa has accounted for the majority of reported human cases. In Uganda, plague cases occur in the West Nile region, near the border with Democratic Republic of Congo. Despite the ongoing risk of contrac...
To determine the prevalence and acquisition of extended-spectrum β-lactamases (ESBLs), plasmid-mediated AmpCs (pAmpCs), and carbapenemases ("MDR Enterobacteriaceae") colonizing children admitted to a pediatric intensive care unit (PICU). Prospective study. 40-bed PICU. Admission and weekly thereafte...
Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumu...
Enterotoxigenic Escherichia coli (ETEC) are an important cause of diarrhea in children under the age of 5 years in developing countries and are the leading bacterial agent of traveler's diarrhea in persons traveling to these countries. ETEC strains secrete heat-labile (LT) and/or heat-stable (ST) en...
We describe an outbreak with an extended-spectrum β-lactamase-producing Klebsiella pneumoniae strain in an intensive care unit in a secondary care hospital in Norway. The outbreak source was a fibreoptic intubation endoscope in which the outbreak strain survived despite chemothermal disinfection in...
The objective of this study was to characterize ESBL-producing Enterobacter cloacae isolated from animals and to compare their clonal distribution with that of human-related isolates. Among 635 clinical E. cloacae from horses, dogs and cats collected in France between 2010 and 2013, 36 were resistan...
Within the last decade, methicillin-resistant Staphylococcus aureus belonging to clonal complex 398 (CC398) has become a worldwide threat associated with livestock. More recently, methicillin-susceptible S. aureus (MSSA) belonging to CC398 have been increasingly reported as a cause of invasive infec...
The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the ident...
The opportunistic yeast Candida glabratais increasingly refractory to antifungal treatment or prophylaxis and relatedly is increasingly implicated in health care-associated infections. To elucidate the epidemiology of these infections, strain typing is required. Sequence-based typing provides multip...
Monopartite begomoviruses (Geminiviridae), which are whitefly-transmitted single-stranded DNA viruses known for causing devastating crop diseases, are often associated with satellite DNAs. Since begomovirus acquisition or exchange of satellite DNAs may lead to adaptation to new plant hosts and emerg...
Ten years after initial publications on livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in 2005, we report on the course of the LA-MRSA CC398 epidemic among patients of the University Hospital Münster. This tertiary care facility is located in the Dutch-German border regio...
No abstract available
Methicillin-resistant Staphylococcus aureus (MRSA) is a nosocomial pathogen in community settings. MRSA colonized individuals may contribute to its dissemination; the risk of MRSA infection is increased in human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) patients, although...
The aim of this nationwide study is to determine the strain type diversity among patients diagnosed with syphilis by PCR during a 4-year period in Denmark. Epidemiological data, including HIV status, for all patients were obtained from the Danish national syphilis registration system. Molecular stra...
No abstract available
Molecular methods for the diagnosis of Neisseria gonorrhoeae are replacing bacterial culture in many settings. This review focuses on recent progress in the development of molecular tests to detect resistant N. gonorrhoeae both to enhance surveillance and to guide decisions about individual patient...
No abstract available
Acinetobacter baumannii causes severe infections that primarily affect intensive care unit (ICU) patients. It has a high prevalence of multidrug resistance, including carbapenems, and a high potential for intra-hospital and inter-hospital transmission. The aim of this study was to determine the orig...
The first week of September 2013, the National Epidemiological Surveillance System identified two cases of cholera in Mexico City. The cultures of both samples were confirmed as Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Initial analyses by PFGE and by PCR-amplification of the vir...
Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the most prevalent Salmonella serotypes that cause gastroenteritis worldwide and the most prevalent serotype causing Salmonella infections in China. A rapid molecular typing method with high throughput and good epidem...
Bartonella bacilliformis is the etiological agent of Carrion's disease, a neglected tropical poverty-linked illness. This infection is endemic of Andean regions and it is estimated that approximately 1.7 million of South Americans are at risk. This bacterium is a fastidious slow growing microorganis...
A major limitation when reconstructing the origin and evolution of HPV-16 is the lack of reliable substitution rate estimates for the viral genes. On the basis of the hypothesis of human HPV-16 co-divergence, we estimated a mean evolutionary rate of 1.47×10(-7) (95% HPD=0.64-2.47×10(-7)) subs/site/y...
Isolated environments such as hot springs are particularly interesting for studying the microbial biogeography. These environments create an 'island effect' leading to genetic divergence. We studied the phylogeographic pattern of thermophilic anoxygenic phototrophic bacteria, belonging to the Roseif...
An explosive outbreak of Legionnaires' disease with 64 reported cases occurred in Ulm/Neu-Ulm in the South of Germany in December 2009/January 2010 caused by Legionella (L.) pneumophila serogroup 1, monoclonal (mAb) subtype Knoxville, sequence type (ST) 62. Here we present the clinical microbiologic...
The aim of this study was to investigate the prevalence and characteristics of staphylococcal enterotoxin B (SEB) producing Staphylococcus aureus (S. aureus) isolated from food sources. A total of 412 S. aureus isolates were recovered from 1970 milk and dairy samples (n = 236) and 2450 meat samples...
Chikungunya virus (CHIKV), an alphavirus and member of the Togaviridae family, is capable of causing severe febrile disease in humans. In December of 2013 the Asian Lineage of CHIKV spread from the Old World to the Americas, spreading rapidly throughout the New World. Given this new emergence in naï...
The purpose of this study was to investigate the epidemiological characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP) in Shanghai Children's Hospital in China. Twenty-two non-duplicate CRKP strains were collected from pediatric patients between March and June in 2014. Antimicrobial s...
Legionnaires' disease (LD) is a globally distributed systemic infectious disease. The burden of LD in many regions is still unclear, especially in Asian countries including China. A survey of Legionella infection using real-time PCR and nested sequence-based typing (SBT) was performed in two hospita...
Ciprofloxacin-resistant shigellosis outbreaks among men who have sex with men (MSM) have not been reported in Asia. During 3 March to 6 May 2015, the Notifiable Disease Surveillance System detected nine non-imported Shigella sonnei infections among human immunodeficiency virus (HIV) -infected Taiwan...
Colonization, infection, and clonal dissemination of vancomycin-resistant enterococcus (VRE) have been reported in the literature. We aimed to investigate the incidence rate of VRE acquisition and route of transmission of VRE within the medical intensive care unit (ICU) to prove whether subclinical...
A vancomycin-intermediate Staphylococcus aureus (VISA) (vancomycin minimum inhibitory concentration: 4mg/L) outbreak occurred in an advanced emergency medical service centre [hereafter referred to as the intensive care unit (ICU)] between 2013 and 2014. Our objective was to evaluate the infection co...
Postprocedural infections by Mycobacterium abscessus complex are increasing worldwide, and the source and route of transmission are infrequently identified. Here the extension of a previous clustering of paediatric patients with surgical site infections due to a single strain of the subspecies M. ma...
Despite vaccination, cyclical peaks of Bordetella pertussis incidence rates are still observed in Canada and other developed countries, making pertussis one of the most prevalent vaccine preventable bacterial diseases. In the postacellular vaccine era, evolution of bacterial strains has resulted in...
Urinary tract infections (UTI) are common in the community. However, information of resistant isolates in this context is limited in Latin America. This study aims to determine the prevalence and risk factors associated with community-onset UTI (CO-UTI) caused by extended-spectrum β-lactamase (ESBL)...
Acinetobacter baumannii is one of the important causes of nosocomial infection especially in burn patients. So, carbapenemase producing strains can make serious therapeutic problems. Molecular epidemiology studies play key role in decreasing the incidence of carbapenemase producing strains. In this...
Extensively drug-resistant Acinetobacter baumannii (XDR-Ab) is an increasingly important cause of healthcare-associated infection. Uncertainties remain concerning optimal control measures for healthcare-associated outbreaks. To describe the epidemiology and control of an XDR-Ab outbreak that involve...
The purpose of this study was to investigate the clinical characteristics of hypervirulent K. pneumoniae (hvKP) induced ventilator-associated pneumonia (VAP) and the microbiological characteristics and epidemiology of the hvKP strains. A retrospective study of 49 mechanically ventilated patients wit...
The objectives of this study were to characterize ESBL-producing Enterobacteriaceae present in 24 neonatal units (NNUs) in eight networks participating in a multicentre probiotic study and to test the hypothesis that specific strains would cluster within individual units and networks. We performed a...
Cronobacter spp. are opportunistic pathogens associated with serious infections in neonates. Increased stress tolerance, including the thermotolerance of some Cronobacter strains, can promote their survival in production facilities and thus raise the possibility of contamination of dried infant form...
The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV...
The aims of this study were to determine the genetic relatedness among 20 clinical Campylobacter jejuni samples isolated from children with diarrhea in Iran and to introduce the best method of discrimination based on flagellin gene (flaA) sequence divergence. A total of 400 stool specimens were obta...
Pulsed-field gel electrophoresis (PFGE) is a reliable method for analyzing outbreaks of methicillin-resistant Staphylococcus aureus (MRSA); however, it is time-consuming and technically demanding. A new strain-differentiation method for MRSA, namely phage open reading frame (ORF) typing (POT), is a...
The phylogenetic and epidemiological relationships of 102 Burkholderia pseudomallei clinical isolates from different geographical and population sources in China were investigated by multilocus sequence typing (MLST). The MLST data were analysed using the e-BURST algorithm, and an unweighted pair-gr...
Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation. Knowledge of the genetic diversity of toxigenic V. cholerae isolates, particularly in Africa, remains scarce. The constraints in improving thi...
"Mycobacterium aviumsubsp.hominissuis" is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandem-repeat (VNTR) analysis. Clinical and household biofilmM. aviumi...
Enterohemorrhagic Escherichia coli (EHEC) is an important cause of diarrhea and hemolytic-uremic syndrome (HUS) worldwide. Australia's worst outbreak of HUS occurred in Adelaide in 1995 and was one of the first major HUS outbreaks attributed to a non-O157 Shiga-toxigenic E. coli (STEC) strain. Molec...
Although the number of outbreaks caused by Yersinia enterocolitica has been very small in Japan, 4 outbreaks were occurred during the 2 years between 2012 and 2013. We describe herein 2 outbreaks which were examined in Tokyo in the present study. Outbreak 1: A total of 39 people (37 high school stud...
To understand the epidemiologic and etiologic characteristics of diarrheagenic Escherichia (E.) coli infections in Shenzhen. Stool samples were collected from acute diarrheal patients in four sentinel hospitals in Shenzhen and diarrheagenic E. coli strains were isolated and identified with multiplex...
In contrast to industrialized countries, until recently Group B Streptococcus (GBS) was infrequently reported in the developing world. This study was aimed at investigating the prevalence of GBS maternal colonization and to analyze the serotype distribution among the isolates. Vagino-rectal swabs co...
We previously reported that the strains of O157:H7 (EcO157) that survived longer in austere soil environment lacked expression of curli, a fitness trait linked with intestinal colonization. In addition, the proportion of curli-positive variants of EcO157 decreased with repeated soil exposure. Here...
Cholera rapid diagnostic tests (RDT) could play a central role in outbreak detection and surveillance in low-resource settings, but their modest performance has hindered their broad adoption. The addition of an enrichment step may improve test specificity. We describe the results of a prospective di...
There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing...
To examine eight strains of Vibrio cholerae O1 isolated in 2003 and 2005 from Puri, India, for antibiotic susceptibility, presence of virulence and regulatory genes, cholera toxin (CT) production, CTX arrangement and genomic profiles. Bacterial strains were tested for antibiotic susceptibility using...
Traditional methods for detection and serotyping of enterovirus infections are virus isolation and immunofluorescence assay (VI-IFA), which are labor-intensive and time-consuming. Recently, VP1 gene has been targeted to develop a CODEHOP-based RT-PCR (VP1-CODEHOP) for the same purpose. In this study...
Shiga toxin-producing (STEC) causes diarrhea and hemorrhagic colitis with life-threatening complications, such as hemolytic uremic syndrome. The aim of this study was to assess the molecular epidemiologic features of non-O157 STEC strains from different resources in China and illustrate the role of...
Despite infection prevention efforts, neonatal intensive care unit (NICU) patients remain at risk of Methicillin-resistant Staphylococcus aureus (MRSA) infection. Modes of transmission for healthcare-associated (HA) and community-associated (CA) MRSA remain poorly understood and may vary by genotype...
Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen responsible for severe disease in humans such as hemolytic uremic syndrome (HUS) and cattle, the principal reservoir. Identification of the clones/lineages is important as several characteristics, among them propensity to cause di...
An outbreak of Clostridium difficile ribotype 027 infection (CDI) occurred at an university hospital, involving 19 departments. To determine what hospital-associated factors drove the outbreak of this particular strain we performed a case-control study. Cases (n = 79), diagnosed with CDI due to C. d...
Enteric fever due to Salmonella Paratyphi A (SPA) is a global problem occurring as outbreaks at times. An unusual SPA (2,12:a:-) variety durazzo has been reported rarely. We report an outbreak of enteric fever due to this variety affecting 43 individuals. The blood samples grew unusual mucoid, lacto...
blaNDM genes are MBL genes that confer resistance to carbapenems. Globally, they are associated with diverse clones and plasmids. In this study, we characterised three isolates of Klebsiella pneumoniae-harbouring blaNDM1 from patients undergoing chronic haemodialysis and renal transplantation. 3 bla...
In China, the spread and outbreak of OXA-48-producing Enterobacteriaceae remains largely unknown. OXA-48-producing isolates were analyzed for genetic relatedness by pulsed-field gel electrophoresis (PFGE), antimicrobial susceptibility by E-test, and sequence type (ST) by multilocus sequence typing....
Since the year 2000 there has been a sharp increase in the prevalence of healthcare-related infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. However, the high community prevalence of ESBL-producing E. coli isolates means that many E. coli typing techniques may...
A total of 125 isolates were recovered from adenoids and/or nasopharynx of 170 children aged 2 to 5 from south-east Poland; they had undergone adenoidectomy for recurrent and/or persistent symptoms of upper respiratory tract infections. Pneumococcal isolates were analyzed by phenotyping (serotyping...
Shigellosis is a leading cause of enteric infections in the United States. We compared antimicrobial resistance in Shigella infections related to overseas travel (travel-associated) and in those acquired domestically by analyzing antimicrobial resistance patterns, geographic distributions, and pulse...
Among the 1660 isolates recovered from invasive pneumococcal disease (IPD) in adults (> = 18 yrs) in 2008-2011, a random sample of ≥50% of each serotype (n = 871) was chosen for MLST analysis and evaluation for the presence and type of pilus islands (PIs). The genetic diversity was high with 206 dif...
This study aimed to analyze the clinical characteristics of patients and molecular mechanisms of the first outbreak mainly caused by sequence types (STs) 208 multidrug resistant (MDR) Acinetobacter baumannii in China. A total of 10 clinical samples were collected from 5 patients who were involved in...
The present work relates to identification and a deep molecular characterization of circulating Mycobacterium tuberculosis complex (MTBC) strains in the Rhône-Alpes region, France from 2000 to 2010. It aimed to provide with a first snapshot of MTBC genetic diversity in conjunction with bacterial dru...
Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). Although the MTBC is highly clonal, between-strain genetic diversity has been observed. In low TB incidence settings, immigration may facilitate the importation of MTBC strains with a potential to complicate TB...
Tuberculosis (TB) is a well-known occupational hazard. Based on more than two decades (1992-2012) of centralized nationwide genotyping of all Mycobacterium tuberculosis culture-positive TB patients in Denmark, we compared M. tuberculosis genotypes from all cases notified as presumed occupational (N...
The most frequently isolated fungi in patients using TPN belongs to the Candida genus. Various infections including venous catheter infections, fungemia, endocarditis and ophthalmitis may be encountered. Upon growth of Candida in the blood cultures from the pediatric (neonatal) unit of our hospital,...
To compare the two Acinetobacter baumannii multi-locus sequence typing (MLST) schemes and to assess their suitability to aid in outbreak analysis we investigated the molecular epidemiology of 99 Acinetobacter baumannii isolates representing outbreak-related and sporadic isolates from 24 hospitals in...
In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of List...
The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Norway is low, but an endemic-like MRSA clone with Staphylococcal protein A (spa)-type t304 has been established especially in nursing homes in the Oslo region causing several large outbreaks. The challenge was that spa-typing a...
Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis that can result in large outbreaks. The birth of genomics and sequencing of C. burnetii strains has revolutionized many fields of study of this infection. Accurate genotyping methods and comparative genomic analysis have ena...
Escherichia coli (E. coli) is one of the most frequent and lethal causes of bloodstream infections (BSIs). We carried out a retrospective multicenter study on antimicrobial resistance and phylogenetic background of clinical E. coli isolates recovered from bloodstream in three hospitals in Shanghai....
The aim of this study was to utilize the multilocus sequence typing (MLST) technique to characterise Streptococcus pneumoniae among clinical isolates in India. MLST was used to determine clonality, to establish genetic relatedness, to check for correlation between serotypes and sequence types (STs)...
No abstract available
Salmonella enterica is one of the most commonly reported causes of bacterial foodborne illness around the world. Understanding the sources of this pathogen and the associated factors that exacerbate its risk to humans will help in developing risk mitigation strategies. The genetic relatedness among...
Clostridium difficile infections caused by the NAP1/B1/027 strain are more severe, difficult to treat, and frequently associated with relapses. A case-control study was designed to examine a C. difficile infection (CDI) outbreak over a 12-month period in a Mexican hospital. The diagnosis of toxigeni...
Bacteria are often grouped by a variety of properties, including biochemical activity, appearance, and more recently, nucleic acid sequence differences. In the case of human pathogens, significant work goes into "typing" strains to understand relatedness. This is especially true when trying to under...
In 2011, a multidrug-resistant Acinetobacter baumannii (MDRAB) outbreak occurred at a Japanese critical care center (CCC) in a tertiary care hospital. Multidrug-resistance in Japan is defined as resistance to the antimicrobials amikacin, carbapenem, and fluoroquinolone. We conducted a retrospective...
Recent years have seen a rise of coagulase-negative staphylococci (CoNS) from common contaminants to agents of nosocomial blood stream infections (BSI's). Molecular typing and establishing a correlation with antibiotic resistance is essential particularly in countries like India where genotyping stu...
is a nosocomial pathogen that usually affects critically ill patients. High mortality rates have been associated with MDR infections. Carbapenem resistance among these isolates is increasing worldwide and is associated with certain International Clones (ICs) and oxacillinases (OXAs). Moreover, this...
Stenotrophomonas maltophilia is an environmental bacterium and an opportunistic pathogen usually associated with healthcare-associated infections, which has recently been recognized as a globally multi-drug resistant organism. The aim of this study was genotyping and physiological characterization o...
This study analyzed clinical and microbiological characteristics of heteroresistant (hVISA) and vancomycin-intermediate Staphylococcus aureus (VISA) from bloodstream infections (BSI) in a Brazilian teaching hospital, between 2011 and 2013. Minimum inhibitory concentrations (MIC) of antimicrobials we...
Clostridium difficile infection (CDI) is a leading and an important cause of diarrhea in a healthcare setting especially in industrialized countries. Community-associated CDI appears to add to the burden on healthcare setting problems. The aim of the study was to investigate the antimicrobial resist...
Nosocomial infections are very common in African hospitals, particularly in neonatal units. These infections are most often caused by bacteria such as Escherichia coli, Klebsiella spp and Staphylococcus spp. Salmonella strains are rarely involved in nosocomial infections. Here, we report the first d...
To investigate the acquisition of Mycobacterium abscessus among ventilator-dependent patients. We prospectively recruited ventilator-dependent patients in five respiratory care wards (RCWs). Respiratory specimens were cultured for mycobacteria on day 1 (D1), 3 months (M3) and 6 months (M6) after enr...
Main problems of system of epidemiologic control for cholera active in Russian Federation, as well as laboratory diagnostics and vaccine prophylaxis of this especially dangerous infection, that had emerged in the contemporary period of the ongoing 7th pandemic of cholera, are discussed. Features of...
The increasing burden of multidrug-resistant bacteria affects the management of several infections. In order to prescribe adequate antibiotics, clinicians facing severe infections such as hospital-acquired pneumonia (HAP) need to promptly identify the pathogens and know their antibiotic susceptibili...
The extent of entry of multidrug-resistant Escherichia coli from the community into the hospital and subsequent clonal spread amongst patients is unclear. To investigate the extent and direction of clonal spread of these bacteria within a large teaching hospital, we prospectively genotyped multidrug...
The spa gene occurs in all strains of Staphylococcus aureus (S. aureus), can function as a genetic marker and might be used distinguish strains at the species level. Hence, due to these advantages, we used spa typing and the Based Upon Repeat Pattern (BURP) to assign the clonal and phylogenetic rela...
As we are approaching the twentieth anniversary of PulseNet, a network of public health and regulatory laboratories that has changed the landscape of foodborne illness surveillance through molecular subtyping, public health microbiology is undergoing another transformation brought about by so-called...
Mycobacterium avium subspecies paratuberculosis (MAP) is the etiological agent of severe chronic intestinal inflammatory disease in ruminants, termed Johne's disease, and can infect many other animal species, including humans. MAP has a long incubation period prior to manifestation of clinical signs...
Enterotoxigenic Escherichia coli (ETEC) has the potential to cause nosocomial infantile diarrhea in a hospital setting. We detected 12 ETEC serotype O128:H45 isolates from diarrheal neonates in our neonatal unit from July through October 2012. These infants developed hospital-acquired and epidemiolo...
Border disease virus (BDV) affects a wide range of ruminants worldwide, mainly domestic sheep and goat. Since 2001 several outbreaks of disease associated to BDV infection have been described in Pyrenean chamois (Rupicapra pyrenaica pyrenaica) in Spain, France and Andorra. In order to reconstruct th...
Crimean Congo hemorrhagic fever virus (CCHFV) is one of the most severe viral zoonozes. It is prevalent throughout Africa, Asia and southern Europe. Limited availability of sequence data has hindered phylogeographic studies. The complete genomic sequence of all three segments of 14 Crimean Congo hem...
Anther-smut fungi belonging to the genus Microbotryum sterilize their host plants by aborting ovaries and replacing pollen by fungal spores. Sibling Microbotryum species are highly specialized on their host plants and they have been widely used as models for studies of ecology and evolution of plant...
Outbreaks of the zoonotic disease tularemia occurred in north-east Bulgaria in the 1960s. Then came 30 years of epidemiological silence until new outbreaks occurred in west Bulgaria in the 1990s. To investigate how bacterial strains of causing tularemia in wildlife and humans in the 1960s and the 1...
Both Ebolavirus and Marburgvirus were detected in several fruit bat species of the family Pteropodidae, suggesting that this taxon plays a key role in the life cycle of filoviruses. After four decades of Zaire Ebolavirus (ZEBOV) outbreaks in Central Africa, the virus was detected for the first time...
Since its discovery in 2012, over 1700 confirmed cases of Middle East Respiratory Syndrome (MERS) have been documented worldwide and more than a third of those cases have died. While the greatest number of cases has occurred in Saudi Arabia, the recent export of MERS-coronavirus (MERS-CoV) to Republ...
Human immunodeficiency virus type 2 (HIV-2) infections are mainly restricted to West Africa; however, in the recent years, the prevalence of HIV-2 is a growing concern in some European countries and the Southwestern region of India. Despite the presence of different HIV-2 groups, only A and B Groups...
Infectious haematopoietic necrosis virus (IHNV) and viral haemorrhagic septicaemia virus (VHSV) are the most important viral pathogens impacting rainbow trout farming. These viruses are persistent in Italy, where they are responsible for severe disease outbreaks (epizootics) that affect the profitab...
Deep-sea hypersaline anoxic basins and other hypersaline environments contain abundant and diverse microbial life that has adapted to these extreme conditions. The bacterial Candidate Division KB1 represents one of several uncultured groups that have been consistently observed in hypersaline microbi...
Recent phylodynamic studies have focused on using tree topology patterns to elucidate interactions among the epidemiological, evolutionary, and demographic characteristics of infectious agents. However, because studies of viral phylodynamics tend to focus on epidemic outbreaks, tree topology signatu...
Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates fro...
Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populatio...
Human adenovirus type 7 (HAdV7) is globally attracting great concern as its high morbidity and severity in respiratory diseases, especially in Asia. To investigate the clinical and epidemiologic characteristics of HAdV7 infection outbreak in East China. The clinical samples were collected from the p...
Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen capable of causing severe disease in humans. Rapid and accurate identification and characterization techniques are essential during outbreak investigations. Current methods for characterization of STEC are expensive and...
Classical phylogenetic methods such as neighbor-joining or maximum likelihood trees, provide limited inferences about the evolution of important pathogens and ignore important evolutionary parameters and uncertainties, which in turn limits decision making related to surveillance, control, and preven...
Current knowledge of community-associated (CA) meticillin-resistant Staphylococcus aureus (MRSA) carriage in hospitalized patients is incomplete. Genotypic characteristics of 637 nasal MRSA isolates from newly admitted patients in South Korea were investigated. Sequence type (ST) 72 accounted for 52...
Whole genome sequencing (WGS) was compared to pulse-field gel electrophoresis (PFGE) of XbaI-digested genomic DNA, as methods by which to evaluate a potential transmission of carbapenem-resistant Klebsiella pneumoniae between 2 hospital inpatients. PFGE result demonstrated only 1-band difference bet...
Methicilin resistance Staphylococcus aureus (MRSA) infections are the major challenges in hospitals, especially in the burn units. The use of molecular typing methods is essential for tracking the spread of S. aureus infection and epidemiological investigations. The aim of this study was to find the...
In the last few years, Klebsiella pneumoniae strains producing K. pneumoniae carbapenemase (KPC) enzymes have emerged as important multidrug-resistant pathogens in hospitalized patients. This report describes KPC-producing isolates collected through the Croatian antimicrobial resistance surveillance...
Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal b...
Between 18 November and 3 December 2011, five renal transplant patients at the Department of Nephrology, Toho University Omori Medical Centre, Tokyo, were diagnosed with Pneumocystis pneumonia (PCP). We used molecular epidemiologic methods to determine whether the patients were infected with the sam...
Listeriosis is a serious foodborne infection that disproportionately affects elderly adults, pregnant women, newborns, and immunocompromised individuals. Diagnosis is made by culturing Listeria monocytogenes from sterile body fluids or from products of conception. This report describes the investiga...
Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and anal...
Three consecutive workers from the same foundry had Mycobacterium massiliense keratitis. The strains isolated from each patient were identical. This is the first report of a non-surgery-related outbreak of non-tuberculous mycobacterial ocular infection. An investigation revealed that injured cornea...
Coagulase-negative staphylococci (CoNS) are a major component of normal human skin and mucosae flora. However, some species of CoNS can lead to infections in immunocompromised patients and premature newborns. The choice of a rapid and reliable typing method is one of the major problems in the epidem...
During October 2011 several residents and staff members at a long-term care facility (LTCF) for elderly fell ill with respiratory symptoms. Several of the residents required hospitalization and one died. Non-typeable Haemophilus influenzae (NTHi) was identified as the causative pathogen. A descripti...
Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors,...
Carbapenem-resistant Acinetobacter baumannii, which are mainly induced by the production of OXA-type β-lactamases, are among the leading causes of nosocomial infections worldwide. Among the β-lactamase genes, the presence of the OXA-51-like gene carrying the upstream insertion sequence, ISAba1, was...
The introduction of pneumococcal conjugate vaccine may change the epidemiology of Streptococcus pneumoniae. The increased prevalence of non-vaccine serotypes as the cause of pneumococcal diseases has already reported in the United States and Europe. However, little attention has been focused on the...
Quantifying the attack ratio of disease is key to epidemiological inference and public health planning. For multi-serotype pathogens, however, different levels of serotype-specific immunity make it difficult to assess the population at risk. In this paper we propose a Bayesian method for estimation...
A number of molecular typing methods have been developed for characterization of Staphylococcus aureus isolates. The utility of these systems depends on the nature of the investigation for which they are used. We compared two commonly used methods of molecular typing, multilocus sequence typing (MLS...
Anthrax, a soil-borne zoonosis caused by the bacterium Bacillus anthracis, is enzootic in areas of North America with frequent outbreaks in west Texas. Despite a long history of study, pathogen transmission during natural outbreaks remains poorly understood. Here we combined case-level spatio-tempor...
One of the strategies utilized to decrease infections in the hospital setting relies on topical antimicrobials and antiseptics. While their use is beneficial, concerns arise over the potential to develop resistance or tolerance to these agents. We examined nosocomial Staphylococcus aureus isolates f...
A high fosfomycin resistance rate was observed in Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) in our previous study, but little is known about its mechanisms. In this study, we explored the prevalence of plasmid-mediated fosfomycin resistance determinants among fosfomy...
Paracoccidioidomycosis is an important systemic fungal infection that occurs throughout Latin America. The etiological agents comprise a species complex that includes two major groups: P. brasiliensis (including subgroups S1, PS2, and PS3) and P. lutzii. A great number of phenotypes may overlap, esp...
Human plague is a severe and often fatal zoonotic disease caused by Yersinia pestis. For public health investigations of human cases, nonintensive whole genome molecular typing tools, capable of defining epidemiologic relationships, are advantageous. Whole genome multilocus sequence typing (wgMLST)...
We studied the bacterial characteristics and incidence of invasive infections caused by group B streptococci (GBS) in adults in Iceland in 1975-2014. A total of 145 isolates were characterized by serotyping, antimicrobial susceptibility, multilocus sequence typing and surface protein gene profiling....
Vancomycin-resistant Enterococcus (VRE) has been identified in China. However, little is known about the spread of VRE isolates. The genetic relatedness of vancomycin-resistant Enterococcus faecium (VREfm) isolates was analyzed by pulsed-field gel electrophoresis (PFGE), their antimicrobial suscepti...
This study shows that the addition of a consensus 4-locus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) loci to the spoligotyping-24-locus MIRU-VNTR typing strategy is a well-standardized approach that can contribute to an improvement of th...
Early recognition and an attempt at obtaining microbiological documentation are recommended in patients with non-community-acquired pneumonia (NCAP), whether hospital-acquired (HAP) or health care-associated (HCAP). We aimed to characterize the clinical features and microbial etiologies of NCAP to a...
Pseudomonas aeruginosa multidrug resistance, and particularly the production of carbapenemases linked to international high-risk clones, is of growing concern. While high levels of carbapenem resistance (>60 %) have been reported in Lithuania, so far, there is no information on the underlying mechan...
Cholera is often caused when drinking water is contaminated through environmental sources. In recent years, the drastic cholera epidemics in Odisha (2007) and Haiti (2010) were associated with natural disasters (flood and Earthquake). Almost every year the state of Assam India witnesses flood in Bra...
Pulsed-field gel electrophoresis (PFGE) is the "gold standard" for epidemiological investigation of methicillin-resistant Staphylococcus aureus (MRSA), but several DNA sequence-based methods have been developed in MRSA typing because of the unambiguous results. Ninety-one MRSA isolates were collecte...
Staphylococcus aureus and coagulase-negative staphylococci (CoNS) colonization among healthcare workers (HCWs) may have implications in development of infections and in spreading of resistance. This study aimed to determine the rate of methicillin-resistant staphylococci carriage in HCWs of spinal s...
Multidrug-resistant tuberculosis (MDR TB) is a significant threat to global health estimated to account for nearly half a million new cases and over 200,000 deaths in 2013. The number of MDR TB cases in the UK has risen over the last 15 years, with ever more complex clinical cases and associated cha...
Enteritidis, Typhimurium and Livingstone are the main Salmonella enterica serovars recovered in Tunisia. Here, we aimed to assess the genetic diversity of fifty-seven Salmonella enterica strains from different sampling periods, origins and settings using pulsed-field gel electrophoresis (PFGE), mult...
Following the resolution of an episode of Clostridium difficile infection (CDI), the factors associated with acquisition of different C. difficile strain types in patients with recurrent infection or persistent colonization have not been evaluated. To explore factors with potential correlation with...
The increase of Escherichia coli producing extended-spectrum β-lactamases (ESBL) in hospitals and their emergence as intestinal colonisers of healthy humans is of concern. Transmission ways and the extent of spread of distinct E. coli clones or ESBL genes among humans and animals via the food chain...
Methicillin-resistant Staphylococcus aureus (MRSA) is prevalent in Japan, and the Staphylococcus cassette chromosome mec (SCCmec) type II is common among hospital-acquired MRSA isolates. Information pertaining to MRSA characteristics is limited, including SCCmec types, in primary or secondary care f...
To investigate a potential outbreak of high-level azithromycin resistant (HL-AziR) gonococcal infections diagnosed in eight patients attending a sexual health clinic in Leeds, North England, between November 2014 and March 2015. Eight cases of infection with gonococci exhibiting azithromycin minimum...
One of the largest and longest Salmonella outbreaks in Germany within the last 10 years occurred in central Germany in 2013. To identify vehicles of infection, we analysed surveillance data, conducted a case-control study and food traceback. We identified 267 cases infected with Salmonella Infantis...
The aim of this study was to determine the origin of virulence and multiresistance of a Klebsiella pneumoniae isolate from an abdominal wound infection of a patient with a gunshot injury in the thoracoabdominal region. The isolate was identified using biochemical tests and Phoenix™ automated system...
Two meticillin-resistant Staphylococcus aureus (MRSA) clones, sequence type (ST) 22 and ST239, have successfully spread globally. Across Australia, ST22 has supplanted ST239 as the main healthcare-associated MRSA. To understand the reasons underlying this shift, the epidemiology and clinical feature...
Histoplasmosis is a systemic mycosis caused by Histoplasma capsulatum, a dimorphic fungal pathogen that can infect both humans and animals. This disease has worldwide distribution and affects mainly immunocompromised individuals. In the environment, H. capsulatum grows as mold but undergoes a morpho...
We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or "epidemic clones" that have been previously associated with outb...
Dengue, classified as a 'neglected topical disease', is currently regarded globally as the most important mosquito-borne viral disease, which inflicts substantial socioeconomic and health burden in many tropical and subtropical regions of the world. While efforts continue towards developing and impr...
Whole-genome sequencing (WGS) of 41 patient and environmental sequence type 22 methicillin-resistant Staphylococcus aureus staphylococcal cassette chromosome mec type IV (ST22-MRSA-IV) isolates recovered over 6 weeks in one acute hospital ward in Dublin, Ireland, where ST22-MRSA IV is endemic, revea...
Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are ban...
Aspergillus flavus is the most common species associated with invasive aspergillosis in Tunisia. The molecular epidemiology of the species is poorly documented. We used five highly discriminative microsatellite markers for the genotyping of clinical and hospital environmental A. flavus strains to as...
Ixodid ticks are important vectors of a wide variety of viral, bacterial and protozoan pathogens of medical and veterinary importance. Although several studies have elucidated tick responses to bacteria, little is known about the tick response to viruses. To gain insight into the response of tick ce...
Cryptococcus gattii, the sister species of Cryptococcus neoformans, is an emerging pathogen which gained importance in connection with the ongoing cryptococcosis outbreak on Vancouver Island. Many molecular studies have divided this species into for major lineages: VGI, VGII, VGIII, and VGIV. This c...
We describe the first nosocomial outbreak of a toxic shock syndrome-positive methicillin-resistant Staphylococcus aureus (MRSA) sequence type 5 Geraldine clone. Infection control interventions that are usually successful were implemented to control the outbreak. Spread of this virulent MRSA strain h...
In this study, we investigated the distribution, phenotypic and molecular typing characters of Campylobacter jejuni in domestic fowl, and livestock populations in East China, to provide some reference for researches on its molecular epidemiology. A total of 1250 samples were collected from different...
Since 2012, three clusters of serogroup C meningococcal disease among men who have sex with men (MSM) have been reported in the United States. During 2012, 13 cases of meningococcal disease among MSM were reported by the New York City Department of Health and Mental Hygiene (1); over a 5-month perio...
DNA-based techniques are frequently used to confirm the relatedness of putative outbreak isolates. These techniques often lack the discriminatory power when analyzing closely related microbes such as E. coli. Here the value of Raman spectroscopy as a typing tool for E. coli in a clinical setting was...
emm typing is the most widely used molecular typing method for the human pathogen Streptococcus pyogenes (group A streptococcus [GAS]). emm typing is based on a small variable region of the emm gene; however, the emm cluster typing system defines GAS types according to the nearly complete sequence o...
The Vibrio cholerae O1 (VCO1) El Tor biotype appeared during the seventh cholera pandemic starting in 1961, and new variants of this biotype have been identified since the early 1990s. This pandemic has affected Vietnam, and a large outbreak was reported in southern Vietnam in 2010. Pulsed-field gel...
Acinetobacter baumannii has emerged worldwide as an important opportunistic nosocomial pathogen and has become a major public health concern. In this study, the draft genome sequence of A. baumannii TCM331 (ST208/CC92), a multidrug-resistant (MDR) isolate harbouring the blaOXA-23 gene isolated in Ch...
Increasing consumption of nitrofurantoin (NIT) for treatment of acute uncomplicated urinary tract infections (UTI) highlights the need to monitor emerging NIT resistance mechanisms. This study investigated the molecular epidemiology of the multidrug-resistant efflux gene oqxAB and its contribution t...
The spread of carbapenem resistant Enterobacteriaceae (CRE) is an emerging clinical problem, of great relevance in Europe and worldwide. The aim of this study was the molecular epidemiology of CRE isolates in Valle d'Aosta region, Italy, and the mechanism of carbapenem resistance. Sixty consecutive...
Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high...
Klebsiella pneumoniae is an opportunistic pathogen often associated with nosocomial infections. A suspected outbreak of K. pneumoniae isolates, exhibiting reduced susceptibility to carbapenem antibiotics, was detected during the month of May 2012 among patients admitted to a haematology unit of a te...
China's Guangdong Province is located along the same latitude as Kolkata, India and Dhaka, Bangladesh, and is also considered a source of epidemic cholera. However, molecular description and the genetic relationships between Vibrio cholerae O1 El Tor isolates in Guangdong remain unclear. In this stu...
The aim of this study was to understand the epidemiology, serotype, antibiotic sensitivity, and clonal structure of Erysipelothrix rhusiopathiae strains in China. Forty-eight strains were collected from seven provinces during the period from 2012 to 2013. Pulse-field electrophoresis identified 32 di...
To investigate the serotypes, antimicrobial resistance, virulence genes and molecular characteristics of food-borne Vibrio parahaemolyticus isolated in Guangdong province in 2014. Sixty V. parahaemolyticus strains were tested in this study. The serotyping and antibiotic resistance test were conducte...
The Malawi Liverpool Wellcome Trust Clinical Research Programme (MLW) has routinely collected specimens for blood culture from febrile patients, and cerebrospinal fluid from patients with suspected meningitis, presenting to Queen Elizabeth Central Hospital (QECH), Blantyre, Malawi, since 1998. We pr...
Alpine Mycobacterium caprae isolates found in cattle and red deer display at least three genetic variations in the region of difference four (RD4) that can be used for further differentiation of the isolates into the subtypes 'Allgäu', 'Karwendel' and 'Lechtal'. Each genomic subtype is thereby chara...
The spread of carbapenemase-producing Gram-negative rods is an emerging global problem. This study describes the epidemiologic features of an outbreak caused by an environmental reservoir of OXA-48-producing Klebsiella pneumoniae caused by persistence of the bacteria during 20 months in an intensive...
The objective of this study was to describe the prevalence and microbiological characteristics of carbapenemase-producing Enterobacteriaceae (CPE) colonizing patients in long-term care hospitals (LTCHs) in Madrid, Spain. Three LTCHs were included in a single-day point-prevalence survey (September 20...
The objective of this study was to describe the nosocomial spread of carbapenemase-producing enterobacteria and characterize a plasmid involved in KPC dissemination. Two Klebsiella pneumoniae, one Escherichia coli and one Citrobacter freundii isolated from two patients were studied. Susceptibility p...
Columnaris disease caused by Flavobacterium columnare is a serious problem in aquaculture, annually causing large economic losses around the world. Despite considerable research, the molecular epidemiology of F. columnare remains poorly understood. We investigated the population structure and spatio...
The study aims were to describe the frequency and dynamics of methicillin-resistant Staphylococcus aureus (MRSA) carriage among healthcare workers (HCWs), and to compare the molecular epidemiology of MRSA isolates from HCWs with those from patients with bacteremia. HCWs were interviewed and three na...
Staphylococci are common causes of healthcare-associated and community-associated infections. However, limited data are available on the prevalence, phenotypes and molecular characteristics of Staphylococci in metro system around the world. 320 surface samples were collected from the Guangzhou metro...
We investigated the prevalence and characteristics of Escherichia coli sequence type 131 (ST131) and its subclones among 268 E. coli isolates. The isolates were collected from 21 Korean hospitals without use of selection criteria and were screened for ST131 status by PCR. ST131 isolates were charact...
Extraintestinal pathogenic Escherichia coli (E. coli) is considered as the main causative agent of urinary tract infections worldwide. The relationship between antimicrobial resistance, phylogenetic groups, patient characteristics and adhesin virulence genes are complex and not fully understood. In...
Although the nosocomial prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Angola is over 60% and one of the highest in Africa, the extent of MRSA in the community is unknown. To fill this gap, we conducted a hospital-based study in which 158 children attending the emergency ward an...
Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this imp...
The aim of this study was to identify the genetic relatedness of multiple drug-resistant (MDR) Acinetobacter baumannii clinical isolates recovered from a hospital in Los Angeles. Twenty-one MDR A. baumannii isolates were collected and their antibiotic susceptibilities determined according to Clinica...
Invasive meningococcal disease (IMD) is a worldwide health issue that is potentially preventable with vaccination. In view of its sporadic nature and the high diversity of Neisseria meningitidis, epidemiological surveillance incorporating detailed isolate characterisation is crucial for effective co...
The global spread of carbapenem-resistant Klebsiella pneumoniae (CR-Kp) has been largely associated with sequence type 258 (ST258) and its related variants (clonal group 258 [CG258]). Here we describe the molecular epidemiology of CR-Kp from five tertiary care hospitals in Medellín, the second large...
Ceftaroline, the active metabolite of the prodrug ceftaroline-fosamil, is an advanced-generation cephalosporin with activity against methicillin-resistant Staphylococcus aureus (MRSA). This investigation provides in vitro susceptibility data for ceftaroline against 1,971 S. aureus isolates collected...
Whitefly-transmitted viruses belonging to the genus Begomovirus (family Geminiviridae) represent a substantial threat to agricultural food production. The rapid evolutionary potential of these single-stranded DNA viruses combined with the polyphagous feeding behavior of their whitefly vector (Bemisi...
A total of 101 Acinetobacter baumannii isolates were collected to determine the mechanisms of quinolone resistance and investigate the occurrence of carbapenem and high-level aminoglycoside resistance genes among quinolone-resistant strains. Among 77 quinolone-resistant A. baumannii harbored mutatio...
Nosocomial infectious outbreaks caused by multidrug-resistant Acinetobacter baumannii have emerged as a serious threat to human health. Phosphoproteomics of pathogenic bacteria has been used to identify the mechanisms of bacterial virulence and antimicrobial resistance. In this study, we used a shot...
The aim of this study was to investigate the basis of the putative persistence of Listeria monocytogenes in a new industrial facility dedicated to the processing of ready-to-eat (RTE) Iberian pork products. Quaternary ammonium compounds, which included benzalkonium chloride (BAC), were repeatedly us...
In a 1-year survey at a university hospital we found that 20·6% (81/392) of patients with antibiotic associated diarrohea where positive for C. difficile. The most common PCR ribotypes were 012 (14·8%), 027 (12·3%), 046 (12·3%) and 014/020 (9·9). The incidence rate was 2·6 cases of C. difficile infe...
Multilocus sequence typing was successfully completed on 494 isolates of Streptococcus uberis from clinical mastitis cases in a study of 52 commercial dairy herds over a 12-month period. In total, 195 sequence types (STs) were identified. S. uberis mastitis cases that occurred in different cows with...
Pasteurella multocida is a rare cause of neonatal bacterial meningitis. We describe such a case and verify two household cats as the source of infection using repetitive-element PCR (rep-PCR) molecular fingering.
The objectives of this study were to estimate the prevalence of MRSA on duck and turkey farms, identify risk factors for human carriage and study transmission between animals and humans. On 10 duck and 10 turkey farms, samples were taken from animals, poultry houses, home residences and humans and c...
OBJECTIVE To determine the role of unit-based transmission that accounts for cases of early Clostridium difficile infection (CDI) during hospitalization for allogeneic stem cell transplant. SETTING Stem cell transplant unit at a tertiary care cancer center. METHODS Serially collected stool from pati...
Main goal of this study was to determine the prevalence and molecular epidemiology of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae among 156 nursing home residents in Bavaria and to compare the results with healthy individuals from the Bavarian community. Intestinal colonisation...
Carbapenem-resistant Klebsiella pneumoniae isolates are an important cause of nosocomial infections. This study evaluated a rapid cost-saving method based on MALDI-TOF technology, was and compared it with phenotypic, genotypic and epidemiological data for characterization of KPC-Kp strains consecuti...
To present results of virological surveillance and epidemiological aspects of dengue in the State of Rio Grande do Norte, Brazil. A total of 1581 cases, reported from 2010 to 2012 at various health centres in the state, were analysed by viral isolation and/or RT-PCR for viral detection and typing. T...
Listeria monocytogenes is capable of infecting almost all animals. However, outbreaks of listeriosis are infrequent in birds. This report describes an outbreak of listeriosis in a small pheasant (Phasianus colchicus) breeder farm with more than 2,000 pheasants from Hubei province of the People's Rep...
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major public health concern worldwide. This is the first nationwide study, performed within the China Gonococcal Antimicrobial Susceptibility Programme (China-GASP), regarding AMR, including ceftriaxone genetic resistance determinants, and...
The objective of this study was to investigate the silver gull as an indicator of environmental contamination by salmonellae and carbapenemase-producing Enterobacteriaceae (CPE) in south-east Australia. A total of 504 cloacal samples were collected from gull chicks at three nesting colonies in New S...
Two proven nosocomial cases of Legionella pneumonia occurred at the Wesley Hospital (Brisbane, Australia) in May 2013. To trace the epidemiology of these cases, whole genome sequence analysis was performed on Legionella pneumophila isolates from the infected patients, prospective isolates collected...
Haemophilus influenzae is an important pathogen able to cause a wide spectrum of diseases in children. Colonization of the upper respiratory tract is a risk factor for developing disease. This study aimed to investigate the oropharyngeal carriage rate of H. influenzae in young children in two Italia...
Pseudomonas aeruginosa is a major cystic fibrosis (CF) pathogen causing chronic respiratory infections and posing a risk for cross-infection between patients with CF. To propose an algorithm for long-term surveillance of P. aeruginosa and assess its suitability for monitoring the epidemiological sit...
Outbreaks of soft tissue or skin infection due to non-tuberculous mycobacteria are reported frequently in scientific journals but in general the infection source in these outbreaks remains unknown. In Venezuela, in two distinct outbreaks, one after breast augmentation surgery and another after hydro...
An outbreak of linezolid-resistant vancomycin-resistant Enterococcus faecium (LRVREfm) occurred in the hepatology ward of a tertiary referral hospital in Ireland between February and September 2014. LRVREfm was isolated from 15 patients; pulsed-field gel electrophoresis confirmed spread of a single...
Next generation sequencing (NGS) technologies have arrived, changing research and infectious disease research into a new era, the "genomic era". Currently, the developed world is introducing NGS in a number of applications, including clinical diagnostics, epidemiology, and microbiology. In developin...
The worldwide emergence of multi-drug resistant (MDR) bacteria in recent years has caused many problems for hospitals and patients, especially intensive care unit patients. Among these clinically important MDR bacteria are Acinetobacter baumannii complex species (A. baumannii, Acinetobacter genomic...
The current Ebola virus disease outbreak in West Africa has revealed serious shortcomings in national and international capacity to detect, monitor, and respond to infectious disease outbreaks as they occur. Recent advances in diagnostics, risk mapping, mathematical modeling, pathogen genome sequenc...
The European epidemiology of MRSA is changing with the emergence of community-associated MRSA (CA-MRSA) and livestock-associated MRSA (LA-MRSA). In this study, we investigated the molecular epidemiology of MRSA during 2 years in 13 ICUs in France, Greece, Italy, Latvia, Luxemburg, Portugal, Slovenia...
Despite tremendous efforts in the fight against polio, Pakistan bears the highest proportion of poliomyelitis cases among the 3 endemic countries including Afghanistan and Nigeria. Apart from insecurity and inaccessibility challenges, the substantial shift of unimmunized children from North Wazirist...
Tuberculosis (TB), a chronic infectious disease caused by Mycobacterium tuberculosis (MTB), poses a serious threat to human health. We investigated the genotypes of MTB in the high prevalence province Xinjiang, China. From March 2010 to May 2013, 381 MTB isolates from patients with pulmonary TB were...
This study describes, for the first time, the genetic and phenotypic diversity among 93 Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected from Guelma, Algeria and Marseille, France. All strains were identified by matrix-assisted laser desorption/ionization time-of-flight mass...
Bloodstream infections (BSIs) are serious diseases associated with high mortality, especially when caused by extensively drug-resistant (XDR) Klebsiella pneumoniae. The prevalence and pandemic strains of extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae isolated from blood cultures of...
We aimed to estimate the prevalence of different Achromobacter species among UK Cystic Fibrosis (CF) patients. nrdA sequence clustering was used to identify 147 Achromobacter isolates from 96 patients from 27 hospitals to species level. Potential cross-infection was investigated by MLST, pulsed-fiel...
Pestiviruses infect a wide variety of animals of the order Artiodactyla, with bovine viral diarrhea virus (BVDV) being an economically important pathogen of livestock globally. BVDV is maintained in the cattle population by infecting fetuses early in gestation and, thus, by generating persistently i...
No abstract available
The objective of this study was to characterize New Delhi metallo-β-lactamase (NDM)-producing Enterobacteriaceae isolates reported in Poland in 2012-14. Representative isolates were typed by PFGE and MLST. NDM and other β-lactamase genes were amplified and sequenced. Plasmids with blaNDM genes were...
Candidemia and other forms of candidiasis are associated with considerable excess mortality and costs. Despite the addition of several new antifungal agents with improved spectrum and potency, the frequency of Candida infection and associated mortality have not decreased in the past two decades. The...
In April and May 2014, two suspected egg-related outbreaks of Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) were investigated by the Belgian National Reference Laboratory of Foodborne Outbreaks. Both the suspected food and human isolates being available, and this for both...
The dissemination of plasmid-mediated multidrug resistance in Enterobacteriaceae is a major public health concern. We investigated the prevalence of plasmid-mediated quinolone resistance (PMQR), 16S rRNA methylases, CTX-M, and acquired AmpC enzymes in ESBL-producing Klebsiella pneumoniae (n=40) from...
The contribution of wild birds as a source of human campylobacteriosis was investigated in Oxfordshire, United Kingdom (UK) over a 10 year period. The probable origin of human Campylobacter jejuni genotypes, as described by multilocus sequence typing, was estimated by comparison with reference popul...
In a community, it is unknown what factors account for transmission of methicillin-resistant Staphylococcus aureus (MRSA). We integrated whole genome sequencing (WGS) and epidemiologic data to identify factors associated with MRSA transmission networks in an urban community. WGS was performed on col...
To compare the genetic population structure of Staphylococcus aureus from China and Europe, 1294 human isolates were characterized by multiple-locus variable number tandem repeat analysis (MLVA). In total, MLVA identified 17 MLVA complexes (MCs), comprising 260 MLVA types (MTs) among the Chinese iso...
In this study we describe the clinical and molecular characteristics of an outbreak due to carbapenem-resistant Klebsiella pneumoniae (CR-KP) producing CTX-M-15 and OXA-48 carbapenemase. Isogenic strains, carbapenem-susceptible K. pneumoniae (CS-KP) producing CTX-M-15, were also involved in the outb...
Since its first isolation in 1996 in Guangdong, China, the highly pathogenic avian influenza virus (HPAIV) H5N1 has circulated in avian hosts for almost two decades and spread to more than 60 countries worldwide. The role of different avian hosts and the domestic-wild bird interface has been critica...
This study investigated the genetic basis of antimicrobial resistance and the epidemiological characteristics of 125 carbapenem-resistant Acinetobacter baumannii (CRAB) isolates collected from 2011 to 2012 in a Korean hospital. All CRAB isolates showed an extensively drug-resistant phenotype, but we...
We evaluated and critically assessed the performance and discriminatory power of a rep-PCR based commercial test DiversiLab® Enterococcus kit (bioMerieux) for typing a set of 65 representative isolates of Enterococcus faecium/VRE and compared it to state-of-the-art typing techniques such as PFGE and...
Candida albicans is a common cause of bloodstream fungal infections in hospitalized patients. To investigate its epidemiology, multilocus sequence typing (MLST) was performed on 285 C. albicans bloodstream isolates from patients in Chang Gung Memorial Hospital at Linkou (CGMHL), Taiwan from 2003 to...
Clonal relationships of Klebsiella pneumoniae strains obtained during an epidemic and after a one-year post-epidemic (non-epidemic) period in the same neonatal intensive care unit (NICU) using pulsed-field gel electrophoresis (PFGE) and repetitive polymerase chain reaction (rep-PCR) by the DiversiLa...
The emergence of multidrug-resistant (MDR) Acinetobacter baumannii has become a serious medical problem worldwide. To clarify the genetic and epidemiological properties of MDR A. baumannii strains isolated from a medical setting in Nepal, 246 Acinetobacter spp. isolates obtained from different patie...
A collection of 1159 enterococcal isolates from five Chinese hospitals were screened for the presence of the novel oxazolidinone resistance gene optrA, which was found in 34 (2.9%) isolates. Pulsed-field gel electrophoresis (PFGE) typing of 29 optrA-carrying Enterococcus faecalis isolates revealed 2...
Both low-level mupirocin resistance (LMR) and high-level mupirocin resistance (HMR) have been identified. The aim of this study was to determine the epidemiology of LMR and HMR in MRSA isolates at five hospitals that have used mupirocin for targeted decolonization as part of successful institutional...
No abstract available
Scedosporiosis is a rare, but often fatal mycotic infection occurring in immunosuppressed as well as in immunocompetent patients. Over a period of 14 months, Scedosporium boydii isolates were sent to our reference laboratory from six immunocompetent patients treated at a single hospital in Germany....
The distribution of carbapenemase genes in Escherichia coli strains isolated between September 2009 and May 2013 in Germany was investigated. Out of 192 isolates with carbapenemase production OXA-48 was found in 44.8%, VIM-1 in 18.8%, NDM-1 in 11.5% and KPC-2 in 6.8%. Patients with VIM-1 producing E...
Outbreaks of Staphylococcus aureus are common in neonatal intensive care units (NICUs). Usually they are documented for methicillin-resistant strains, while reports involving methicillin-susceptible S. aureus (MSSA) strains are rare. In this study we report the epidemiological and molecular investig...
Since a well-documented incidence peak in 2011/12 in European countries, infections due to the cell wall-less bacterium Mycoplasma pneumoniae have gained the increased attention of clinicians, microbiologists and health authorities. Despite the mild or asymptomatic clinical course of most M. pneumon...
An increase of Enterobacteriaceae isolates with reduced susceptibility to cefepime (FEP) and amoxicillin/clavulanate (AMC) has been observed in our area. The aim of this study was to characterize this antibiotic resistance phenotype and its molecular epidemiology. A total of 33 Enterobacteriaceae st...
We characterized an outbreak of imipenem-resistant Acinetobacter baumannii with clinical and environmental isolates from a tertiary care hospital in San Luis Potosi, Mexico. During a 4-month period, a total of 32 nonrepetitive imipenem-resistant clinical isolates of A. baumannii were collected. All...
Conflicting reports have been published on the association between Clostridium difficile ribotypes and severe disease outcomes in patients with C. difficile infection (CDI); several so-called hypervirulent ribotypes have been described. We performed a multicenter study to assess severe disease prese...
Although new serotypes of enterohemorrhagic Escherichia coli (EHEC) emerge constantly, the mechanisms by which these new pathogens arise and the reasons emerging serotypes tend to carry more virulence genes than other E. coli are not understood. An insertion sequence (IS) excision enhancer (IEE) was...
We applied an emm cluster typing system to group A Streptococcus strains in New Zealand, including those associated with acute rheumatic fever (ARF). We observed few so-called rheumatogenic emm types but found a high proportion of emm types previously associated with pyoderma, further suggesting a r...
Over a four-month period, ten patients were suspected of having acquired nosocomial infection to P. aeruginosa in the ear, nose, and throat department. Environmental and clinical isolates were compared. Only water from a drinking water fountain was contaminated by P. aeruginosa. This isolate and tho...
Fast and reliable discrimination of methicillin-resistant Staphylococcus aureus (MRSA) isolates is essential in identifying an outbreak. Molecular typing methods, such as S. aureus protein A (spa) typing, multi locus sequence typing (MLST) and pulse field gel electrophoresis (PFGE) are generally use...
Candida parapsilosis (sensu lato), which represents a fungal complex composed of three genetically related species - Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis, has emerged as an important yeast causing fungemia worldwide. The goal of the present work was to a...
Twenty-one multiresistant Enterobacter cloacae isolates producing OXA-48 (n=10), CTX-M-15 (n=7) or both (n=4) β-lactamases were detected in a Spanish hospital during a 1-year period (June 2013 to June 2014). The isolates were also resistant to non-β-lactam antimicrobials, further complicating the th...
In March 2014, after an increase of notifications of domestically acquired hepatitis A virus infections, an outbreak investigation was launched in Norway. Sequenced-based typing results showed that these cases were associated with a strain that was identical to one causing an ongoing multinational o...
A new method is proposed to infer unobserved epidemic subpopulations by exploiting the synchronization properties of multistrain epidemic models. A model for dengue fever is driven by simulated data from secondary infective populations. Primary infective populations in the driven system synchronize...
The identification of circulating TB strains in the community and drug sensitivity patterns is essential for the tuberculosis control program. This study was undertaken to identify M. tuberculosis strains circulating in selected communities in Ethiopia as well as to evaluate the drug sensitivity pat...
Human enteroviruses (EVs) and parechoviruses (HPeVs) belong to the family Picornaviridae. Although most EV and HPeV infections remain asymptomatic, both pathogens can cause a wide spectrum of clinical manifestations ranging from respiratory or gastrointestinal symptoms to myocarditis, neonatal sepsi...
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and n...
A significant increase in HIV-1 diagnoses was reported among Injecting Drug Users (IDUs) in the Athens (17-fold) and Bucharest (9-fold) metropolitan areas starting 2011. Molecular analyses were conducted on HIV-1 sequences from IDUs comprising 51% and 20% of the diagnosed cases among IDUs during 201...
Enterobacter cloacae is among the most important pathogens responsible for nosocomial infections and outbreaks. In this study, 77 Enterobacter isolates were collected: 27 isolates from Algerian hospitals (in Constantine, Annaba, and Skikda) and 50 isolates from Marseille, France. All strains were id...
It remains unclear whether lineages of influenza A(H3N2) virus can persist in the tropics and seed temperate areas. We used viral gene sequence data sampled from Peru to test this source-sink model for a Latin American country. Viruses were obtained during 2010-2012 from influenza surveillance cohor...
Baseline methicillin-resistant Staphylococcus aureus (MRSA) isolates from patients with nosocomial and community-acquired pneumonia collected during Phase 3 trials for ceftobiprole were characterized. Eighty-four unique isolates from patients enrolled in Europe (50.0%), Asia-Western Pacific region (...
Global spread and evolutionary links of an epidemic Clostridium difficile strain (PCR-ribotype 027) have been noted in recent decades. However, in Japan, no outbreaks caused by type 027 have been reported to date. A total of 120 C. difficile isolates from patients at 15 hospitals during non-outbreak...
Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of near...
Meticillin-resistant Staphylococcus aureus (MRSA) bacteraemia cases have declined since 2003, and have mostly been due to two epidemic (E) strains, E15 (multi-locus sequence type clonal complex CC22) and E16 (CC30). By contrast, the incidence of meticillin-susceptible S. aureus (MSSA) bacteraemia ha...
From 24 December to 24 July 2015, 174 cases were reported in a nationwide salmonellosis outbreak in Sweden: 108 cases were connected to a single restaurant. A spice mix, containing dried vegetables from the restaurant tested positive for the outbreak strain. Additional spice mixes with similar conte...
Group A streptococci (GAS) is responsible of several human diseases ranging from mild infection to severe invasive toxin-mediated disease and post-infectious sequelae. Accordingly, a GAS surveillance program based on molecular techniques is advisable for its epidemiological control. Pulsed-field gel...
Host-adaptation of Streptococcus agalactiae subpopulations has been described whereby strains that are commonly associated with asymptomatic carriage or disease in people differ phenotypically and genotypically from those causing mastitis in dairy cattle. Based on multilocus sequence typing (MLST),...
The aim of this study was to determine if mycobacterial lineages affect infection risk, clustering, and disease progression among Mycobacterium tuberculosis cases in The Netherlands. Multivariate negative binomial regression models adjusted for patient-related factors and stratified by patient ethni...
The OmpK36 porin plays a role in carbapenem resistance and may contribute to bacterial virulence in Klebsiella pneumoniae. This study aimed to investigate the characteristics of different groups of K. pneumoniae separated by ompK36 typing. Among 226 nonduplicate K. pneumoniae bloodstream isolates co...
Due to the clinical threat posed by multidrug-resistant (MDR) Pseudomonas aeruginosa and importance of virulence factors produced in infection, 21 carbapenem-resistant P. aeruginosa were analyzed. 42.8% metallo-beta-lactamases-positive strains were identified. 85.7% of strains were meropenem resista...
This study investigated the molecular features of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae from hospital- and community-acquired (HA/CA) infections in the region of Mahdia, Tunisia. Among 336 K. pneumoniae isolates recovered from both clinical contexts between July 2009 a...
We evaluated temporal fluctuations in macrolide resistance rates, analysing genetic determinants of resistance and clonal evolution in a population of 2744 S. pyogenes isolates collected in the period 2000-2013. The total resistance rate to erythromycin of the isolates was 17.9 %. A maximum of eryth...
Neisseria meningitidis is a leading cause of meningitis and septicaemia. The hyperinvasive ST-11 clonal complex (cc11) caused serogroup C (MenC) outbreaks in the US military in the 1960s and UK universities in the 1990s, a global Hajj-associated serogroup W (MenW) outbreak in 2000-2001, and subseque...
The objective of this study was to determine the activity of fidaxomicin and comparator antimicrobials against Clostridium difficile isolated from patients with C. difficile infection (CDI) in Australian hospitals and in the community. One private and one public laboratory from five states in Austra...
In August and September 2014, unexpected clusters of enterovirus-D68 (EV-D68) infections associated with severe respiratory disease emerged from North-America. In September, the European Centre for Disease Prevention and Control (ECDC) asked European countries to strengthen respiratory sample screen...
The first outbreaks of bacterial canker of kiwifruit caused by Pseudomonas syringae pv. actinidiae biovar 3 were detected in France in 2010. P. syringae pv. actinidiae causes leaf spots, dieback, and canker that sometimes lead to the death of the vine. P. syringae pv. actinidifoliorum, which is path...
Characterizing the impact of HIV transmission routes on viral genetic diversity can improve the understanding of the mechanisms of virus evolution and adaptation. HIV vertical transmission can occur in utero, during delivery, or while breastfeeding. The present study investigated the phylodynamics o...
Klebsiella pneumoniae is a common colonizer of the gastrointestinal tract of humans, companion animals, and livestock. To better understand potential contributions of foodborne K. pneumoniae to human clinical infections, we compared K. pneumoniae isolates from retail meat products and human clinical...
Here we describe the international scenario of Vibrio cholerae with a comparative analysis of different aspects of typing. Representative V. cholerae strains (n=108) associated with endemic cholera regions from 29 states of India and worldwide were subjected to microbiological, molecular and phyloge...
We describe a large hospital outbreak (93 bloodstream infections) of colistin-resistant Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae isolates which was mirrored by increased colistin consumption. The outbreak was mostly traced to the clonal expansion of an mgrB deletion mutant o...
Multilocus sequence typing (MLST) is the gold standard genotyping technique for many microorganisms. This classification approach satisfies the requirements for a high-resolution, standardized, and archivable taxonomic system. Here, we describe the development of a novel MLST system to assist with t...
Legionella is the causative agent for Legionnaires' disease (LD) and is responsible for several large outbreaks in the world. More than 90% of LD cases are caused by Legionella pneumophila, and studies on the origin and transmission routes of this pathogen rely on adequate molecular characterization...
HIV sequence data can be used to reconstruct local transmission networks. Along international borders, like the San Diego-Tijuana region, understanding the dynamics of HIV transmission across reported risks, racial/ethnic groups, and geography can help direct effective prevention efforts on both sid...
To describe successful termination of an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) colonization within a neonatal service. Multisite neonatal intensive care unit and special care nurseries within a single health care service. Forty-four cases of VREfm-colonized neonatal inpatient...
Acinetobacter baumannii has become one of the major infection threats in intensive care units (ICUs) globally. Since 2008, A. baumannii has been the leading cause of ventilator-associated pneumonia (VAP) in our ICU at an infectious disease hospital in southern Vietnam. The emergence of this pathogen...
Rickettsia spp. are the causative agents of a number of diseases in humans. These bacteria are transmitted by arthropods, including ixodid ticks. DNA of several Rickettsia spp. was identified in Ixodes persulcatus ticks, however, the association of Ixodes trianguliceps ticks with Rickettsia spp. is...
We describe a case of an infant with recurrent bacteremia caused by Streptococcus equi subsp. zooepidemicus, likely transmitted from mother to infant. Our case highlights the importance of an epidemiological history and molecular diagnostics in ascertaining insights into transmission, pathogenesis,...
The remote and indigenous populations of Western Australia (WA) have one of the highest notification rates of gonorrhoea in the world. Despite this, the low rate of antimicrobial resistance in Neisseria gonorrhoeae from these regions permits the use of amoxycillin as empirical therapy. We describe t...
In 2013, an unusual increase of paratyphoid fever cases in travellers returning from Cambodia was reported in Japan. From December 2012 to September 2013, 18 cases of Salmonella Paratyphi A infection were identified. Microbiological analyses revealed that most isolates had the same clonal identity,...
Group A Streptococcus (GAS) genotype emm89 is increasingly recognized as a leading cause of disease worldwide, yet factors that underlie the success of this emm type are unknown. Surveillance identified a sustained nationwide increase in emm89 invasive GAS disease in the United Kingdom, prompting lo...
Salmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred...
A growing tendency for community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) to be involved in nosocomial infections was reported. The predominance of SCCmec type IV or V CA-MRSA in soft tissue infection has also been indicated in Northern Taiwan. To establish basic information...
The aim of this study was to analyze the molecular epidemiologic characteristics of Acinetobacter baumannii. A total of 398 isolates were collected in 7 regions of South China from January to June of 2012. Drug sensitivity was tested toward 15 commonly used antibiotics; thus, 146 multi-drug-resistan...
Barley yellow dwarf virus-GPV (BYDV-GPV) is transmitted by Rhopalosiphum padi and Schizaphis graminum in a persistent nonpropagative manner. To improve our understanding of its transmission mechanism by aphid vectors, we used two approaches, isobaric tags for relative and absolute quantitation (iTRA...
Aspergillus fumigatus is the leading cause of invasive aspergillosis. Adequate treatment is complicated by an increase in azole resistance. Here, the incidence of voriconazole, posaconazole and itraconazole resistance in clinical isolates from high-risk patients from either the haematology ward or t...
A prospective, noninterventional survey was conducted among Clostridium difficile positive patients identified in the time period of July until October 2012 in 18 hospitals distributed across all nine Austrian provinces. Participating hospitals were asked to send stool samples or isolates from ten s...
The introduction of rabbit hemorrhagic disease virus (RHDV) into Australia and New Zealand during the 1990s as a means of controlling feral rabbits is an important case study in viral emergence. Both epidemics are exceptional in that the founder viruses share an origin and the timing of their releas...
We developed a new method of typing for anginosus group streptococci (SAG). It is the first SAG-dedicated, PCR-based method, which allows to determine the relationship between strains. The method is based on the detection of tandem repeats among 9 genomic loci and is classified as multilocus variabl...
"Candidatus Neoehrlichia mikurensis" is the tick-borne agent of neoehrlichiosis, an infectious disease that primarily affects immunocompromised patients. So far, the genetic variability of "Ca. Neoehrlichia" has been studied only by comparing 16S rRNA genes and groEL operon sequences. We describe th...
Ireland has the highest rate of vancomycin-resistant Enterococcus faecium (VREfm) isolated from blood of nosocomial patients in Europe, which rose from 33% (110/330) in 2007 to 45% (178/392) in 2012. No other European country had a VREfm rate from blood cultures of >25%. Our aim was to elucidate the...
Canine distemper virus (CDV) (Paramyxoviridae-Morbillivirus) is a worldwide spread virus causing a fatal systemic disease in a broad range of carnivore hosts. In this study we performed Bayesian inferences using 208 full-length hemagglutinin gene nucleotide sequences isolated in 16 countries during...
Determination of microbial genetic relatedness is important for improving efficiency of infection control measures during hospital outbreaks. This study aimed to analyze the clonal relationships of clinical and environmental Acinetobacter baumannii strains isolated during an outbreak in the intensiv...
Most nosocomial infections by Staphylococcus epidermidis and Staphylococcus aureus have gained considerable attention due to an increase of infections caused by these strains that have been reported in recent years throughout the world. Most notably, it is important to underline the presence of S. e...
We investigated the clinical and molecular characteristics of Candida albicans bloodstream infection (BSI) in children from a tertiary-level medical centre in Taiwan over a 9-year period from January 2003 to December 2011. We performed multilocus sequence typing (MLST) to investigate the genetic rel...
Clostridium difficile infection (CDI) is increasingly recognized as a significant community acquired pathogen that causes disease in the community. The aim of the study was to investigate prospectively the incidence of community-acquired-CDI (CA-CDI) in Kuwait. Of the 2584 patients with diarrhea, 16...
In Finland, occurrence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) has previously been sporadic and related to travel. We describe the first outbreak of colonisation with KPC-KP strain ST512; it affected nine patients in a 137-bed primary care hospital. The index case was...
Dehong prefecture, Yunnan province on China's southwestern border was the gateway of the country's AIDS epidemic. Studies on HIV-1 molecular epidemiology will provide key information on virus transmission dynamics and help to inform HIV prevention strategies. HIV-1 infected youths (age 16-25 years)...
Salmonellosis is a significant cause of foodborne gastroenteritis in Australia, and rates of illness have increased over recent years. We adopt a Bayesian source attribution model to estimate the contribution of different animal reservoirs to illness due to Salmonella spp. in South Australia between...
Whole-genome sequencing is becoming a leading technology in the typing and epidemiology of microbial pathogens, but the increase in genomic information necessitates significant investment in bioinformatic resources and expertise, and currently used methodologies struggle with genetically heterogeneo...
Whole-genome sequencing (WGS) has emerged today as an ultimate typing tool to characterize Listeria monocytogenes outbreaks. However, data analysis and interlaboratory comparability of WGS data are still challenging for most public health laboratories. Therefore, we have developed and evaluated a ne...
Outbreaks of bloody diarrhea in swine herds in the late 2000s signaled the reemergence of an economically significant disease, swine dysentery, in the United States. Investigations confirmed the emergence of a novel spirochete in swine, provisionally designated "Brachyspira hampsonii," with two gene...
Over 700,000 cases of cholera were reported in Haiti between October 2010 and February 2015. In November 2011, the Cuban Medical Team serving in Haiti established a laboratory-supported sentinel surveillance system for cholera in 10 public hospitals (one in each of Haiti's 10 departments), to estima...
When epidemiological and evolutionary dynamics occur on similar timescales, pathogen genomes sampled from infected hosts carry a signature of the dynamics of epidemic spread. Phylodynamic inference methods aim to extract this signature from genetic data. We discuss the contribution of phylodynamics...
French Polynesia is an overseas territory located in the South Pacific. The incidence of tuberculosis in French Polynesia has been stable since 2000 with an average of 20 cases/y/100,000 inhabitants. Molecular epidemiology of Mycobacterium tuberculosis in French Polynesia is unknown because M. tuber...
Aspergillus fumigatus, the major etiological agent of human and animal aspergillosis, is a toxigenic fungus largely regarded as a single species by macroscopic and microscopic features. However, molecular studies have demonstrated that several morphologically identified A. fumigatus strains might be...
Methicillin-resistant Staphylococcus aureus (MRSA) health care-associated infections (HAIs) are a cause of extended hospitalizations and escalating health care costs. We typed 49 MRSA HAIs and their corresponding admission nasal MRSA isolates to determine strain-relatedness and better define the rol...
This study addresses the potential association of Escherichia coli O157:H7 genetic clusters with severe clinical manifestations in humans. The genotypes used in this model-based clustering had been delineated on the basis of lineage-specific polymorphism assay, Shiga toxin-encoding bacteriophage ins...
The epidemiological and molecular characteristics of eight linezolid nonsusceptible Enterococcus faecalis isolated from a teaching hospital in China (January to July 2014) were investigated. The target site modifications and cfr gene associated with linezolid resistance were not found. Results of th...
The aim of this study was to characterize the spread of carbapenemase-producing Klebsiella pneumoniae (CPKP) in a tertiary level hospital using ongoing active surveillance with rectal swab cultures. Furthermore, this study analyzed the presence of CPKP in the clinical samples (CS) of a single patien...
Cryptococcosis is caused by members of the Cryptococcus neoformans/Cryptococcus gattii species complex. Based on molecular identification, these two species have been further differentiated into molecular types. The aim of this work was to characterize clinical cryptococcal isolates recovered from s...
Campylobacter jejuni is a major food-borne pathogen that causes human gastroenteritis in many developed countries. In our study, we applied multilocus sequence typing (MLST) technology to 167 C. jejuni isolates from diverse sources in Eastern China to examine their genetic diversity. MLST defined 94...
Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explo...
Rift Valley Fever virus (RVFV) is a member of Bunyaviridae family that causes a febrile disease affecting mainly ruminants and occasionally humans in Africa, with symptoms that range from mid to severe. RVFV has a tri-segmented ssRNA genome that permits reassortment and could generate more virulent...
Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and ca...
Antimicrobial stewardship is a key component in the reduction of healthcare-associated infections, particularly Clostridium difficile infection (CDI). We successfully restricted the use of cephalosporins and, subsequently, fluoroquinolones. From an endemically high level of >280 cases per year in 20...
This study aimed to characterize the genomic context of the bla SPM-1 gene in Brazilian strains belonging to the pandemic Pseudomonas aeruginosa clone SP/ST277. WGS of clone SP/ST277 strains was performed using a Nextera paired-end library in an Illumina HiSeq 2500 sequencer. bla SPM-1 context was a...
Since the World Health Assembly's 1988 resolution to eradicate poliomyelitis, one of the main tools of the World Health Organization (WHO) Global Polio Eradication Initiative (GPEI) has been the live, attenuated oral poliovirus vaccine (OPV). OPV might require several doses to induce immunity but pr...
Numerous viruses can be transmitted by their corresponding vector insects; however, the molecular mechanisms enabling virus transmission by vector insects have been poorly understood, especially the identity of vector components interacting with the virus. Here, we used the yeast two-hybrid system t...
Methicillin-resistant Staphylococcus aureus (MRSA) infection and colonization, involving MRSA strains which differ from common human health care-associated clones, have become serious emerging conditions in equine veterinary hospitals. In 2010, MRSA spa type t535 caused an outbreak involving both ho...
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major concern globally; however, no comprehensive AMR data for gonococcal isolates cultured after 2006 in Korea have been published internationally. We determined the susceptibility of N. gonorrhoeae isolates cultured in 2011-13, the mecha...
Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to un...
Multi-drug resistant Klebsiella pneumoniae strains are a common cause of health care associated infections worldwide. Clonal spread of Klebsiella pneumoniae isolates carrying plasmid mediated CTX-M-15 have been commonly reported. Limited data is available regarding dissemination of chromosomally enc...
Staphylococcus aureus (S. aureus) is the most common cause of bone and joint infections. However, limited information is available on the distribution of S. aureus geno- and phenotypes causing orthopaedic infections. The aim of this study was to identify the dominating types causing infections in or...
Diseases caused by zoonotic viruses (viruses transmittable between humans and animals) are a major threat to public health throughout the world. By studying virus migration and mutation patterns, the field of phylogeography provides a valuable tool for improving their surveillance. A key component i...
Highly pathogenic avian influenza (HPAI) viruses threaten human and animal health yet their emergence is poorly understood, partly because sampling of the HPAI Asian-origin H5N1 lineage immediately after its identification in 1996 was comparatively sparse. The discovery of a novel H5N8 virus in 2013...
Advances in DNA sequencing have greatly enhanced the molecular epidemiology studies. In order to assess evolutionary and phylogenetic relation of Mycobacterium tuberculosis isolates several gene targets were evaluated. In this study, appropriate fragments of 5 highly variable genes (rpsL, mprA, lipR...
The Mycobacterium abscessus complex are the rapidly growing mycobacteria (RGM) most commonly causing lung disease, especially in cystic fibrosis (CF) patients. Ireland has the world's highest CF incidence. The molecular epidemiology of M. abscessus complex in Ireland is unreported. We performed rpoB...
In November 2011, The Rockefeller University Center for Clinical and Translational Science (CCTS), the Laboratory of Microbiology and Infectious Diseases, and Clinical Directors Network (CDN) launched a research and learning collaborative project with six community health centers in the New York Cit...
No abstract available
The community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic in the United States is attributed to the spread of the USA300 clone. An epidemic of CA-MRSA closely related to USA300 has occurred in northern South America (USA300 Latin-American variant, USA300-LV). Using phyl...
Between December 2010 and July 2011, 252 cases of STEC O157 PT8 stx1 + 2 infection were reported in England, Scotland and Wales. This was the largest outbreak of STEC reported in England and the second largest in the UK to date. Eighty cases were hospitalized, with two cases of haemolytic uraemic sy...
The objective of this study was to identify the Staphylococcus aureus clonal types currently circulating in animals, humans in contact with animals and the environment in Portugal based on genetic relatedness, virulence potential and antimicrobial/biocide susceptibility. Seventy-four S. aureus isola...
The advent of molecular typing using MIRU-VNTR mini-satellites has largely facilitated tuberculosis (TB) molecular epidemiological studies. Apart from detecting the chains of transmission and risk factors, these markers have also allowed to study the phenomena of mixed strain infections versus micro...
Our goals were to study the molecular epidemiology and antimicrobial susceptibilities of C. difficile strains in Israel. Microbiology laboratories serving 6 general hospitals (GH) and 10 long-term care facilities (LTCF) were asked to submit all stool samples in January-February 2014 that tested posi...
Clostridium difficile infection (CDI) became a public health problem for the global spreading of the so-called hypervirulent PCR ribotypes (RTs) 027 and 078, associated with increases in the transmission and severity of the disease. However, especially in Europe, several RTs are prevalent, and the c...
In Denmark, the incidence of vancomycin-resistant Enterococcus faecium (VREfm) has increased since 2012. The aim of this study was to investigate the epidemiology and clonal relatedness of VREfm isolates in Danish hospitals in 2012-13 using WGS. The second aim was to evaluate if WGS-based typing cou...
No abstract available
Multiple-locus variable number-tandem repeat analysis (MLVA) of Mycobacterium avium subspecies paratuberculosis (MAP) isolates may contribute to the knowledge of strain diversity in Argentina. Although the diversity of MAP has been previously investigated in Argentina using IS900-RFLP, a small numbe...
The objectives of the present study were to determine Helicobacter pylori via culture, polymerase chain reaction and histopathological diagnosis in 101 children ranging in age from 4 to 18 years, to identify the association among restriction fragment length polymorphism types and clinical disease an...
Molecular epidemiology (ME) is one of the main areas in tuberculosis research which is widely used to study the transmission epidemics and outbreaks of tubercle bacilli. It exploits the presence of various polymorphisms in the genome of the bacteria that can be widely used as genetic markers. Many D...
In 2010, two infants became ill at a hospital in Mexico. Subsequently, a range of clinical, environmental, and powdered and rehydrated infant formula isolates were identified by using a combination of phenotyping and PCR probes. The strains were clustered according to pulsed-field gel electrophoresi...
Outbreaks of Salmonella enterica serotype Enteritidis infections associated with eggs occurred in French Polynesia during 2008-2013. Molecular analysis of isolates by using clustered regularly interspaced short palindromic repeat polymorphisms and multilocus variable-number tandem-repeat analysis wa...
During 2007-2010, 13 545 confirmed human verocytotoxin (VT)-producing Escherichia coli (VTEC) infections were reported in the European Union, including 777 haemolytic uraemic syndrome (HUS) cases. Clinical manifestations were reported for 53% of cases, 64% of which presented with diarrhoea alone and...
Multilocus sequence typing (MLST) is commonly used to understand the genetic background of invasive pneumococcal disease (IPD) isolates. This study was conducted to identify serotype and genetic change among IPD isolates in Canadian children following vaccine use. Clinical isolates collected from ch...
No abstract available
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is one of the worldwide concerns of antimicrobial chemotherapy. An accumulation of ten patients in five families (A-E) suffering from skin and soft tissue infection (SSTI) of CA-MRSA was experienced in 2012, in Fuchu-shi, Tok...
Campylobacter jejuni is a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbia...
Waterborne epidemics of tularaemia caused by Francisella tularensis are increasingly reported in Turkey. We have used whole genome sequencing to investigate if F. tularensis isolated from patients could be traced back to drinking water sources. Tonsil swabs from 33 patients diagnosed with oropharyng...
Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent source of infection in the neonatal intensive care unit (NICU), often associated with significant morbidity. Active detection and isolation (ADI) programs aim to reduce transmission. We describe a comprehensive analysis of the clinical...
Widespread infections with community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) have occurred in the United States with the dissemination of the USA300 strain beginning in 2000. We examined 105 isolates obtained from children treated at the University of Chicago from 1994 to...
The shapes of phylogenetic trees relating virus populations are determined by the adaptation of viruses within each host, and by the transmission of viruses among hosts. Phylodynamic inference attempts to reverse this flow of information, estimating parameters of these processes from the shape of a...
Enterovirus (EV) infection is common in infants, but the information with regard to the molecular epidemiology and the associations between types and clinical variables is very scarce. This study includes 195 children <3 months old with fever, attended from March 2010 to December 2012 in an emergenc...
Educational and rehabilitation programmes increase the quality-of-life of patients with cystic fibrosis, but patients are discouraged to participate because of the risk of cross-infections. Isolates of Pseudomonas aeruginosa, Staphylococcus aureus and Haemophilus influenzae cultured one year before...
Using a novel combination of whole-genome sequencing (WGS) analysis and geographic metadata, we traced the origins of Salmonella Bareilly isolates collected in 2012 during a widespread food-borne outbreak in the United States associated with scraped tuna imported from India. Using next-generation se...
This study determined the mechanisms and patterns of antimicrobial resistance among the isolates obtained from different wards of a teaching hospital in the city of Mashhad in north-east Iran. Between January 2012 and the end of June 2012, 36 isolates of Acinetobacter baumannii were collected from d...
We aimed to identify the source of Staphylococcus aureus contaminating hands of food handlers. Nasal samples and direct fingertip imprints were collected on 2 occasions from food handlers and characterized to determine likely sources of hand contamination. Most hand contamination was attributable to...
Asymptomatic colonization may contribute to Clostridium difficile transmission. Few data identify which patients are at risk for colonization. We performed a prospective cohort study of C. difficile colonization and risk factors for C. difficile acquisition and loss in hospitalized patients. Patient...
The purpose of this study was to determine the incidence of Clostridium difficile infections (CDI) and to characterise the isolates in 14 departments of ten academic hospitals in Slovakia. During a one-month study (September 2012) all unformed stool samples were investigated using a rapid test to de...
A. baumannii has emerged as an important nosocomial pathogen with an outstanding ability to acquire multidrug resistant mechanisms. In this study, we investigate the molecular epidemiology and carbapenem resistance mechanisms of A. baumannii in Tripoli, Northern Lebanon. One hundred sixteen non-dupl...
Routine surveillance in a neonatal intensive care unit (NICU) showed an increased detection of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) in August 2012, following nearly a year without detection. To describe the investigation and interventions by a hospital infec...
An appreciation of the genetic diversity of Mycobacterium tuberculosis (Mtb) is needed for effective planning of strategies in tuberculosis (TB) control. Large sequence polymorphisms (LSPs) are the molecular epidemiological and evolutionary markers for classification of Mtb into East Asian (EA) or B...
In 2011, a nationwide outbreak of tularaemia occurred in Norway with 180 recorded cases. It was associated with the largest peak in lemming density seen in 40 years. Francisella tularensis was isolated from 18 patients. To study the geographical distribution of F.tularensis genotypes in Norway and c...
Acinetobacter baumannii is one of the most important nosocomial pathogens worldwide. This study aimed to use multilocus sequence typing (MLST) for the epidemiological surveillance of A. baumannii isolates in Taiwan and analyze the clinical presentations and patients' outcome. MLST according to both...
Data on community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) in Israel are scarce. The objective of this study was to characterize the major CA-MRSA clones in Israel. All clinical MRSA isolates detected in the community during a period of 2.5 years (2011-2013) from individual...
Accurate and rapid typing of pathogens is essential for effective surveillance and outbreak detection. Conventional serotyping of Escherichia coli is a delicate, laborious, time-consuming, and expensive procedure. With whole-genome sequencing (WGS) becoming cheaper, it has vast potential in routine...
The incidence of vancomycin-resistant enterococcus (VRE) in China is increasing, the molecular epidemiology of VRE in China is only partly known. This study was conducted to assess the molecular characterization of resistance, virulence and clonality of 69 vancomycin-resistant Enterococcus faecium (...
Whole genome sequencing (WGS) of pathogens enables the sources and patterns of transmission to be identified during specific disease outbreaks and promises to transform epidemiological research on communicable diseases. This review discusses new insights into disease spread and transmission that hav...
The objectives of this study were to determine CTX-M-producing Escherichia coli ST131 strain prevalence in stool specimens from healthy subjects in central China and to molecularly characterize clonal groups. From November 2013 to January 2014, stool specimens from healthy individuals in Hunan Provi...
While whitefly-transmitted begomoviruses are economically important constraints to tomato production in Kuwait, little is known about genomic features of these viruses from Kuwait. A begomovirus isolated from severely diseased tomatoes, collected over a two-year period in the main tomato-growing are...
Molecular typing methods are critical for epidemiological investigations, facilitating disease outbreak detection and source identification. Study of the epidemiology of the emerging human pathogen Arcobacter butzleri is currently hampered by the lack of a subtyping method that is easily deployable...
One of the central objectives in the field of phylodynamics is the quantification of population dynamic processes using genetic sequence data or in some cases phenotypic data. Phylodynamics has been successfully applied to many different processes, such as the spread of infectious diseases, within-h...
The HIV-1 subtype A variant dominating the HIV-1 epidemics in former Soviet Union (FSU) countries (A(FSU)) represents one of the major clades of the HIV-1 pandemic. This variant was reported to have begun spreading among injecting drug users (IDUs) in the Ukrainian city of Odessa in late 1994. Two c...
Chlamydia trachomatis genogroups using ompA and multilocus sequence typing (MLST) were determined in consecutive isolates from school students aged 18 or older in the district of Brescia, Italy, 2012-2013. Among 40 samples, 4 ompA genovars and 18 STs were identified. Genovar E predominated (70 %) in...
We studied Staphylococcus aureus and Streptococcus pneumoniae carriage among elderly adults in Jakarta, Indonesia. Nasopharyngeal swabs were collected from 149 adults aged 60-97 years. Both S. aureus and S. pneumoniae were identified by conventional and molecular methods. Methicillin-resistant Staph...
We analyzed 1,093 Vibrio cholerae isolates from the Democratic Republic of the Congo during 1997-2012 and found increasing antimicrobial drug resistance over time. Our study also demonstrated that the 2011-2012 epidemic was caused by an El Tor variant clonal complex with a single antimicrobial drug...
The molecular epidemiology and carbapenem resistance mechanisms of clinical isolates of Acinetobacter baumannii obtained from a south Indian tertiary care hospital were investigated by repetitive extragenic palindromic sequence PCR (REP-PCR) and multi-locus sequence typing (MLST). Analysis of resist...
Phylogeographic studies inform about routes of pathogen dissemination and are instrumental for improving import/export controls. Genomes of 17 isolates of the bacterial wilt and potato brown rot pathogen Ralstonia solanacearum race 3 biovar 2 (R3bv2), a Select Agent in the United States, were thus a...
A total of 1085 strains of Acinetobacter sp. obtained from 280 medical institutions in the Chugoku and Shikoku areas of Japan were investigated between 2011 and 2013. Among these strains, 20 (1.84 %) showing meropenem or imipenem resistance with a MIC of >4 μg ml- 1 were detected. Of these 20 strain...
Although heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) has been increasingly reported, the true prevalence of hVISA is unclear, especially in Asia. In this study, the genotype-specific prevalence of hVISA among meticillin-resistant S. aureus (MRSA) clinical isolates collected f...
This study describes an interhospital spread of carbapenem-resistant Klebsiella pneumoniae (CRKP) producing NDM-7 carbapenemase that started in December 2013 in Madrid, Spain. NDM-7-producing CRKP were isolated from urine, rectal swabs or blood samples from seven patients admitted to three different...
In Portugal, listeriosis has been notifiable since April 2014, but there is no active surveillance programme for the disease. A retrospective study involving 25 national hospitals led to the detection of an outbreak that occurred between March 2009 and February 2012. The amount of time between the s...
Mixed infections have been considered as a potential obstacle for tuberculosis treatment and control. To date, few studies have been done to determine the rate of mixed infections of Mycobacterium tuberculosis in China. In this study, we used the standard 24-loci MIRU-VNTR method to genotype the rep...
To quantify the extent of inter- and intra-nursing home transmission of multidrug-resistant gram-negative bacteria (MDRGN) among residents with advanced dementia and characterize MDRGN colonization among these residents. Prospective cohort study. Twenty-two nursing homes in the greater Boston, Massa...
Ticks are important vectors of human pathogens. The knowledge of disease causing agents harboured by ticks in Norway is limited. The focus of this study was (a) to detect the bacteria of medical importance in ticks collected from the vegetation at locations in the southern part of the country and (b...
We analyzed in parallel 27 pediatric Clostridium difficile isolates by repetitive sequence-based polymerase chain reaction (RepPCR), pulsed-field gel electrophoresis (PFGE), and whole-genome next-generation sequencing. Next-generation sequencing distinguished 3 groups of isolates that were indisting...
We report an outbreak of Salmonella Enteritidis phage type 14b (PT14b) in the United Kingdom (UK) between May and September 2014 where Public Health England launched an investigation to identify the source of infection and implement control measures. During the same period, outbreaks caused by a Sal...
Cholera continues to be a global threat, with high rates of morbidity and mortality. In 2011, a cholera outbreak occurred in Palawan, Philippines, affecting more than 500 people, and 20 individuals died. Vibrio cholerae O1 was confirmed as the etiological agent. Source attribution is critical in cho...
Reliable molecular typing methods are necessary to investigate the epidemiology of bacterial pathogens. Reference methods such as multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) are costly and time consuming. Here, we compared our newly developed double-locus sequence t...
In Brazil, since 2009, there has been an ever increasing widespread of the bla(KPC-2) gene, mainly in Klebsiella pneumoniae. This study aims to assess the molecular epidemiology and genetic background of this gene in Enterobacteriaceae (non-K. pneumoniae) species from 9 Brazilian states between 2009...
The objective of this work was to investigate correlations between Acinetobacter baumannii isolates from neurosurgical intensive care unit patients and its environment. This is a prospective, observational study. The minimal inhibitory concentrations of antimicrobial agents against 27 clinical and 2...
Tetracycline resistance has been postulated as a potential phenotypic marker of livestock-associated lineage ST398 amongst meticillin-resistant Staphylococcus aureus (MRSA) clinical isolates in some European hospitals. The objective of this study was to determine if this marker could also be applied...
Group A streptococcus (GAS) is an important cause of morbidity and mortality worldwide. Surveillance of emm types has important implications, as it can provide baseline information for possible implementation of vaccination. A total of 1,349 GAS pediatric isolates were collected during a 7-year peri...
Acinetobacter baumannii is clustered with other phenotypically similar species into what has commonly become known as the ACB complex: A. calcoaceticus, A. pittii and, A. nosocomialis. The ecology and pathology of most of these species are not well understood, mainly because current specific phenoty...
Current sequencing technologies have created unprecedented opportunities for studying microbial populations. For pathogens with comparatively low per-site mutation rates, such as DNA viruses and bacteria, whole-genome sequencing can reveal the accumulation of novel genetic variation between populati...
Although vancomycin-resistant enterococci (VRE) are reported in Brazil since 1996, data on their impact over settings of different complexity are scarce. We performed a study aimed at identifying determinants of VRE emergence and spread in a public hospital consortium (comprising 2 hospitals, with 3...
The presence of clusters (identical genotypes infecting different patients) suggests patient-to-patient transmission or a common source for strains. We report the results of a genotyping study based on microsatellite markers of Candida albicans (n = 179) and Candida parapsilosis (n = 76) causing can...
Although much is known about the mechanisms affecting cholera spread, cholera outbreaks occur annually in Iran. The aim of this study was to characterize and assess the clonal correlation of strains obtained from an outbreak in 2013 in Iran. Thirty-three strains of Vibrio cholerae were isolated from...
An outbreak of severe respiratory illness associated with enterovirus D68 (EV-D68) infection was reported in mid-August 2014 in the United States. In this study, we evaluated the diagnostic utility of an EV-D68-specific real-time reverse transcription-PCR (rRT-PCR) that was recently developed by the...
This study was conducted to investigate the clinical features of hospital-associated infections (HAIs) caused by methicillin-resistant Staphylococcus aureus (MRSA) in Chinese children, and the molecular characteristics of the bacteria. Patients with HAIs caused by MRSA were identified retrospectivel...
Tuberculosis (TB) was once a major killer in Europe, but it is unclear how the strains and patterns of infection at 'peak TB' relate to what we see today. Here we describe 14 genome sequences of M. tuberculosis, representing 12 distinct genotypes, obtained from human remains from eighteenth-century...
Characterization of 14,079 circulating dengue viruses in a cross-border surveillance program, UNITEDengue, revealed that the 2013 outbreaks in Singapore and Malaysia were associated with replacement of predominant serotype. While the predominant virus in Singapore switched from DENV2 to DENV1, DENV2...
Porcine circovirus type 2 is one of the most widespread and economically relevant infections of swine. Four genotypes have been recognized, but currently, only three (PCV2a, PCV2b and PCV2d) are effectively circulating. The widespread livestock trade and rapid viral evolution have contributed to det...
Here we report a retrospective clinical and molecular study conducted in a tertiary care facility in southern Madrid, Spain, from January 2009 to February 2014 to investigate the epidemiology of carbapenemase-producing Klebsiella pneumoniae (CPKp). Carbapenemase genes were identified in 97 non-dupli...
The aim of this clinical investigation was to identify and quantify the microbial species adhering to toothbrush bristles after controlled brushing and storage in different antimicrobial agents. Sixteen healthy participants were enrolled in this study and randomly submitted to 4 interventions in a c...
Several antimicrobial agents and proton pump inhibitors (PPIs) have been identified as risk factors for Clostridium difficile infections (CDIs). Nationwide laboratory-based surveillance of CDIs in Finland since 2008 has shown variation in regional CDI rates. We evaluated whether regional differences...
Our aim was to determine and characterize S. aureus (SA) isolated from infections in newborns for antibiotic resistance, virulence factors, genotypes, epidemiology and antibiotic consumption. Prospective surveillance of infections was conducted. Data about antibiotic treatment were analyzed. Antimic...
During March 25-May 5, 2014, we investigated 11 outbreaks of peste des petits ruminants in Heilongjiang Province, China. We found that the most likely source of the outbreaks was animals from livestock markets in Shandong. Peste des petits ruminants viruses belonging to lineages II and IV were detec...
The molecular epidemiology of pediatric Clostridium difficile infection (CDI) is poorly understood. We aimed to identify the restriction endonuclease analysis (REA) groups causing CDI and to determine risk factors and outcomes associated with CDI caused by epidemic strains in children. Retrospective...
Tuberculosis (TB) is an ancient disease with an enormous global impact. Despite declining global incidence, the diagnosis, phenotyping, and epidemiological investigation of TB require significant clinical microbiology laboratory resources. Current methods for the detection and characterization of My...
Helicobacter pylori is a highly genetically diverse bacterial species, which can persist in the gastric environment for decades. Recent studies have shown that single infections predominate in developed countries, whereas mixed infections are more prevalent in developing countries. Mixed infections...
The noroviruses are now considered a leading cause of outbreaks of non-bacterial gastroenteritis worldwide. Vaccine strategies against norovirus are currently under consideration but depend on a detailed knowledge of the capsid genotypes. This study examined the incidence of norovirus outbreaks in V...
Enterovirus D68 was implicated in a widespread outbreak of severe respiratory illness across the USA in 2014 and has also been reported sporadically in patients with acute flaccid myelitis. We aimed to investigate the association between enterovirus D68 infection and acute flaccid myelitis during th...
Reasons for the successful global dissemination of multidrug-resistant Escherichia coli sequence type 131 (ST131) are undefined, but may include enhanced transmissibility or ability to colonize the intestine compared with other strains. We identified a household in which 2 young children had urinary...
Severe Acinetobacter baumannii infections in immunocompetent patients are uncommon, and the virulence mechanisms of this organism are not fully understood. Following an outbreak of fatal A. baumannii infections in a cohort of relatively immunocompetent patients (low comorbidity and illness severity...
In January 2014 a possible outbreak of Burkholderia cepacia bacteremia occurred in a hemodialysis center situated in La Linea de la Concepción (Cadiz). An investigation was begun to confirm the outbreak, identify the source, and implement control measures. A descriptive analysis was performed to des...
In this study, we comprehensively described the clinical risk factors, outcome, epidemiology, and molecular basis associated with an outbreak of extensively drug-resistant KPC-2-producing Klebsiella pneumoniae involving 15 patients in a teaching hospital from May 1 to June 27, 2013. Most of the pati...
The objective of this study was to characterise isolates of methicillin-susceptible Staphylococcus aureus (MSSA) with resistance to clindamycin and/or tobramycin in southeast Sweden, including the previously described ECT-R clone (t002) found in Östergötland County, focusing on clonal relatedness, v...
To explore temporal associations between planned antibiotic stewardship and infection control interventions and the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA). Retrospective ecological study and time-series analysis integrating typing data from the Scottish MRSA ref...
Compartmentalized HIV-1 replication within the central nervous system (CNS) likely provides a foundation for neurocognitive impairment and a potentially important tissue reservoir. The timing of emergence and character of this local CNS replication has not been defined in a population of subjects. W...
Flies may act as potential vectors for the spread of resistant bacteria to different environments. This study was intended to evaluate the presence of Escherichia coli strains resistant to cephalosporins in flies captured in the areas surrounding five broiler farms. Phenotypic and molecular characte...
Acinetobacter baumannii is a Gram-negative bacterial agent involved in nosocomial infections. In this five-year retrospective study, phylogenetic relationships among carbapenem-resistant A. baumannii strains that were isolated at Teikyo University Hospital in Tokyo metropolis, Japan, were explored....
Information about the molecular structure of MRSA strains provides significant insights into the epidemiology of this important pathogen. To investigate the molecular characteristics of MRSA isolates, MRSA isolates were subjected to molecular typing by means of spa typing, multilocus sequence typing...
N. meningitidis is a major cause of meningitis and septicemia and a major public health problem in many countries. The disease, that can be fulminant, has a high mortality and may cause serious sequelae, even in cases of apparently optimal medical treatment. Chemoprophylaxis may prevent secondary ca...
This study characterized Neisseria meningitidis serogroup C strains in China in order to establish their genetic relatedness and describe the use of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) to provide useful epidemiological information. A total of 215 N. meningitidis serogroup...
Stenotrophomonas maltophilia is an emerging nosocomial pathogen responsible for serious human infections. This study was carried out to determine antibiotic susceptibility, resistance mechanisms (integrons, sul1 and sul2), and genetic relatedness (Enterobacterial Repetitive Intergenic Consensus [ERI...
No abstract available
Methicillin-resistant S. aureus (MRSA) is one of the most important organisms causing hospital-acquired infections worldwide. Molecular analysis of MRSA strains from Taif, Saudi Arabia, had not been previously done. Phenotypic and molecular characteristics of MRSA isolated from Taif hospitals were i...
Pseudomonas aeruginosa is an important nosocomial pathogen, commonly causing infections in immunocompromised patients. The aim of this study was to examine the genetic relatedness of metallo-beta-lactamase (MBL) producing carbapenem resistant Pseudomonas aeruginosa clinical isolates collected from 2...
Genotyping results and epidemiologic investigation were used to confirm tuberculosis transmission from a cadaver to an embalmer. This investigation highlights the utility of genotyping in identifying unsuspected epidemiologic links and unusual transmission settings. In addition, the investigation pr...
As most newly characterized emerging infectious diseases are considered to be zoonotic, a modern pre-eminence ascribed within this classification lies clearly within the viral taxonomic realm. In particular, RNA viruses deserve special concern given their documented impact on conservation biology, v...
The molecular characteristics and epidemiology of carbapenemase-producing Escherichia coli (CPEC) isolates from Shanghai, China, were investigated using 21 imipenem-resistant E. coli isolates obtained from a Shanghai teaching hospital from 2011 to 2014. The presence of bla KPC, bla IMP, bla VIM, bla...
Invasive Mycobacterium chimaera infections were diagnosed in 2012 in 2 heart surgery patients on extracorporeal circulation. We launched an outbreak investigation to identify the source and extent of the potential outbreak and to implement preventive measures. We collected water samples from operati...
OXA-48 is a highly prevalent carbapenemase and has been isolated worldwide. Here, we investigate the in vivo horizontal gene transfer (HGT) of blaOXA-48 from Klebsiella pneumoniae to Escherichia coli in an infected patient. Bacterial isolates were characterized by susceptibility testing, multilocus...
The objective of this study was to perform a multinational survey of patients' colonization by metallo-β-lactamase (MBL)-producing Enterobacteriaceae, including their molecular characterization. Patients in 18 hospital units across Europe and Israel (n = 17 945) were screened between mid-2008 and mi...
Streptococcus dysgalactiae subsp. equisimilis (SDSE) isolates are the most common group C streptococci in humans and reports of invasive infections associated with SDSE have been increasing. Molecular epidemiology studies are an important strategy to trace the emergence and spread of possible well-f...
Recently, we reported a high prevalence (16%) of urogenital Chlamydia trachomatis infections among women in a rural setting in South Africa. Molecular epidemiological studies on C. trachomatis infections could provide insights into the characteristics of this epidemic, yet such data are not availabl...
An influenza A pandemic occurred in 2009-2010. A novel H1N1 virus (hereafter H1N1pdm) was responsible for this outbreak. H1N1pdm viruses have been largely seen in recent human influenza A viruses. This virus was descended from a triple-reassorted swine virus consisting of human, avian, and swine ori...
MRSA population dynamics is undergoing significant changes, and for this reason it is important to know which clones are circulating in our nosocomial environment. A total of 118 MRSA isolates were collected from clinical samples from patients with previous hospital or healthcare contact (named as h...
Methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) are classified epidemiologically as health care-associated hospital onset (HAHO)-, health care-associated community onset (HACO)-, or community-associated (CA)-MRSA. Clinical and molecular differences between HAHO- and H...
Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance. In this study, the genome of an ST10 outbreak A. baumannii isolate LAC-4 was completely sequenced to better understand its epidemiology, antibiotic resistance genetic determinants and potential virulence factors...
Culex tritaeniorhynchus (Diptera: Culicidae), an important vector of Japanese encephalitis belongs to the Culex vishnui subgroup which includes two other vector species namely, Cx. Vishnui and Cx. pseudovishnui. Many varieties and types of Cx. tritaeniorhynchus have been reported, besides population...
Malaria parasites are continually evolving to evade the immune system and human attempts to control the disease. To eliminate malaria from regions where it is deeply entrenched we need ways of monitoring what is going on in the parasite population, detecting problematic changes as soon as they arise...
Multidrug-resistant (MDR) Klebsiella pneumoniae has become a leading cause of nosocomial infections worldwide. Despite its prominence, little is known about the genetic diversity of K. pneumoniae in resource-poor hospital settings. Through whole-genome sequencing (WGS), we reconstructed an outbreak...
Outbreaks of shigellosis have been documented in men who have sex with men (MSM), associated with interpersonal transmission and underlying HIV infection. We observed a rise in Shigella flexneri isolates identified in a downtown tertiary-care hospital laboratory located within the city centre commun...
Enterococcus faecalis (E. faecalis) is a common cause of nosocomial infection in immunocompromised patients. The presence and dissemination of high-risk clonal complexes, such as CC2, is an ongoing problem in hospitals. The aim of this work was to characterize 24 E. faecalis isolates from ICU patien...
Determine whether the NAP1 strain identified by polymerase chain reaction (PCR)-based stool assay is correlated with CDI severity and clinical outcomes. Medical records of adult patients with positive stool Xpert® Clostridium difficile PCR assay for an initial episode of CDI between January 2012 and...
We aimed to describe bacterial etiology of acute otitis media (AOM) and characterize resistance, serotypes and genotype profiles of AOM-causing pneumococci recovered in Moscow children. Children with AOM and an available middle ear fluid specimen were prospectively enrolled in this study. Streptococ...
Phylogeography improves our understanding of spatial epidemiology. However, application to practical problems requires choices among computational tools to balance statistical rigor, computational complexity, sensitivity to sampling strategy and interpretability. We introduce a fast, heuristic algor...
Several outbreaks of Enterovirus 68 (EV-D68) have recently been reported in the USA and Canada, causing substantial hospitalisation of children with severe respiratory disease. The acute flaccid paralysis detected in the USA and Canada among children with EV-D68 infection has raised concerns about t...
Sequence type 131 (ST131) is a predominant lineage among extraintestinal pathogenic Escherichia coli. It plays a major role in the worldwide dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. The ST131 pandemic is mainly the result of clonal expansion of the single well-adapted...
Staphylococcus aureus is the predominant cause of bacteremia worldwide. We assessed the molecular epidemiology and antibiotic resistance of methicillin-resistant S aureus isolates causing bacteremia in southern Mississippi. Diverse genetic backgrounds in terms of staphylococcal cassette chromosome m...
In this study, fungemia cases from four tertiary hospitals located in Shanghai and Anhui province in China from March 2012 to December 2013 were enrolled to investigate clinical features, species distribution, antifungal susceptibility and strain relatedness. During the study period, 137 non-duplica...
Cholera, an infectious disease caused by Vibrio cholerae, is a major public health problem and is a particularly burden in developing countries including Nepal. Although the recent worldwide outbreaks of cholera have been due to V. cholerae El Tor, the classical biotypes are still predominant in Nep...
Epidemiological data on the aetiologic agents of feline sporotrichosis in Malaysia have not been reported, though human sporotrichosis in Malaysia is reported to be transmitted primarily via cat scratch. To the best of our knowledge, the present report is the first study of the molecular epidemiolog...
No abstract available
The magnitude and scope of Clostridium difficile infection in the United States continue to evolve. In 2011, we performed active population- and laboratory-based surveillance across 10 geographic areas in the United States to identify cases of C. difficile infection (stool specimens positive for C....
In Japanese Red Cross (JRC) blood centers, blood collected from donors with serum alanine aminotransferase (ALT) levels of more than 60 U/L are disqualified even if serologically negative for transfusion-transmitted infections (TTIs). To assess potential risks of TTIs in plasma with elevated serum A...
Escherichia coli is the leading cause of various infections, both in community and nosocomial settings. Our objective was to determine the antibiotic resistance rates and the phylogenetic groups of invasive E. coli and to assess the relationship between these characteristics according to the communi...
To examine the epidemiology of pneumococcal infection in Galicia (Spain) after the incorporation of the pneumococcal conjugate vaccine, and to determine serotype distribution, antibiotic susceptibility, risk factors and associated mortality in cases of invasive pneumococcal disease (IPD) during 2011...
To describe epidemiologic features and identify risk factors for methicillin-resistant Staphylococcus aureus (MRSA) acquisition in a level III neonatal intensive care unit (NICU). A prospective, cohort study in a university-affiliated NICU with an infection control program including weekly nasal cul...
Nosocomial outbreaks of multidrug-resistant Acinetobacter baumannii are of worldwide concern. Using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and multiple locus variable number tandem repeat sequence (VNTR) analysis (MLVA), the present work examines the genetic dive...
Prevention and management of Escherichia coli bloodstream infections (EC-BSIs) have become increasingly complicated by antimicrobial resistance and rapid dissemination. We investigated the antimicrobial epidemiology and phylogenetic background of clinical E. coli isolates from patients with bloodstr...
To identify risk factors associated with carbapenem-resistant Klebsiella pneumoniae (CRKP) infection/colonization and death and to investigate the resistance and homology of CRKP. A retrospective 1:1 case-control study was conducted at Changhai Hospital, China, from January 2010 to December 2011.The...
The biosynthesis of nano-silica silver nanocomposite (NSAgNC) and it is as antibacterial effect on gram-negative bacteria viz.Escherichia coli and Pseudomonas aeruginosa has been investigated for disinfection of water. The as-synthesized NSAgNC exhibited antibacterial activity in a dose dependent ma...
Here, I review the population structure and phylogeography of the two contrasting families of Mycobacterium tuberculosis, Beijing and Ural, in the context of strain pathobiology and human history and migration. Proprietary database (12-loci MIRU-VNTR profiles of 3067 Beijing genotype isolates) was s...
The mechanism by which carbapenem non-susceptible Acinetobacter nosocomialis (CNSAN) is disseminated is rarely described in the literature. In this study, we delineated the molecular epidemiology of CNSAN isolated from patients in a medical center in Taiwan. Fifty-four non-duplicate bloodstream isol...
The objective of the study is to report a multidrug-resistant outbreak of Providencia stuartii that occurred in inpatients in the Athens area in 2012 resulting from a very successful transmissible A/C multidrug-resistant plasmid. Thirteen multidrug-resistant P. stuartii clinical isolates from 5 hosp...
The zoonotic bacterium Corynebacterium ulcerans may be pathogenic both in humans and animals: toxigenic strains can cause diphtheria or diphtheria-like disease in humans via diphtheria toxin, while strains producing the dermonecrotic exotoxin phospholipase D may lead to caseous lymphadenitis primari...
Although Malta is historically linked with the zoonosis brucellosis, there had not been a case of the disease in either the human or livestock population for several years. However, in July 2013 a case of human brucellosis was identified on the island. To determine whether this recent case originate...
This study compared the pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), multilocus variable-number of tanden-repeat analysis (MLVA), and multilocus sequence typing (MLST) methods for typing 188 Salmonella Enteritidis strains from different sou...
Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, im...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of both hospital- and community-acquired infections worldwide. However, data about the molecular epidemiology of MRSA in North Africa are still scarce. All MRSA isolates recovered between January 2006 and July 2011 from one Algerian...
Porcine epidemic diarrhea has become pandemic in the Asian pig-breeding industry, causing significant economic loss. In the present study, 11 complete genomes of porcine epidemic diarrhea virus (PEDV) field isolates from China were determined and analyzed. Frequently occurring mutations were observe...
Clostridium difficile infection has gained importance in recent years as a result of the rapid spread of epidemic strains, including hypervirulent strains. This study reports the molecular epidemiology of C. difficile obtained from hospitalized patients in Chile. Seven hundred and nineteen isolates...
No abstract available
RNA interference (RNAi) was shown over 18 years ago to be a mechanism by which arbovirus replication and transmission could be controlled in arthropod vectors. During the intervening period, research on RNAi has defined many of the components and mechanisms of this antiviral pathway in arthropods, y...
Previous studies found conflicting results regarding associations between urogenital Chlamydia trachomatis infections and ethnicity or urogenital symptoms among at-risk populations using either ompA-based genotyping or high-resolution multilocus sequence typing (MLST). This study applied high-resolu...
Here we describe an outbreak caused by a pandrug-resistant Providencia stuartii strain involving 15 critically ill patients in a Greek intensive care unit (ICU) during September-November 2011. All isolates harboured the blaVIM-1 gene and a class 1 integron structure of 1913 bp as well as blaSHV-5 an...
We argue in favor of a concerted and coordinated response to stop tuberculosis (TB) by monitoring global TB spread, drug-resistance surveillance and populations at risk using available molecular and web tools to identify circulating clones of Mycobacterium tuberculosis complex (MTBC). We took specif...
All 16 Klebsiella pneumoniae isolates and both Escherichia coli isolates harbored the bla(OXA-232) and bla(CTX-M-15) genes. Furthermore, all 16 K. pneumoniae isolates belonged to a unique pulsed-field gel electrophoresis clone and were assigned to an identical sequence type (ST14). The 2 E. coli iso...
Group B Streptococcus (GBS) is one of the major pathogens of severe newborn sepsis and meningitis. Understanding its regional molecular epidemiology is helpful for regulating efficient prevention practice. A total of 160 GBS strains were collected from colonized pregnant women in six hospital settin...
Recent genotyping studies of Mycobacterium tuberculosis in Ethiopia have reported the identification of a new phylogenetically distinct M. tuberculosis lineage, lineage 7. We therefore investigated the genetic diversity and association of specific M. tuberculosis lineages with sociodemographic and c...
Microbial whole-genome sequencing (WGS) is poised to transform many of the currently used approaches in medical microbiology. Recent reports on the application of WGS to understand genetic evolution and reconstruct transmission pathways have provided valuable information that will influence infectio...
The infection route of Helicobacter pylori has been recognized to be mainly intrafamilial, preferentially mother-to-child, especially in developed countries. To determine the transmission route, we examined whether multilocus sequence typing (MLST) was useful for analysis of intrafamilial infection....
No abstract available
Viral outbreaks, such as the 2014 ebolavirus, can spread rapidly and have complex evolutionary dynamics, including coinfection and bulk transmission of multiple viral populations. Genomic surveillance can be hindered when the spread of the outbreak exceeds the evolutionary rate, in which case consen...
Listeria (L.) monocytogenes causes orally acquired infections and is of major importance in ruminants. Little is known about L. monocytogenes transmission between farm environment and ruminants. In order to determine potential sources of infection, we investigated the distribution of L. monocytogene...
Listeriosis is a frequent silage-associated disease in ruminants. The slugs Arion vulgaris are invaders in gardens, vegetable crops and meadows for silage production. Field and laboratory studies were conducted to clarify whether slugs could host Listeria monocytogenes and thereby constitute a threa...
Escherichia coli serogroup O111 is among the six most commonly reported non-O157:H7 Shiga toxin-producing E. coli (STEC), which are emerging as important foodborne pathogens. We have assembled a collection of environmental and clinical strains of E. coli O111 from diverse sources and investigated va...
Outside Africa, the global phylogeography of HIV is characterized by compartmentalized local epidemics that are typically dominated by a single subtype, which indicates strong founder effects. We hypothesized that the competition of viral strains at the epidemic level may involve an advantage of the...
In Japan, publicly subsidized Haemophilus influenzae serotype b vaccines became available in 2011; consequently, the incidence of invasive H. influenzae infection in paediatric patients of less than 5 years of age decreased dramatically. In 2013, the first case of H. influenzae serotype f (Hif) meni...
The prevalence of Clostridium difficile infections has increased due to the emergence of epidemic variants from diverse genetic lineages. Here we describe the emergence of a novel variant during an outbreak in a Costa Rican hospital that was associated with severe clinical presentations. This C. dif...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health concern associated with residence in a long-term care facility (LTCF). The aim of this prospective study was to characterize MRSA isolated from residents over a 1-year period and their physical environment over a 2-year peri...
Staphylococcus aureus or methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of surgical site infections (SSIs). The aim of our study was to characterize molecularly S. aureus isolates from SSIs in orthopedic patients in Shanghai, China. Eighty-two S. aureus isolates (46 methicilli...
Mosquito-borne alphaviruses have the potential to cause large outbreaks throughout the world. Here we investigated the causative agent of an unexpected Sindbis virus (SINV) outbreak during August-September, 2013, in a previously nonendemic region of Sweden. Mosquitoes were collected using carbon dio...
Vibrio parahaemolyticus carrying the tdh gene, encoding the thermostable direct hemolysin (TDH), or the trh gene, encoding the TDH-related hemolysin (TRH), are both considered virulent strains. There are, however, disproportionally fewer reports of infections caused by seafood contaminated with trh-...
We previously reported a shift in the electrophoretic type (ET) of invasive MenC in Canada from predominantly ET-15 to ET-37 in the post-MenC conjugate vaccine period. This study sought to confirm this trend by examining all culture-confirmed invasive MenC case isolates in Canada in the period from...
During 2014, henipavirus infection caused severe illness among humans and horses in southern Philippines; fatality rates among humans were high. Horse-to-human and human-to-human transmission occurred. The most likely source of horse infection was fruit bats. Ongoing surveillance is needed for rapid...
Ciprofloxacin resistance (CipR) among gonococcal strains in San Francisco (SF) increased between 2001 and 2006 and decreased between 2007 and 2009. Molecular typing of isolates obtained from 2005 to 2009 was performed to elucidate changes in CipR prevalence. A total of 2526 samples were collected at...
In Nakhon Phanom, Thailand, we identified 38 hospitalized patients with Streptococcus suis infection during 2006-2012. Deafness developed in 12 patients; none died. Thirty-five reported recent exposure to pigs/pork. Annual incidence was 0.1-2.2 cases/100,000 population (0.2-3.2 in persons ≥20 years...
Gonorrhoea and widely spread antimicrobial resistance (AMR) in its etiological agent Neisseria gonorrhoeae are major public health concerns worldwide. Gonococcal AMR surveillance nationally and internationally, to identify emerging resistance and inform treatment guidelines, is imperative for public...
With an increase in the use of colistin methansulfonate (CMS) to treat carbapenem-resistant Acinetobacter baumannii infections, colistin resistance is emerging. Patients with infection or colonization due to colistin-resistant A. baumannii were identified at a hospital system in Pennsylvania. Clinic...
The aim of this study was to investigate the rate of asymptomatic colonization rate of Clostridium difficile among both healthcare workers (HCWs) and patients in a hospital ward in Sweden. In a prospective observational study, asymptomatic HCWs (n = 22) (22/60; 37%) attending patients in an infectio...
Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequ...
Clostridium difficile is the most commonly identified pathogen among health care-associated infections in the United States. There is a need for accurate and low-cost typing tools that produce comparable data across studies (i.e., portable data) to help characterize isolates during epidemiologic inv...
The present study was designed to provide a snapshot on carbapenemase-producing Pseudomonas aeruginosa (n=11) and Acinetobacter baumannii (n=7) isolates in hospitalized patients (November 2011, January-March 2012) from two main hospitals in Bucharest, south Romania. Clonality among isolates was esta...
The aim of the study was to investigate the molecular epidemiologic of Staphylococcus aureus isolated from seven staphylococcal food-poisoning (SFP) outbreaks between 2006 and 2013 in Xi'an, northwest China. A total of seven S. aureus isolates associated with seven SFP outbreaks were obtained and ch...
Inactivation of pathogenic microbial samples is often necessary for the protection of researchers and to comply with local and federal regulations. By its nature, biological inactivation causes changes to microbial samples, potentially affecting observed experimental results. While inactivation-indu...
The aim of this study was to investigate the prevalence and characteristics of imipenem-resistant Acinetobacter baumanni isolated from surgical wards in a university hospital, China. A total of 143 non-duplicate A. baumannii were isolated from 517 inpatients in surgery intensive care units (ICUs), b...
No abstract available
To systematically review the evidence for the impact of study design and setting on the interpretation of tuberculosis (TB) transmission using clustering derived from Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) strain typing. MEDLINE, EMBASE, CINHAL, Web of...
Acinetobacter baumannii is an increasingly common pathogen in healthcare settings globally. It is frequently resistant to multiple antimicrobial agents and there are recent reports on strains that are pandrug resistant. The aim of the study was to characterize the mechanisms of carbapenem resistance...
Burn intensive care unit (BICU) patients are specifically exposed to deep-seated nosocomial infections due to Candida albicans. Superficial carriage of C. albicans is a potential source of infection and dissemination, and typing methods could be useful to trace the different isolates. Multilocus seq...
Escherichia coli is one of the most common clinical pathogens causing nosocomial infection. The widespread cefotaxime-beta lactamases (CTX) has increased the multidrug resistance (MDR) of E. coli and has brought great trouble to the doctor treating the infection. ESBL-positive E. coli isolates were...
A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framewor...
A multilocus sequence typing (MLST) scheme including 7 housekeeping genes was used to evaluate whether the current spread of multidrug-resistant Enterobacter cloacae isolates worldwide might be associated to specific successful clones. Fifty E. cloacae clinical isolates of worldwide origin, with var...
Ceftaroline is a novel cephalosporin with activity against Gram-positive organisms, including meticillin-resistant Staphylococcus aureus (MRSA). The objective of this study was to investigate the susceptibility to ceftaroline of hospital-associated MRSA (HA-MRSA) isolates causing acute bacterial ski...
The aim of this study was to investigate the prevalence and the mechanisms of carbapenem and colistin resistance in Acinetobacter baumannii clinical isolates in an Algerian hospital. Twelve isolates were collected between October 2013 and March 2014. All isolates were resistant to almost all antibio...
Here we report on a long-term outbreak from 2009 to 2012 with an XDR Pseudomonas aeruginosa on two wards at a university hospital in southern Germany. Whole-genome sequencing was performed on the outbreak isolates and a core genome was constructed for molecular epidemiological analysis. We applied a...
Twenty-one women and their respective singleton infants participated in this study, contributing with samples of breast milk and faeces (at days 7, 14 and 35 after birth), respectively, used for Staphylococcus aureus recovery. The aim was to track the carriage of S. aureus in milk and infant faeces...
To investigate molecular epidemiology of extended-spectrum β-lactamase/ESBL and plasmid-mediated AmpC β-lactamase/pAmpC producing Gram-negative bacteria causing urinary tract infections (UTIs) in Zenica-Doboj Canton, Bosnia and Herzegovina, in the period Decembar 2009-May 2010. Antibiotic susceptibi...
Parasites including helminthes, protozoa, and medical arthropod vectors are a major cause of global infectious diseases, affecting one-sixth of the world's population, which are responsible for enormous levels of morbidity and mortality important and remain impediments to economic development especi...
The aim of this study was to describe an outbreak of Burkholderia stabilis colonization among patients in a nasal ward. Multilocus sequence typing (MLST) was used for the molecular typing of B. stabilis isolates. Microbiological records were reviewed to delineate the colonization outbreak period. On...
RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq an...
Fungal invasions are increasingly recognized as a significant component of global changes, threatening ecosystem health and damaging food production. Invasive fungi also provide excellent models to evaluate the generality of results based on other eukaryotes. We first consider here the reasons why f...
Molecular typing of 246 Staphylococcus aureus isolates from unselected patients in Thailand showed that 10 (4.1%) were actually Staphylococcus argenteus. Contrary to the suggestion that S. argenteus is less virulent than S. aureus, we demonstrated comparable rates of morbidity, death, and health car...
The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Acinetobacter baumannii (CRAB) were determined in hospitals in the states of the Cooperation Council for the Arab States of the Gulf (Gulf Cooperation Council [GCC]), namely, Saudi Arabia, United Arab Emirates, Oman, Qat...
Some important virulence factors have been elucidated in Klebsiella pneumoniae infections. We investigated the relationship between virulence factors and multilocus sequence types (STs) and assessed the risk factors for bacteremia in patients with pneumonia due to K. pneumoniae. From April 2004 thro...
Pseudomonas aeruginosa is an opportunistic pathogen, one of the leading causes of nosocomial infections such as pneumonia, urinary tract infections, and bacteraemia. The bacterial resistance to structurally unrelated antibiotics and its spread within hospitals limits the efficient antimicrobial opti...
Puerperal infection is a common complication during postnatal period in developing countries. Bacterial species, drug resistance, and genetic characteristics were investigated for a total of 470 isolates from puerperal infections in Bangladesh for a 2-year period (2010-2012). The most common species...
On August 8 2014, the World Health Organization (WHO) declared the outbreak of Ebola Virus Disease (EVD) evolving in West Africa since December 2013, a Public Health Emergency of International Concern (PHEIC). It is expected that the outbreak of Ebolavirus Disease (EVD) in West Africa will lead to i...
OBJECTIVE To identify risk factors related to Mycobacterium abscessus subsp. bolletii infection during an outbreak, associated with laparoscopic surgery and to propose recommendations for preventing new cases. DESIGN A retrospective cohort study. SETTING A private hospital in Manaus, Brazil. PATIENT...
Scrub typhus, an acute febrile illness that is widespread in the Asia-Pacific region, is caused by the bacterium Orientia tsutsugamushi, which displays high levels of antigenic variation. We conducted an investigation to identify the circulating genotypes of O. tsutsugamushi in 3 scrub typhus-endemi...
Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging from minor infections to life-threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its gen...
Legionnaires' disease (LD) is an often severe and potentially fatal form of bacterial pneumonia caused by an extensive list of Legionella species. These ubiquitous freshwater and soil inhabitants cause human respiratory disease when amplified in man-made water or cooling systems and their aerosols e...
In Colombia, Shigella sonnei is one of the most frequently isolated serotypes (53.4%) in human clinical samples associated with diarrheal acute disease. The identification of DNA restriction patterns by pulsed field gel electrophoresis is the basis for the molecular surveillance of S. sonnei . To es...
Salmonella is an important zoonotic pathogen and its prevalence in the chicken meat and eggs acts as a continuous threat to human population. The current studies covering a time period of three years, was carried out to report the isolation of salmonellae from the chicken tissues, eggs and feed ingr...
Listeriosis patient isolates in Germany have shown a new identical pulsed-field gel electrophoresis (PFGE) pattern since 2012 (n = 66). Almost all isolates (Listeria monocytogenes serotype 1/2a) belonged to cases living in southern Germany, indicating an outbreak with a so far unknown source. Case n...
On 12 June 2015, Corynebacterium diphtheriae was identified in a skin swab from a burns patient in Scotland. The isolate was confirmed to be genotypically and phenotypically toxigenic. Multilocus sequence typing of three patient isolates yielded sequence type ST 125. The patient was clinically well....
Globally, hepatitis C Virus (HCV) infection is responsible for a large proportion of persons with liver disease, including cancer. The infection is highly prevalent in sub-Saharan Africa. West Africa was identified as a geographic origin of two HCV genotypes. However, little is known about the genet...
With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (tMRCA) for rapidly evolving viruses. Coupled with an increasing abundance...
In June 2014, a staphylococcal food poisoning outbreak occurred at an international equine sports event in Luxembourg requiring the hospitalisation of 31 persons. We conducted a microbiological investigation of patients and buffet items, a case-control study and a carriage study of catering staff. I...
Between 1 August and 6 September 2013, an outbreak of Legionnaires' disease (LD) with 159 suspected cases occurred in Warstein, North Rhine-Westphalia, Germany. The outbreak consisted of 78 laboratory-confirmed cases of LD, including one fatality, with a case fatality rate of 1%. Legionella pneumoph...
Avian pathogenic Escherichia coli (APEC) are the major cause of colibacillosis in poultry production. In this study, a total of 22 E. coli isolated from colibacillosis field cases and 10 avian faecal E. coli (AFEC) were analysed. All strains were characterised phenotypically by susceptibility testin...
Next to official surveillance system in Poland, established by Public Statistic Act in 1995, other surveillance data collection system exists - historically connected with Ministry of Health Decree, which is not in force from 1995 y. Data in this system comes from National Sanitary Inspection labora...
Streptococcus pneumoniae is a common pathogenic cause of pediatric infections. This study investigated the serotype distribution, antimicrobial susceptibility, and molecular epidemiology of pneumococci before the introduction of conjugate vaccines in Shanghai, China. A total of 284 clinical pneumoco...
Hand, foot, and mouth disease (HFMD) is an infectious disease caused by human enterovirus 71 (EV71), coxsackievirus A16 (CVA16) and other enteroviruses. It is of interest that other enteroviruses associated with HFMD in Jinan have been rarely reported. The aim of the present study is to detect and c...
The information about disease burden and epidemiology of invasive listeriosis in Asia is scarce. From 2000 to 2013, a total of 338 patients with invasive listeriosis (bacteremia, meningitis, and peritonitis) were treated at four medical centers in Taiwan. The incidence (per 10,000 admissions) of inv...
We characterized 12 clinical isolates of Klebsiella oxytoca with the extended-spectrum β-lactamase (ESBL) phenotype (high minimum inhibitory concentration [MIC] values of ceftriaxone) recovered over 9 months at a university hospital in Japan. To determine the clonality of the isolates, we used pulse...
We investigated the pathogenicity, invasiveness, and genetic relatedness of 17 clinical Listeria monocytogenes stains isolated over a period of nine years (2006-2014). All isolates were phenotypically characterised and growth patterns were determined. The antimicrobial susceptibility of L. monocytog...
In March 2014, a Yersinia pseudotuberculosis (YP) outbreak was detected by a municipal authority in southern Finland. We conducted epidemiological, microbiological and traceback investigations to identify the source. We defined a case as a person with YP infection notified to the National Infectious...
Coxiella burnetii, the etiologic bacterium of Q fever zoonosis, is still difficult to control. Ruminants are often carriers and involved in human epidemics. MLVA is a promising genotyping method for molecular epidemiology. Different techniques are used to resolve the MLVA band profiles such as elect...
Recently, newly defined clades of Mycobacterium tuberculosis complex (MTBC) strains, namely Ethiopia 1-3 and Ethiopia H37Rv-like strains, and other clades associated with pulmonary TB (PTB) were identified in Ethiopia. In this study, we investigated whether these new strain types exhibit an increase...
Residents in nursing homes (NHs) always represent potential reservoirs for Staphylococcus aureus and methicillin-resistant S. aureus (MRSA). To our knowledge, there is no epidemiological information up till now that describes the prevalence and molecular characteristics of S. aureus in nursing home...
Infections with multidrug-resistant (MDR) microorganisms are an increasing threat to hospitalized patients. Although rapid typing of MDR microorganisms is required to apply targeted prevention measures, technical barriers often prevent this. We aimed to assess whether extended-spectrum beta-lactamas...
To determine the epidemiological and molecular characteristics of 12 Staphylococcus aureus isolates presenting heteroresistance to vancomycin in laboratories of two cities in Santa Catarina, southern Brazil. Epidemiological data, including the city of isolation, health institution, and date of isola...
The aim of this study was to assess the epidemiology of meningitis and/or encephalitis in Poland in 2013. In the last three years in Poland, about 3000 cases of meningitis and/or encephalitis of viral or bacterial etiology were recorded annually. Assessment of the epidemiological situation of mening...
In Italy, Klebsiella pneumoniae carbapenemase producing K. pneumoniae (KPC-Kp) strains are highly endemic and KPC producing CC258 is reported as the widely predominating clone. In Palermo, Italy, previous reports have confirmed this pattern. However, recent preliminary findings suggest that an epide...
Assess the best approach to type methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcal protein A (spa) typing, multiple-locus variable number tandem repeat analysis (MLVA) or both. Discriminatory power of spa typing and MLVA was determined using 20,771 MRSA isolates. There were twice as...
To characterize temporal shifts in extended-spectrum β-lactamases (ESBLs) and clones of clinical Escherichia coli isolates. All ESBL-producing E. coli isolates from a Portuguese hospital (n = 112; June 2006-June 2007 and January-December 2010) were characterized by identification of phylogenetic gro...
Listeria monocytogenes infection is an important cause of illness and hospitalization in vulnerable individuals. In the present study, we describe a community outbreak of Listeria monocytogenes in the North-East region of Scotland, which was epidemiologically, environmentally and microbiologically l...
The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in c...
This paper considers the experience of genotyping and sequencing technologies in laboratories of specialized anti-epidemic team (SAET) during the XXII Olympic Winter Games and XI Paralympic Winter Games of 2014 in Sochi. The work carried out during the pre-Olympic period on performance of readiness...
Clostridium difficile infection (CDI) is a leading cause of healthcare-associated morbidity and mortality worldwide. In Thailand, CDI exhibits low recurrence and mortality and its molecular epidemiology is unknown. CDI surveillance was conducted in a tertiary facility (Siriraj Hospital, Bangkok). A...
In June 2013, a diarrheal outbreak occurred among high school students in Incheon, South Korea. We investigated the outbreak to identify the pathogen and mode of transmission. A case-control study using a self-administered questionnaire was conducted by local authorities and the Korean Centers for D...
The detection of West Nile virus (WNV) nucleic acid in a blood donation from Vienna, Austria, as well as in Culex pipiens pupae and egg rafts, sampled close to the donor's residence, is reported. Complete genomic sequences of the human- and mosquito-derived viruses were established, genetically comp...
Molecular typing of Candida albicans is important for studying the population structure and epidemiology of this opportunistic yeast, such as population dynamics, nosocomial infections, multiple infections and microevolution. The genetic diversity of C. albicans has been rarely studied in China. In...
Genotyping studies like spoligotyping are valuable tools in understanding the genetic diversity and epidemiology of Mycobacterium tuberculosis. Though there are reports of spoligotyping of M. tuberculosis isolates from pulmonary specimens from different parts of India, spoligotyping of extra pulmona...
There is a huge need to develop molecular typing methods which are simple to perform, rapid and cost effective to confirm clonality of nosocomial isolates in outbreak situations. The aim of the study was to investigate a hospital outbreak of multi-drug resistant (MDR) Klebsiellapneumoniae septicemia...
Pulsed field gel electrophoresis (PFGE) is generally accepted as one of the most discriminatory methods available for genotyping Campylobacter jejuni. PFGE has been extensively used in epidemiological studies, including outbreak investigation, persistence of genotypes in a human population, environm...
Genotyping approaches are important for tracking infectious agents and can be used for various purposes. Pulsed-Field Gel Electrophoresis (PFGE) is among the highly discriminatory genotyping approaches commonly used for characterizing Clostridium difficile. Other genotyping methods used for C. diffi...
Pulsed-Field Gel Electrophoresis (PFGE) subtyping has been used extensively to characterize various bacterial species and to facilitate comparative analysis of geographically diverse populations. To this end, standardized protocols for many different genera and species have been developed, particula...
In early July 2008, a cluster of six Salmonella Agona was identified in the Republic of Ireland. A dispersed, common source outbreak was suspected. Later in July a further case was identified and the Health Protection Agency in the UK indicated that they had 32 cases of S. Agona since Feb 2008. This...
Epidemiologically linked clusters are confirmed by typing strains with molecular typing such as pulsed-field gel electrophoresis (PFGE). We compared six extended-spectrum β-lactamase producing E. coli of a PFGE-related cluster with Matrix-assisted laser desorption/ionization-time of flight mass-spec...
Despite worldwide dissemination of New Delhi metallo-β-lactamase1 (blaNDM-1), outbreaks remain uncommon in China. In this study, we describe the characteristics of the outbreak-related blaNDM-1-producing K. pneumonia isolates in a neonatal unit in Shandong province, China. We recovered 21 non-repeti...
Besides mosquitoes, ticks are regarded as the primary source of vector-borne infectious diseases. Indeed, a wide variety of severe infectious human diseases, including those involving viruses, are transmitted by ticks in many parts of the world. To date, there are no published reports on the use of...
Bovine rhinitis viruses (BRV) are established etiological agents of bovine respiratory disease complex however little research into their epidemiology and ecology has been published for several decades. In the U.S., only bovine rhinitis A virus 1 (BRAV1) has been identified while bovine rhinitis A v...
In this paper, we examine 2 case reports for different reptile-related Salmonella enterica subspecies enterica serotypes. In case 1, a 5-year-old boy presented with gastroenteritis caused by S. enterica subspecies enterica serovar Poona. The suspected source of infection was a turtle kept at the pat...
The prevention and control of methicillin-resistant Staphylococcus aureus (MRSA) are important, particularly in emergency units. The active surveillance of MRSA was prospectively performed at the emergency medical center of Nagasaki University Hospital. After obtaining nasal swab specimens, a fully...
Cholera is a major cause of illness in the developing world. During the monsoon season, small sporadic clusters of cholera cases are reported on an annual basis in Karnataka, India. During the monsoons of 2013, there was a cholera outbreak in Badami, a remote area of Bagalkot district in Karnataka....
This study was a detailed investigation of Staphylococcus epidermidis clinical isolates exhibiting linezolid resistance. Thirty-six linezolid-resistant S. epidermidis from eight German hospitals, including isolates from suspected hospital-associated outbreaks between January 2012 and April 2013, wer...
Since Group B Streptococcus (GBS, Streptococcus agalactiae) clinical isolates are believed to be uniformly susceptible to β-lactams, penicillin G has been used as the first-line agent for the prevention and treatment of GBS infections. However, the existence and characteristics of GBS isolates with...
No abstract available
Surveillance of Salmonella enterica subsp. enterica serovar Enteritidis is generally considered to benefit from molecular techniques like multiple-locus variable-number of tandem repeats analysis (MLVA), which allow early detection and confinement of outbreaks. Here, a surveillance study, including...
The aim of this study is to report the occurrence of the first outbreak of food poisoning caused by Salmonella Alachua in Brazil, as well as the antimicrobial susceptibility and the genetic relatedness of Salmonella Alachua strains isolated from clinical and food samples. To elucidate the outbreak,...
Acinetobacter baumannii is usually multi-drug resistant (MDR), including third generation cephalosporins, amino glycosides and fluoroquinolone. Resistance to these antibiotics is mediated by multiple factors such as: lactamases, efflux pumps and other mechanisms of resistance. Pulsed-field gel elect...
In 2008, the New Jersey Department of Health (NJDOH) identified a 21.1% increase in reported invasive pneumococcal disease (IPD). In 2009, NJDOH piloted nucleic acid-based serotyping to characterize serotypes causing IPD. From April through September, NJDOH received specimens from 149 of 302 (49%) c...
The goal of this work was to present the data of the study of the peculiarities of the generation factors of humoral immunity in the response to the infection with the pandemic influenza A (HIN1) pdmO9 in patients with different epidemiological anamnesis. High ability of the influenza viruses to spr...
Dengue fever is the commonest arthropod-borne infection worldwide. In recent years, rapid growth in global air travel has resulted in a considerable increase in the incidence of imported cases. In Romania it is now the second most frequent cause for hospitalization (after malaria) in patients arrivi...
The aim of this study was to determine the prevalence and characteristics of Staphylococcus aureus isolates from the patients, staff, air and environments of an ICU in a hospital in Tehran. During this study, 37 S. aureus isolates were collected and analyzed via the spa typing method. Of the 37 S. a...
Asymptomatic carriage of methicillin-resistant Staphylococcus aureus (MRSA) can predispose the host to a wide range of infections. To inform public health strategies, this study sought to determine the prevalence and the phenotypic and genotypic characteristics of MRSA from nasal swabs of health car...
Bacteriology has embraced the next-generation sequencing revolution, swiftly moving from the time of single genome sequencing to the age of genomic epidemiology. Hundreds and now even thousands of genomes are being sequenced for single bacterial species, allowing unprecedented levels of resolution a...
As part of the European Clostridium difficile infections (CDI) surveillance Network (ECDIS-Net), which aims to build capacity for CDI surveillance in Europe, we constructed a new network of hospital-based laboratories in Poland. We performed a survey in 13 randomly selected hospital-laboratories in...
No abstract available
To investigate the antimicrobial susceptibility and clonal relationship of Acinetobacter baumannii strains isolated in an Italian ICU. Epidemiological, observational, retrospective, longitudinal study. The ICU of the University Hospital of Sassari, Italy. Pulsed Field Gel Electrophoresis (PFGE) and...
Healthcare-Associated Infections (HAIs) are an important cause of morbidity and mortality worldwide and have a significant economic impact for health systems. Molecular epidemiology tools have a central role in HAI prevention programs. In order to give an overview of their specific advantages and di...
The study investigated the presence of CTX-M-15 type extended spectrum beta-lactamases (ESBL), compared their genetic arrangements and plasmid types in gram negative isolates of hospital and food origin in north-east India. From September 2013 to April 2014, a total of 252 consecutive, non-duplicate...
Anaplasma phagocytophilum is a zoonotic obligate intracellular bacterium known to be transmitted by ticks belonging to the Ixodes persulcatus complex. This bacterium can infect several mammalian species, and is known to cause diseases with variable symptoms in many domestic animals. Specifically, it...
Staphylococcus lugdunensis can cause community- and healthcare-associated infections. This study investigated the molecular characteristics of S. lugdunensis isolates collected at our hospital and compared the characteristics of the infectious and commensal isolates. We collected the S. lugdunensis...
In Brazil, ventilator-associated pneumonia (VAP) caused by carbapenem resistant Acinetobacter baumannii and Pseudomonas aeruginosa isolates are associated with significant mortality, morbidity and costs. Studies on the clonal relatedness of these isolates could lay the foundation for effective infec...
Streptococcus pneumoniae is a potentially deadly human pathogen associated with high morbidity, mortality and global economic burden. The universally used bacterial genotyping methods are multilocus sequence typing and pulsed field gel electrophoresis. However, another highly discriminatory, rapid a...
The mucoralean fungi are emerging causative agents of primary cutaneous infections presenting in the form of necrotizing fasciitis. The aim of this study was to investigate a series of suspected necrotizing fasciitis cases by Apophysomyces species over one-year period in a northern Indian hospital....
The shiga-toxin (Stx)-producing human pathogen Escherichia coli serotype O157:H7 is a highly pathogenic subgroup of Stx-producing E. coli (STEC) with food-borne etiology and bovine reservoir. Each year in the U. S., approximately 100,000 patients are infected with enterohemorrhagic E. coli (EHEC) of...
Lower respiratory tract infections (LRTI) account for 20-30 % of all hospital-acquired contagions. They are characterized by high mortality of hospitalized patients. The most serious form of LRTI is pneumonia, and the most common etiological factors in such cases are bacteria. The article gives the...
Since its isolation in 1966 in Kenya, rice yellow mottle virus (RYMV) has been reported throughout Africa resulting in one of the economically most important tropical plant emerging diseases. A thorough understanding of RYMV evolution and dispersal is critical to manage viral spread in tropical area...
Many of the pathogens perceived to pose the greatest risk to humans are viral zoonoses, responsible for a range of emerging and endemic infectious diseases. Phylogeography is a useful tool to understand the processes that give rise to spatial patterns and drive dynamics in virus populations. Increas...
Increased incidence of infections due to Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) was noted among patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) at a single hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-pro...
We recently reported the rapid expansion of an HIV-1 subtype F cluster among men who have sex with men (MSM) in the region of Galicia, Northwest Spain. Here we update this outbreak, analyze near full-length genomes, determine phylogenetic relationships, and estimate its origin. For this study, we us...
The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology....
Continuous phylogeography is a growing approach to studying the spatiotemporal origins of RNA viruses because of its realistic spatial reconstruction advantages over discrete phylogeography. While the generalized linear model has been demonstrated as an effective tool for simultaneously assessing th...
H6N1 influenza A is an avian virus but in 2013 infected a human in Taiwan. We studied the phylogeography of avian origin H6N1 viruses in the Influenza Research Database and the Global Initiative on Sharing Avian Influenza Data EpiFlu Database in order to characterize their recent evolutionary spread...
The HIV-1 epidemic among men who have sex with men (MSM) has been spreading throughout China. Shanghai, a central gathering place for MSM, is facing a continuously increasing incidence of HIV-1 infection. In order to better understand the dynamics of HIV-1 diversity and its influence on patient's im...
The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impac...
Unlike hospitals or the community, nursing homes provide a unique healthcare environment for patients. There have been no reports regarding methicillin-resistant Staphylococcus aureus (MRSA) carriage among nursing home residents and staff in Taiwan. From May to November 2012, a total of 523 subjects...
Whole Genome Sequencing (WGS) is emerging as a very powerful tool for the management, outbreak analyses, surveillance and determining drug resistance of human infectious pathogens including Mycobacterium tuberculosis and MRSA. WGS can also discriminate relapse TB from re-infection and the resolution...
The Australian Group on Antimicrobial Resistance performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2013 survey focussed for the first time on blood stream infections. Four thousand nine hundred and fifty-eight E...
From 1 January to 31 December 2013, 26 institutions around Australia participated in the Australian Enterococcal Sepsis Outcome Programme (AESOP). The aim of AESOP 2013 was to determine the proportion of enterococcal bacteraemia isolates in Australia that are antimicrobial resistant, and to characte...
From 1 January to 31 December 2013, around Australia 26 institutions around Australia participated in the Australian Staphylococcal Sepsis Outcome Programme (ASSOP). The aim of ASSOP 2013 was to determine the proportion of Staphylococcus aureus bacteraemia (SAB) isolates in Australia that are antimi...
In North America and Europe, the binary toxin positive Clostridium difficile strains of the ribotypes 027 and 078 have been associated with death, toxic megacolon and other adverse outcomes. Following an increase in C. difficile infections (CDIs) in Queensland, a prevalence study involving 175 hospi...
Bovine Anaplasmosis caused by Anaplasma marginale is a worldwide disease prevalent in tropical and subtropical regions where Rhipicephalus microplus is considered the most significant biological vector. Molecular markers previously applied for A. marginale typing are efficient for isolate discrimina...
Although heteroresistance is common in a wide range of microorganisms, carbapenem heteroresistance among invasive Escherichia coli infections has not been reported. The objective of this study was to evaluate the clinical significance of carbapenem heteroresistance and to identify risk factors for i...
Mycoplasma bovis is a major bovine pathogen associated with bovine respiratory disease complex and is responsible for substantial economic losses worldwide. M. bovis is also associated with other clinical presentations in cattle, including mastitis, otitis, arthritis, and reproductive disorders. To...
In addition to being a human pathogen, Staphylococcus aureus causes an array of infections in economically important livestock animals, particularly pigs. In Asia, there have been few reports on livestock-associated meticillin-resistant S. aureus (LA-MRSA), mostly from developed countries, with very...
An exploratory study in five conventional pig production clusters was carried out to investigate the dynamic and diversity of Salmonella spp. within different production stages and sample site categories (pooled feces, direct and non-direct environment). Observing two production cycles per productio...
Despite more than 50 years of vaccination, pertussis is still an endemic disease, with regular epidemic outbreaks. With the exception of Poland, European countries have replaced whole-cell vaccines (WCVs) by acellular vaccines (ACVs) in the 1990s. Worldwide, antigenic divergence in vaccine antigens...
This study investigated the molecular characteristics of azithromycin-resistant Streptococcus pneumoniae in Taiwan. A total of 486 non-duplicate isolates of azithromycin-resistant S. pneumoniae recovered from various clinical sources of patients treated at 22 different hospitals in Taiwan from 2006...
An outbreak of Legionnaires’ disease with 334 confirmed cases was identified on 7 November 2014 in Vila Franca de Xira, Portugal and declared controlled by 21 November. Epidemiological, environmental and microbiological analysis identified industrial wet cooling systems to be the probable source of...
The high frequency of fluoroquinolone resistance in Escherichia coli is a feature of clinical bacteriology in China, where the molecular epidemiology and genetic characteristics of this resistance in county hospitals remain unclear. A total of 590 nonduplicate E. coli isolates from 30 county hospita...
Increasing numbers of infections following transrectal prostate biopsy (TPB) at our hospital led us to investigate clinical and bacterial risk factors to determine if the colonizing rectal Escherichia coli population is the source. We performed an observational cohort study of men undergoing TPB (1...
Rapidly fatal cases of invasive fungal infections due to a fungus later identified as Saprochaete clavata were reported in France in May 2012. The objectives of this study were to determine the clonal relatedness of the isolates and to investigate possible sources of contamination. A nationwide aler...
Human immunodeficiency virus type 1 (HIV-1) subtype CRF01_AE originated in Africa and then passed to Thailand, where it established a major epidemic. Despite the global presence of CRF01_AE, little is known about its subsequent dispersal pattern. We assembled a global data set of 2736 CRF01_AE seque...
Human adenoviruses (HAdV) of species B, C, and E (HAdV-B, -C, -E) are frequent causative agents of acute respiratory infections worldwide. No specific analysis has been done on the epidemiological and clinical features of HAdV in pediatric pneumonia in China. Nasopharyngeal aspirates were collected...
Staphylococcus schweitzeri has been recently considered to be a highly divergent Staphylococcus aureus clade and usually colonises nonhuman primates and bats in sub-Saharan Africa. Its transmissibility to humans remains unclear. We therefore investigated the transmission of S. aureus and S. schweitz...
Staphylococcus aureus is one of the most important human pathogens and meticillin-resistant S. aureus (MRSA) presents a major cause of healthcare- and community-acquired infections. This study investigated the spatial and temporal changes of S. aureus causing bacteraemia in Europe over a five-year i...
Resistance to cephalosporins in Haemophilus influenzae is usually caused by characteristic alterations in penicillin-binding protein 3 (PBP3), encoded by the ftsI gene. Resistance to extended-spectrum cephalosporins is associated with high-level PBP3-mediated resistance (high-rPBP3), defined by the...
We first describe two novel variants of blaKPC, blaKPC-16 and blaKPC-17, which were identified in three Klebsiella pneumoniae isolates from a patient in Taiwan. KPC-16 and KPC-17 differed from KPC-2 by two (P202S and F207L) and a single (F207L) amino acid substitutions, respectively. All three isola...
The aim of this study was to determine the clinical characteristics, molecular epidemiology and biofilm production of Acinetobacter baumannii clinical isolates obtained from a tertiary-care hospital in Mexico. Clinical isolates of A. baumannii (n=152) isolated from 2007 to 2012 were included. Clonal...
The aim of this study was to explore the population structure of multidrug-resistant (MDR) tuberculosis strains and distribution of resistance-associated nucleotide alteration among the different genotype MDR strains in China. The genotypes of 376 MDR strain were analyzed by 15-loci MIRU-VNTR and RD...
Clostridium difficile infection control strategies require an understanding of its epidemiology. In this study, we analysed the toxin genotypes of 130 non-duplicate clinical isolates of C. difficile from a university hospital in Tokyo, Japan. Multilocus sequence typing (MLST) and eBURST analysis wer...
The purpose of this study was to investigate the molecular characteristics of 83 clinical Cryptococcus neoformans/C. gattii species complex isolated in Beijing, China, between 2007 and 2013. Restriction fragment length polymorphism of the gene URA5 (URA5-RFLP), multilocus sequence typing (MLST), and...
To study the serotypes, antimicrobial resistance, virulence genes and molecular characteristics of Vibrio parahaemolyticus isolated from outbreaks and sporadic cases in Guangdong, 2013. 36 Vibrio parahaemolyticus strains isolated from outbreaks and 43 strains from sporadic cases were sero-typed and...
In the province of Gipuzkoa, Spain (≈700,000 inhabitants), 7-12 episodes of human listeriosis were recorded annually during 2009-2012. However, during January 2013-February 2014, 27 episodes were detected, including 11 pregnancy-associated cases. Fifteen cases in 2 epidemiologically unrelated outbre...
We report the recent epidemiology and estimated seroprevalence of human hantavirus infections in the Netherlands. Sixty-two cases were reported during December 2008-December 2013. The estimated seroprevalence in the screened municipalities in 2006-2007 was 1.7% (95% CI 1.3%-2.3%). Findings suggest t...
Detection of carbapenemase-producing Enterobacteriaceae (CPE) is an important task at microbiology laboratories in hospitals. As the prevalence of CPE is increasing worldwide, the implementation of phenotypically based screening as well as confirmatory procedures to detect CPE are important for micr...
No abstract available
No abstract available
The spread of carbapenem resistant Enterobacteriaceae (CRE) has recently become a matter of concern in public health, mainly due to the wide distribution of carbapenemase genes. Italy is a country considered endemic for the spread of blaKPC Klebsiella pneumoniae (KP). The aim of this study was to de...
We collected nasal, axilla, and groin swabs from 252 adult patients from 2 nephrology centers in Hong Kong. Staphylococcus lugdunensis carriage was detected in 51.6% patients (groin, 39.3%; axilla, 19.8%; nose, 17.9%). The carriage rates of methicillin-sensitive S. lugdunensis and methicillin-resist...
A total of 1,187 Vibrio cholerae isolates were received during 2011 cholera outbreaks from 16 provinces in different geographical location to Iranian reference Health laboratory. A random selection was performed, and 61 isolates were subjected to further investigations. Cholera cases were come up fr...
An outbreak of human botulism was due to consumption of ham containing botulinum neurotoxins B and E. A Clostridium botulinum type E strain isolated from ham was assigned to a new subtype (E12) based on bont/E gene sequencing and belongs to a new multilocus sequence subtype, as analyzed by whole-gen...
In the remote Japanese community of Saku, a rural town in the Nagano Prefecture, a large proportion of outpatient urinary tract infections was caused by well-recognized globally dispersed clonal lineages of uropathogenic Escherichia coli (UPEC). However, most of these strains were drug susceptible,...
The emergence of drug-resistant forms of tuberculosis (TB) represents a major public health concern. Understanding the transmission routes of the disease is a key factor for its control and for the implementation of efficient interventions. Mycobacterial interspersed repetitive-unit-variable-number...
New sequencing technologies have made it possible to generate bacterial genomes at clinically relevant timescales and price levels. The use of whole-genome sequencing (WGS) has proved useful for investigating transmission at different scales. WGS data are highly effective at determining whether indi...
A total of 274 samples were screened for toxigenic Clostridium difficile using a combination of several commercially available assays, and positive isolates ribotyped. A two-step algorithm assisted in demonstrating an increased prevalence of C. difficile infection in South Australia of 9·8%, most of...
Bacterial infections causing mastitis in sheep can result in severe economic losses for farmers. A large survey of milk samples from ewes with mastitis in Sardinia, Italy, indicated an increasing prevalence of Pseudomonas aeruginosa infections. It has been shown previously that during chronic, biofi...
Until recently, the origin of the HIV-1 group M pandemic largely remained a scientific mystery. The use of comprehensive evolutionary analyses has revealed a unique story regarding viral migration, starting in the 1920s in Kinshasa, and the social and infrastructural changes associated with the earl...
This study assessed pneumococcal carriage in the early periods after routine use of 13-valent pneumococcal conjugate vaccine (PCV13) in Hong Kong. Nasopharyngeal swabs were obtained from 1110 children (<5 years) admitted with acute illness during September 2010-August 2013. Pneumococcal carriage rat...
Despite the low nutrient level and constant presence of secondary disinfectants, bacterial re-growth still occurs in drinking water distribution systems. The molecular mechanisms that starved bacteria use to survive low-level chlorine-based disinfectants are not well understood. The objective of thi...
The genetic diversity of 89 clinical Legionella isolates, collected between 1987 and 2012, in 22 hospitals from the five regions of Portugal, was analysed in this study using monoclonal antibodies (MAbs) of the Dresden panel and the sequence-based typing (SBT) protocol. The eBURST algorithm was used...
Organisms of the Burkholderia cepacia complex are especially important pathogens in cystic fibrosis (CF), with a propensity for patient-to-patient spread and long-term respiratory colonization. B. cenocepacia and Burkholderia multivorans account for the majority of infections in CF, and major epidem...
An unusual increase in the number of Campylobacter concisus isolates found in stool cultures provoked an outbreak investigation at Bern University Hospital. No epidemiological links were found between the cases, and the Campylobacter isolates were clonally unrelated. A change in culture conditions t...
We aimed to investigate the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) isolates in the province of Palermo, Sicily, Italy, by characterizing 183 isolates identified in the years 2004-2012. A comparison with 104 MTBC strains identified in the same geographic area in the years...
A main export market for chicken meat from industrialized countries is sub-Saharan Africa. We hypothesized that antibiotic resistant bacteria could be exported to developing countries through chicken meat trade. The objective was to investigate the occurrence and molecular types of ESBL-producing En...
Infections caused by multidrug resistant bacteria act as a risk factor for mortality in burns patients. So keeping in view the crucial importance of reliable therapeutic decisions of multidrug resistance bacteria and role of hospital environment in bacteria colonization, our study is based on the ev...
Typing of bacterial isolates has been used for decades to study local outbreaks as well as in national and international surveillances for monitoring newly emerging resistant clones. Despite being recognized as a nosocomial pathogen, the precise modes of transmission of Stenotrophomonas maltophilia...
Several mumps outbreaks have been reported in Europe and in the United States among highly vaccinated populations. Biological diagnosis is classically based on the detection of mumps-specific IgM, but the ability of serological tests to confirm mumps infection seems to be limited among vaccinated pa...
Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bac...
The combination of new genotyping tools and a more exhaustive sampling policy in the analysis of infection by Mycobacterium tuberculosis has shown that infection by this pathogen is more complex than initially expected. Mixed infections, coexistence of clonal variants from a parental strain, and com...
Chlamydia trachomatis is a pathogen of worldwide importance, causing more than 100 million cases of sexually transmitted infections annually. Whole-genome sequencing is a powerful high resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mu...
Hepatitis C virus (HCV) has a naturally occurring polymorphism, Q80K, in the nonstructural protein 3 (NS3) gene encoding the viral protease, which has been associated with reduced susceptibility to the direct-acting antiviral inhibitor simeprevir. Q80K is observed predominantly in HCV genotype 1a an...
No abstract available
There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecologic...
Swine dysentery is a mucohaemorrhagic colitis of pigs caused by infection with Brachyspira hyodysenteriae. The disease can be controlled by treatment with antimicrobial agents, with the pleuromutilins tiamulin and valnemulin being widely used. In recent years, the occurrence of B. hyodysenteriae wit...
Escherichia coli O157:H7 is, to date, the major E. coli serotype causing food-borne human disease worldwide. Strains of O157 with other H antigens also have been recovered. We analyzed a collection of historic O157 strains (n = 400) isolated in the late 1980s to early 1990s in the United States. Str...
Molecular PorA subtyping provides information that increasingly requires the adaptation of standard public health approaches to outbreak management. We report an outbreak of a rare subtype of meningococcal infection not previously identified in the United Kingdom (UK). The outbreak occurred in the W...
A retrospective investigation was performed to evaluate whole-genome sequencing as a benchmark for comparing molecular subtyping methods for Salmonella enterica serotype Enteritidis and survey the population structure of commonly encountered S. enterica serotype Enteritidis outbreak isolates in the...
Characterize the clinical and molecular epidemiology of new methicillin-resistant Staphylococcus aureus (MRSA) acquisitions at nasal and extranasal sites among high-risk nursing home (NH) residents. Multicenter prospective observational study. Six NHs in southeast Michigan. A total of 120 NH residen...
For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more th...
The increase in carbapenem-resistant Enterobacteriaceae (CRE) infections is a critical public health issue. We recently experienced the largest single-center pediatric outbreak of carbapenem-resistant Klebsiella pneumoniae (CRKP) at our hospital. The objective of this study was to describe the molec...
Non-tuberculous mycobacteria (NTM) are important environmental pathogens capable of causing a spectrum of infection. The different species exhibit varied geographical prevalence worldwide. Identification of the infecting organism may be helpful in determining the clinical significance of the isolate...
A widespread salmonellosis outbreak linked to consumption of hummus made from contaminated tahini imported from Turkey occurred in New Zealand in November 2012. This article summarizes the outbreak detection, investigation, and control. The New Zealand Enteric Reference Laboratory alerted public hea...
Compared with other developed countries, vancomycin-resistant enterococci (VRE) are not widespread in clinical environments in Japan. There have been no VRE outbreaks and only a few VRE strains have sporadically been isolated in our university hospital in Gunma, Japan. To examine the drug susceptibi...
The Mycobacterium tuberculosis genotypes obtained from elderly Finns were assessed and compared with those obtained from younger Finns to comprehend the epidemiology of tuberculosis (TB) in Finland. From 2008 to 2011, a total of 1021 M. tuberculosis isolates were characterized by spoligotyping and 1...
The growing problem of widespread viral infections is a challenge for modern medicine. Emerging reports of dengue virus infections in Europe create a new epidemic problem. The virus responsible for causing the symptoms of the disease is transmitted by mosquitoes. Over 50% of the world's population l...
Aspergillus respiratory infection is a common complication in cystic fibrosis (CF) and is associated with loss of pulmonary function and allergic disease. Fifty-three Aspergillus isolates recovered from CF patients were identified to species by Internal Transcribed Spacer Region (ITS), β-tubulin, an...
Streptococcus pyogenes (group A Streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of m...
Emerging and re-emerging infectious diseases of zoonotic origin like highly pathogenic avian influenza pose a significant threat to human and animal health due to their elevated transmissibility. Identifying the drivers of such viruses is challenging, and estimation of spatial diffusion is complicat...
No abstract available
Despite the spread of penicillin-resistant, ampicillin-susceptible Enterococcus faecalis (PRASEF) isolates in diverse countries, the mechanisms leading to this unusual resistance phenotype have not yet been investigated. The aim of this study was to evaluate whether polymorphism in the pbp4 gene is...
Mycoplasma pneumoniae is a leading cause of respiratory infections, including community-acquired pneumonia (CAP). Currently, pathogen-specific testing is not routinely performed in the primary care setting, and the United States lacks a systematic surveillance program for M. pneumoniae. Documentatio...
Methicillin-resistant Staphylococcus aureus (MRSA) belonging to the multilocus sequence type clonal complex 59 (MLST CC59) is the predominant community-associated MRSA clone in Asia. This clone, which is primarily linked with the spa type t437, has so far only been reported in low numbers among larg...
Intra-familial infection is considered to be one of the main routes of transmission for Helicobacter pylori in Japan. We assessed the genomic profiles of H. pylori isolates from family members by multi-locus sequence typing (MLST) and identified the original strain infecting the index child. A total...
Nosocomial fungal bloodstream infections (BSI) are increasing significantly in hospitalized patients and Candida parapsilosis has emerged as an important pathogen responsible for numerous outbreaks. The objective of this study was to evaluate C. parapsilosis sensu lato infection scenarios, regarding...
Aedes aegypti and A. albopictus represent the two most important species of mosquitoes in relation to dengue virus transmission both in the Americas and Asia. However, the study of theses species generally requires the establishment of a colony for the larvae to hatch, or waiting for the adult devel...
As a precursor to planned arboviral vector incrimination studies, an integrated systematics approach was adopted using morphology and DNA barcoding to examine the Culex fauna present in Turkey. The mitochondrial COI gene (658bp) were sequenced from 185 specimens collected across 11 Turkish provinces...
A total of 123 enterotoxigenic Escherichia coli (ETEC) isolates from diarrheal patients from June to December 2012 in Shanghai, China, were examined to determine their genetic relatedness using multilocus sequence typing and pulsed-field gel electrophoresis (PFGE) and for the presence of virulence g...
Fourteen postoperative infections caused by Serratia marcescens were detected in patients on the neurosurgical wards and spinal surgery ward of a 2640-bed hospital between 26th December 2012 and 5th June 2013. To investigate the source of the outbreak, identify risk factors and implement infection c...
The Ebola virus (EBOV) epidemic in Western Africa is the largest in recorded history and control efforts have so far failed to stem the rapid growth in the number of infections. Mathematical models serve a key role in estimating epidemic growth rates and the reproduction number (R0) from surveillanc...
Burkholderia cepacia has been linked to healthcare-associated infections and colonization caused by contamination of alcohol-free mouthwash used in patients undergoing mechanical ventilation. The purpose of our study was to establish the source of a clustering of healthcare-associated B. cepacia iso...
Mycoplasma amphoriforme has been associated with infection in patients with primary antibody deficiency (PAD). Little is known about the natural history of infection with this organism and its ability to be transmitted in the community. The bacterial load was estimated in sequential sputum samples f...
An increase of invasive meningococcal disease caused by Neisseria meningitidis serogroup Y has been noted in Sweden since 2005, and to a lower extent throughout Europe. The present study describes the epidemiology of invasive N. meningitidis isolates in Sweden in the period between 2010 and 2012, wi...
Despite its global relevance, our understanding of how influenza A virus transmission impacts the overall population dynamics of this RNA virus remains incomplete. To define this dynamic, we inserted neutral barcodes into the influenza A virus genome to generate a population of viruses that can be i...
The emergence of Panton-Valentine leukocidin (PVL)-positive methicillin-resistant Staphylococcus aureus (MRSA) is a public health concern worldwide. PVL is associated with community-associated MRSA and is linked to skin and soft tissue infections (SSTIs). However, PVL genes have also been detected i...
For over 10 years, DNA barcoding has been used to identify specimens and discern species. Its potential benefits in parasitology were recognized early, but its utility and uptake remain unclear. Here we review studies using DNA barcoding in parasites and vectors affecting humans and find that the te...
Group B streptococcus is the most common cause of neonatal infections. We studied the clinical and molecular epidemiology of invasive group B streptococcus infection in children younger than 3 months in the Netherlands over 25 years. We assessed the effect of the Dutch guidelines, introduced in 1999...
After the first isolation of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in 2003, this MRSA variant quickly became the predominant MRSA obtained from humans as part of the Dutch national MRSA surveillance. Previous studies have suggested that human-to-human transmissio...
Leptospirosis is a worldwide zoonotic disease whose transmission is linked through multiple factors in the animal-human-ecosystem interface. The data on leptospirosis reported to the World Organization for Animal Health (OIE) for Latin America and Caribbean (LAC) countries/sovereign territories from...
Dengue fever, a mosquito-borne viral disease, has become a major public health problem with marked expansion in recent decades. Dengue has now become hyperendemic in India with co-circulation of all the four serotypes. Herein, we report an unprecedented outbreak which occurred during August to Octob...
Human-to-human-transmitted Corynebacterium diphtheriae was historically the main pathogen causing diphtheria and has therefore been studied extensively in the past. More recently, diphtheria caused by toxigenic Corynebacterium ulcerans is an emerging disease in several industrial countries, includin...
During a prospective surveillance using PCR for the detection of plasmid-mediated AmpC β-lactamase (pAmpC)-producing Enterobacteriaceae, outbreaks due to pAmpC-producing Klebsiella pneumoniae (pAmpC-Kp) occurred in an adult liver transplantation unit (aLTU) and a paediatric liver transplantation uni...
The present study was carried out to evaluate the prevalence of the clonal subgroup O16:H5-ST131 and the H30 and H30-Rx subclones among E. coli isolates causing extraintestinal infections and to know their virulence potential. The ST131 clonal group accounted for 490 (16%) of the 2995 isolates obtai...
Whole-genome sequencing of pathogens has recently been used to investigate disease outbreaks and is likely to play a growing role in real-time epidemiological studies. Methods to analyze high-resolution genomic data in this context are still lacking, and inferring transmission dynamics from such dat...
Species of the Burkholderia cepacia complex are associated with opportunistic infection in patients with cystic fibrosis. For years now, B. multivorans and B. cenocepacia have been the most frequently isolated species within the complex in such patients. However, between 2008 and 2012, the overall i...
Molecular methods to differentiate serotypes, mating types and molecular types of Cryptococcus neoformans and C. gattii are important tools to understand epidemiology and pathogenesis of these pathogens. In this study, a multiplex polymerase chain reaction (PCR) approach was applied to sero-mating t...
Staphylococcus aureus is a versatile bacterium, which can lead to various infectious diseases. Various molecular typing methods are applied to the evolution and epidemiology surveys of S. aureus, mostly for methicillin-resistant S. aureus (MRSA). However, methicillin-susceptible S. aureus (MSSA) is...
Smartphone touchscreens are known as pathogen carriers in clinical environments. However, despite a rapidly growing number of smartphone users worldwide, little is known about bacterial contamination of smartphone touchscreens in non-clinical settings. Such data are needed to better understand the h...
Scant attention has been paid to Lyme disease, Borrelia burgdorferi, Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports of B. burgdorferi and I. scapularis in North Dakota, however, prompted a more detailed examin...
spa typing of methicillin-resistant Staphylococcus aureus (MRSA) has traditionally been done by PCR amplification and Sanger sequencing of the spa repeat region. At Hvidovre Hospital, Denmark, whole-genome sequencing (WGS) of all MRSA isolates has been performed routinely since January 2013, and an...
Seven imipenem-resistant Pseudomonas aeruginosa isolates were recovered from the sputum samples of pneumonia patients in southwestern China. They had identical antibiotic resistance patterns and indistinguishable pulsed-field gel electrophoresis profiles. Nucleotide sequence analysis revealed a 4-bp...
No abstract available
The current Ebola virus epidemic in West Africa has been spreading at least since December 2013. The first confirmed case of Ebola virus in Sierra Leone was identified on May 25. Based on viral genetic sequencing data from 72 individuals in Sierra Leone collected between the end of May and mid June,...
Bovine mastitis due to Mycoplasma californicum is often accompanied by huge economic losses, and the disease spreads very quickly. An appropriate molecular epidemiological analysis is needed to prevent and control infectious disease, but molecular epidemiological analysis methods for M. californicum...
The national tuberculosis strain typing service (TB-STS) was introduced in England in 2010. The TB-STS involves MIRU-VNTR typing of isolates from all TB patients for the prospective identification, reporting and investigation of TB strain typing clusters. As part of a mixed-method evaluation, we rep...
This article reports a significant outbreak of Clostridium difficile ribotype 027 infection in a residential care home in the UK. Five of six affected residents died within one month of diagnosis. Investigation of the facility revealed problems with hand hygiene and environmental cleaning. Affected...
Staphylococcal food poisoning (SFP), one of the commonest food-borne diseases, results from the ingestion of one or more staphylococcal enterotoxins (SEs) produced in foods by Staphylococcus aureus. In the present study, 203 S. aureus strains originating from 83 outbreaks that had occurred in Tokyo...
In the last decade, non-multiresistant methicillin-resistant Staphylococcus aureus (NM-MRSA) has been described as an important agent in bloodstream infections in our hospital. This prospective cohort study, conducted from February 2009 through January 2010 in the neonatal unit, evaluated 403 newbor...
The study included 79 vancomycin-resistant Enterococcus faecium (VRE) strains isolated from 33 patients after kidney (n = 19) or liver (n = 14) transplantation; these patients were hospitalized between 2010 and 2012. The strains were obtained from infected persons as well as from carriers. All exami...
Internationally, recent progress in clinical microbiology has involved adapting for multi-drug-resistant organisms (MDROs) such as carbapenemase-producing Enterobacteriaceae (CRE) using selective culture media and the active surveillance test using real-time PCR, matrix-assisted laser desorption-ion...
No abstract available
An outbreak of extended-spectrum β-lactamase (ESBL)-producing Shigella sonnei infections occurred in a school for disabled children in Gyeongbuk Province, Republic of Korea, in 2008. Five students were affected. Pulsed-field gel electrophoresis (PFGE) analysis revealed that all of the ESBL-producing...
Tetracycline-resistance (Tet(R)) has been postulated as a marker of the livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage CC398. to determine the spa-types and assigned MLST clonal complexes (CCs) among all 98 MRSA-Tet(R) strains recovered during 2011-2012 (from differe...
The aim of this study was to characterise carbapenem-resistant Klebsiella pneumoniae isolates that caused an outbreak in a hospital in the south of Spain, originating from a patient transferred in 2012 from Italy. Forty-four K. pneumoniae isolates, recovered from 28 patients, were screened by PCR fo...
This study investigated the molecular epidemiology of Acinetobacter baumannii in the University of Debrecen in relation to antibiotic consumption. Overall and ward-specific antibiotic consumption was measured by the number of defined daily doses (DDD) per 100 bed-days between 2002 and 2012. Consumpt...
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae has disseminated rapidly in China. We aimed to analyze the molecular epidemiology of four KPC-producing K. pneumoniae strains isolated from a suspected clonal outbreak during a 3-month period and to track the dissemination of KPC-prod...
Clostridium difficile is responsible for more than 90 % of cases of antibiotic-associated diarrhea and pseudomembranous colitis. The most important virulence factors are two toxins called enterotoxin A and cytotoxin B; some C. difficile strains contain the C. difficile binary toxin (CDT). The aim of...
No abstract available
Pseudorabies (PR) or Aujeszky's disease (AD), caused by pseudorabies virus (PRV), is an economically important viral disease worldwide. Recently, PR outbreaks occurred in a large number of Bartha-K61-vaccinated swine herds in many regions of China. Here, we isolated a PRV variant, named TJ strain, f...
No abstract available
This study describes phenotypic, genotypic and antibiotic susceptibility patterns of the strains isolated from the 2012 Sierra Leone cholera outbreak. Rectal swabs were collected from patients and cultured for Vibrio cholerae O1. The isolates were subjected to multiplex PCR, mismatch amplification m...
Residents of nursing homes (NHs) are often hospitalized and could present a potential reservoir for methicillin-resistant Staphylococcus aureus (MRSA). The aim of the study was to determine the prevalence for MRSA carriage in residents and staff in Croatian NHs and to characterize MRSA strains using...
A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97%...
In 2002, an outbreak of necrotizing enterocolitis in a Canadian neonatal intensive care unit was associated with a proposed novel species of Clostridium, "Clostridium neonatale." To date, there are no data about the isolation, identification, or clinical significance of this species. Additionally, C...
A total of 95 human Campylobacter jejuni isolates acquired from domestic infections and collected from three districts in Finland during the seasonal peak (June to September) in 2012 were analyzed by PCR-based multilocus sequence typing (MLST) and by whole-genome sequencing (WGS). Four predominant s...
From around the year 2000, Northern Europe experienced a rise in impetigo caused by Staphylococcus aureus resistant to fusidic acid. A single clone of S. aureus was found to be the bacterial pathogen involved in the impetigo outbreak in Norway, Sweden, the UK and Ireland, termed 'the epidemic Europe...
The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, signif...
The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently c...
Ticks are considered to be second worldwide to mosquitoes as vectors of human diseases and the most important vectors of disease-causing pathogens in domestic and wild animals. A number of emerging tick-borne pathogens are already discovered; however, the proportion of undiagnosed infectious disease...
To perform the first multinational Enterobacter cloacae clonality study, using the MLST scheme newly developed in Japan. The analysis included 195 rectal carriage E. cloacae isolates resistant to expanded-spectrum cephalosporins (ESCs), collected from patients in 12 hospital units across Europe and...
Multilocus sequence typing (MLST), a sequence-based typing method for bacterial pathogens, is currently the best method for long-term epidemiological study and to understand the population structure of the bacteria. This investigation was carried out to study the diversity of Pasteurella multocida i...
Carbapenem-resistant Pseudomonas aeruginosa has become a serious health threat worldwide due to the limited options available for its treatment. Understanding its epidemiology contributes to the control of antibiotic resistance. The aim of this study was to describe the clinical and molecular charac...
Mycobacterium xenopi is an opportunistic mycobacterial pathogen of increasing clinical importance. Surveillance of M. xenopi is hampered by the absence of tools for genotyping and molecular epidemiology. In this study, we describe the development and evaluation of an effective multilocus sequence ty...
Despite the success of combined antiretroviral therapy in controlling viral replication in human immunodeficiency virus (HIV)-infected individuals, HIV-associated neurocognitive disorders, commonly referred to as neuroAIDS, remain a frequent and poorly understood complication. Infection of CD8(+) ly...
To study the molecular characteristics of carbapenemase-producing Enterobacteriaceae (CPE) in post-acute-care hospitals (PACHs) in Israel and to analyse the temporal changes between 2008 and 2013. CPE isolates were obtained during two cross-sectional, point prevalence national surveys of PACHs in Is...
Leptospira spp. isolated from patients during a multiyear outbreak in Thailand were genotyped using multilocus sequence typing and a majority were identified as ST34, especially in earlier years. We tested whether ST34 isolates were better adapted to survive in various pH levels, temperatures, and w...
Due to the effect of midgut bacteria on proliferation of parasites and their potential as paratransgenesis tools, their identification in malaria vector mosquitoes is important. Anopheles culicifacies s.l. is one of the main malaria vectors in Asia; however, its midgut microbiota remains un-studied....
An outbreak of foot-and-mouth disease (FMD) affecting cattle and water buffalo (Bubalus bubalis) occurred in Egypt during 2012/2013. The present study was undertaken to determine the current strains of the FMD virus (FMDV) and the prevalence of FMD among cattle and buffalo in Gharbia, Egypt. The dia...
Mycoplasma hyopneumoniae is the major cause of enzootic pneumonia (EP) in domestic pigs, a disease with low mortality but high morbidity, having a great economic impact for producers. In Switzerland EP has been successfully eradicated, however, sporadic outbreaks are observed with no obvious source....
Recently, serotype O75 was found to be prominent among the non-ST131 ciprofloxacin-resistant Escherichia coli, and they were all lactose non-fermenters. In this study, we investigated the prevalence and characteristics of lactose non-fermenters in urinary isolates of E. coli. A total of 167 E. coli...
We tested 19 sera from Austrian patients with acute hepatitis A. A serum from a 48-year-old female patient yielded HAV-nucleic acid that showed 99.7% homology to the HAV-sequence obtained from samples taken during the current outbreak in several European countries, which is associated with consumpti...
Carbapenem-resistant isolates of Pseudomonas aeruginosa producing metallo-β-lactamases (MBLs) are increasingly reported worldwide and often belong to particular 'high-risk clones'. This study aimed to characterize a comprehensive collection of MBL-producing P. aeruginosa isolates referred to the UK...
In 2010, we investigated anthrax outbreak in Bhutan. A total of 43 domestic animals died, and cutaneous anthrax developed in 9 persons, and 1 died. All affected persons had contact with the carcasses of infected animals. Comprehensive preparedness and response guidelines are needed to increase publi...
Six high school students in Tochigi prefecture, Japan, developed gastroenteritis after eating at a pork cutlet shop. Molecular epidemiologic analyses showed that the causative agent was genotype G1P[8] rotavirus (RV), this being detected in stool samples from both the patients and the asymptomatic f...
During testing for Staphylococcus aureus in an intensive care unit in France in 2011, we found that methicillin-sensitive S. aureus clonal complex 398 was the most frequent clone (29/125, 23.2%). It was isolated from patients (5/89, 5.6%), health care workers (2/63, 3.2%), and environmental sites (1...
Pathogenic Yersinia enterocolitica strains are associated with biotypes 1B, 2-5, while environmental strains with biotype 1A. In this work a method for Y. enterocolitica genotyping based on HRMA to determine SNPs was developed and the genetic diversity of 50 strains was determined. The strains were...
As routine diagnostic assays for human parechoviruses (HPeVs) have not been included in the enteroviruses surveillance network in Taiwan, HPeVs may be the actual pathogens of hundreds of untypeable enteroviruses-suspected isolates. In this study, these untypeable isolates collected from 2007 through...
In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to charact...
Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae pose an increasing challenge in hospitals. To describe the benefits of using molecular techniques to investigate the spread of ESBL-producing Klebsiella pneumoniae (ESBL-KP) within a tertiary referral centre. Following the identifi...
Streptococcus agalactiae frequently colonizes the urogenital tract, and it is a major cause of bacterial septicemia, meningitis, and pneumonia in newborns. For typing purposes, a microarray targeting group B streptococcus (GBS) virulence-associated markers and resistance genes was designed and valid...
We report a case of congenital candidiasis in triplets, in the context of premature labor at 25 weeks gestation, without symptomatic vaginitis or chorioamnionitis. All three infants died as a result of prematurity, aggravated by systemic candidiasis. Multi-locus sequence typing confirmed vertical tr...
Reconstructing the evolutionary history, demographic signal and dispersal processes from viral genome sequences contributes to our understanding of the epidemiological dynamics underlying epizootic events. In this study, a Bayesian phylogenetic framework was used to explore the phylodynamics and spa...
Molecular epidemiology of Mycobacterium tuberculosis, its transmission dynamics and population structure have become important determinants of targeted tuberculosis control programs. Here we describe recent changes in the distribution of M. tuberculosis genotypes in New South Wales (NSW), Australia...
The hard tick Ixodes uriae parasitises a wide range of seabird species in the circumpolar areas of both Northern and Southern hemispheres and has been shown to be infected with Borrelia burgdorferi sensu lato, the bacterial agents of Lyme borreliosis. Although it is assumed that seabirds represent v...
While all verotoxin-producing Escherichia coli O157:H7 bacteria are considered potential pathogens, their genetic subtypes appear to differ in their levels of virulence. The aim of this study was to compare the distribution of subtypes of E. coli O157:H7 in the cattle reservoir and in human cases wi...
Although Kingella kingae is the most common etiology of osteoarticular infections in young children, is a frequent cause of bacteremia in those younger than 4 years, and has been involved in clusters of invasive infections among daycare center attendees, the population structure of the species has n...
One hundred and one methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates were classified into 10 genotypes based on their polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) coa pattern. PCR-RFLP coa patterns correlated with the clonal complex (CC) with the...
Helicobacter pylori infects a significant proportion of the world population and it is associated with pathologies which include chronic atrophic gastritis, peptic ulcer, and gastric neoplasias such as gastric adenocarcinoma and MALT lymphoma. Costa Rica has a high prevalence of the infection and an...
Our study showed the antibiotic susceptibility profile of toxigenic Clostridium difficile isolated from nosocomial and community-acquired CDI between 2008 and 2010. MICs of 200 C. difficile strains were determined using E®test method in the case of erythromycin, clindamycin, moxifloxacin, rifampicin...
We characterized 30 community-associated extended-spectrum-β-lactamase-producing Escherichia coli isolates collected from five hospitals in the United States. Nineteen sequence types were identified. All sequence type 131 (ST131) isolates had the fimH30 allele. IncFII-FIA-FIB was the most common rep...
The distribution of Campylobacter jejuni capsular serotypes in the Philadelphia region from 2007 to 2012 was determined using molecular methods. Compared with the last U.S. survey in 1990, there does not appear to be a major shift in circulating capsular types.
The aim of this study was to characterize by a multi-level approach extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae isolates other than E. coli from Portuguese hospitals. Eighty-eight ESBL-producing clinical isolates (69 Klebsiella pneumoniae, 13 Enterobacter cloacae complex, 3 Kle...
Cryptococcosis is a systemic fungal infection that affects humans and animals, mainly due to Cryptococcus neoformans and Cryptococcus gattii. Following the epidemic of acquired immunodeficiency syndrome (AIDS), fungal infections by C. neoformans have become more common among immunocompromised patien...
Methicillin-resistant Staphylococcus aureus (MRSA) burden is increasing worldwide in hospitals [healthcare-associated (HA)-MRSA] and in communities [community-associated (CA)-MRSA]. However, the impact of CA-MRSA within hospitals remains limited, particularly in Latin America. A countrywide represen...
The rapid emergence and dissemination of carbapenem resistance in Enterobacteriaceae complicates the treatment of infections caused by these organisms. We collected clinical isolates with meropenem inhibition zones of ≤ 22 mm from January 1, 2009, through December 31, 2010. We attempted to amplify t...
There have recently been significant changes in diagnostic practices for detecting enterovirus (EV) infections across England and Wales. Reports of laboratory-confirmed EV infections submitted by National Health Service (NHS) hospital laboratories to Public Health England (PHE) over a 12-year period...
Carbapenem-resistant Acinetobacter baumannii (CRAB) is an increasingly common nosocomial pathogen. We sought to identify clinical and microbiological predictors of 14-day mortality among patients with CRAB bacteraemia. This case-control study included all adult patients in one Israeli hospital with...
A variety of molecular typing techniques have been developed to investigate the clonal relationship among bacterial isolates, including those associated with nosocomial infections. In this study, the authors evaluated whole-genome mapping as a tool to investigate the genetic relatedness between Pseu...
Arthropod-borne viruses significantly impact human health. They span multiple families, all of which include viruses not known to cause disease. Characterizing these representatives could provide insights into the origins of their disease-causing counterparts. Field-caught Aedes aegypti mosquitoes f...
The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) has been increasing in the general population, and there is concern that close or physical contact, such as in professional and collegiate sports, may increase spread of MRSA. We sought to determine the prevalence of MRSA colonizat...
Bacterial strain typing is commonly employed in studies involving epidemiology, population ecology, and microbial source tracking to identify sources of fecal contamination. Methods for differentiating strains generally use either a collection of phenotypic traits or rely on some interrogation of th...
We investigated 400 cases of dengue-like illness in persons hospitalized during an outbreak in Al Hudaydah, Yemen, in 2012. Overall, 116 dengue and 49 chikungunya cases were diagnosed. Dengue virus type 2 was the predominant serotype. The co-circulation of these viruses indicates that mosquitoborne...
We confirmed infection of 2 patients with Borrelia miyamotoi in Japan by retrospective surveillance of Lyme disease patients and detection of B. miyamotoi DNA in serum samples. One patient also showed seroconversion for antibody against recombinant glycerophosphodiester phosphodiesterase of B. miyam...
Levofloxacin resistance in Haemophilus influenzae has increased significantly in Taiwan, from 2.0% in 2004 to 24.3% in 2010 (p<0.001). Clinical and molecular investigations of 182 levofloxacin-resistant isolates revealed that the increase was mainly the result of the spread of several clones in the...
Nosocomial Candida albicans infections are a significant problem in neonatal intensive care units (NICUs). We investigated the clonality of C. albicans isolates recovered over an 8-year period from neonates at a NICU. We also validated multilocus sequence typing (MLST) compared with pulsed-field gel...
From August to September 2008, the Centers for Disease Control and Prevention (CDC) assisted the Alaska Division of Public Health with an outbreak investigation of campylobacteriosis occurring among the residents of Southcentral Alaska. During the investigation, pulsed-field gel electrophoresis (PFG...
We investigated a Q fever outbreak with human patients showing high fever, respiratory tract symptoms, headache and retrosternal pain in southern Hungary in the spring and summer of 2013. Seventy human cases were confirmed by analysing their serum and blood samples with micro-immunofluorescence test...
Mycobacterium tuberculosis isolates of the Manila sublineage are genetically homogeneous. In this study, we used whole-genome sequencing (WGS) to type a collection of 36 M. tuberculosis isolates of the Manila family. WGS enabled the subtyping of these 36 isolates into at least 10 distinct clusters....
Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93...
Intestinal inflammation was evaluated using faecal lactoferrin and ribotype in 196 hospitalized adults with Clostridium difficile infection to determine the impact of ribotype 027 in long-term care facilities (LTCFs). LTCF residents (n=28) had greater antibiotic use (P=0.049) and more ribotype 027 i...
Tuberculosis (TB) remains a major cause of morbidity and mortality worldwide. It is expected that combining multiple molecular methods will further help in focusing contact investigations. We performed a population-based molecular epidemiological study in six sites in China between 1 June 2009 and 3...
We characterized 53 OXA-48-producing Klebsiella pneumoniae (OXA-48-Kp) isolated between 2011 and 2013 in 21 French hospitals. All the isolates were genotyped using MLST and PFGE and the population structure of the species was determined by a nucleotide-based analysis of the entire K. pneumoniae MLST...
Clinical background and molecular epidemiology of Clostridium difficile infection (CDI) in the University Hospital Centre Split were investigated from January 2010 to December 2011. In total, 54 patients with first episode of CDI were consecutively included in the study based on the positive EIA tes...
Group A rotaviruses are a major cause of severe gastroenteritis in children worldwide. Currently, two rotavirus vaccines are being used in vaccination programs, and one of the factors involved in lower vaccine efficacy is the mismatch among the circulating strains and the vaccine strains. Thus, the...
This report describes an outbreak of Clostridium difficile infection (CDI) in a nephrology ward in 2012, caused by the fluoroquinolone- and clindamycin-resistant polymerase chain reaction (PCR) ribotype 027 strains. An increase in the number of cases of diarrhoea was noted among patients hospitalise...
Fungal nosocomial infections continue to be a serious problem among hospitalized patients, decreasing quality of life and adding millions of euros to healthcare costs. The aim of this study was to describe the pattern of fungi associated with the hands of healthcare workers and to genotype Candida p...
Francisella noatunensis subsp orientalis (FNO) is an emerging pathogen of warm water tilapia in a number of different countries. The disease caused by this bacterium in fish is characterized by a systemic granulomatous infection that causes high mortality rates during outbreaks. FNO has been previou...
Pneumocystis jiroveci infections can cause pneumocystis pneumonia (PCP) or lead to colonization without signs of PCP. Over the years, different genotypes of P. jiroveci have been discovered. Genomic typing of P. jiroveci in different subpopulations can contribute to unravelling the pathogenesis, tra...
Japanese encephalitis (JE) is an arthropod-borne disease associated with the majority of viral encephalitis cases in the Asia-Pacific region. The causative agent, Japanese encephalitis virus (JEV), has been phylogenetically divided into five genotypes. Recent surveillance data indicate that genotype...
Background: In May 2013, an outbreak of gastroenteritis occurred in a high school in Incheon, South Korea. We investigated the outbreak in order to identify the pathogen and mode of transmission. A case-control study was performed using standardized questionnaires with a case definition of illness w...
A nosocomial outbreak of Acinetobacter baumannii (AB) infections occurred among intensive care units (ICU) (surgery, medical, cardiovascular surgery, coronary unit) of Recep Tayyip Erdogan University Medical School (Rize, Turkey) between January 2011 and May 2012. The identification of isolates and...
Multidrug-resistant tuberculosis (MDR-TB) poses a serious challenge to the global control of the disease. The purpose of this study was to characterize MDR-TB patients from Poland and to determine the extent of MDR-TB disease attributable to recent transmission. The study included all 46 patients di...
Ventilator-associated pneumonia (VAP) is a serious healthcare-associated infection that affects up to 30 % of intubated and mechanically ventilated patients in intensive care units (ICUs) worldwide. The bacterial aetiology and corresponding antimicrobial susceptibility of VAP is highly variable, and...
Outbreaks associated with rapidly growing mycobacteria (RGM) have been increasingly reported worldwide, including in Brazil. Among the RGM, the Mycobacterium abscessus complex is the most pathogenic and related to multidrug resistance. The aim of this study was to evaluate the antimicrobial suscepti...
Although pertussis disease is vaccine preventable, Washington State experienced a substantial rise in pertussis incidence beginning in 2011. By June 2012, the reported cases reached 2,520 (37.5 cases per 100,000 residents), a 1,300% increase compared with the same period in 2011. We assessed the mol...
In the United States, most Clostridium botulinum type A strains isolated during laboratory investigations of human botulism demonstrate the presence of an expressed type A botulinum neurotoxin (BoNT/A) gene and an unexpressed BoNT/B gene. These strains are designated type A(B). The most common pulse...
Microbial subtyping approaches are commonly used for source attribution of human salmonellosis. Such methods require data on Salmonella in animals and humans, outbreaks, infection abroad and amounts of food available for consumption. A source attribution model was applied to 24 European countries, r...
Leptospirosis is a zoonotic infection that is caused by the pathogenic species of Leptospira. Rats are the most important reservoirs of these organisms. Our study aimed to characterize Leptospira isolates from humans and rats and elucidate the Leptospira-rat-human relationship in Luzon, Philippines....
Research on African Staphylococcus aureus has been largely neglected in the past, despite the cultural and geographical diversity in Africa, which has a significant impact on the epidemiology of this pathogen. The polarity between developed urban societies and remote rural populations (e.g. Pygmies)...
Brucellosis caused by Brucella abortus is one of the most important zoonoses in the world. Multiple-locus variable-number tandem repeat analysis (MLVA16) has been shown be a useful tool to epidemiological traceback studies in B. abortus infection. Thus, the present study aimed (i) to evaluate the ge...
Selecting suitable controls for outbreak investigations is often difficult and if done inappropriately will lead to biased inferences. Till receipts and other sales records are frequently available on food premises, but their applicability has not been fully explored. Using data from an investigatio...
An outbreak of anthrax was reported in Lianyungang, Jiangsu Province, China in 2012. Laboratory confirmation of cases was made by detection of Bacillus anthracis genes rpoB, pagA, and cap using real-time polymerase chain reaction (PCR); source tracking was conducted by multiple locus variable-number...
Human noroviruses are the leading cause of epidemic and sporadic gastroenteritis across all age groups. Although the disease is usually self-limiting, in the United States norovirus gastroenteritis causes an estimated 56,000 to 71,000 hospitalizations and 570 to 800 deaths each year. This minireview...
Acute hemorrhagic pneumonia caused by Streptococcus zooepidemicus has emerged as a major disease of shelter dogs and greyhounds. S. zooepidemicus strains differing in multilocus sequence typing (MLST), protective protein (SzP), and M-like protein (SzM) sequences were identified from 9 outbreaks in T...
Previous studies report high prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) colonization among imprisoned populations. However, there are no data on that prevalence in Brazilian correctional institutions. We tested 302 male prisoners for nasopharyngeal colonization with Staphylococ...
This study aimed to investigate the prevalence of Campylobacter jejuni in potential contamination sources that are not regularly monitored such as free-living urban pigeons and crows, dogs, cats and urban environmental water and to assess the possible impact on the epidemiology of campylobacteriosis...
We collected all Staphylococcus aureus isolates from the National Children's Hospital in Costa Rica to evaluate the prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA). Of 299 S. aureus isolates, 61% were MRSA. Most MRSA isolates (94.5%) carried SCCmec IV, and...
Methicillin-resistant Staphylococcus aureus (MRSA) strains have been responsible for many nosocomial outbreaks. Within hospitals, colonized employees often act as reservoirs for the spread of this organism. This study collected clinical samples of 91 patients admitted to the intensive care unit (ICU...
Acinetobacter baumannii is one of the most important antibiotic-resistant nosocomial bacteria. We investigated changes in the clinical and molecular epidemiology of A. baumannii over a 10-year period. We compared the data from 2 prospective multicenter cohort studies in Spain, one performed in 2000...
No abstract available
Host immunity is a major driver of pathogen evolution and thus a major determinant of pathogen diversity. Explanations for pathogen diversity traditionally assume simple interactions between pathogens and the immune system, a view encapsulated by the susceptible-infected-recovered (SIR) model. Howev...
No abstract available
The molecular epidemiology of 66 NDM-producing isolates from 2 Pakistani hospitals was investigated, with their genetic relatedness determined using repetitive sequence-based PCR (Rep-PCR). PCR-based replicon typing and screening for antibiotic resistance genes encoding carbapenemases, other β-lacta...
Streptococcus pyogenes [Group A Streptococcus (GAS)] is one of the most important human pathogens, responsible for numerous diseases with diverse clinical manifestations. As the epidemiology of GAS infections evolves, a rapid and reliable characterization of the isolates remains essential for epidem...
Infections caused by Mycobacterium avium and its subspecies are reported as emerging disease in many countries worldwide. In our study we applied the multilocus sequence typing technology to 98 German M. avium strains originating from different hosts and specimens to examine the degree of the geneti...
Hepatitis B virus (HBV) is the leading cause of liver disease and infects an estimated 240 million people worldwide. It is characterised by a high degree of genetic heterogeneity because of the use of a reverse transcriptase during viral replication. The ten genotypes (A-J) that have been described...
Clostridium difficile is a major nosocomial pathogen of present times. The analysis of 624 C. difficile strains from 11 hospitals in the Czech Republic in 2013 revealed that 40% of isolates belonged to ribotype 176. These results suggest that the incidence of CDI (C. difficile infection) in the Czec...
On September 2 and 6, 2013, Mexico's National System of Epidemiological Surveillance identified two cases of cholera in Mexico City. Rectal swab cultures from both patients were confirmed as toxigenic Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Pulsed-field gel electrophoresis and...
This study involves longitudinal and point-in-time surveys of Salmonella carriage and environmental contamination on two commercial cage layer farms positive for Salmonella enterica subsp. enterica serovar Typhimurium (flock A age, 32 weeks; flock B age, 34 weeks). Salmonella-positive fecal, egg bel...
Group A Streptococcus (GAS)-related disease is responsible for high mortality and morbidity in the Pacific region. The high diversity of circulating strains in this region has hindered vaccine development due to apparently low vaccine coverage of type-specific vaccines. Prospective passive surveilla...
Recent advances in the molecular identification and serotyping of Streptococcus pneumoniae are useful for culture-negative samples; however, there are limitations associated with these methods. We aimed to assess the value of molecular assays for invasive pneumococcal disease (IPD) surveillance in S...
Microbiological data regarding Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacter spp. are scarce. In this study, 11 unique KPC-producing Enterobacter isolates were identified among 44 ertapenem-nonsusceptible Enterobacter isolates collected between 2009 and 2013 at a hospital system i...
Legionnaires' disease is an important cause of community-acquired and hospital-acquired pneumonia. Although uncommon, Legionnaires' disease continues to cause disease outbreaks of public health significance. The disease is caused by any species of the Gram-negative aerobic bacteria belonging to the...
Variable-number tandem repeats (VNTRs) mutate rapidly and can be useful markers for genotyping. While multilocus VNTR analysis (MLVA) is increasingly used in the detection and investigation of food-borne outbreaks caused by Salmonella enterica serovar Typhimurium (S. Typhimurium) and other bacterial...
Outbreaks of viral diseases are frequently associated with the consumption of minimally processed shellfish. Among the viruses in these outbreaks, hepatitis A virus (HAV) and human norovirus (NoV) have been increasingly reported as the most common food-borne pathogens. These viruses must be concentr...
This study was intended to investigate the trend in vancomycin susceptibility and correlation with molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) causing invasive infections. A total of 670 MRSA isolates were collected from patients with invasive infections as part o...
Microcystis aeruginosa is a bloom-forming cyanobacteria, which currently has a cosmopolitan distribution. Since M. aeruginosa can produce toxic compounds across all continents that it inhabits, it is of major public health relevance to assess its origin and dispersal. Thus, we conducted a worldwide...
Hepatitis B virus (HBV) infection is the leading cause of severe chronic liver disease. This article provides a critical view of the importance of genomic medicine for the study of HBV infection and its clinical outcomes in Latin America. Three levels of evolutionary adaptation may correlate with th...
Several virulent Clostridium difficile clones, designated as polymerase chain reaction (PCR) ribotypes 017, 027, or 078, are well recognized in western countries. However, the ribotype distribution of clinical C. difficile isolates in Taiwan remains unclear. Between 2010 and 2012, we identified thre...
Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are an important cause of morbidity and mortality, especially in children. We compared 58 epidemiologically unrelated ESBL-producing E. coli strains that caused infections. They were isolated between 2008 and 201...
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major concern worldwide and gonococcal AMR surveillance globally is imperative for public health purposes. In Eastern Europe, gonococcal AMR surveillance is exceedingly rare. However, in 2004 the Russian gonococcal antimicrobial susceptibi...
Seven high-risk clones of vancomycin-resistant Enterococcus faecium (VREF) belonging to clonal complex 17 were identified using multilocus sequence typing (MLST) among clinical isolates from Saudi Arabia. Among these isolates, a new hospital-associated sequence type (ST795), VanB(2)-type teicoplanin...
Clostridium difficile infections (CDI) in hospitalized patients are known to be closely related to antibiotic exposure. Although several substances can cause CDI, the risk differs between individual agents. In Vienna and other eastern parts of Austria, CDI ribotype 027 is currently highly prevalent....
Extended-spectrum β-lactamases (ESBLs), including the AmpC type, are important mechanisms of resistance among Enterobacteriaeceae. CTX-M type extended-spectrum β- lactamases, of which there are now over 90 variants, are distributed globally, yet appear to vary in regional distribution. AmpC β-lactam...
Streptococcus pneumoniae serotype 19A was the main serotype responsible for invasive pneumococcal disease (IPD) in the Paris area in 2007 and 2009 in both adults and children. To verify if a particular clone is emerging, we determined the populational structure of S. pneumoniae isolates. Eighty-four...
The molecular epidemiology and prevalence of virulence factors of isolates from patients with Klebsiella pneumoniae liver abscess (KLA) in mainland China are unknown. Klebsiella pneumoniae isolates were obtained from drainage samples aseptically collected from patients with pyogenic liver abscess (P...
β-lactamase production has been sporadically reported in the emerging Kingella kingae pathogen but the phenomenon has not been studied in-depth. We investigated the prevalence of β-lactamase production among K. kingae isolates from different geographical origins and genetically characterized β-lacta...
This study presents the serotype distribution and the antibiotic resistance profile of 953 colonising group B Streptococcus (GBS) recovered from women of child bearing age (15 to 49 years) between 2005 and 2012 in the Lisbon and Tagus Valley region, Portugal. Overall, serotypes Ia, II, III, and V we...
Dengue is endemic and affects people in all Indonesian provinces. Increasing dengue cases have been observed every year in Sukabumi in West Java province. Despite the endemicity, limited data is available on the genetic of dengue viruses (DENV) circulating in the country. To understand the dynamics...
Little is known about prevailing ribotypes of Clostridium difficile infection in Romania where CDI is not a mandatory notifiable disease. We studied 64 non-duplicate C. difficile isolates from patients hospitalised at the National Institute of Infectious Diseases, Bucharest, Romania between March 20...
Carbapenem-resistant Acinetobacter baumannii (CRAb) is emerging worldwide as a public health problem in various settings. The aim of this study was to investigate the prevalence of CRAb isolates in Italy and to characterize their resistance mechanisms and genetic relatedness. A countrywide cross-sec...
Whole-genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics f...
To investigate the resistance to carbapenems in Enterobacteriaceae and the underlying resistance mechanisms in North Lebanon between 2008 and 2012. A total of 2767 Enterobacteriaceae isolates recovered from clinical samples collected in Nini Hospital (North Lebanon) were screened for a decrease in s...
Leptospirosis is the most common bacterial zoonoses and has been identified as an important emerging global public health problem in Southeast Asia. Rodents are important reservoirs for human leptospirosis, but epidemiological data is lacking. We sampled rodents living in different habitats from sev...
Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogen of public health importance. The prevalence of MRSA and its antimicrobial resistance pattern, as well as SCCmec and spa types, remain unclear both in the community and in the hospitals of the western region of Iran. One hundred MRSA is...
Staphylococcus epidermidis is a pathogen that is frequently encountered in the hospital environment. Healthcare workers (HCWs) can serve as a reservoir for the transmission of S. epidermidis to patients. The aim of this study was to compare and identify differences between S. epidermidis isolated fr...
Inmates of Rikers Island jail potentially introduce Staphylococcus aureus into New York State prisons upon transfer. In this study, methicillin-resistant Staphylococcus aureus isolates (n = 452), collected from infected inmates (2009 to 2013), were characterized. spa type t008 was the predominant cl...
Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium absc...
An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. Data from the Korea Influenza and Respiratory Surveillance System (KINRESS) showed an unusually...
To characterize the diversity of human Salmonella isolates from one of the administrative regions of the Czech Republic in a time horizon of four years using different typing methods. The following phenotyping methods were used: serotyping, phage typing, and the disk diffusion method for antimicrobi...
To help assess the clinical and public health risks associated with different Shiga toxin-producing Escherichia coli (STEC) strains, an empirical classification scheme was used to classify STEC into five "seropathotypes" (seropathotype A [high risk] to seropathotypes D and E [minimal risk]). This de...
No abstract available
The incidence of community-onset (CO) methicillin-resistant Staphylococcus aureus (MRSA) bacteremia rose from the late 1990s through the 2000s. However, hospital-onset (HO) MRSA rates have recently declined in the United States and Europe. Data were abstracted from infection prevention databases bet...
Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and the host transmission history. Here, we examine in detail the limitations of this relationship. First, all splits in a pathogen phylogeny of more than 1 host occu...
This study investigated the phylogeny and molecular epidemiology of Australian porcine enterotoxigenic Escherichia coli (ETEC) isolates (n=70) by performing multilocus sequence typing (MLST), random amplified polymorphic DNA (RAPD) analysis, virulence gene analysis, plasmid, bacteriocin, integron an...
Community-genotype methicillin-resistant Staphylococcus aureus (CG-MRSA) isolates are known to be more virulent and clinically aggressive in children. The goal of the present study was characterize the molecular epidemiology of MRSA isolates causing infections in Colombian children. An observational...
The dog-associated Staphylococcus pseudintermedius is a rare pathogen in humans. Here we describe a cluster of infections caused by the methicillin-resistant S. pseudintermedius clone ST71-J-t02-II-III. It involved four elderly patients at a tertiary hospital. Three patients had wound infections, an...
Totals of 8.7% (103/1,190) and 21.0% (249/1,190) of the Streptococcus pneumoniae isolates recovered from specimens collected in the United States during the 2011-2012 AWARE (Assessing Worldwide Antimicrobial Resistance Evaluation) Surveillance Program were ceftriaxone nonsusceptible according to the...
Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12...
No abstract available
Co-trimoxazole (trimethoprim/sulfamethoxazole) is clinically valuable in treating skin and soft tissue infections (SSTIs) caused by community-associated methicillin-resistant Staphylococcus aureus (MRSA). The genetic basis of emerging trimethoprim/sulfamethoxazole resistance in S. aureus from Africa...
Catheter-related bloodstream infections (CR-BSIs) have become the most common cause of healthcare-associated bloodstream infections in neonatal intensive care units (ICUs). Microbiological evidence implicating catheters as the source of bloodstream infection is necessary to establish the diagnosis o...
Carbapenem-resistant Enterobacteriaceae (CRE) have spread globally and represent a serious and growing threat to public health. Rapid methods for tracking plasmids carrying carbapenemase genes could greatly benefit infection control efforts. Here, we demonstrate that real-time, direct tracking of a...
In the present work, we studied the genetic diversity of Mycobacterium tuberculosis clinical isolates from patients according to their gender, age, and geographic location in Mexico. We did not observe any statistically significant differences in regard to age or gender. We found that spoligo intern...
Methicillin-resistant Staphylococcus aureus (MRSA) infections pose a major challenge in health care, yet the limited heterogeneity within this group hinders molecular investigations of related outbreaks. Pulsed-field gel electrophoresis (PFGE) has been the gold standard approach but is impractical f...
Repetitive element polymerase chain reaction (rep-PCR) typing has been used for methicillin-resistant Staphylococcus aureus (MRSA) strain characterization. The goal of this study was to determine if a rapid commercial rep-PCR system, DiversiLab™ (DL; bioMérieux, Durham, NC, USA), could be used for M...
No abstract available
No abstract available
Beta-lactam resistance in Haemophilus influenzae due to ftsI mutations causing altered penicillin-binding protein 3 (PBP3) is increasing worldwide. Low-level resistant isolates with the N526K substitution (group II low-rPBP3) predominate in most geographical regions, while high-level resistant isola...
In 2010, Winnipeg, Canada, experienced a doubling of invasive pneumococcal disease (IPD) rates, with a significant increase in the number of cases due to Streptococcus pneumoniae serotype 12F, which previously had accounted for very few cases each year. All serotype 12F IPD cases reported between Se...
Cryptococcosis is a fungal infection mostly caused by Cryptococcus neoformans. We identified agents of cryptococcosis diagnosed in Germany from 2004 to 2010. We used multi-locus sequence typing (MLST) to understand the molecular epidemiology of cryptococcosis. Sero- and mating types of individual pa...
The aim of this study was to determine the prevalence, SCCmec types, presence of the Panton-Valentine leukocidin (PVL) gene, and susceptibility to antibiotics of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from hospitalized children. From August 2009 to September 2011, 291 S....
Between August 2011 and January 2013, an outbreak of Salmonella enterica serovar Stanley (S. Stanley) infections affected 10 European Union (EU) countries, with a total of 710 cases recorded. Following an urgent inquiry in the Epidemic Intelligence Information System for food- and waterborne disease...
In April and May 2011, there was a serious food-poisoning outbreak in Japan caused by enterohemorrhagic Escherichia coli (EHEC) strains O111:H8 and O157:H7 from raw beef dishes at branches of a barbecue restaurant. This outbreak involved 181 infected patients, including 34 hemolytic-uremic syndrome...
Mycobacterium avium subsp. paratuberculosis is the etiological agent of paratuberculosis, a granulomatous enteritis affecting a wide range of domestic and wild ruminants worldwide. A variety of molecular typing tools are used to distinguish M. avium subsp. paratuberculosis strains, contributing to a...
The Paramyxoviridae form an increasingly diverse viral family, infecting a wide variety of different hosts. In recent years, they have been linked to disease emergence in many different animal populations and in humans. Bats and rodents have been identified as major animal populations capable of har...
In hospitals, Clostridium difficile infection (CDI) surveillance relies on unvalidated guidelines or threshold criteria to identify outbreaks. This can result in false-positive and -negative cluster alarms. The application of statistical methods to identify and understand CDI clusters may be a usefu...
The first French outbreak of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 clone was investigated. After outbreak investigation, hygiene measures were implemented in all family households and childminders' homes. Several decontamination procedures were performed, wh...
Shigella dysenteriae type 1 (Sd1) causes recurrent epidemics of dysentery associated with high mortality in many regions of the world. Sd1 infects humans at very low infectious doses (10 CFU), and treatment is complicated by the rapid emergence of antibiotic resistant Sd1 strains. Sd1 is only detect...
We aimed to determine the incidence of Clostridium difficile infection (CDI), the molecular epidemiology of circulating C. difficile strains and risk factors for CDI among hospitalised children in the Auckland region. A cross-sectional study was undertaken of hospitalised children <15 years of age i...
Enterococcus is a major cause of important nosocomial infections. Linezolid, the first member of an entirely new class of antibiotics (oxazolidinones), is effective against serious infections caused by Enterococcus. However, resistance to linezolid has been discovered throughout the world rapidly. F...
Limited clinical experience exists regarding the management of prosthetic joint infection (PJI) due to multidrug-resistant (MDR) Gram-negative organisms. We review three cases of carbapenem-resistant Klebsiella pneumoniae (CRKP) complicating PJI. This was a retrospective study of all patients at a t...
In this study, we report the early expansion, evolution, and characterization of a multiresistant Klebsiella pneumoniae clone that was isolated with increasing frequency from inpatients in a tertiary-care university hospital in Brazil. Seven carbapenem- and quinolone-resistant and polymyxin B-suscep...
In 2009, a severe epidemic of dengue disease occurred in Sri Lanka, with higher mortality and morbidity than any previously recorded epidemic in the country. It corresponded to a shift to dengue virus 1 as the major disease-causing serotype in Sri Lanka. Dengue disease reached epidemic levels in the...
Since 2003, a rising incidence of Clostridium difficile infection (CDI) in North America and Europe has coincided with outbreaks of C. difficile PCR ribotype 027. This ribotype was not observed in Poland until 2008. In the period 2008-2010, outbreaks of antibiotic-associated diarrhoea occurred in th...
Klebsiella pneumoniae is a frequent nosocomial pathogen, with the multidrug-resistant (MDR) K. pneumoniae being a major public health concern, frequently causing difficult-to-treat infections worldwide. The aim of this study was to investigate the molecular characterization of clinical MDR Klebsiell...
A total of 178 strains of V. parahaemolyticus isolated from 13,607 acute diarrheal patients admitted in the Infectious Diseases Hospital, Kolkata has been examined for serovar prevalence, antimicrobial susceptibility and genetic traits with reference to virulence, and clonal lineages. Clinical sympt...
To determine whether, and to what extent, influenza A subtype H3 viruses were present in feral swine in the United States, we conducted serologic and virologic surveillance during October 2011-September 2012. These animals were periodically exposed to and infected with A(H3N2) viruses, suggesting th...
During 2010, outbreaks of serogroup C meningococcal (MenC) disease occurred in 2 oil refineries in São Paulo State, Brazil, leading to mass vaccination of employees at 1 refinery with a meningococcal polysaccharide A/C vaccine. A cross-sectional study was conducted to assess the prevalence of mening...
Prolonged outbreaks of multidrug-resistant Streptococcus pneumoniae in health care facilities are uncommon. We found persistent transmission of a fluroquinolone-resistant S. pneumoniae clone during 2006-2011 in a post-acute care facility in Israel, despite mandatory vaccination and fluoroquinolone r...
Tularemia outbreaks occurred in northwestern Spain in 1997-1998 and 2007-2008 and affected >1,000 persons. We assessed isolates involved in these outbreaks by using pulsed-field gel electrophoresis with 2 restriction enzymes and multilocus variable number tandem repeat analysis of 16 genomic loci of...
No abstract available
No abstract available
It is common practice to define a bacterium with unequal antibiotic susceptibility phenotypes as a different genotype. Here, we describe the utility of this practice for Acinetobacter baumannii. We determined antibiotic susceptibility for 19 clinical isolates of A baumannii. Repetitive sequence poly...
Neisseria meningitidis, the cause of meningococcal disease, has been the subject of sophisticated molecular epidemiological investigation as a consequence of the significant public health threat posed by this organism. The use of multilocus sequence typing and whole genome sequencing classifies the...
Pathogenic Escherichia coli strains cause a wide variety of intestinal and extraintestinal infections. The widespread geographical clonal dissemination of intestinal pathogenic E. coli strains, such as E. coli O157:H7, is well recognized, and its spread is most often attributed to contaminated food...
No abstract available
After the last reported cases of rabies in a human in 1959 and a nonhuman animal in 1961, Taiwan was considered free from rabies. However, during 2012-2013, an outbreak occurred among ferret badgers in Taiwan. To examine the origin of this virus strain, we sequenced 3 complete genomes and acquired m...
The prevalence of community-associated meticillin-resistant Staphylococcus aureus (CA-MRSA) is increasing throughout the world and is an important cause of skin and soft tissue infection (SSTI) in children and neonates. To describe the successful control of an outbreak caused by a new strain of CA-M...
Streptococcus gallolyticus subsp. gallolyticus (formerly known as S. bovis biotype I) is a commensal of the gastrointestinal tract in animals and in up to 15% of healthy humans. Furthermore, it is a facultative pathogen that can cause infectious endocarditis, mastitis, and septicemia. The number of...
Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infe...
Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the most significant pathogens affecting global public health and health care systems. In Canada and the United States, the spread of MRSA is primarily attributed to a single dominant epidemic clone: CMRSA10/USA300. Despite this, t...
Bacterial gene islands add to the genetic repertoire of opportunistic pathogens. Here, we perform comparative analyses of three Pseudomonas aeruginosa strains isolated sequentially over a 3-week period from a patient with ventilator-associated pneumonia (VAP) who received clindamycin and piperacilli...
The term 'zero tolerance' has recently been applied to healthcare-associated infections, implying that such events are always preventable. This may not be the case for healthcare-associated infections such as methicillin-resistant Staphylococcus aureus (MRSA) bacteraemia. We combined information fro...
Salmonella sp. continues to be one of the most important foodborne pathogens. Control measures in terms of cleaning and disinfection on food production plants are very important for limiting the risk of contaminated food products to reach the consumer. In the last decade concern has arisen that bact...
Serogroup B meningococcal (MenB) isolates currently account for approximately 90% of invasive meningococcal disease (IMD) in Greece with ST-162 clonal complex predominating. The potential of a multicomponent meningococcal B vaccine (4CMenB) recently licensed in Europe was investigated in order to fi...
Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of both healthcare-associated MRSA (HA-MRSA) and community-associated MRSA (CA-MRSA) infections. Severe MRSA infections have been associated with the virulence factor Panton-Valentine leukocidin (PVL). The aim of this study was...
A cluster of seven human cases of listeriosis occurred in Austria and in Germany between April 2011 and July 2013. The Listeria monocytogenes serovar (SV) 1/2b isolates shared pulsed-field gel electrophoresis (PFGE) and fluorescent amplified fragment length polymorphism (fAFLP) patterns indistinguis...
In a previous prospective multicenter study in Spain, we found that OXA-1 and inhibitor-resistant TEM (IRT) β-lactamases constitute the most common plasmid-borne mechanisms of genuine amoxicillin-clavulanate (AMC) resistance in Escherichia coli. In the present study, we investigated the population s...
Treponema pallidum strains are closely related at the genome level but cause distinct diseases. Subspecies pallidum (TPA) is the causative agent of syphilis, subspecies pertenue (TPE) causes yaws while subspecies endemicum (TEN) causes bejel (endemic syphilis). Compared to the majority of treponemal...
A total of 180 non-duplicate carbapenem-resistant Klebsiella pneumoniae isolates were recovered from patients hospitalized between December 2010 and January 2012 at a Chinese hospital. Eight KPC-2, four NDM-1, one VIM-2, and five KPC-2 plus IMP-4 producers were identified and all were multidrug resi...
A 42-plex clustered regularly interspaced short palindromic repeat (CRISPR)-based typing technique (spoligotyping) was recently developed at the French National Reference Center for Legionella. It allows the subtyping of the Legionella pneumophila sequence type 1/Paris pulsotype. In this report, we...
Multidrug-resistant nosocomial pathogens present a major burden for hospitals. Rapid cluster identification and pathogen profiling, i.e., of antibiotic resistance and virulence genes, are crucial for effective infection control. Methicillin-resistant Staphylococcus aureus (MRSA), in particular, is n...
Antimicrobial drug resistance in Neisseria gonorrhoeae has become an increasing public health problem. Hence, surveillance of resistance development is of crucial importance to implement adequate treatment guidelines. Data on the spread of antibiotic resistance among gonococcal isolates in Germany,...
Clostridium difficile infection (CDI) is the most frequent infectious cause of health care-associated diarrhea. Three cases of CDI, in children age 2, 3, and 14 years, occurred in the hematology/oncology ward of our children's hospital over 48 hours. We aimed to assess environmental contamination wi...
Vibrio parahaemolyticus (Vp) is found naturally in coastal saltwater. In the United States, Vp causes an estimated 35,000 domestically acquired foodborne infections annually, of which most are attributable to consumption of raw or undercooked shellfish. Illness typically consists of mild to moderate...
Cholera has been a recurrent epidemic disease in human populations for the past 200years. We present herein a comparative characterization of clinical Vibrio cholerae strains isolated from two consecutive cholera outbreaks in 2012 and associated environmental strains from western India. The clinical...
Mountain lions (Puma concolor) throughout North and South America are infected with puma lentivirus clade B (PLVB). A second, highly divergent lentiviral clade, PLVA, infects mountain lions in southern California and Florida. Bobcats (Lynx rufus) in these two geographic regions are also infected wit...
Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract disease in infants and young children and an important respiratory pathogen in the elderly and immunocompromised. While population-wide molecular epidemiology studies have shown multiple cocirculating RSV genotyp...
Despite the fact that the NDM-1 carbapenemase has successfully disseminated worldwide, outbreaks remain uncommon in the European region. We describe the characteristics of the first outbreaks caused by NDM-1-producing Klebsiella pneumoniae clonal isolates in Greece. Between January 2010 and June 201...
Clostridium difficile infection is the most common cause of severe cases of antibiotic-associated diarrhea (AAD) and is a significant health burden. Recent increases in the rate of C. difficile infection have paralleled the emergence of a specific phylogenetic clade of C. difficile strains (ribotype...
In December 2012, a 32-year-old woman with no previous medical history and no previous antibiotic treatment had a fever and diarrhea 2 days after a cesarean section in which cefazolin was used as a prophylactic antimicrobial agent. She was transferred to our hospital 5 days after the cesarean for se...
Pertussis is increasing due to multiple factors including increasing awareness by clinicians, decreased effectiveness of vaccines, and improved testing. While Bordetella pertussis is the causative agent of pertussis other Bordetella species such as B. parapertussis, and B. holmesii, have been associ...
Compounding pharmacies often prepare parenteral nutrition (PN) and must adhere to rigorous standards to avoid contamination of the sterile preparation. In March 2011, Serratia marcescens bloodstream infections (BSIs) were identified in 5 patients receiving PN from a single compounding pharmacy. An i...
Trichosporon asahii has been recognized as an emerging opportunistic agent for invasive infections, mainly in immunocompromised patients. Urinary tract infections by this pathogen may also occur, especially in patients with urinary obstruction or those undergoing vesical catheterization and antibiot...
After the massive outbreak of infections with Shiga toxin-producing Escherichia coli (STEC) of serotype O104:H4 in Germany in the summer of 2011, post-outbreak surveillance for further infections with this type of STEC was maintained until the end of 2011. This surveillance was based on national man...
Genomics is increasingly being used to investigate disease outbreaks, but an important question remains unanswered--how well do genomic data capture known transmission events, particularly for pathogens with long carriage periods or large within-host population sizes? Here we present a novel Bayesia...
The genome sequence of one OXA-48-producing Klebsiella pneumoniae belonging to sequence type (ST) 405, and three belonging to ST11, were used to design and test ST-specific PCR assays for typing OXA-48-producing K. pneumoniae. The approach proved to be useful for in-house development of rapid PCR ty...
We investigated the prevalence of vulvovaginal candidiasis due to C. africana in an STD clinic in India and analysed the genetic relatedness of these C. africana isolates with those outside India. A total of 283 germ-tube-positive yeasts were identified by VITEK2. Molecular characterisation of all i...
Despite having a low occurrence rate, Listeria monocytogenes is one of the most prominent foodborne pathogens in Australia. The organism is responsible for severe outbreaks with high case fatality and substantial economic losses due to food recalls. In this study, we analyze the incidence trends of...
No abstract available
Two-hundred MRSA strains from inpatients with healthcare-associated (HA) and 100 MRSA strains from outpatients with community-associated (CA) skin and soft tissue infections (SSTIs) were tested for antimicrobial susceptibility, staphylococcal cassette chromosome mec (SCCmec) typing, Panton-Valentine...
Vertical transmission from mother to child, the main route of chronic hepatitis B virus (HBV) infection in the East Asia, is considered one of the most important predictors for the response to antiviral therapies as well as its complications such as cirrhosis and hepatocellular carcinoma. Therefore,...
We report the investigation of an outbreak of colonization by a wild-type Enterobacter cloacae and its AmpC-hyper-producing derivative E cloacae in a neonatal intensive care unit. E cloacae hyper-producing AmpC β-lactamase isolates were found from neonate specimens and from environmental samples. Al...
We analyzed the prevalence and characteristics of Vibrio parahaemolyticus among patients with acute infectious diarrhea in the southern coastal region of China. V. parahaemolyticus was the leading cause of bacterial infectious diarrhea in this region during 2007-2012. Serotype O3:K6 strains were mos...
Introduction : One of the major worldwide public health problems today are the infections caused by carbapenem-resistant Enterobacteriaceae (CRE), among which carbapenem-resistant Klebsiella pneumoniae (CRKP), constitutes one of the most common pathogens causing nosocomial infection. This study was...
Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of infection in the pediatric population. Initially, MRSA was restricted to hospitals; however, outbreaks in the community among people without health care-related risk factors have been reported worldwide. Currently, MRSA is a f...
Enterococcus spp is currently considered as one of the most important nosocomial pathogens . The antibiotic resistance of this group of bacteria is a particularly important problem in health centers. To characterize the antibiotic resistance of 50 Enterococcus spp strains isolated from hospitalized...
Part of the success of methicillin-resistant Staphylococcus aureus (MRSA) as a pathogen responds to the rapid spread of pandemic lineages with diverse virulence and antimicrobial susceptibility profiles. In Colombia, several healthcare-associated MRSA (HA-MRSA) clones have been found, including the...
A recent longitudinal study in the Dadaab refugee camp near the Kenya-Somalia border identified unusual biannual respiratory syncytial virus (RSV) epidemics. We characterized the genetic variability of the associated RSV strains to determine if viral diversity contributed to this unusual epidemic pa...
No abstract available
Possible cross-transmission of hospital-associated enterococci between human patients, medical staff, and hospital environments has been extensively studied. However, limited information is available for veterinary hospital-associated Enterococcus isolates. This study investigated the possibility of...
Pulsed-field gel electrophoresis (PFGE) is a common method used to type methicillin-resistant Staphylococcus aureus (MRSA) in nosocomial investigations and epidemiological studies but is time-consuming and methodologically challenging. We compared typing results obtained using a commercial repetitiv...
Streptococcus pyogenes (group A Streptococcus [GAS]) causes a wide variety of diseases, ranging from mild noninvasive to severe invasive infections. Mutations in regulatory components have been implicated in the switch from colonization to invasive phenotypes. The inactivation of the sil locus, comp...
Mycobacterium abscessus is a rapidly growing mycobacterium that causes respiratory tract infections in predisposed patients, such as those with cystic fibrosis and nosocomial skin and soft tissue infections. In order to investigate the clonal relationships between the strains causing epidemic episod...
Yersinia pseudotuberculosis is an enteropathogen that has an animal reservoir and causes human infections, mostly in temperate and cold countries. Most of the methods previously used to subdivide Y. pseudotuberculosis were performed on small numbers of isolates from a specific geographical area. One...
Carbapenemase-producing Enterobacteriaceae (CPE) strains are encountered with increasing frequency in Europe. In November 2010 the European Centre for Disease Control (ECDC) graded Ireland as only having sporadic occurrence of CPE. To describe the epidemiological and molecular typing analysis of the...
Prevalent since pre-history, human tuberculosis - caused by the pathogen Mycobacterium tuberculosis - remains a major source of death worldwide. Moreover, increasing drug resistance poses the threat of disease resurgence. However, the expanding application of genomic techniques is providing new aven...
To investigate the characterization of bla(OxA-23) gene regions in isolates of Acinetobacter baumannii from Taizhou Municipal Hospital. Fifty-nine non-repetitive, multiresistant (including imipenem-resistant) isolates of A. baumannii were recovered from clinical infections in hospitalized patients f...
In epidemiology, the identification of 'who infected whom' allows us to quantify key characteristics such as incubation periods, heterogeneity in transmission rates, duration of infectiousness, and the existence of high-risk groups. Although invaluable, the existence of many plausible infection path...
Ochrobactrum anthropi (O. anthropi), is a non-fermenting gram-negative bacillus usually found in the environment. Nevertheless, during the past decade it has been identified as pathogenic to immunocompromised patients. In this study, we assessed the usefulness of the automated repetitive extragenic...
Despite scientific advances in typing of C. difficile strains very little is known about how hospital staff use typing results during periods of increased incidence (PIIs). This qualitative study, undertaken alongside a randomised controlled trial (RCT), explored this issue. The trial compared ribot...
Over a 6-year period (2007-2012), the emergence of Enterobacter cloacae isolates resistant to β-lactams and with reduced susceptibility to carbapenems was observed in Hospital Universitario 12 de Octubre (Madrid, Spain). To determine the possible role of metallo-β-lactamases (MBLs) in the resistance...
No abstract available
Shiga toxin-producing Escherichia coli (STEC) are important food-borne pathogens associated with cases of diarrhea, hemorrhagic colitis and hemolytic uremic syndrome (HUS). E. coli O157:H7 is the dominant serotype in Argentina and also in Neuquén Province, in which HUS incidence is above the nationa...
The prevalence of plasmid-mediated quinolone resistance (PMQR) determinants was investigated in a Tunisian collection of 300 uropathogenic Escherichia coli. PMQR genes were detected in 68 isolates (22.7%) as follows: aac(6')-Ib-cr (n=66), qnrB1 (n=3), qnrA6 (n=1), and qnrS1 (n=1). Three isolates car...
Southern rice black-streaked dwarf virus (SRBSDV), transmitted by the white-backed planthopper (Sogatella furcifera) in a persistent-propagative manner, has caused serious yield losses in Asia. Here in a yeast two-hybrid system, protein interactions between SRBSDV P7-1 as a bait protein and a cDNA l...
This study was performed to investigate the prevalence and molecular epidemiology of Pseudomonas aeruginosa isolates from Korea that produce enzymes with extended-spectrum (ES) activity to β-lactams. A total of 205 non-duplicate P. aeruginosa clinical isolates were collected from 18 university hospi...
The study investigated the genetic relationship of carbapenem-resistant Acinetobacter baumannii clinical isolated from inpatients during 2008-2011 from 11 Brazilian states. Antimicrobial susceptibility profile was determined by disc diffusion method and Etest. Polymerase chain reaction was applied f...
After the first outbreak of Clostridium difficile PCR ribotype (RT) 027 in Germany in 2007, no further outbreaks were reported until the recent re-emergence of RT 027 in Hesse, a federal state with 6 million inhabitants located in south-west Germany. We undertook a survey to determine the prevalence...
In this study, the prevalence of M types of Group A Streptococcus (GAS) in North India, invasive behavior of prevalent M types, and inflammatory immune response by host cells were studied. A total of 1,047 clinical samples were collected between 2004 and 2010. Confirmation of GAS was determined by s...
Surface-expressed protein antigens such as factor H-binding protein (fHbp), Neisserial adhesin A (NadA), Neisserial heparin-binding antigen (NHBA) and Porin protein A (PorA); all express sequence variability that can affect their function as protective immunogens when used in meningococcal serogroup...
Xanthomonas arboricola is an important bacterial species, the pathovars of which are responsible for bacterial blight diseases on stone fruit, hazelnut, Persian walnut, poplar, strawberry, poinsettia and banana. In this study, we evaluated variable number tandem repeats (VNTR) as a molecular typing...
Single-locus blaOXA-51-like sequence-based typing (SBT) was evaluated for its ability to determine correctly sequence types (STs) in Acinetobacter baumannii clinical isolates, in comparison with the Pasteur's multilocus sequence typing (MLST) reference method and 3-locus sequence typing (3-LST). The...
MALDI-TOF mass spectrometry (MALDI-TOF MS) is increasingly used as a reliable technique for species identification of bacterial pathogens. In this study we investigated the question of whether MALDI-TOF MS can be used for accurate sub-differentiation of strains and isolates of two important nosocomi...
A sublineage of Mycobacterium tuberculosis called RD(Rio) was described in 2007. Although only recently described, this strain may have been present previously in the population, and its identification in clinical isolates will elucidate bacterial transmission dynamics and host-pathogen interactions...
On 31 May 2011, after notification of Klebsiella pneumoniae (KP)(OXA-48;CTX-M-15) in two patients, nosocomial transmission was suspected in a Dutch hospital. Hospital-wide infection control measures and an outbreak investigation were initiated. A total of 72,147 patients were categorised into groups...
Salmonella enterica serovar Typhi is transmitted by fecally contaminated food and water and causes approximately 22 million typhoid fever infections worldwide each year. Most cases occur in developing countries, where approximately 4% of patients develop intestinal perforation (IP). In Kasese Distri...
During active surveillance at the Mediterranean Institute for Transplantation and Advanced Specialized Therapies (ISMETT, Palermo, Italy) with the CARBA screening medium, five pairs of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae and Escherichia coli strains were isolated in eac...
Klebsiella oxytoca acts as a pathobiont in the dysbiotic human intestinal microbiota, causing antibiotic-associated hemorrhagic colitis (AAHC), but it also infects other organs, resulting in pneumonia and urinary tract and skin infections. The virulence of K. oxytoca is still poorly understood. The...
The study aims were: (i) to define the prevalence of and risk factors for colonization by extended spectrum β-lactamase (ESBL) -producing Enterobacteriaceae (EPE) among healthcare workers (HCWs) and family members (FMs) of EPE-colonized patients in rehabilitation units and (ii) to compare EPE isolat...
Mycobacterium bovis is the causative agent of bovine tuberculosis (TB), a disease that affects approximately 5% of Argentinean cattle. Among the molecular methods for genotyping, the most convenient are spoligotyping and variable number of tandem repeats (VNTR). A total of 378 samples from bovines w...
B. cepacia complex have emerged as an important opportunistic pathogen in hospitalized and immunocompromised patients. Small hospital outbreaks are frequent and are usually due to a single contaminated environmental source. In this study we were going to investigate the role of B.cepacia complex in...
Fowl cholera, caused by Pasteurella multocida, remains a major problem of poultry worldwide. In the current report, we describe an outbreak in free range organic broilers. In addition to culturing samples from dead broilers, we attempted to isolate P. multocida from feral cats trapped on the farm. T...
A total of 60 Mycobacterium tuberculosis isolates collected from patients in prisons in Kazakhstan and 125 from the civilian sector were examined using mycobacterial interspersed repetitive units-variable number of tandem repeat analysis in 2012. The proportion of tuberculosis strains with unique ge...
In summer 2012, an outbreak of hantavirus infections occurred among overnight visitors to Yosemite National Park in California, USA. An investigation encompassing clinical, epidemiologic, laboratory, and environmental factors identified 10 cases among residents of 3 states. Eight case-patients exper...
Methicillin-resistant Staphylococcus aureus (MRSA) plays an important role in nosocomial infections including those in communities. MRSA enables colonization in the nares and throats of healthy people. In this study, investigation of MRSA prevalence from the throats of healthy subjects in southern T...
In August 2012, the Arkansas Department of Health (ADH) was notified of gastrointestinal illness outbreaks in two Arkansas state prisons. ADH investigated the outbreaks and conducted case-control studies to identify the source of the illnesses. This report describes the results of these investigatio...
The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological p...
This report describes the investigation and public health management of a community-based outbreak of severe adenovirus serotype 14p1 respiratory infection affecting the Tayside area during 2011. It is the first report of an adenovirus outbreak involving prisons. An outbreak-based/incident managemen...
We examined the molecular epidemiology of Acinetobacter baumannii clinical isolates from two cities (Tehran and Tabriz) of Iran. DiversiLab repetitive extragenic palindromic PCR (rep-PCR), multilocus sequence typing and sequence group multiplex PCR were performed. The presence of resistance mechanis...
Shigella species are an important cause of diarrhea in developing countries. These bacteria normally acquire their antibiotic resistance via several different mobile genetic elements including plasmids, transposons, and integrons involving gene cassettes. During a diarrhea surveillance study in Thim...
Infections caused by multidrug-resistant (MDR) Acinetobacter baumannii have become an important healthcare-associated problem, particularly in intensive care units (ICUs). To investigate the emergence of carbapenem- and colistin-resistant A. baumannii infections in two Sicilian hospitals. From Octob...
Mycobacterium kansasii is a pulmonary pathogen that has been grown readily from municipal water, but rarely isolated from natural waters. A definitive link between water exposure and disease has not been demonstrated and the environmental niche for this organism is poorly understood. Strain typing o...
In Sweden the prevalence of Enterobacteriaceae with transferable resistance to extended-spectrum cephalosporins (ESCs) is low. However, in broilers ESC-resistant Escherichia coli is common, with a clear dominance of blaCMY-2. Antimicrobials are rarely used in broiler production in Sweden and cephalo...
Infection with Clostridium difficile is the primary infective cause of antibiotic-associated diarrhoea. In 2008, a major outbreak of CD027 took place in North Zealand, Denmark. We described this infection in a single medical department. Patients positive for C. difficile enlisted at Medical Departme...
Coxiella burnetii causes Q fever in humans and Coxiellosis in animals; symptoms range from general malaise to fever, pneumonia, endocarditis and death. Livestock are a significant source of human infection as they shed C. burnetii cells in birth tissues, milk, urine and feces. Although prevalence of...
No abstract available
Our aim was to describe the epidemiology and incidence of community-onset invasive S. aureus disease in children presenting to our hospital, and to compare the clonal complexes and virulence genes of S. aureus strains causing invasive and non-invasive disease. The virulence gene repertoire of invasi...
We describe, for the first time, a cluster of lethal fulminant health-care associated Clostridium difficile (CD) colitis in Italy, observed in the intensive care unit (ICU) of an Italian tertiary care hospital in Rome. For all cases the cause of ICU admission was CD-related septic shock. Three out o...
Gastroenteritis outbreaks in prisons represent a public health risk worldwide. Identifying and characterizing the etiological agents of gastroenteritis outbreaks in prisons is important for implementing effective prevention and infection control measures. We present the first studied case of a gastr...
We describe a foodborne outbreak in Italy caused by enteroinvasive Escherichia coli (EIEC), an enteric pathogen uncommon in industrialized countries. On 14 April 2012 a number of employees of the city of Milan Fire Brigade (FB) were admitted to hospital with severe diarrhoea after attending their ca...
Staphylococcus epidermidis is an abundant member of the microbiota of the human skin and wet mucosa, which is commonly associated with sight-threatening infections in eyes with predisposing factors. Ocular S. epidermidis has become notorious because of its capability to form biofilms on different oc...
Salmonella serovar Dublin causes disease in cattle and leads to considerable production losses. In humans, severe invasive disease and high mortality rates are reported. The presently available typing methods provide insufficient discrimination within Salm. Dublin for epidemiological investigations....
Dengue is the most rapidly spreading mosquito-borne viral disease in the world, and as a larger proportion of the population is being affected, more unusual manifestations are being reported. Very few studies have documented unusual manifestations of dengue in South India. This prospective study was...
A series of extensively drug-resistant isolates of Pseudomonas aeruginosa from two outbreaks in UK hospitals were characterized by whole genome sequencing (WGS). Although these isolates were resistant to antibiotics other than colistin, we confirmed that they are still sensitive to disinfectants. Th...
Pseudomonas aeruginosa is an important opportunistic pathogen responsible for nosocomial infections and is currently reported to be a worldwide nosocomial menace. The aim of this study was to investigate the epidemiological traits and the distribution of metallo-β-lactamases (MBLs)-producing P. aeru...
Salmonella enterica serovar Kottbus has been continuously isolated from poultry and poultry meat, especially from turkey. We investigated by comparative molecular typing 95 S. Kottbus isolates obtained in Germany between 2000 and 2011 from poultry/poultry meat, pig/pork, cattle, reptiles, the enviro...
A meticillin-resistant Staphylococcus aureus (MRSA) strain with additional β-lactam-inducible aminoglycoside resistance was previously reported by a group at the Kitasato University in Japan. In addition to gentamicin, the 'Kitasato strain' was resistant to arbekacin (ABK), which is primarily used a...
Lung infection with Pseudomonas aeruginosa is common in lung transplant recipients and may lead to severe complications. Bacteriological surveillance aims to detect transmission of microbes between hospital environment and patients. We sought to determine whether genotyping of P. aeruginosa isolates...
We investigated the extent of lymphocytic choriomeningitis virus (LCMV) infection in employees and rodents at 3 commercial breeding facilities. Of 97 employees tested, 31 (32%) had IgM and/or IgG to LCMV, and aseptic meningitis was diagnosed in 4 employees. Of 1,820 rodents tested in 1 facility, 382...
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High-throughput sequencing technologies are now allowing us to study patterns of community assembly for diverse microbial assemblages across environmental gradients and during succession. Here we discuss potential explanations for similarities and differences in bacterial and fungal community assemb...
We report the epidemiological and clinical features of the first outbreak of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) type 2 in Switzerland. The outbreak took place in the medical intensive care unit (MICU) of our tertiary care hospital and affected three severely ill pat...
Here we report an outbreak of Klebsiella pneumoniae infections harboring extended spectrum β-lactamases (ESBL) and armA 16Sr RNA methylase that were detected in pediatric and neonatal intensive care units during the 2010 and 2011 surveys of 100 clinical strains of K. pneumoniae from Annaba hospitals...
It is unclear whether patients colonized with methicillin-resistant Staphylococcus aureus (MRSA) continue to harbor the same genotype during hospital readmissions. We characterized 140 MRSA strains isolated from 33 persistent MRSA carriers with hospital readmissions. Nearly half of the patients cont...
The molecular epidemiology of group B Streptococcus (GBS) in Ireland was investigated. Invasive (n = 132) and non-invasive (n = 45) isolates, collected in 2007-2011, were analysed by multilocus locus sequence typing, capsular polysaccharide (CPS) serotyping, profiling of surface proteins, pilus isla...
Klebsiella pneumoniae causes a range of clinical disease in paediatric patients and is of increasing concern due to growing antibiotic resistance, yet little is known about the relative distribution of commensal and pathogens throughout the population structure of K. pneumoniae. We conducted a prosp...
The aim of this study was to characterize vancomycin-resistant Enterococcus faecium (VREfm) isolates phenotypically and molecularly, and investigate associations between the virulence factors enterococcal surface protein (esp), hyaluronidase (hyl), and collagen adhesin (acm) and colonization/infecti...
Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees ("who infected whom") from epidemiological and genetic data. Making use of pathogen genome sequences in such analyses remains a challenge, however, with a variety of heuristic...
We aimed at evaluating the prevalence of Listeria species isolated from food samples and characterizing food and human cases isolates. Between 2005 and 2007, one hundred food samples collected in the markets of Tunis were analysed in our study. Five strains of Listeria monocytogenes responsible for...
The emergence of Neisseria gonorrhoeae with decreased susceptibility to extended spectrum cephalosporins raises the prospect of untreatable gonorrhoea. In the absence of new treatments, efforts to slow the increasing incidence of resistant gonococcus require insight into the factors that contribute...
A survey was performed in May 2013 to assess methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization in healthy children attending 26 municipal daycare centres in Palermo, Italy. Of the 500 children, ten (2 %) tested positive. Eight MRSA isolates were tst1-positive ST22-MRSA-IVa, spa t...
Vibrio cholerae serogroup O139 was first identified in 1992 in India and Bangladesh, in association with major epidemics of cholera in both countries; cases were noted shortly thereafter in China. We characterized 211 V. cholerae O139 isolates that were isolated at multiple sites in China between 19...
Shigella flexneri is the major cause of shigellosis in developing countries. A new S. flexneri serotype, Xv, appeared in 2000 and replaced serotype 2a as the most prevalent serotype in China. Serotype Xv is a variant of serotype X, with phosphoethanolamine modification of its O antigen mediated by a...
Transmissible strains of Pseudomonas aeruginosa have been described for cystic fibrosis (CF) and may be associated with a worse prognosis. Using a comprehensive strain biobank spanning 3 decades, we sought to determine the prevalence and stability of chronic P. aeruginosa infection in an adult popul...
No abstract available
No abstract available
Molecular typing and antifungal susceptibility testing of 34 clinical Serbian Cryptococcus neoformans isolates from 25 patients was retrospectively performed. Amplified fragment length polymorphism (AFLP) fingerprinting was used for genotyping, whereas a novel real-time PCR was used to determine the...
Serogroup O1 Vibrio cholerae is the most common agents to cause epidemic and pandemic cholera disease. In this study, multilocus sequence typing (MLST) was performed on 160 serogroup O1 strains (including 42 toxigenic and 118 non-toxigenic), and the virulence/fitness gene profiles of 16 loci were fu...
Invasive fungal infections due to Aspergillus species have become a major cause of morbidity and mortality among immunocompromised patients. In order to determine the possible relationship between environmental contamination by Aspergillus and the occurrence of invasive aspergillosis, a 1-year prosp...
Microbial typing is often employed to determine the source and routes of infections, confirm or rule out outbreaks, trace cross-transmission of healthcare-associated pathogens, recognize virulent strains and evaluate the effectiveness of control measures. Conventional microbial typing methods have o...
Bovine viral diarrhea virus (BVDV) has been recognized as an important pathogen of livestock in Canada. The high mutation rate of this virus leads to a great degree of diversity between isolates resulting in the ability to infer precise evolutionary relationships. Many studies have attempted to eluc...
Avian botulism is a paralytic disease caused by Clostridium botulinum-produced botulinum neurotoxins (BoNTs), most commonly of type C/D. It is a serious disease of waterbirds and poultry flocks in many countries in Europe. The objective of this study was to compare the genetic relatedness of avian C...
Thermotolerant Campylobacter spp. are frequently the cause of human gastroenteritis and have assumed more importance in Italy following the increased consumption of raw milk. Our objectives were to determine the prevalence and genotypes of Campylobacter spp. in dairy herds and to investigate the pos...
Enterococcus faecium NRRL B-2354 is a surrogate microorganism used in place of pathogens for validation of thermal processing technologies and systems. We evaluated the safety of strain NRRL B-2354 based on its genomic and functional characteristics. The genome of E. faecium NRRL B-2354 was sequence...
Patterns in virus dispersal and epidemiology of viral diseases can be revealed by phylogeographic studies. Currently knowledge about phylogeography of Dengue virus (DENV) Types 1 and 2 is limited. We carried out the phylogeographic analyses for DENV-1 and DENV-2, by the Bayesian Markov Chain Monte C...
The largest Salmonella enterica serovar Newport outbreak (n=106) ever reported in Germany occurred in October and November 2011. Twenty associated cases were reported in the Netherlands. The outbreak investigation included an analytical epidemiological study, molecular typing of human and food isola...
Although most reports describing patients infected with methicillin-resistant Staphylococcus aureus enterocolitis have been published in Japan, this concept remains a matter of debate and diagnostic criteria have not yet been defined. The general status of a 74-year-old Japanese man referred to our...
Determining the prevalence of children in day-care centres (DCCs) carrying faecal extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and molecularly characterizing those belonging to the Escherichia coli species. Stools were collected from children's diapers (January-April 2012) in ra...
To assess the molecular characterization of disseminated vancomycin-resistant enterococci (VRE) in the intensive care units, 546 enterococci isolates were collected from different clinical samples in a prospective observational study. The results showed that a total number of 33 isolates (6 %) were...
Acinetobacter baumannii is generally the most frequently isolated Acinetobacter species. Sequence analysis techniques allow reliable identification of Acinetobacter isolates at the species level. Forty-eight clinical isolates of Acinetobacter spp. were obtained from blood cultures at Tohoku Universi...
A growing number of β-lactamases have been reported in Pseudomonas aeruginosa clinical isolates. The aim of this study was to investigate the diversity of β-lactamases in the collection of 51 ceftazidime-resistant P. aeruginosa clinical isolates in four hospitals of southern China. Among these isola...
A multicenter collection comprising of 171 Streptococcus agalactiae isolates from pregnant women recovered between 2007 and 2010 and 46 from unmatched neonates with invasive infections was subjected to antimicrobial susceptibility testing and genetic characterization. High rates of erythromycin resi...
Since 2007, Kenya has experienced an increase in cholera outbreaks characterized by a high fatality rate. In this study, we characterized 81 Vibrio cholerae isolates from diarrhoeal stool samples in Nyanza, a cholera-endemic lake region of Kenya, for virulence properties, clonality and antibiotic su...
Staphylococcus aureus nasal carriage increases infection risk. However, few studies have investigated S. aureus acquisition/loss over >1 year, and fewer still used molecular typing. 1123 adults attending five Oxfordshire general practices had nasal swabs taken. 571 were re-swabbed after one month th...
Enterococci are a major cause of health care-associated infections and account for approximately 10% of all bacteremias globally. The aim of this study was to determine the proportion of enterococcal bacteremia isolates in Australia that are antimicrobial resistant, with particular emphasis on susce...
Urinary tract infection (UTI) is common amongst children and recurs in 10-30 % of cases. The differences between Escherichia coli strains causing UTI among hospitalised children and adults remains to be fully elucidated. Here, we examined the genetic relatedness and virulence gene (VG) profiles of a...
Vibrio parahaemolyticus is one of the most important seafood-borne bacterial in recent years and is the leading causal agent of human acute gastroenteritis, primarily following the consumption of raw, undercooked or mishandled marine products. Until 1996, infections caused by V. parahaemolyticus wer...
This study aims to investigate the characteristics of genomic variation of pandemic A/H1N1/2009 influenza virus isolated in Fujian Province, China. Complete genome sequence analysis was performed on 14 strains of pandemic A/H1N1/2009 influenza virus isolated from Fujian during 2009-2012. All virus s...
The increase in the prevalence of epidemic strains of methicillin resistant Staphylococcus aureus (MRSA) in hospitals and community requires special attention of infection control. The aim of this study was to determine the pathogenic phenotype (i.e. infectivity and resistotype) and genotypic charac...
We sampled 7,511 black-headed gulls for influenza virus in the Netherlands during 2006-2010 and found that subtypes H13 and H16 caused annual epidemics in fledglings on colony sites. Our findings validate targeted surveillance of wild waterbirds and clarify underlying factors for influenza virus eme...
Cholera remains a major public health problem. To compare the relative contribution of strains from the environment with strains isolated from patients during outbreaks, we performed multilocus variable tandem repeat analyses on samples collected during the 2010 and 2011 outbreak seasons in 2 geogra...
To evaluate the clfB typing method in discriminating the ST239 methicillin-resistant Staphylococcus aureus (MRSA) isolated from patients under nosocomial infection in Tianjin first central hospital so as to access the clinical risk factors and outcomes of the MRSA nosocomial infection from ICU and n...
Campylobacteriosis is a collective term, used for infectious, emerging foodborne disease caused by Campylobacter species comprising Gram negative, curved, and microaerophilic pathogens. The true incidence of human campylobacteriosis is unknown for most countries of the world including Bangladesh. Bu...
Healthcare-associated infections due to multidrug-resistant Gram-negative bacteria (MDR-GNB) are a leading cause of morbidity and mortality worldwide. These evidence-based guidelines have been produced after a systematic review of published studies on infection prevention and control interventions a...
Vancomycin-resistant enterococci (VRE) are a serious problem all over the world. The present study was conducted to investigate antimicrobial resistance patterns, genotypes, clonal relationship, and virulence fac- tors of VRE species isolated from rectal swab samples of hospitalized patients, patien...
This study analyzed 42 Acinetobacter baumannii strains collected between 2009-2012 from different hospitals in Beyrouth and North Lebanon to better understand the epidemiology and carbapenem resistance mechanisms in our collection and to compare the robustness of pulsed field gel electrophoresis (PF...
Progress in control of bovine tuberculosis (bTB) is often not uniform, usually due to the effect of one or more sometimes unknown epidemiological factors impairing the success of eradication programs. Use of spatial analysis can help to identify clusters of persistence of disease, leading to the ide...
Carbapenem-resistant Acinetobacter baumannii have emerged globally. The objective of this study was to investigate the epidemiology, clonal diversity and resistance mechanisms of imipenem non-susceptible A. baumannii isolates in France. Between December 2010 and August 2011, 132 notifications were c...
Staphylococcus aureus is one of the major pathogens that causes bacteremia; therefore, it is important to understand the long-term molecular epidemiology of S. aureus bacteremia infections. In particular, little is known about the population structure of methicillin-sensitive S. aureus (MSSA) compar...
This study evaluated the relationship between previous colonization of the oropharynx and development of ventilator-associated pneumonia through the classification of genomic fingerprint pattern by pulsed-field gel electrophoresis of both oxacillin-resistant and oxacillin-susceptible Staphylococcus...
The aims of this study were to investigate drug resistance rates, types of extended spectrum beta lactamases (ESBLs), and molecular epidemiological characteristics of 43 Shigella sonnei isolates. Ampicillin-sulbactam, amoxicillin-clavulanate, chloramphenicol, and ciprofloxacin were the most active a...
Dengue virus (DENV) represents a major threat to public health worldwide. Early DENV diagnosis should not only detect the infection but also identify patients with a higher likelihood to develop severe cases. Previous studies have suggested the potential for NS1 to serve as a viral marker for dengue...
Forty domestic and travel-associated Campylobacter jejuni isolates were analyzed by profiling 7 pathogenic genes (cdtB, cadF, Cj0131, ciaB, racR, wlaN, and virB11) along with multilocus sequence typing (MLST) and antimicrobial susceptibility testing. cdtB, cadF, and Cj0131 were present in all isolat...
Salmonella enterica serovar Typhimurium is the most important serovar associated with human salmonellosis worldwide. Here we aimed to explore the molecular epidemiology and genetic characteristics of this serovar in Guangdong, China. We evaluated the molecular epidemiology and genetic characteristic...
The epidemiology of invasive Haemophilus influenzae (Hi) has changed since the introduction of the Hi type b (Hib) vaccine. The aim of this study was to analyze the clinical and molecular epidemiology of Hi invasive disease in adults. Clinical data of the 82 patients with Hi invasive infections were...
Highly pathogenic Y. enterocolitica bioserotype 1B/O8 is considered to be an important etiological agent of yersiniosis in Poland. Infections caused by Y. enterocolitica 1B/O8 became an important public health problem in Poland, especially because of their high potential of virulence and the unknown...
Shiga toxin-producing Escherichia coli (STEC) cause infections in humans ranging from asymptomatic carriage to bloody diarrhoea and haemolytic uremic syndrome (HUS). Here we present whole genome comparison of Norwegian non-O157 STEC strains with the aim to distinguish between strains with the potent...
Comparative evaluation of biological properties of parahemolytic vibrios that had determined outbreaks and sporadic cases of food toxic infection in Primorsky Region in 2012 and previous years. Materials AND METHODS: 40 clinical strains of Vibrio parahaemolyticus isolated in 2012 were studied in com...
In the last decades, there has been an increase of cholera epidemics caused by multidrug resistant strains. Particularly, the integrative and conjugative element (ICE) seems to play a major role in the emergence of multidrug resistant Vibrio cholerae. This study fully characterized, by whole genome...
We have previously reported in Xishuangbanna (Banna) Dai Autonomous Prefecture, a well-developed tourist destination in the southwest border of China, that HIV-1 transmitted dominantly through heterosexual contact with less divergent genotypes and few drug resistant mutations. Due to the rapid incre...
Outbreaks of mucohemorrhagic diarrhea in pigs caused by Brachyspira hyodysenteriae in the late 2000s indicated the re-emergence of Swine Dysentery (SD) in the U.S. Although the clinical disease was absent in the U.S. since the early 1990s, it continued to cause significant economic losses to other s...
Pseudomonas aeruginosa (PA) has a non-clonal, epidemic population with a few widely distributed and frequently encountered sequence types (STs) called 'high-risk clusters'. Clinical P. aeruginosa (clinPA) has been studied in all inhabited continents excepted in Africa, where a very few isolates have...
Klebsiella spp. is a common cause of bovine mastitis, but information regarding its molecular epidemiology is lacking from many parts of the world. On using mass spectrometry and partial sequencing of the rpoB gene, it was found that over a one year study, K. variicola and Enterobacter cloacae were...
The aim of this study was to assess the epidemiology of meningitis and/or encephalitis in Poland in 2012. About 2 500-3 000 cases of meningitis and/or encephalitis of viral or bacterial etiology are recorded in Poland every year. Assessment of the epidemiological situation of meningitis and/or encep...
According to official records, dengue was introduced in Brazil in the 80's; since then several epidemics have occurred. Meanwhile, in Rio Grande do Sul (RS, Southern Brazil) the first autochthonous case occurred only in 2007. In this study we report laboratory surveillance of dengue cases and season...
The lone star tick (Amblyomma americanum) is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variatio...
Genotyping of noroviruses that had circulated in the territory of Nizhny Novgorod during 6 epidemic seasons (2006 - 2012), detection of dominating genovariants and analysis of their change. Feces samples from children hospitalized in an intestinal infection department of one of the infectious diseas...
In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applic...
Dengue is a vector-borne disease in the tropical and subtropical region of the world and is transmitted by the mosquito Aedes aegypti. In the state of Amazonas, Brazil during the 2011 outbreak of dengue all the four Dengue virus (DENV) serotypes circulating simultaneously were observed. The aim of t...
Escherichia coli colonies isolated from the bone marrow of fresh dead hens of laying flocks with the E. coli peritonitis syndrome (EPS) were genotyped using pulsed-field gel electrophoresis (PFGE). Typing is important from an epidemiological point of view and also if the use of autogenous (auto)vacc...
Wild and domestic ruminants are susceptible to Bluetongue virus (BTV) infection. Three BTV serotypes (BTV-4, BTV-1 and BTV-8) have been detected in Spain in the last decade. Even though control strategies have been applied to livestock, BTV circulation has been frequently detected in wild ruminant p...
Vibrio parahaemolyticus is one of the leading causative agents of foodborne diseases in humans. In this study, the proteome profiles of the pandemic strain V. parahaemolyticus SC192 belonging to the O3:K6 serovar during the planktonic and biofilm stages were analyzed by two-dimensional liquid chroma...
Following a large outbreak of foodborne gastrointestinal (GI) disease, a multiplex PCR approach was used retrospectively to investigate faecal specimens from 88 of the 413 reported cases. Gene targets from a range of bacterial GI pathogens were detected, including Salmonella species, Shigella specie...
Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquit...
Infectious disease emergence represents a global threat to human, agricultural animal and wildlife health. West Nile virus (WNV) first emerged in the Americas in 1999 following its introduction to New York from the Old World. This flavivirus rapidly spread across much of North America, causing human...
The objective of the following study is to detect genes encoding carbapenem resistance in Klebsiella pneumoniae sepsis outbreak in a neonatal intensive care unit (NICU). Antibiotic sensitivity test was performed by standard Kirby Bauer disc diffusion technique and minimum inhibitory concentrations o...
Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals a...
Between November 2010, and May 2011, eleven cases of cholera, unrelated to a concurrent outbreak on the island of Hispaniola, were recorded, and the causative agent, Vibrio cholerae serogroup O75, was traced to oysters harvested from Apalachicola Bay, Florida. From the 11 diagnosed cases, eight isol...
No abstract available
Dengue has been reported from plains as well as hilly regions of India including some parts of Northeast India. In July-August 2012, outbreak of fever with unknown origin (FUO) indicative of Dengue was reported in Pasighat, East Siang district of Arunachal Pradesh (AP) state. Serum samples (n = 164)...
During September 2010, an outbreak of acute hemorrhagic conjunctivitis reemerged in Jiangsu, three years after the nationwide epidemic in China in 2007. In total, 2409 cases were reported, 2118 of which were reported in September; 79.8% of those affected were students or teachers, with a median age...
Whiteflies from the Bemisia tabaci species complex have the ability to transmit a large number of plant viruses and are some of the most detrimental pests in agriculture. Although whiteflies are known to transmit both DNA and RNA viruses, most of the diversity has been recorded for the former, speci...
Designing an ideal vaccine against HIV-1 has been difficult due to enormous genetic variability as a result of high replication rate and lack of proofreading activity of reverse transcriptase leading to emergence of genetic variants and recombinants. Tat transactivates HIV-1 LTR, resulting in a rema...
Molecular typing and fingerprinting of microbial pathogens represent an essential tool for the epidemiological surveillance, outbreak detection and control of infectious diseases. Indeed, epidemiological investigation without genotyping data may not provide comprehensive information to allow the mos...
No abstract available
Hand, foot, and mouth disease (HFMD) has been one of the most common infectious diseases in Shijiazhuang City, as is the situation in China overall. In the National HFMD surveillance system, the pathogen detection was focused on EV-A71 and CVA16, and therefore, information on the other EVs is very l...
We developed a multilocus sequence typing (MLST) scheme for Mycobacterium abscessus sensu lato, based on the partial sequencing of seven housekeeping genes: argH, cya, glpK, gnd, murC, pta and purH. This scheme was used to characterize a collection of 227 isolates recovered between 1994 and 2010 in...
The aim of this study was to determine the prevalence of Staphylococcus aureus and risk factors for the acquisition of MRSA (Methicillin Resistant Staphylococcus aureus) as the main cause of skin and soft tissue infections. S. aureus were characterized for the presence of PVL, TSST-1 and mecA genes....
To establish a PCR-based genotyping method for clinical Klebsiella pneumoniae. The prevalence of six serotype markers, 41 large variably presented gene clusters, and seven additional virulence markers were screened by PCR in 327 clinical K. pneumoniae strains from China. Detection of serotype marker...
Analysis of occurrence of the third type secretory system (TTSS) effectors in clinical P. aeruginosa strains. Intra-hospital (n = 164) and extra-hospital (n = 30) strains of P. aeruginosa were studied. Detection of exoS and exoU genes was carried out by PCR in DNA Engine Dyad Thermal Cycler ("Bio-Ra...
To propose a standardized protocol for the evaluation of Legionella contamination in air. A bathroom having a Legionella contamination in water >1,000 cfu/l was selected in 10 different healthcare facilities. Air contamination was assessed by active (Surface Air System, SAS) and passive (Index of Mi...
The emergence of Acinetobacter baumannii during recent decades as an important nosocomial pathogen responsible of worldwide, intensively documented, outbreaks has resulted in a need for effective epidemiological typing methods. Throughout the years, many typing methods for A. baumannii epidemiologic...
A prospective study was conducted to investigate the incidence, clinical profiles and outcome of ICU-onset CDI in a 50-bed medical ICU at a university hospital in China. Stools were collected from patients who developed ICU-onset diarrhea and was screened for tcdA (toxin A gene) and tcdB (toxin B ge...
Typical Klebsiella pneumoniae is an opportunistic pathogen, which mostly affects those with weakened immune systems and tends to cause nosocomial infections. A subset of hypervirulent K. pneumoniae serotypes with elevated production of capsule polysaccharide can affect previously healthy persons and...
Toxigenic strains of Clostridium difficile may be disseminating. Here we prospectively screened patients with nosocomial diarrhoea in two hospitals in Brazil. To identify C. difficile polymerase chain reaction ribotypes 027/078 strains, we used high resolution melting and multiplex polymerase chain...
The notion "molecular epidemiology" was introduced into scientific literature by Kilburn E. et al. in 1973. The first period of development of infectious diseases molecular epidemiology may be called "genotypic" (1980-1990s). During this period methodology of molecular marking of pathogens for purpo...
No abstract available
Mycobacterium bovis is the main causative agent of animal tuberculosis (TB) and it may cause TB in humans. Molecular typing of M. bovis isolates provides precise epidemiological data on issues of inter- or intra-herd transmission and wildlife reservoirs. Techniques used for typing M. bovis have evol...
No abstract available
The information of molecular characteristics and antimicrobial susceptibility pattern of methicillin-resistant Staphylococcus aureus (MRSA) is essential for control and treatment of diseases caused by this medically important pathogen. A total of 577 clinical MRSA bloodstream isolates from six major...
Stenotrophomonas ssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species, S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromis...
The epidemiology of Staphylococcus aureus in the community in Ghana was never investigated prior to this study. The aims of the study were: i) to assess prevalence of nasal S. aureus carriage in Ghanaian people living in an urban and a rural area, and ii) to identify phenotypic and genotypic traits...
Enterococci are Gram-positive cocci saprophyte of the human gastrointestinal tract, diners who act as opportunistic pathogens. They can cause infections in patients hospitalized for a long time or who have received multiple antibiotic therapy. Enterococcus faecalis and Enterococcus faecium are the m...
The emergence of extensively drug-resistant Acinetobacter baumannii (XDRAB) is a serious threat to hospitalized patients. From 2008 to 2010, surveillance detected 25 hospital-acquired infection (HAI) cases caused by XDRAB at a medical center in Taipei. The site of XDRAB infection was bloodstream (n...
Infectious laryngotracheitis (ILT) is an economically important respiratory disease of poultry that affects the poultry industry worldwide. The disease is caused by gallid herpesvirus I (GaHV-1), a member of the genus Iltovirus, family Herpesviridae, subfamily Alphaherpesvirinae. The current inciden...
No abstract available
Candidemia is an infectious complication mainly affecting hospitalized patients, particularly those admitted to intensive care units. Patient mortality can reach up to 40%. Candidemia is typically nosocomially-acquired, and horizontal transmission of Candida spp. can lead to the presence of outbreak...
Zoonotic viruses represent emerging or re-emerging pathogens that pose significant public health threats throughout the world. It is therefore crucial to advance current surveillance mechanisms for these viruses through outlets such as phylogeography. Despite the abundance of zoonotic viral sequence...
Bioinformatics and phylogeography models use viral sequence data to analyze spread of epidemics and pandemics. However, few of these models have included analytical methods for testing whether certain predictors such as population density, rates of disease migration, and climate are drivers of spati...
One of the most successful public health applications of next-generation sequencing is whole-genome sequencing of pathogens to not only detect and characterize outbreaks, but also to inform outbreak management. Using genomics, infection control teams can now track, with extraordinarily high resoluti...
Viral gastroenteritis is the most common causal agent of public health problems worldwide. Noroviruses cause nonbacterial acute gastroenteritis in humans of all ages. In this study, we investigated the occurrence of norovirus infection in children with acute gastroenteritis admitted to university ho...
Measuring epidemic parameters early in an outbreak is essential to inform control efforts. Using the viral genome sequence and collection date from 78 infections in the 2014 Ebola virus outbreak in Sierra Leone, we estimate key epidemiological parameters such as infectious period duration (approxima...
Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detec...
Multidrug-resistant Acinetobacter baumannii commonly causes hospital outbreaks. However, within an outbreak, it can be difficult to identify the routes of cross-infection rapidly and accurately enough to inform infection control. Here, we describe a protracted hospital outbreak of multidrug-resistan...
Intercontinental migratory waterfowl are the primary vectors for dispersion of H5N1 viruses and have been implicated in several zoonotic epidemics and pandemics. Recent investigations have established that with a single mutation, the virus gains the ability to transmit between humans. Consequently,...
Crop diseases emerge without warning. In many cases, diseases cross borders, or even oceans, before plant pathologists have time to identify and characterize the causative agents. Genome sequencing, in combination with intensive sampling of pathogen populations and application of population genetic...
Linezolid (LNZ) is a promising antimicrobial agent for the treatment of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB). To investigate the efficacy of LNZ among MDR-TB and XDR-TB in China, the LNZ susceptibility of 158 MDR-TB isolates from the national drug resistan...
The extracellular proteins (ECPs) of enterohemorrhagic Escherichia coli (EHEC) can cause hemorrhagic colitis which may cause life threatening hemolytic-uremic syndrome, while that of enteroaggregative E. coli (EAEC) can clump to intestinal membranes. Liquid chromatography-electrospray ionization-tan...
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There has been a worldwide increase in community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) infections. CA-MRSA isolates commonly produce the Panton-Valentine leukocidin toxin encoded by the pvl genes lukF-PV and lukS-PV. This study investigated the clinical and molecular epi...
An outbreak at a university in Georgia was identified after 83 cases of probable pneumonia were reported among students. Respiratory specimens were obtained from 21 students for the outbreak investigation. The TaqMan array card (TAC), a quantitative PCR (qPCR)-based multipathogen detection technolog...
Previous research revealed a 6-fold higher incidence of tuberculosis (TB) amongst aborigines compared to Han Chinese in Taiwan. To investigate the reasons for this disparity, we genotyped Mycobacterium tuberculosis (MTB) strains obtained from members of different aboriginal tribes in different geogr...
Legionella pneumophila is an opportunistic pathogen of humans where the source of infection is usually from contaminated man-made water systems. When an outbreak of Legionnaires' disease caused by L. pneumophila occurs, it is necessary to discover the source of infection. A seven allele sequence-bas...
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This study aimed to characterize meticillin-resistant Staphylococcus aureus (MRSA) lineages circulating in a Brazilian teaching hospital. MRSA isolates from nasal swabs were evaluated to assess antimicrobial susceptibility, staphylococcal cassette chromosome mec (SCCmec), Panton-Valentine leucocidin...
New strains of meticillin-resistant Staphylococcus aureus (MRSA) may be associated with changes in rates of disease or clinical presentation. Conventional typing techniques may not detect new clonal variants that underlie changes in epidemiology or clinical phenotype. To investigate the role of clon...
To describe the prevalence and population structure of Staphylococcus aureus bacteria that colonize pigs at slaughterhouses in northeastern China, nose swabs were collected from pigs in two slaughterhouses in Harbin, Heilongjiang Province, China in 2009. S. aureus isolates were characterized by mult...
The genotypes of Mycobacterium tuberculosis (MTB) have been found to be related to the risk of transmission and the development of drug resistance of this pathogen. Thus, exploring the molecular characteristics of MTB is helpful for understanding and controlling the spread of strains in areas with a...
The global spread and increasing incidence of carbapenem-resistant Enterobacteriaceae have resulted in treatment and public health concerns. Here, we present an investigation of the molecular mechanisms and clonality of carbapenem-non-susceptible Escherichia coli (CnSEC) based on a nationwide survey...
A total of 330 clinical Vibrio cholerae O1 serogroups from China dating between 1961 and 2010 were investigated. By phenotypic biotyping and genetic analysis, during the seventh pandemic of V. cholerae O1 in China, the isolates of hybrid biotype (mixed classical phenotypes) were present during the e...
Culicoides biting midges (Diptera: Ceratopogonidae) are a major vector group responsible for the biological transmission of a wide variety of globally significant arboviruses, including bluetongue virus (BTV). In this review we examine current biological resources for the study of this genus, with a...
The Escherichia coli sequence type 131 (ST131) clone is notorious for extraintestinal infections, fluoroquinolone resistance, and extended-spectrum beta-lactamase (ESBL) production, attributable to a CTX-M-15-encoding mobile element. Here, we applied pulsed-field gel electrophoresis (PFGE) and whole...
Clostridium difficile infection (CDI) is caused by toxin-producing strains. It accounts for 20-30 % of antibiotic-associated diarrhoea and particularly accounts for 90 % of pseudomembranous colitis. The epidemiological study of C. difficile is thus important. In this study, we report the molecular e...
Staphylococcus aureus is an opportunistic pathogen commonly identified from food poisoning-associated foodstuffs. From 1996 to the present, S. aureus isolates have been found to exhibit increasing resistance to antimicrobial drugs. The aim of this study was to assess the molecular epidemiology prope...
Francisellosis, caused by the bacterium Francisella noatunensis subsp. noatunensis, remains a serious threat to Atlantic cod (Gadhus morhua) farming in Norway and potentially in other countries. As outbreak strains appear clonal in population structure, access to highly discriminatory typing tools i...
Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-genome sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission u...
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Sequence-based typing (SBT) combined with monoclonal antibody subgrouping of Legionella pneumophila isolates is at present considered to be the reference standard during epidemiological investigation of Legionnaires' disease outbreaks. In some isolates of L. pneumophila, the seventh allele of the st...
We report six confirmed cases of Legionnaires' disease in Scotland caused by Legionella longbeachae serogroup 1, identified over a four-week period in August–September 2013. All cases required admission to hospital intensive care facilities. All cases were amateur gardeners with frequent exposure to...
Although the molecular typing of Pseudomonas aeruginosa is important to understand the local epidemiology of this opportunistic pathogen, it remains challenging. Our aim was to develop a simple typing method based on the sequencing of two highly variable loci. Single-strand sequencing of three highl...
Avian pathogenic Escherichia coli (APEC) causes economically significant infections in poultry. The genetic diversity of APEC and phylogenetic relationships within and between APEC and other pathogenic E. coli are not yet well understood. We used multilocus sequence typing (MLST), PCR-based phylogro...
Leptospirosis is a worldwide zoonosis which is responsible for the typical form of Weil's disease. The epidemiological surveillance of the Leptospira species agent is important for host prevalence control. Although the genotyping methods have progressed, the identification of some serovars remains a...
Enterococcus faecium has recently emerged as a multidrug-resistant nosocomial pathogen involved in outbreaks worldwide. A high rate of resistance to different antibiotics has been associated with virulent clonal complex 17 isolates carrying the esp and hyl genes and the purK1 allele. Twelve clinical...
National surveillance of Legionnaires' disease (LD) is important to inform control measures and facilitate international networking for timely reporting. This study is the first to describe the molecular epidemiology of LD in Israel. Case notifications for 2006-2011, collated through mandatory repor...
Since 1994, when Brucella ceti was first isolated from an aborted dolphin fetus, several cases have been reported worldwide. The first case of B. ceti in the Mediterranean (and in Italy), however, was recorded only in 2012, off the coast of Tuscany. Extensive studies, using serological and microbiol...
Infections caused by carbapenem-resistant Pseudomonas aeruginosa strains represent a major therapeutic and epidemiological problem. The aim of this study was to characterize carbapenem resistance in 89 clinical strains of P. aeruginosa isolated from three hospitals in western Algeria between October...
We aimed to analyse the clinical epidemiology and genetic diversity of invasive pneumococcal disease (IPD) episodes attributed to the Spain(23F)-ST81 (PMEN1) clone. Fifty-eight (2.7%) of 2117 invasive pneumococci isolated from adult patients during the 1990-2012 period shared a PFGE pattern related...
Pneumococci are an important cause of acute exacerbations in patients with chronic obstructive pulmonary disease (COPD). In the last decade, the pneumococcal population has changed, mainly due to the introduction of the 7-valent conjugate vaccine (PCV7). We analysed the antimicrobial susceptibility...
A study was designed to characterize 35 non-repeat isolates of VIM- and IMP-producing Enterobacteriaceae obtained from the SMART surveillance program. Characterization was done by polymerase chain reaction, sequencing, and multi-locus sequencing. The VIM-1, -2, -5, -26, -27, -33, and IMP-1 and -26-p...
Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum, is a bacterial disease of fish, which is both geographically widespread and difficult to control. Previously, application of various molecular typing methods has failed to reliably discriminate between R. salmoninarum isolates ori...
On May 24, 2010, a cluster of 17 human Salmonella enterica serotype Chester clinical isolates with indistinguishable pulsed-field gel electrophoresis (PFGE) patterns was reported to PulseNet, the national molecular subtyping network for foodborne disease surveillance. This PFGE pattern had not been...
Our objective was to investigate the plasmid replicon-types involved in spread of ESBLs among Bulgarian Klebsiella pneumoniae and Escherichia coli. Sixty-three isolates, with transferable beta-lactam resistance determinants, collected between 2007 and 2009 in six medical institutions, were analysed...
The first penicillin-non-susceptible pneumococci (PNSP) were identified in Iceland in 1988. A rapid increase followed, associated with expansion of a single multiresistant clone, Spain(6B)-2, peaking at 19.8% in 1993. After interventions led to reduced antimicrobial use in children, the prevalence o...
On 9 October 2011, the University Hospital of North Norway alerted the Norwegian Institute of Public Health (NIPH) about an increase in Shigella sonnei infections in Tromsø. The isolates had an identical ‘multilocus variable-number tandem repeat analysis’ (MLVA) profile. Most cases had consumed food...
Nasal colonization with coagulase-negative Staphylococcus (CoNS) has been described as a risk factor for subsequent systemic infection. In this study, we evaluated the genetic profile of CoNS isolates colonizing the nares of children admitted to a neonatal intensive care unit (NICU). We assessed CoN...
The Philippines has an extremely high rate of tuberculosis but little is known about M. tuberculosis genotypes and transmission dynamics in this country. The aim of this study was to determine the proportion of household contacts who develop active TB due to direct transmission from an index case in...
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Tuberculosis genotypic clustering is used as a proxy for recent transmission. The association between clustering and recent transmission becomes problematic when the genotyping method lacks specificity in defining a cluster, as well as for clusters with extensive jurisdictional histories and/or comm...
Pasteurella multocida was isolated from poultry on six farms (one free-range duck farm, one free-range turkey farm, one conventional enclosed turkey farm, and three free-range layer farms) suffering fowl cholera outbreaks. In addition, historical isolates from previous outbreaks were available for t...
Multilocus sequence typing (MLST) analysis has been emerging as a powerful tool for genotyping specific bacterial species. MLST utilizes internal fragments of multiple housekeeping genes and the combination of each allele defines the sequence type for each isolate. MLST databases contain reference d...
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The goal of our study was to use spatial scan statics to determine whether the night roosts of European starlings (Sturnus vulgaris) act as point sources for the dissemination of Escherichia coli O157:H7 among dairy farms. From 2007 to 2009, we collected bovine faecal samples (n = 9000) and starling...
There are limited data available on the epidemiology and prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in the human population that encode the recently described mecA homologue, mecC. To address this knowledge gap we undertook a prospective prevalence study in England to determine...
To determine the prevalence, risk factors, and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) colonization at the time of admission to acute medical units and to develop a cost-effective screening strategy. Nasal and groin screening cultures were performed for patients...
Mycobacterium tuberculosis still represents a serious cause of morbidity and mortality worldwide. The aim of this study was to determine the transmission rate and genetic lineages of M. tuberculosis circulating in Croatia during a 3-y period, between 2009 and 2011. A total of 1587 M. tuberculosis st...
The occurrence and dissemination of methicillin-resistant Staphylococcus aureus (MRSA) in healthcare settings and the community and its risk of being introduced into hospitals are matters of great concern. The purpose of this study was to conduct a miniaturized epidemiological analysis of S. aureus-...
This review focuses on new or improved technologies currently being applied, or likely to be applied in the future, to worldwide research on plant virus epidemiology. Recent technological advances and innovations provide many opportunities to improve understanding of the way diverse types of plant v...
The aim of this study was to determine the geographical distribution of hepatitis C virus genotypes/subtypes among people who inject drugs (PWID) recruited at 22 needle exchange sites and drug outpatient services in all seven Planning and Statistical Regions of Hungary. Of 198 such PWID, 147 (74.2%)...
Haemophilus influenzae, particularly H influenzae serotype b (Hib), is an important pathogen that causes serious diseases like meningitis and septicaemia. Since the introduction of Hib conjugate vaccines in the 1990s, the epidemiology of invasive H influenzae disease has changed substantially, with...
Pertussis has shown a striking resurgence in the United States, with a return to record numbers of reported cases as last observed in the 1950s. Bordetella pertussis isolates lacking pertactin, a key antigen component of the acellular pertussis vaccine, have been observed, suggesting that B. pertuss...
Next generation sequencing (NGS) is being increasingly used for the detection and characterization of pathogens during outbreaks. This technology allows rapid sequencing of pathogen full genomes, useful not only for accurate genotyping and molecular epidemiology, but also for identification of drug...
Staphylococcus aureus colonization is a risk factor for invasive disease. There is a need to understand S. aureus colonization in infancy as the burden of S. aureus infections in infants is high. We aimed to investigate the transmission of S. aureus between mothers and their newborns during the firs...
Extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae have been notifiable according to the Swedish Communicable Disease Act since 2007. A major increase in the number of cases has been observed, with 2099 cases in 2007 and 7225 cases in 2012. The majority of the isolates are Escherichi...
This study describes the analysis of 432 isolates of Yersinia enterocolitica by pulsed-field gel electrophoresis (PFGE). PFGE had a high level of discrimination with biotype 1A isolates (Simpson's Diversity Index 0.997), but with the clinically important biotypes 2, 3 and 4, the discriminatory abili...
In 2012, Texas has reported the highest number of West Nile virus (WNV) cases in the United States to the Centers for Disease Control and Prevention. In this report, we conducted a retrospective chart review of 57 patients with WNV disease and analyzed the clinical features of these patients. Our re...
Antibiotic resistance of Escherichia coli isolated from urinary tract infections (UTIs) is increasing worldwide. A total of 41 E. coli isolates were obtained from urine samples from hospitalized patients with a UTI in three hospitals in the northern districts of the West Bank, Palestine during March...
Expended spectrum β-lactamase (ESBL)-producing Enterobacter cloacae is an important nosocomial pathogen. In this study, the prevalence and the molecular epidemiology of ESBL producing E. cloacae strains isolated from various hospitals in Annaba, Algeria were investigated. The study involved 63 isola...
During the molecular epidemiological study of a legionellosis outbreak, we obtained sequence based typing (SBT) profiles from uncultured respiratory samples of 15 affected patients. We detected several distinct allelic profiles some of which were a mixture of alleles present in the more common profi...
We analyzed the phylogenetic and time-space relationships (phylodynamics) of 181 isolates of vesicular stomatitis New Jersey virus (VSNJV) causing disease in Mexico and the United States (US) from 2005 through 2012. We detail the emergence of a genetic lineage in southern Mexico causing outbreaks in...
Salmonella enterica subsp. enterica serovars Typhimurium (S. Typhimurium) and Heidelberg (S. Heidelberg) are major causes of foodborne salmonellosis, accounting for a fifth of all annual salmonellosis cases in the United States. Rapid, efficient and accurate methods for identification are required f...
Transmission of Staphylococcus aureus colonization in community-based populations is not well understood. We sought to describe the molecular epidemiology of S. aureus colonization in the Old Order Amish. The study was a prospective, observational study of healthy adults and their same-sex siblings...
Production and wild animals are major sources of human salmonellosis and animals raised for food also play an important role in transmission of antimicrobial resistant Salmonella strains to humans. Furthermore, in sub-Saharan Africa non-typhoidal Salmonella serotypes are common bloodstream isolates...
A total of 1,870 nonduplicate clinical Enterobacteriaceae from 13 teaching hospitals located in 11 provinces of mainland China from 2011 to 2012 were screened for the presence of the blaNDM gene. The high-throughput MiSeq sequencing method and comparative genomics were used to analyze the genetic en...
Since the establishment of sequence-based typing as the gold standard for DNA-based typing of Legionella pneumophila, the Legionella laboratory at the Centers for Disease Control and Prevention (CDC) has conducted routine sequence-based typing (SBT) analysis of all incoming L. pneumophila serogroup...
In Asia, Salmonella Paratyphi A is an emerging infection, and travelers are increasingly at risk. During October 2009-November 2009, an outbreak in S. Paratyphi A infection was noted in Israeli travelers returning from Nepal. An outbreak investigation included a standardized exposure questionnaire a...
Methicillin-resistant Staphylococcus aureus (MRSA) typing is an important epidemiologic tool for monitoring trends and preventing outbreaks. However, the efficiency of various MRSA typing methods for each SCCmec MRSA isolate is rarely evaluated. A total of 157 MRSA isolates from four different regio...
Isolates of Streptococcus suis from different Western countries as well as those from China and Vietnam have been previously well characterized. So far, the genetic characteristics and relationship between S. suis strains isolated from both humans and pigs in Thailand are unknown. In this study, a t...
Vibrio cholerae is ubiquitous in aquatic environment inhabiting marine, fresh and brackish waters. V. cholerae serotypes O1 and O139 cause the devastating diarrheal disease cholera, which is often fatal without proper treatment. Little is known regarding the abundance and diversity of clinically imp...
During 2003-2012, 8 clusters of meningococcal disease were identified in Rio de Janeiro State, Brazil, all caused by serogroup C Neisseria meningitidis. The isolates were assigned to 3 clonal complexes (cc): cc11, cc32, and cc103. These hyperinvasive disease lineages were associated with endemic dis...
The usefulness of variable number tandem repeat (VNTR) typing based on limited numbers of loci has previously proven inferior compared to IS6110-RFLP typing when applied to the study of the molecular epidemiology of bovine tuberculosis (BTB) in both livestock and wildlife in southern Africa. In this...
This study reports on an investigation of Mycobacterium tuberculosis cases in mostly captive wild animals using molecular typing tools [Variable Number of Tandem Repeat (VNTR) typing and Restriction Fragment Length Polymorphism typing]. The investigation included cases from (i) the National Zoologic...
A total of 720 Vibrio cholerae O1 strains were recovered for investigation from an outbreak of cholera in South Africa between November 2008 and April 2009. Strains were characterized by serotype testing. Antimicrobial susceptibility testing. Genetic diversity of 248 strains was investigated using p...
Multiple locus variable number tandem repeats (VNTRs) analysis (MLVA) has become a reliable tool, able to establish genetic relationships for epidemiological surveillance and molecular subtyping of pathogens such as verotoxigenic Escherichia coli (VTEC). This emerging pathogen whose primary reservoi...
Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multidrug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit-variable-...
Multidrug-resistant Pseudomonas aeruginosa is a serious challenge for antimicrobial therapy of nosocomial infections, as it possesses several mechanisms of antimicrobial resistance. In Central Greece, a sudden increase of infections caused by carbapenem-resistant P. aeruginosa was observed during 20...
Tuberculosis (TB) persists as a public health problem in Iran. Characterization of Mycobacterium tuberculosis isolates circulating in this area will contribute to understand and control the spread of the strains. The aims of this study were to understand the genetic diversity and drug susceptibility...
With the increasing incidence of Salmonella enterica serovar Enteritidis (SE) infections, five SE foodborne outbreaks were identified between 2008 and 2010 on Jeju Island, Republic of Korea. In this study, the genetic relatedness of isolates recovered from the five outbreaks was investigated to iden...
Campylobacter jejuni is responsible for the majority of bacterial foodborne gastroenteritis in the US, usually due to the consumption of undercooked poultry. Research on which avian species transmit the bacterium is limited, especially in the US. We sampled wild birds in three families-Anatidae, Sco...
In the Netherlands, extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli bacteria are highly prevalent in poultry, and chicken meat has been implicated as a source of ESBL-producing E. coli present in the human population. The current study describes the isolation of ESBL-producing E....
Rapid and accurate strain identification is paramount in the battle against microbial outbreaks, and several subtyping approaches have been developed. One such method uses clustered regular interspaced short palindromic repeats (CRISPRs), DNA repeat elements that are present in approximately half of...
This work is an approach to the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) bovine infections in Tunisia. A total of 35 MTBC isolates from both lateral retropharyngeal lymph node samples of cattle slaughtered in different Tunisian regions were genotyped by spoligotyping and v...
In this paper we aim to provide insight into the complexity of outbreak management in an intensive care unit (ICU) setting. In October 2010 four patients on the ICU of our tertiary care centre were colonized or infected with a multidrug-resistant strain of Pseudomonas aeruginosa (MDR-PA). An outbrea...
In December 2011 and early 2012 four neonates died from Pseudomonas aeruginosa bacteraemia in hospitals in Northern Ireland. To assess whether P. aeruginosa was associated with the neonatal unit taps and whether waterborne isolates were consistent with patient isolates. Thirty taps and eight flow st...
A recent increase in virulence of pathogenic Streptococcus dysgalactiae subsp. equisimilis (SDSE) has been widely proposed. Such an increase may be partly explained by the acquisition of new virulence traits by horizontal gene transfer from related streptococci such as Streptococcus pyogenes (GAS) a...
Coalescent methods are widely used to infer the demographic history of populations from gene genealogies. These approaches-often referred to as phylodynamic methods-have proven especially useful for reconstructing the dynamics of rapidly evolving viral pathogens. Yet, population dynamics inferred fr...
Acinetobacter baumannii is a notorious opportunistic pathogen mainly associated with hospital-acquired infections. Studies on the clonal relatedness of isolates could lay the foundation for effective infection control. A snapshot study was performed to investigate the clonal relatedness of A. bauman...
Increasing rates of Clostridium difficile infection (CDI) among those without traditional risk factors have been reported mainly in Europe and North America. Here we describe the epidemiology, clinical features and ribotypes of CDI at National University Hospital (NUH), a 1000-bed tertiary care hosp...
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Cholera outbreaks annually occur in many parts of Iran. The aim of this study was to investigate the biotype and genotype diversity of V. cholerae isolates from recent outbreak (2012) in Iran and to characterize the ctxB allelic sequence of isolates. The ctxB sequence of all isolates was analyzed an...
Vibrio parahaemolyticus infection has been considered the leading cause of bacterial illnesses mainly associated with seafood consumption in Guangdong province in China. In this study, epidemiological and etiological characteristics of 36 V. parahaemolyticus outbreaks that occurred from 2008 to 2010...
Salmonella enterica serovar Newport pattern JJPX01.0061 has been identified as causing several multistate outbreaks in the last 10 years, primarily due to contamination of tomatoes grown in Virginia. The goal of this study was to evaluate gulls as a potential vehicle of S. Newport pattern 61 contami...
Erwinia amylovora causes a major disease of pome fruit trees worldwide, and is regulated as a quarantine organism in many countries. While some diversity of isolates has been observed, molecular epidemiology of this bacterium is hindered by a lack of simple molecular typing techniques with sufficien...
Streptococcus gallolyticus is often found as a member of the normal gut microflora in various animals. However, it has been reported to cause mastitis in cattle, septicaemia in pigeons, and meningitis, septicaemia and endocarditis in humans. However, little is known about the epidemiology and crucia...
The Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-KP) sequence type (ST)-258/512 clone is the dominant clone by which KPC has disseminated worldwide. Standard typing methods are time-consuming and are therefore impractical for identification of this clone in the course of...
The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) is increasing in patients with cystic fibrosis (CF). We report a molecular characterization, antimicrobial resistance, and Panton-Valentine leukocidin (PVL) toxin gene detection of MRSA strains from 28 Brazilian pediatric CF patien...
Escherichia coli belonging to clonal group ST131 has emerged as a significant contributor to infection caused by antibiotic-resistant E. coli worldwide. We investigated the risk factors for infections caused by ST131 E. coli and their clinical implications. One thousand and seventy-seven E. coli iso...
Two plasmids carrying bla(KPC-2) isolated from carbapenem-resistant Escherichia coli (CR-EC) and carbapenem-resistant Klebsiella pneumoniae (CR-KP), respectively, were completely sequenced. The CR-KP strain was selected from an outbreak in 2012, and the CR-EC strain was the first blaKPC-2-carrying E...
A community outbreak of legionellosis occurred in Barrow-in-Furness, Cumbria, during July and August 2002. A descriptive study and active case-finding were instigated and all known wet cooling systems and other potential sources were investigated. Genotypic and phenotypic analysis, and amplified fra...
Phenotypic and genetic characterization of 62 Staphylococcus aureus isolates recovered in Nigeria indicated a high proportion of Panton-Valentine leukocidin-positive isolates and a high genetic diversity among the 22 methicillin-resistant S. aureus. This underlines the need for infection control in...
Escherichia coli ST131 is an important cause of multidrug-resistant infections. Thus, the aim of this study was to evaluate the concomitant presence of resistance plasmids and pathogenicity islands (PAIs) in ST131 E. coli. From 97 extraintestinal E. coli characterized for antimicrobial susceptibilit...
No study to date has compared multilocus variable-number tandem-repeat analysis (MLVA) and whole-genome sequencing (WGS) in an investigation of the transmission of Clostridium difficile infection. Isolates from 61 adults with ongoing and/or recurrent C. difficile infections and 17 asymptomatic carri...
In 2012, 28 out of 140 staff working for a film crew in a Beijing movie and television base experienced a sudden onset of fever, sore throat, and/or tiredness, headache within the 24 hour period of July 26-27. All of the patients visited the hospital and were diagnosed as having tonsillopharyngitis....
Multilocus variable-number tandem repeat analysis (MLVA) is a promising subtyping tool to complement pulsed-field gel electrophoresis for discriminating closely related strains of some monomorphic organisms, including Shigella sonnei, which is one of the major foodborne pathogens. However, MLVA resu...
Contamination of retail meat with extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been reported, but only limited data have been documented in Japan. One hundred fifty-three retail foods including chicken meat, beef, pork, and vegetables were purchased from 29 supermarkets betwee...
In recent decades, bacterial meningitis rates have decreased secondary to the success of routine vaccinations. Ironically, the decreased incidence may contribute to the challenge of establishing accurate and timely diagnoses. Studies have suggested that in immunocompetent patients with normal cerebr...
Highly pathogenic avian influenza A (HPAI) H5N1 is endemic in China. It is expanding its borders over time and the associated economic and health consequences are critically important. To determine the evolutionary history and phylodynamics of HPAI H5N1, a comprehensive analysis of the demographic,...
Pneumococcal vaccine-naïve mother-child dyads in South Africa had nasopharyngeal swabs taken 9 times within the first 2 years of the children's lives between January 2007 and May 2009. To quantify the strength of the association of serotype-specific carriage in mother-child dyads, a stochastic trans...
Staphylococcus aureus is the most common pathogen cultured from diabetic foot infection including diabetic foot osteomyelitis. This French multicentre study determined the genetic content of S. aureus isolated from 157 consecutive cases admitted to 12 diabetic foot centres between 2008 and 2011. We...
A large outbreak caused by expanded-spectrum cephalosporin-resistant Klebsiella pneumoniae (ESCRKP) was observed in a neonatal intensive care unit (NICU) in central Italy. The outbreak involved 127 neonates (99 colonizations and 28 infections, with seven cases of sepsis and two deaths) over a period...
Streptococcus pneumoniae causes a substantial proportion of community-acquired pneumonia (CAP) and healthcare-associated pneumonia (HCAP) in the United States. Limited data are available regarding the pneumococcal serotypes causing CAP and HCAP. Adults aged ≥ 50 years presenting to participating US...
The purpose of this study is to analyze isolates of Clostridium difficile from patients with nosocomial acquired infection in respect to their molecular type and antimicrobial susceptibility. Fifty-nine randomly selected clinical isolates were characterized. Molecular typing was performed by rep-PCR...
The control, prediction, and understanding of epidemiological processes require insight into how infectious pathogens transmit in a population. The chain of transmission can in principle be reconstructed with phylogenetic methods which analyze the evolutionary history using pathogen sequence data. T...
Neisseria meningitidis is an unusual pathogen among the causes of acute bacterial conjunctivitis. Meningococcal conjunctivitis may present as primary or secondary infection, while primary meningococcal conjunctivitis may emerge as invasive or non-invasive forms. N.meningitidis W135 strain is not com...
Staphylococcus aureus is one of the most frequent agents causing hospital infections. S.aureus has a great ability to adapt itself to variety of conditions and successful clones can be epidemic and even pandemic by its ability spread from one continent to another. The aims of this study were to dete...
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The advent of high-throughput whole-genome sequencing has the potential to revolutionize the conduct of outbreak investigation. Because of its ultimate resolution power for differentiating between closely related pathogen strains, whole-genome sequencing could augment the traditional epidemiologic i...
OXA-48 β-lactamase is one of the several emerging carbapenemases. Pre-2007 reports were almost exclusively from Turkey, but subsequently its distribution has expanded. We report an early and prolonged outbreak in the UK of Klebsiella pneumoniae producing OXA-48 carbapenemase affecting a predominantl...
In 2012, there were 208 laboratory-confirmed cases of invasive meningococcal disease (IMD) analysed by the National Neisseria Network, and 222 cases notified to the National Notifiable Diseases Surveillance System, thus laboratory data were available for 93.7% of cases of IMD in Australia in 2012. I...
Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and h...
The investigation of an outbreak of hemorrhagic-uremic syndrome in Norway in 2006 indicated that the outbreak strain Escherichia coli O103:H25 could originate from sheep. A national survey of the Norwegian sheep population was performed, with the aim of identifying and describing a possible reservoi...
The emergence and spread of Type 2 Porcine Reproductive and Respiratory Syndrome virus (Type 2 PRRSV) in North America is heavily influenced by the multiple site production system used in the hog industry. However, it is unclear how anthropogenic factors such has this have shaped the current spatial...
Transmission of Mycobacterium tuberculosis continues at high rates among Greenland-born persons in Greenland and Denmark, with 203 and 450 notified cases per 10(5) population, respectively, in the year 2010. Here, we document that the predominant M. tuberculosis outbreak strain C2/1112-15 of Danish...
Carbapenem-resistant Acinetobacter baumannii has emerged as an important cause of nosocomial infections with high morbidity and mortality. The carbapenemases, especially class D carbapenem-hydrolyzing oxacillinases (CHDLs), play an important role, but the relationship between their prevalence trend...
No abstract available
Yersinia pseudotuberculosis human infections caused by serotype O:1 and O:3 isolates have been common in Finland and have also caused outbreaks. Epidemiological studies on the outbreaks have been limited by the lack of accurate typing methods. During the recent years, multilocus variable-number tand...
The aim of this study was to better understand methicillin-resistant Staphylococcus aureus (MRSA) at the molecular level by investigating the genotypic characteristics and evolutionary patterns of MRSA clones in Shenyang, China. We analyzed the molecular epidemiology of 60 MRSA isolates in Shenyang,...
Clostridium difficile causes outbreaks of infectious diarrhoea, most commonly occurring in healthcare institutions. Recently, concern has been raised with reports of C. difficile disease in those traditionally thought to be at low risk i.e. community acquired rather than healthcare acquired. This ha...
Methicillin -resistant Staphylocccus aureus (MRSA) and multirresistant entorococci are still problematic in nosocomial infections and new challenges have emerged for their containment. MRSA has increased the multiresistant profile; it has been described vancomycin and linezolid resistant isolates an...
Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed...
A large epidemic of foot-and-mouth disease (FMD) occurred in the United Kingdom (UK) over a seven month period in Northwest England from late 1967 to the summer of 1968. This was preceded by a number of smaller FMD outbreaks in the country, two in 1967, in Hampshire and Warwickshire and one in North...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major human pathogen worldwide. However, data on MRSA prevalence in the African continent are scarce and nonexistent for São Tomé and Príncipe. In November 2010 and April 2012, a total of 332 individuals (258 patients and 74 health care workers...
Nursing homes represent a unique and important methicillin-resistant Staphylococcus aureus (MRSA) reservoir. Not only are strains imported from hospitals and the community, strains can be transported back into these settings from nursing homes. Since MRSA bacteria are prevalent in nursing homes and...
Campylobacteriosis is a frequently reported, food-borne, human bacterial disease that can be associated with ruminant reservoirs, although public health messages primarily focus on poultry. In Washington State, the two counties with the highest concentrations of dairy cattle also report the highest...
Antibiotic resistance in Streptococcus pneumoniae is a major concern worldwide. However, it is unclear whether resistance is associated with only a few highly prevalent clones or numerous and diverse clones. We monitored 349 healthy children and obtained nasopharyngeal cultures at five time points c...
Healthcare-associated infections are a worldwide threat to hospitalized patients, especially those in intensive care units. The prevalence of these infections in Egypt, and their antimicrobial resistance patterns and mechanisms, were investigated in this study. A total of 547 cases of healthcare-ass...
To investigate and compare the characteristics of invasive hospital-associated (HA) and community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) infections in Chinese children. Clinical data on 59 paediatric patients with invasive MRSA isolated from the normally sterile sites bet...
The molecular epidemiology of C. jejuni and C. coli clinical strains isolated from children with gastroenteritis, was investigated using the multilocus sequence typing method (MLST). This analysis establishes for the first time in Greece and constitutes an important tool for the epidemiological surv...
This article reports an outbreak of colonization by Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) sequence type (ST) 258 in a neonatal intensive care unit (NICU) in Palermo, Italy. KPC-Kp ST258 was detected by an active surveillance culture programme. Between 18th September an...
We investigated the prevalence, genetics, and clonality of fluoroquinolone non-susceptible isolates of Streptococcus pyogenes in the central part of Italy. S. pyogenes strains (n = 197) were isolated during 2012 from patients with tonsillopharyngitis, skin, wound or invasive infections and screened...
Foot-and-mouth disease virus (FMDV) is a highly contagious and genetically variable virus. Sporadic introductions of this virus into FMD-free countries may cause outbreaks with devastating consequences. In 2010 and 2011, incursions of the FMDV O/SEA/Mya-98 strain, normally restricted to countries in...
The food-borne pathogen Listeria monocytogenes is genetically heterogeneous. Although some clonal groups have been implicated in multiple outbreaks, there is currently no consensus on how "epidemic clones" should be defined. The objectives of this work were to compare the patterns of sequence divers...
In this study, we report the first outbreak of KPC-2-producing Klebsiella pneumoniae isolates from three patients admitted to a neurosurgery department in a South Korean teaching hospital. Multilocus sequence typing showed that the isolates were identical to the previous KPC producers in South Korea...
Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBLE) outbreaks in intensive care units (ICUs) associated with contaminated handwashing sinks have been reported. To conduct a regional study to assess whether handwashing sinks in 135 ICU patient rooms are a potential source of contami...
Pseudomonas aeruginosa is one of the primary pathogens in patients with cystic fibrosis (CF) and a major cause of morbidity and mortality. Reports of the spread of epidemic or transmissible strains of P. aeruginosa within and across CF centers raised the possibility of clonal spread among siblings w...
Between 1998 and 2008 all dengue virus serotypes circulated in the Departamento de Santander, an endemic region in northeastern Colombia. No information is available as to the role of serotype 1 (DENV-1) with respect to epidemiology of dengue. To analyze the relationship between changes in DENV-1 pr...
A genital and potentially fatal form of Pasteurella multocida infection was reported on two turkey-breeding farms on which birds were vaccinated against Pasteurella multocida. Both outbreaks were linked to the use of semen from young vaccinated toms with a history of respiratory pasteurellosis follo...
During October 2007, a large outbreak of suspected dengue fever (DF) was reported in Moreh township, Manipur: the first widespread outbreak in Northeast India. A cross sectional study was carried out in Moreh. The information on outbreak was collected and then described in time, place and person cha...
The present report aims to molecularly characterize seven clinical L. pneumophila (L. pn.) sg 1 isolated from nosocomial acquired infections in Apulia region, using the European Working Group on Legionella Infections (EWGLI), sequence-based typing (SBT) and amplified fragment length polymorphism (AF...
Methicillin-resistant Staphylococcus aureus (MRSA) causes serious nosocomial and community acquired infections. Resistance to methicillin is mediated by the mecA gene, which is inserted in a mobile genetic element called staphylococcal cassette chromosome mec (SCCmec). We determined the SCCmec types...
Listeria monocytogenes was isolated in two neonates born consecutively in the same hospital in France. The isolates had indistinguishable pulsed-field electrophoresis profiles. Retrospective epidemiological investigations found no evidence of a food-borne or environmental source. Infection control p...
An increase in the number of cases of postoperative empyema due to S. marcescens was recognized in the intensive care unit (ICU) of our Division of Thoracic Surgery between 3 and 19 March 2013. Pleural samples from patients and environmental samples from the operating room and ICU were obtained. A t...
Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important cl...
Having shown that Lucus Augusti Hospital in Lugo, Spain, has been affected by Escherichia coli clone O25:H4-ST131 producing CTX-M-15, the present study was carried out to evaluate the prevalence of this clone among the extended-spectrum β-lactamase (ESBL)-producing E. coli isolates and to identify n...
We investigated whether an increase in enterococcal bloodstream infections (BSIs) depends on the emergence of Enterococcus faecium in an area with low vancomycin-resistant enterococci prevalence. From 1999 to 2012, a linear increase in E. faecium BSI rates (0.009 per 1,000 patient-days per year; P <...
A total of 1878 non-duplicate clinical Escherichia coli isolates (comprising 1711 urinary isolates and 167 blood-culture isolates), which were collected from multiple centres in Hong Kong during 1996-2008, were used to investigate the prevalence and molecular epidemiology of plasmid-mediated fosfomy...
There is increasing concern regarding the association between certain methicillin-resistant Staphylococcus aureus (MRSA) genotypes and poor clinical outcome. To assess this issue, a large cohort of 579 subjects with MRSA bacteraemia was prospectively followed from June 2008 to December 2009, in 21 h...
Among 1588 non-duplicated Staphylococcus aureus isolates from 10 cities in China, 60 isolates were susceptible to oxacillin (MIC50: 1 μg/mL; MIC90: 2 μg/mL) but were mecA-positive. Twenty-one spa and 5 staphylococcal cassette chromosome mec (SCCmec) types were detected, and combined with multilocus...
Acinetobacter baumannii pigmented strains are not common in clinical settings. Here, we report an outbreak caused by indigo-pigmented A. baumannii strains isolated in an acute care hospital in Argentina from March to September 2012. Pan-PCR assays exposed a unique pattern belonging to the recently d...
Mycobacterium bovis populations in countries with persistent bovine tuberculosis usually show a prevalent spoligotype with a wide geographical distribution. This study applied mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing to a random panel of 115 M. bovi...
The global spread of methicillin-resistant Staphylococcus aureus (MRSA) is a serious problem, particularly in mainland China. In order to better understand the national molecular epidemiology and resistance profiles of hospital-associated MRSA (HA-MRSA) in China, a laboratory-based multicenter surve...
Elucidation of the molecular phylogeny of shrew-borne hantaviruses in sub-Saharan Africa has been hampered by the lack of full-length viral genomes. In this report, we present the complete genome analysis of a newfound hantavirus, designated Bowé virus, detected in ethanol-fixed intercostal muscle o...
A limited number of Pseudomonas aeruginosa genotypes (mainly ST-111, ST-175, and ST-235), known as high-risk clones, are responsible for epidemics of nosocomial infections by multidrug-resistant (MDR) or extensively drug-resistant (XDR) strains worldwide. We explored the potential biological paramet...
No abstract available
In Dakar kennels where morbidity and mortality attributed to diseases transmitted by ticks were high, we conducted a field study to assess the prevalence of Ehrlichia canis, Anaplasma platys and Babesia spp. infections in two kennels (n = 34 dogs) and to study the impact of tick protection. The firs...
Three neonates and 5 health care workers were identified as colonized with methicillin-resistant Staphylococcus aureus (MRSA) out of 222 individuals screened during an outbreak investigation in an 18-bed neonatal intensive care unit. Two of 3 MRSA neonatal isolates demonstrated identical pulsed-fiel...
As a follow-up of the "spoligoriftyping" development, we present here an extension of this technique which includes the detection of isoniazid resistance-associated mutations in a new 59-plex assay, i.e., tuberculosis-spoligo-rifampin-isoniazid typing (TB-SPRINT), running on microbead-based multiple...
In this study, we analyzed the clinical and molecular epidemiology of invasive serotype 5 (Ser5) pneumococcal isolates in four teaching hospitals in the Barcelona, Spain, area (from 1997 to 2011). Among 5,093 invasive pneumococcal isolates collected, 134 (2.6%) Ser5 isolates were detected. Although...
We investigated a cluster of 10 Burkholderia cepacia complex-positive cultures among ventilated patients and those with a tracheostomy in an acute care hospital. Isolates from 5 patients had outbreak-strain-related Burkholderia contaminans. Isolates of B. cepacia complex unrelated to the outbreak st...
Biochemical profiles, PFGE typing and MLST analysis were used to investigate an outbreak of septicaemic pasteurellosis in a free-range pig farm in Spain. Signs of coughing, dyspnoea and a visible inflammation of the ventral area of the neck (jowl), which acquired a cyanotic and necrotic appearance,...
A major community outbreak of salmonellosis occurred in France in October 2010. Classical epidemiological investigations led to the identification of beef burgers as the cause of the outbreak and the presence of the emerging monophasic Salmonella Typhimurium 4,5,12:i:-. The objective of this study w...
Measles is a highly contagious viral infection causing congenital infections with a risk of neurological complications in the newborn. Two cases of measles, which occurred in pregnant women within 14 days before the delivery, are described. Mother-to-child transmission of the virus was documented in...
Elizabethkingia meningoseptica is a nosocomial-adapted Gram-negative bacillus intrinsically resistant to antibiotics commonly used in the intensive care setting. An outbreak investigation commenced when five patients developed E. meningoseptica infection in two intensive care units (ICUs). Analysis...
Outbreaks of urinary tract infections (UTIs) due to contaminated ureteroscopes have been rarely reported. To report such an outbreak at a regional teaching hospital in southern Taiwan. From October to December 2010, ertapenem-resistant Enterobacter cloacae were identified from urine cultures of 15 p...
We screened 650 isolates from historical collection of Vibrio cholerae O1 during the 7th cholera pandemic in China, by amplifying and sequencing the cholera toxin subunit gene ctxB. Ten isolates were identified as harboring three novel ctxB genotypes based on amino acid residue substitutions. Within...
The epidemiology of invasive Haemophilus influenzae has changed in recent years. β-Lactamase-negative ampicillin-resistant (BLNAR) invasive isolates have recently been described in Europe but their clinical significance is unclear. Our main goal was to determine whether invasive H. influenzae remain...
The importance of livestock as a source of bacterial pathogens with the potential for epidemic spread in human populations is unclear. In recent years, there has been a global increase in community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections of healthy humans, but an...
Foot-and-mouth disease (FMD) is endemic in Kenya where four serotypes (O, A, SAT 1 and SAT 2) of the virus are currently in circulation. Within 2010 and 2011, the National Laboratory recorded an increase in the number of FMD outbreaks caused by serotype O virus. The characteristics of these viruses...
Aspergillus terreus is a common soil saprophyte. After Aspergillus fumigatus and Scedosporium apiospermum it ranks third amongst the filamentous fungi colonizing the airways of patients with cystic fibrosis. In this context, the clinical presentation of A. terreus infection mainly corresponds to all...
Carbapenem-resistant Acinetobacter baumannii has spread rapidly across China and is currently reported to be a worldwide nosocomial menace. In light of its increasing clinical significance, this study aimed to investigate the molecular epidemiology of carbapenem-resistant and carbapenem-susceptible...
All notified MRSA cases in Skåne County have been followed since 2000. We have investigated the MRSA epidemiology over time, method of acquisition, whether some spa types are more prone to spread, and/or cause more infections, and the connection between spa type and country of acquisition/origin. Al...
A total of 1,021 extended-spectrum-β-lactamase-producing Escherichia coli (ESBLEC) isolates obtained in 2006 during a Spanish national survey conducted in 44 hospitals were analyzed for the presence of the O25b:H4-B2-ST131 (sequence type 131) clonal group. Overall, 195 (19%) O25b-ST131 isolates were...
During the 30 months of surveillance period, 85 pAmpC-producing isolates were detected (prevalence 0.56% overall): blaCMY-2 gene in 70 E. coli, 2 K. pneumoniae and 6 P. mirabilis isolates; and the blaDHA-1 gene in 4 E. coli and 3 K. pneumoniae. In 8.23% of them, other β-lactamases (predominantly OXA...
Emerging and re-emerging viruses continue to surface all over the world. Some of these viruses have the potential for rapid and global spread with high morbidity and mortality, such as the SARS coronavirus outbreak. It is extremely urgent and important to identify a novel virus near-instantaneously...
Emerging pathogens that originate from invasive species have caused numerous significant epidemics. Some bacteria of genus Bartonella are rodent-borne pathogens that can cause disease in humans and animals alike. We analyzed gltA sequences of 191 strains of rat-associated bartonellae from 29 rodent...
Arbovirus screening in invertebrate vectors is an important component of the vector-borne disease surveillance programs. Turkey has been shown to harbor medically important mosquito-borne arboviruses such as West Nile Virus (WNV). However, limited information about infections in vectors are currentl...
Escherichia coli sequence type 131 (ST131), typically fluoroquinolone-resistant (FQ-R) and/or extended-spectrum β-lactamase (ESBL)-producing, has emerged globally. We assessed its prevalence and characteristics among US veterans. In 2011, 595 de-identified E. coli clinical isolates were collected sy...
Nosocomial transmission of Candida spp. has not been fully explored and previous studies have shown conflicting results. To evaluate the possible nosocomial transmission of Candida spp. on an intensive care unit (ICU). A prospective study was conducted for a period of 19 months, including all patien...
Pasteurella multocida, the causative agent of fowl cholera, is a serious threat to poultry farming. In this study, we isolated and identified 40 P. multocida strains in fowl cholera outbreaks in Jiangsu province, China. The identified P. multocida was further characterized using multi-locus sequence...
Congenital cytomegalovirus (CMV) infection is caused by maternal primary infection as well as CMV reinfection or reactivation during pregnancy, although differences in the clinical impact between these modes of infection remain to be clarified. To investigate the latest prevalence and risk of multip...
Evaluation of multilocus variable number tandem repeat analysis (MLVA) to subtype all isolates of Vero cytotoxin-producing Escherichia coli O157 phage type 8 in England and Wales. Over a 13 month period from December 2010, 483 isolates of VTEC O157 PT8 were tested by MLVA; 39% were received in the f...
To investigate the prevalence and genetic background of Escherichia coli collected from different patient populations in the Euroregion Meuse-Rhine. Susceptibility testing was performed on 1651 E. coli isolates with broth microdilution. Their genetic background was determined using pulsed-field gel...
The epidemiology of enteroviral infection in South Korea during 1999-2011 chronicles nationwide outbreaks and changing detection and subtyping methods used over the 13-year period. Of 14,657 patients whose samples were tested, 4,762 (32.5%) samples were positive for human enterovirus (human EV); as...
We report an increase in the proportion of genotype GI.6 norovirus outbreaks in the United States from 1.4% in 2010 to 7.7% in 2012 (p<0.001). Compared with non-GI.6 outbreaks, GI.6 outbreaks were characterized by summer seasonality, foodborne transmission, and non-health care settings.
Two major Treponema pallidum subtypes, 14 d/g and 14 d/f, were identified in a population of 119 patients with syphilis in Paris, France, characterized by a high proportion of men who have sex with men. A new subtype named 11 q/j was characterized, and a reinfection case was determined in 1 patient...
Streptococcus pneumoniae infections have resulted in significant morbidity and mortality worldwide in children and adults. In Canada, Streptococcus pneumoniae remains one of the leading causes of infectious disease including pneumonia, meningitis, bacteremia and otitis media. Although the widespread...
No abstract available
Clostridium difficile infection is almost unrecognized in mainland China. We have undertaken a study in a large Chinese teaching hospital in Changsha, Hunan, China, to identify cases of C. difficile, record patient characteristics, and define the molecular epidemiology with respect to ribotype distr...
An outbreak of shiga-toxin producing Escherichia coli infections occurred in southwest France in June 2012. The outbreak was investigated to identify the source of infection, and guide control measures. Confirmed outbreak cases were patients who developed bloody diarrhoea or haemolytic uremic syndro...
CTX-M-producing Escherichia coli is the predominant type of extended-spectrum β-lactamase (ESBL)-producing E. coli worldwide. In this study, molecular typing was conducted for 139 CTX-M-producing E. coli isolates, phenotypically positive for ESBLs, isolated from environmental water, swine, healthy h...
No abstract available
The recent emergence of multidrug-resistant Escherichia coli sequence type 131 (ST131) has coincided with an increase in general antibiotic resistance of E. coli, suggesting that ST131 has a contributing role in resistance. However, there is little information about the contribution of ST131 to diff...
This study assessed the relationship between nasal colonization and ventilator-associated pneumonia (VAP) by Staphylococcus aureus, as well the role of the environment in the transmission of this organism. We performed a cohort study of patients with VAP caused by methicillin-resistant S aureus (MRS...
Between September 2000 and November 2005, approximately 10% of the retrospectively examined human adenovirus (HAdV)-positive pediatric cases of acute respiratory disease (ARD) requiring hospitalization at the Hospital Nacional de Pediatria Juan P. Garrahan in Buenos Aires, Argentina, were found to h...
A repeated cross-sectional study was conducted to determine the prevalence of Campylobacter spp. and the population structure of C. jejuni in European starlings and ducks cohabiting multiple public access sites in an urban area of New Zealand. The country's geographical isolation and relatively rece...
Genetic characterisation of linezolid-resistant Gram-positive cocci in a multicentre study in China has not been reported previously. To study the mechanism underlying the resistance of linezolid-resistant isolates, nine Enterococcus faecalis, one Enterococcus faecium and three Staphylococcus cohnii...
In summer 2011, two outbreaks of a unique, multidrug-resistant strain of Salmonella enterica serovar Typhimurium phage type 120 (DT120) occurred mainly in the Midlands, England. The first outbreak occurred among guests attending a wedding in July 2011 ('Wedding outbreak'), followed by a more geograp...
Staphylococcal cassette chromosome mec is a genetic mobile element that carries the gene mecA mediating the methicillin resistance in staphylococci. The aim of this study is to type the Staphylococcal cassette chromosome mec (SCCmec) in 64 non-redundant methicillin-resistant Staphylococcus aureus (M...
Previous studies in intensively raised piglets have detected a high prevalence of the epidemic Clostridium difficile PCR ribotype 078. In this article we present a longitudinal survey of C. difficile colonisation in a population of Iberian pigs reared under a free-range system. A total of 160 faecal...
Staphylococcus aureus from bacteraemia at multiple hospitals in China were genetically characterised to improve understanding of its epidemiology. A total of 236 consecutive, non-duplicate S. aureus bacteraemia isolates were collected at 16 Chinese hospitals. Isolates were characterised by antimicro...
Klebsiella pneumoniae outbreaks possessing extended-spectrum β-lactamase- (ESBL) mediated resistance to third-generation cephalosporins have increased significantly in hospital and community settings worldwide. The study objective was to characterize prevalent genetic determinants of TEM, SHV and CT...
The emergence of highly virulent and successful Streptococcus pyogenes (group A streptococci - GAS) clones has been attributed to the exchange of virulence factors by lateral gene transfer mechanisms, which strongly contribute to genomic diversity. We characterized a collection of 191 GAS isolates r...
Dengue virus infection has become an increasingly serious threat to public health in Nepal. Detection and/or serotyping of dengue virus has been reported in the past; however, little is known about the critical phase among dengue patients in Nepal. Rapid immunochromatographic tests and reverse trans...
On 20 March 2012, the Minnesota Department of Health (MDH) was notified of multiple Facebook postings suggestive of a foodborne outbreak of Group A Streptococcus (GAS) pharyngitis occurring among attendees of a high school dance team banquet. An investigation was initiated. Associations between GAS...
No abstract available
Campylobacter remains one of the most common bacterial causes of gastroenteritis worldwide. Tracking sources of this organism is challenging due to the large numbers of human cases, and the prevalence of this organism throughout the environment due to growth in a wide range of animal species. Many m...
We previously reported HIV-1 infection in Warao Amerindians from Venezuela. The aim of this study was to evaluate the extent and the dynamic of HIV-1 dissemination in eight Warao communities. HIV-1 infection was evaluated in 576 Warao Amerindians from the Orinoco Delta. Partial HIV-1 pol sequences w...
The case is presented of a woman with intrauterine infection and post-partum bacteraemia due to Streptococcus gallolyticus subsp. pasteurianus, who delivered an infant via Caesarean section. Furthermore, we comment on the possibility of vaginal colonization of this organism as a portal of entry in c...
Although it is understood that low-risk human papillomavirus (HPV) genotypes are associated with genital warts, there have been very few published studies reporting the genotype-specific prevalence of HPV among Chinese population. The aim of the study was to assess the prevalence of HPV genotypes in...
To describe the changing prevalence of healthcare- and community-associated MRSA. Susceptibility phenotypes of MRSA were observed from 2000 to 2012 using routine susceptibility data. Phenotypic definitions of major clones were validated by genotyping isolates from a nested period prevalence survey i...
Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimicrobial susceptibility of isolates from a UK-wide survey of Campylobacter in retail poul...
Infection of humans and animals caused by Salmonella is a major public health problem worldwide. Among the more than 2500 serovars, S. Infantis has been one of the 15 most isolated serovars in the world. Despite its clinical importance, little is known about the molecular characteristics of S. Infan...
We describe the epidemiological and microbiological process in the clearing of a foodborne outbreak of Yersinia pseudotuberculosis O:1 linked to raw carrots and frequency of the associated reactive extra-gastrointestinal manifestations. The patient samples were investigated by routine culture or ant...
Our understanding of the sources of Mycobacterium avium infection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this assumption, a high-re...
Although numerous studies have documented outbreaks of carbapenem-resistant Klebsiella pneumoniae (CRKP) possessing various carbapenemases, reports on outbreaks due to CRKP possessing extended-spectrum β-lactamases (ESBLs) and/or AmpCs with porin lesions have been limited. Here, we describe an outbr...
Molecular epidemiology studies on cryptococcemia are limited. This study aimed to describe the clinical features of patients with bloodstream infections by Cryptococcus sp. in a public tertiary hospital in Mato Grosso do Sul, as well as identify the fungus' molecular type and determine its antifunga...
The widespread occurrence of Wolbachia in arthropods and nematodes suggests that this intracellular, maternally inherited endosymbiont has the ability to cross species boundaries. However, direct evidence for such a horizontal transmission of Wolbachia in nature is scarce. Here, we compare the well-...
The influenza virus has been a challenge to science due to its ability to withstand new environmental conditions. Taking into account the development of virus sequence databases, computational approaches can be helpful to understand virus behavior over time. Furthermore, they can suggest new directi...
Between October 2012 and May 2013, five cases of invasive meningococcal disease in young men who have sex with men (MSM) living in Berlin were notified to local health authorities in Germany. Three of the five cases died. All were caused by serogroup C variants with the finetype P1.5-1,10-8:F3-6. Aw...
Sixty-five CTX-M-2/15/14 extended-spectrum-β-lactamase-producing Enterobacteriaceae were isolated from 258,888 mastitic milk samples from Japanese dairy farms between 2007 and 2011. CTX-M-2-producing Klebsiella pneumoniae and CTX-M-15-producing Escherichia coli were the predominant strains isolated....
In China, Klebsiella pneumoniae carbapenemase (KPC) -producing K. pneumoniae isolates have been identified. However, little is known about the spread and outbreak of KPC-producing enterobacterial pathogens. In this study, 48 non-duplicated KPC-producing isolates were analysed for genetic relatedness...
To investigate the epidemiological traits of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa (MPPA) clinical isolates collected by the Asian Network for Surveillance of Resistant Pathogens (ANSORP). A total of 16 MPPA clinical isolates were collected from six Asian countries in 2000 to 20...
To control the spread of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals, infection control measures such as hand hygiene practices were introduced into the teaching hospitals in Shanghai, China, in 2008. Currently, there is limited information characterizing the latest hospital-acqu...
Carbapenem resistance among Acinetobacter baumannii strains isolated from clinical settings in Brazil has increased dramatically in the last 10 years due to the emergence and dissemination of OXA-type carbapenemase encoding genes. This study aimed to characterize the presence of carbapenem-hydrolyzi...
Bluetongue (BT) is an economically important endemic disease of livestock in tropics and subtropics. In addition, its recent spread to temperate regions like North America and Northern Europe is of serious concern. Rapid serotyping and characterization of BT virus (BTV) is an essential step in the i...
Since 1998, 9 of the 26 serotypes of bluetongue virus (BTV) have spread throughout Europe, and serotype 8 has suddenly emerged in northern Europe, causing considerable economic losses, direct (mortality and morbidity) but also indirect, due to restriction in animal movements. Therefore, many new typ...
Although extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) has emerged as a significant community-acquired pathogen, there is little epidemiological information regarding community-onset bacteremia due to ESBL-EC. A retrospective observational study from 2006 through 2011 was perfor...
We retrospectively studied 22 patients with catheter-related candidemia caused by Candida albicans. Strains isolated simultaneously from blood and catheter tips were genotyped using six microsatellite markers. Matches between genotypes of isolates recovered from both sample sources were found in 20/...
From 2001 to 2008, 119 pediatric cases of meningococcal disease caused by serogroup W were reported in France. They cases represented 4% of all meningococcal disease cases in children and were mostly in infants (54%). Meningitis occurred in 78 (66%) patients but differed by isolate. Isolates of the...
Escherichia coli is a common uropathogen causing community-acquired urinary tract infections (UTIs). Out of 4735 E. coli community-acquired UTIs, 10.2% were extended spectrum β-lactamases (ESBL)-producing. The identified ESBL types were CTX-M-15 (96.4%), SHV-2a (3%), and TLA-1 (1%). Of the isolates,...
Mycobacterium tuberculosis is classified into six phylogenetic lineages, each of which can be divided into sublineages. Sublineages of the same lineage have phenotypic differences, including their capacity to cause disease (pathogenicity). 1) To test the hypothesis that different sublineages of line...
To study the clinical and molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) infection in children. A total of 37 MRSA strains were isolated from hospitalized patients in Children's Hospital of Fudan University from March 2009 to November 2011. The clinical characteristi...
No abstract available
No abstract available
Enterocytozoon bieneusi (phylum Microsporidia) is a human pathogen with a broad host range. Following the sequencing of 3.8 Mb of the estimated 6-Mb E. bieneusi genome, simple sequence repeats (micro- and minisatellites) were identified. Sequencing of four such repeats from various human and animal...
Shiga toxin-producing Escherichia coli O26:H11/H(-) strains showing the characteristics of the emerging human-pathogenic ST29 clone (stx2a(+) only, eae(+), plasmid gene profile hlyA(+) etpD(+)) were detected from human patients and healthy cattle, indicating a possible reservoir. Sheep also appear t...
To determine whether methicillin-susceptible S. aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) are present in commercial pig farms and food products from supermarkets in China, we characterized S. aureus isolates from 250 samples associated with swine and animal-related food pr...
This study describes the course of an OXA-48-producing Enterobacteriaceae (OPE) outbreak that started in March 2012 in a neonatal intensive care unit (NICU) in Jerusalem, Israel. During the peak of the outbreak (January to August 2012), there were 49 patients who had proven or suspected acquisition...
Clostridium difficile infection (CDI) causes nearly half a million cases of diarrhea and colitis in the United States each year. Although the importance of the gut microbiota in C. difficile pathogenesis is well recognized, components of the human gut flora critical for colonization resistance are n...
Antimicrobial susceptibility, integron carriage, genetic relationship and presence of some important virulence genes of the integron-carrier strains of Shigella sonnei (n = 230) and Shigella flexneri (n = 22) isolated from stool samples of patients in Hungary between 1998 and 2008 were investigated....
Extended-spectrum β-lactamases (ESBLs), particularly CTX-M- type ESBLs, are among the most important resistance determinants spreading worldwide in Enterobacteriaceae. The aim of this study was to characterize a collection of 163 ESBL-producing Escherichia coli collected in Tunisia, their ESBL-encod...
Acinetobacter baumannii is an important microorganism responsible for a number of nosocomial outbreaks, in particular, in intensive care units (ICUs). We investigated a nosocomial infection caused by multidrug-resistant (MDR) A. baumannii in a neonatal intensive care unit (NICU) in Korea. A. baumann...
Salmonella enterica serovar Weltevreden and Vibrio fluvialis were identified as etiological agents of a foodborne gastroenteritis outbreak after an Iftar feast in North Dumdum. Of the 278 cases admitted to the Infectious Diseases Hospital, Kolkata, 44 stool samples were tested for the enteric pathog...
Torque teno sus viruses (TTSuV1-2), members of the newly established family Anelloviridae are considered non-pathogenic emerging viral agents of Suidae species. However, the genetic diversity, phylogeny and evolutionary processes responsible for the emergence and spread of TTSuVs in wild boars remai...
Salmonella enterica serovar 4,[5],12:b:- is a monophasic serovar not able to express the second-phase flagellar antigen (H2 antigen). In Germany, the serovar is occasionally isolated from poultry, reptiles, fish, food, and humans. In this study, a selection of 67 epidemiologically unrelated Salmonel...
Worldwide HIV-1 pandemic is becoming increasingly complex, with growing heterogeneity of subtypes and recombinant viruses. Previous studies have documented HIV-1 subtype B as the predominant one in Serbia, with limited presence and genetic diversity of non B subtypes. In recent years, MSM transmissi...
To analyse the ongoing epidemiology of KPC-producing Enterobacteriaceae after a non-ST258 KPC-3-producing Klebsiella pneumoniae outbreak in a university hospital in Madrid, Spain. Enterobacterial isolates (one per patient based on bacterial identification and typing patterns) with carbapenem MICs hi...
Pneumocystis jirovecii pneumonia (PCP) is an opportunistic infection with airborne transmission and remains a major cause of respiratory illness among immunocompromised individuals. In recent years, several outbreaks of PCP, occurring mostly in kidney transplant recipients, have been reported. Curre...
Typing of Clostridium difficile facilitates understanding of the epidemiology of the infection. Some evaluations have shown that certain strain types (for example, ribotype 027) are more virulent than others and are associated with worse clinical outcomes. Although restriction endonuclease analysis...
Pseudomonas aeruginosa is an important nosocomial pathogen that exhibits multiple resistances to antibiotics with increasing frequency, making patient treatment more difficult. The aim of the study is to ascertain the population structure of this clinical pathogen in the Hospital Son Llàtzer, Spain....
In 2008, 150 people gathered for a wedding celebration in Baden-Württemberg, Germany. Three hours after ingestion of a variety of foods including pancakes filled with minced chicken, several guests exhibited symptoms of acute gastroenteritis such as vomiting, diarrhea, fever, and ague. Twelve guests...
The distribution of methicillin-resistant Staphylococcus aureus (MRSA) clones is dynamic and geographically unique. To understand the changing epidemiology of MRSA infections in China, we performed a prospective, multicity surveillance study with molecular typing and phenotypic analysis to determine...
We compared two PCR methods for molecular typing the medically important filamentous fungus Aspergillus terreus. In a set of 46 strains investigated we found 19 and 12 different fingerprinting types obtained by random amplified polymorphic DNA PCR (RAPD) and semi-automated repetitive element PCR (re...
An outbreak of Clostridium difficile infection (CDI) at Höglandet Hospital Eksjö in southern Sweden in 2011 was mainly due to a multidrug-resistant PCR ribotype 046 (30% of all samples). Diagnostics used routinely was the Vidas CDAB assay, but to control the outbreak the rapid loop-mediated isotherm...
No abstract available
The introduction of Haemophilus influenzae serotype b (Hib) conjugate vaccines has changed the epidemiology of invasive H. influenzae disease, with a shift in the predominant serotype from Hib to nonencapsulated H. influenzae (ncHi). The objective of this study was to identify the genotypes/clones a...
Seventy-six Pseudomonas aeruginosa isolates recovered from chronically (n=18) and nonchronically (n=18) colonized cystic fibrosis (CF) patients (2002 to 2009) were grouped in separate polyclonal populations. International CF epidemic clones were not identified, but the high-risk clone ST274, also fo...
To assess the within-farm dynamics of extended-spectrum β-lactamase (ESBL)/AmpC-producing Escherichia coli in veal calves. Three veal-calf fattening farms were screened. Faecal samples from all calves within a compartment (109-150 per farm) were taken upon arrival on the farm (T0) and after 3, 6, 8...
Contagious agalactia (CA) is a serious disease of small dairy ruminants that has a substantial economic impact on the goat and sheep milk industries. The main aetiological agent of the disease is Mycoplasma agalactiae, although other species, such as Mycoplasma mycoides subsp. capri, Mycoplasma capr...
Rapid and easy-to-use molecular subtyping methods are being explored and used for the surveillance of bacterial diseases, including multiple-loci variable number of tandem repeats (VNTR) analysis (MLVA). In this study, we assessed different VNTR combinations for the subtyping of Vibrio cholerae sero...
Shiga toxin-producing Escherichia coli (STEC) are associated with foodborne illnesses, including hemolytic uremic syndrome in humans. Cattle and consequently, beef products are considered a major source of STEC. E. coli O157:H7 has been regulated as an adulterant in ground beef since 1996. The Unite...
Chlamydia pecorum is a significant pathogen of domestic livestock and wildlife. We have developed a C. pecorum-specific multilocus sequence analysis (MLSA) scheme to examine the genetic diversity of and relationships between Australian sheep, cattle, and koala isolates. An MLSA of seven concatenated...
To determine the spread of Staphylococcus aureus within and between nursing home (NH) residents in the Euregion Meuse-Rhine, a cross-border region of the Netherlands and Germany, we investigated the prevalence of antibiotic resistance, genetic background and population structure of both methicillin-...
The prevalence and genetic characteristics of Escherichia coli and Klebsiella pneumoniae clinical isolates producing extended-spectrum β-lactamase (ESBL) were examined. Between October 2010 and March 2011, E. coli (n=460) and K. pneumoniae (n=78) isolates were collected at a tertiary care hospital i...
Staphylococcus aureus is a frequent cause of nosocomial pneumonia and bacteremia worldwide. Classical and molecular epidemiology approaches were used to study a S. aureus outbreak in the intensive care unit (ICU) of one of the largest public hospitals in Quito. Staphylococcus aureus isolates from 17...
This study aimed at characterizing the phenotypic and toxigenic status of circulating strains of cholera during outbreaks in Nigeria, employing molecular typing techniques. Two hundred and one samples of rectal swabs, stool, vomitus, water (from the well, borehole, sachet, stream, and tap) and disin...
Before introduction of Haemophilus influenzae type b (Hib) vaccines, rates of Hib disease in Alaska's indigenous people were among the highest in the world. Vaccination reduced rates dramatically; however, invasive H. influenzae type a (Hia) disease has emerged. Cases of invasive disease were identi...
Scarlet fever is one of a variety of diseases caused by group A Streptococcus (GAS). During 2011, a scarlet fever epidemic characterized by peak monthly incidence rates 2.9-6.7 times higher than those in 2006-2010 occurred in Beijing, China. During the epidemic, hospital-based enhanced surveillance...
To investigate the spread of methicillin-resistant Staphylococcus aureus (MRSA) isolated from a cluster of clinical cases at a veterinary hospital by molecular epidemiological techniques. Antimicrobial susceptibility testing, spa typing, multilocus sequence typing and pulsed-field gel electrophoresi...
We report new sequence types of 14 penicillinase-producing Neisseria gonorrhoeae, isolated from sexually transmitted disease clinic attendees in Manaus, Brazil. They were characterized by WI/WII/WIII groups, susceptibility testing and Multi-Antigen Sequencing Typing/Mutilocus Sequence Typing protoco...
Citrus Huanglongbing (HLB) also known as citrus greening is one of the most devastating diseases of citrus worldwide. The disease is caused by Candidatus Liberibacter bacterium, vectored by the psyllid Diaphorina citri Kuwayama and Trioza erytreae Del Guercio. Citrus plants infected by the HLB bacte...
Measles has been controlled effectively in some countries because of high coverage rates with an effective vaccine. However, measles outbreaks still occasionally occur in areas with high vaccine coverage as a result of imported transmission. To identify the sources of measles infection and to determ...
The aims of our study were analysis of the occurrence of infections by members of the Enterobacteriaceae family in 6 Polish neonatal intensive care units in 2009, their drug resistance, the epidemiology of extended-spectrum β-lactamase (ESBL)-producing strains and the possibility of using modern too...
The prevalence of carbapenemase-producing Enterobacteriaceae (CPE) has increased during the past 10 years. Its detection is frequently difficult, because they do not always show a minimum inhibitory concentration (MIC) value for carbapenems in the resistance range. Both broth microdilution and agar...
Tuberculosis (TB), caused by the Mycobacterium tuberculosis complex (MTBC), is a serious infection in humans and animals. Ethiopia is one of the countries in Sub-Saharan Africa with the highest burden of TB. However, limited information is available on the genotypic characteristics of M. tuberculosi...
The methicillin-susceptible Staphylococcus aureus (MSSA) clone sequence type (ST) 398 has increasingly been identified as a pathogen in diverse geographic settings, yet its epidemiology remains incompletely understood. In this case-control study of MSSA infections, we identified ST398 MSSA as both a...
A single strain of Mycobacterium massiliense (BRA 100), a subspecies of the Mycobacterium abscessus complex, has been responsible for an epidemic of post-surgical infections in Brazil. Outside Brazil, this is the first report to describe a single emerging strain of M. massiliense (TPE 101) associate...
16S rRNA methylase-producing Gram-negative bacteria are highly resistant to all clinically important aminoglycosides. We analyzed clinical strains of 16S rRNA methylase-producing Acinetobactor baumannii and Pseudomonas aeruginosa obtained from clinical isolates in medical settings in Vietnam. From 2...
In industrialized countries, Clostridium difficile is the major cause of nosocomial diarrhea. This study involved a broad overview of baseline epidemiology for C. difficile in Taiwan. Point prevalence was estimated from a prospective survey conducted in the respiratory care wards of six hospitals in...
We report the molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) with resistance to tigecycline and to daptomycin isolated from intensive-care-unit patients in Brazil over a 6-month period. Thirty-six isolates (25 from infection sites, 11 from nasal sites) recovered fro...
Bacterial pathogens impose a heavy health burden worldwide. In the new era of high-throughput sequencing and online bioinformatics, real-time genome typing of infecting agents, and in particular those with potential severe clinical outcomes, holds promise for guiding clinical care to limit the detri...
Emerging carbapenem resistance among Acinetobacter baumannii clinical isolates is a worldwide problem. Infections caused by A. baumannii are increasing and demonstrate high mortality rates. This study aimed to establish a nationwide surveillance of antimicrobial susceptibility, carbapenemase genes,...
Mycoplasma hominis is an opportunistic human mycoplasma species that can cause various urogenital infections and, less frequently, extragenital infections. The objective of this work was to study the genetic diversity of this species using a molecular typing method based on multiple-locus variable-n...
Fifty consecutive MRSA blood isolates were evaluated: 30(60%) carried SCCmec type II (single PFGE clone; sequence type 5 or ST105); 12 (26%), IV; 5 (10%), III; 3 (6%), I. Brazilian endemic clone, carrying SCCmec type III, has been the main nosocomial clone in Brazil; however, this study showed that...
This study aims to investigate the prevalence of a novel cell wall-anchored protein gene, sasX, and to obtain information on the genetic basis for the pathogenic potential of the MRSA strains isolated from Chinese children. The molecular and virulence characteristics of the clinical strains were ana...
Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdiv...
Salmonella enterica serotype Typhimurium is one of the leading causes of salmonellosis in Mauritius, where it has also been associated with outbreaks of foodborne illness. However, little is known about its molecular epidemiology in the country. This study was therefore undertaken to investigate the...
The aim of the study was to characterize isolates of Escherichia coli from an outbreak of septicemia in a Norwegian sheep flock in 2008 with emphasis on virulence, serological grouping, phylogenicity and homology. Six E. coli isolates from succumbed neonatal lambs and four E. coli isolates collected...
Strains of the Burkholderia cepacia complex (Bcc) are opportunistic pathogens capable of causing serious infection in cystic fibrosis patients. Recently we identified a suspected outbreak of infection with Bcc strains at the University Hospital Olomouc. Seventy-four Bcc strains were isolated from 52...
Serratia marcescens causes health care-associated infections with important morbidity and mortality. Particularly, outbreaks produced by multidrug-resistant isolates of this species, which is already naturally resistant to several antibiotics, including colistin, are usually described with high rate...
Pneumocystis jirovecii causes pneumonia, a severe opportunistic infection in immunosuppressed patients that has both person-to-person airborne transmission and environmental transmission as important routes of infection. An increasing incidence of P. jirovecii in Northern Ireland prompted a detailed...
It has been hypothesized that biogeographical boundaries are a feature of Burkholderia pseudomallei ecology, and they impact the epidemiology of melioidosis on a global scale. This study examined the relatedness of B. pseudomallei sourced from islands in the Torres Strait of Northern Australia to de...
Sequence-based typing is essential for understanding the epidemiology of Campylobacter infections, a major worldwide cause of bacterial gastroenteritis. We demonstrate the practical and rapid exploitation of whole-genome sequencing to provide routine definitive characterization of Campylobacter jeju...
We examined the environmental dissemination of Acinetobacter nosocomialis multilocus sequence typing clonal complex 260/71 in Rio de Janeiro, Brazil, including water from a dam and food samples. The increasing use of sequence based methods has demonstrated a large, previously unpredicted, disseminat...
No abstract available
Enterohemorrhagic Escherichia coli (EHEC) causes diarrhea, often with severe complications. Rapid and discriminatory typing of EHEC using advanced molecular methods is needed for determination of the genetic relatedness of clones responsible for foodborne outbreaks and for finding out the transmissi...
Mumps is a vaccine-preventable disease that usually occurs as a self-limiting parotitis, but it can also lead to several life-threatening complications, including pancreatitis, meningitis, and encephalitis. The molecular epidemiology of the virus is poorly understood. The present study describes an...
Staphylococcus aureus (SA) nasal colonization plays a critical role in the pathogenesis of staphylococcal infections and SA eradication from the nares has proven to be effective in reducing endogenous infections. To understand SA nasal colonization and its relation with consequent disease, assessmen...
The rates of escape and reversion in response to selection pressure arising from the host immune system, notably the cytotoxic T-lymphocyte (CTL) response, are key factors determining the evolution of HIV. Existing methods for estimating these parameters from cross-sectional population data using or...
NotI, the most prevalent restriction enzyme used for typing Moraxella catarrhalis, failed to digest genomic DNA from respiratory samples. An improved pulsed-field gel electrophoresis (PFGE) methodology determined SpeI as the best choice for typing this bacterial species, with a good restriction of c...
Salmonella enterica subsp. enterica serovar Newport (S. Newport) is the third most prevalent cause of food-borne salmonellosis. Rapid, efficient, and accurate methods for identification are required to track specific strains of S. Newport during outbreaks. By exploiting the hypervariable nature of v...
The flea-borne rickettsioses murine typhus (Rickettsia typhi) and flea-borne spotted fever (FBSF) (Rickettsia felis) are febrile diseases distributed among humans worldwide. Murine typhus has been known to be endemic to Kenya since the 1950s, but FBSF was only recently documented in northeastern (20...
Between 20 000 and 35 000 cases of salmonellosis are detected annually in Germany, but only a few Salmonella are resistant to third-generation cephalosporins. The German National Reference Centre for Salmonella and other Enterics obtained 150 Salmonella enterica isolates from human infections betwee...
Dengue is the most prevalent arboviral disease of humans. The host and virus variables associated with dengue virus (DENV) transmission from symptomatic dengue cases (n = 208) to Aedes aegypti mosquitoes during 407 independent exposure events was defined. The 50% mosquito infectious dose for each of...
The success of Streptococcus pneumoniae (pneumococcus) in both colonisation and disease is associated with the increased prevalence of genetic clones expressing virulence factors that assist host invasion. We studied the distribution of pneumococcal clones in paediatric carriage as part of an ongoin...
Vancomycin-resistant Enterococcus faecium (VRE) may cause outbreaks in neonatal intensive care units (NICU). We describe a biphasic VRE outbreak and identify risk factors for VRE acquisition. After the occurrence of 2 cases of VRE infections in a 44-bed NICU, a bundle of interventions was implemente...
To determine the methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) contamination rate of white coats (WC) and surgical scrubs (SS) worn by personnel at the Ontario Veterinary College Health Sciences Centre (OVCHSC) and to identify ris...
Strains of Klebsiella pneumoniae producing KPC-carbapenemase have emerged as one of the most important multidrug-resistant Gram-negative nosocomial pathogens. Here, we report the first isolation and subsequent dissemination of a K. pneumoniae ST512 producing KPC-3 carbapenemase in a hospital in sout...
In a prospective study (2009-2011) in healthcare institutions from the Canary Islands (Spain), 6 out of 298 carbapenem non-susceptible Pseudomonas aeruginosa isolates produced a metallo-β-lactamase: four IMP-15, two VIM-2 (including one IMP-15-positive isolate) and one VIM-1. Multilocus sequence typ...
Forty-six Helicobacter cinaedi isolates from the same hospital were analyzed by multilocus sequence typing. Most H. cinaedi isolates exhibited clonal complex 9 and were mainly isolated from immunocompromised patients in the same ward. Three Helicobacter fennelliae isolates were obtained from the sam...
The population structure of 3,776 Mycobacterium tuberculosis isolates was determined using variable-number tandem-repeat (VNTR) typing. The degree of clonality was so high that a more relaxed definition of clustering cannot be applied. Among recent immigrants with non-Euro-American isolates, transmi...
Genotyping of Mycobacterium tuberculosis strains became indispensable for understanding tuberculosis transmission dynamics and designing measures to combat the disease. Unfortunately, typing involves sophisticated laboratory analysis, is expensive, and requires a high level of technical expertise, w...
Investigation of Staphylococcus aureus outbreaks, and particularly those due to methicillin-resistant S. aureus (MRSA) in hospitals, can identify infection reservoirs and prevent further colonization and infection. During outbreaks, S. aureus genomes develop single nucleotide polymorphisms (SNPs), s...
To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using...
The empirical treatment with trimethoprim or ciprofloxacin of urinary tract infections (UTIs) is now questioned, partly due to the global expansion of a few resistant clonal groups of Escherichia coli. In this study we investigated the clonal structure of 34 strains of E. coli (collected from non-pr...
Variable number of tandem repeats (VNTR) loci were recently identified in Japanese isolates of Mycobacterium intracellulare. We hypothesised that some mycobacterial genotypes are more virulent than others, resulting in particular genotypes being associated with disease phenotype and progression. To...
Molecular typing is a valuable tool for gaining insight into spread of Mycobacterium tuberculosis. Typing allows for clustering of cases whose isolates share an identical genotype, revealing epidemiologic relatedness. Observed distributions of genotypic cluster sizes of tuberculosis (TB) are highly...
We describe an outbreak of 5 osteoarticular infections among 24 daycare center attendees. Polymerase chain reaction revealed Kingella kingae in the joint fluid of 1 child and in 85% of throat samples from healthy contacts. Multilocus sequence typing performed on the joint fluid and carriage isolates...
We investigated Bacillus cereus-positive tracheal aspirates from infants on ventilators in a neonatal intensive care unit. Multilocus sequence typing determined a genetic match between strains isolated from samples from a case-patient and from the air flow sensor in the ventilator. Changing the ster...
Dengue is a resurging mosquito-borne disease that is often contracted in U.S. travelers to Latin America, Asia, and the Caribbean. The clinical symptoms range from a simple febrile illness to hemorrhagic fever or shock. The clinical course has a wide range of outcomes, and adequate supportive care c...
The purpose of the CANWARD study was to assess the antimicrobial activity of a variety of available agents against 22,746 pathogens isolated from patients in Canadian hospitals between 2007 and 2011. Between 2007 and 2011, 27,123 pathogens were collected from tertiary-care centres from across Canada...
To compare the demographics, antimicrobial susceptibilities and molecular epidemiology of community-associated (CA) and healthcare-associated (HA) methicillin-resistant Staphylococcus aureus (MRSA) in Canada. Between 2007 and 2011, 1266 MRSA were collected from inpatients and outpatients attending t...
The purpose of this study was to describe the association between age groups and antimicrobial resistance in the most commonly identified pathogens in Canadian hospitals. Between 2007 and 2011, 27,123 clinically significant isolates, comprising 3580 isolates from children ≤ 18 years old, 12,119 isol...
OBJECTIVE. To quantify the association between admission to an intensive care unit (ICU) room most recently occupied by a patient positive for extended-spectrum β-lactamase (EBSL)-producing gram-negative bacteria and acquisition of infection or colonization with that pathogen. DESIGN. Retrospective...
From September 2010 to December 2011, 26 KPC-3-producing Enterobacter cloacae isolates were identified from 16 patients at a single hospital. Analyses revealed the blaKPC gene to be localized on multiple plasmids in a diverse nonclonal E. cloacae genetic background. These findings highlight the pote...
Little information is available on the differences in frequency of pyrogenic exotoxin genes between strains of group A streptococci that cause scarlet fever and those that cause pharyngotonsillitis in children in Taiwan. This study retrospectively monitored the presence of pyrogenic exotoxin genes,...
Among 82 clinical isolates of the Acinetobacter calcoaceticus-baumannii complex recovered in 13 hospitals of Sichuan, China, in 2011, 13 were Acinetobacter pittii and 2 were Acinetobacter nosocomialis. Multilocus sequence typing revealed a novel sequence type (ST) of A. nosocomialis and 7 novel STs...
No literature is available on the prevalence and clinical aspects of beta-haemolytic group G Streptococcus anginosus group in central Taiwan. In this study, we used 16S rRNA gene sequencing and 16S-23S rDNA intergenic spacer sequencing (where necessary) as the gold standard for molecular identificat...
To determine the molecular epidemiology and presence of virulence genes in community-acquired (CA) and hospital-acquired (HA) methicillin-resistant Staphylococcus aureus (MRSA) isolates and their relationship to clinical outcomes. An observational and prospective study of infections caused by MRSA w...
Methicillin is the drug of choice to treat infections caused by resistant strains of Staphylococcus aureus. However, methicillin-resistant S. aureus (MRSA) is now becoming endemic in many hospitals worldwide and is the cause of nosocomial outbreaks. To assess clonality and dissemination of MRSA stra...
Genotyping of Candida albicans strains causing candidemia can uncover the presence of endemic genotypes in the hospital. Using a highly reproducible and discriminatory microsatellite marker panel, we studied the genetic diversity of 217 C. albicans isolates from the blood cultures of 202 patients wi...
A population-based study combining (i) antimicrobial, (ii) genetic, and (iii) virulence analyses with molecular evolutionary analyses revealed segregative characteristics distinguishing human clinical and bovine Escherichia coli O157 strains from western Canada. Human (n = 50) and bovine (n = 50) st...
Sepsis is now the leading direct cause of maternal death in the United Kingdom, and Streptococcus pyogenes is the leading pathogen. We combined conventional and genomic analyses to define the duration and scale of a lethal outbreak. Two postpartum deaths caused by S. pyogenes occurred within 24 h; o...
Overseas travel, as a risk factor for the acquisition of infections due to antimicrobial-resistant organisms, has recently been linked to carbapenemase-producing Gram-negative bacteria. Multiresistant Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii strains were isolated from a w...
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of infection in the community (CA-MRSA), but in spite of its relevance, no data exist concerning its epidemiology in Portugal. In this study, we aimed to evaluate the prevalence, population structure, and origin of MRSA in the Por...
A panel of 29 multidrug-resistant (MDR) Pseudomonas aeruginosa isolates recovered from seven hospitals as part of a country-wide surveillance of antimicrobial resistance in Bulgarian hospitals was studied. Molecular typing through multiple-locus variable number tandem-repeat analysis (MLVA6) yielded...
From October to December 2007, an outbreak of Burkholderia cenocepacia occurred in a secondary care hospital. The 19 B cenocepacia isolated from the patients, the chlorhexidine solutions of each different ward, and the purified water that diluted these solutions exhibited an identical pulsed-field g...
The increasing incidence of Clostridium difficile infection (CDI) in Bulgaria has indicated the need to implement better surveillance approaches. The aim of the present work was to improve the current surveillance of CDI in Bulgaria by introducing innovative methods for identification and typing. On...
The recent advances in sequencing technologies have given all microbiology laboratories access to whole genome sequencing. Providing that tools for the automated analysis of sequence data and databases for associated meta-data are developed, whole genome sequencing will become a routine tool for lar...
Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment....
Melissococcus plutonius is the bacterial pathogen that causes European Foulbrood of honeybees, a globally important honeybee brood disease. We have used next-generation sequencing to identify highly polymorphic regions in an otherwise genetically homogenous organism, and used these loci to create a...
College students living in residential halls are at increased risk of meningococcal disease. Unlike that for serogroups prevented by quadrivalent meningococcal vaccines, public health response to outbreaks of serogroup B meningococcal disease is limited by lack of a US licensed vaccine. In March 201...
We investigated the molecular characteristics of multidrug-resistant, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae isolated in community settings and in hospitals in Antananarivo, Madagascar. Forty-nine E. coli, K. pneumoniae, K. oxytoca and E. cloacae ESBL-producing isolates we...
During an 8-month period, 24 Corynebacterium striatum isolates recovered from lower respiratory tract specimens of 10 hospitalized patients were characterized. The organisms were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and by 16S rRNA...
A selection of plasmid-mediated AmpC-producing Escherichia coli isolates carrying blaCMY-2 from Swedish broilers were characterized to establish their relatedness to and a possible overlap with human clinical E. coli isolates. The results showed diversity among the E. coli isolated from broilers, in...
An outbreak of Legionnaires' disease with 113 confirmed cases was reported in the town of Mataró, Spain, in August 2002. In this study, we compared three different typing methods and characterized the clinical isolates by comparing them with other clinical isolates with the same ST from our own data...
Populations of the food-borne pathogen Listeria monocytogenes are genetically structured into a small number of major clonal groups, some of which have been implicated in multiple outbreaks. The goal of this study was to develop and evaluate an optimized multilocus variable number of tandem repeat (...
Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain. To explore the potential of metagenomics, which is the direct seq...
No abstract available
Shiga toxin-producing Escherichia coli (STEC) are an important cause of diarrhea and the major cause of postdiarrheal hemolytic uremic syndrome. Non-O157 STEC infections are being recognized with greater frequency because of changing laboratory practices. Foodborne Diseases Active Surveillance Netwo...
In 2003, nosocomial infections caused by vancomycin-resistant enterococci (VRE) occurred rarely in Taiwan. Between 2003 and 2010, however, the average prevalence of vancomycin resistance among enterococci spp. increased from 2% to 16% in community hospitals and from 3% to 21% in medical centers of T...
Numerous reports have documented isolated transmission events or clonal outbreaks of multidrug-resistant Mycobacterium tuberculosis strains, but knowledge of their epidemic spread remains limited. In this study, we evaluated drug resistance, strain diversity, and clustering rates in patients diagnos...
Capillary-based PCR ribotyping was used to quantify the presence/absence and relative abundance of 98 Clostridium difficile ribotypes from clinical cases of disease at health care institutions in six states of the United States. Regionally important ribotypes were identified, and institutions in clo...
We report the characteristics of 115 extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli clinical isolates, from 115 unique Danish patients, over a 1-year study interval (1 October 2008 to 30 September 2009). Forty-four (38%) of the ESBL isolates represented sequence type 131 (ST13)1,...
Dermatophytosis caused by Microsporum canis is a heterogeneous disease with variable clinical manifestations. M. canis is a zoophilic dermatophyte and the most frequent fungi isolated from dogs, cats and children in Brazil. The aim of this study was to investigate the genetic variability of M. canis...
An outbreak of foot-and-mouth disease caused by serotype O virus occurred in cattle and pigs in South Korea during November 2010-April 2011. The highest rates of case and virus detection were observed 44 days after the first case was detected. Detection rates declined rapidly after culling and compl...
To record surveillance, antibiotic resistance of uropathogens of hospitalized patients over a period of 18 months. Urine samples from wards and cabins were used for isolating urinary tract infection (UTI)-causing bacteria that were cultured on suitable selective media and identified by biochemical t...
Strains of the enteric pathogen Vibrio parahaemolyticus harboring the thermostable hemolysin (TDH) encoding gene tdh is known to cause epidemic and pandemic diarrhea. In industrialized countries, this pathogen causes sporadic or outbreaks of diarrheal illness associated with consumption of raw or im...
No abstract available
No abstract available
Mycobacterium tuberculosis variant Beijing B0/W148 is regarded as a successful clone of M. tuberculosis that is widespread in the former Soviet Union and respective immigrant communities. Understanding the pathobiology and phylogeography of this notorious strain may help to clarify its origin and ev...
A methicillin-resistant Staphylococcus aureus (MRSA) outbreak occurred in an advanced emergency medical service center between 2010 and 2011. Our objective was to evaluate the status of the MRSA outbreak, as monitored by molecular analysis. Twenty-eight MRSA strains were isolated from blood samples...
Mupirocin is used for the decolonization of methicillin-resistant Staphylococcus aureus (MRSA). High-level mupirocin resistance (Hi-Mup(R)) is of concern, having been associated with therapeutic failure. Our main objective was to assess the emergence and mode/s of spread of Hi-Mup(R) in the MRSA pop...
Methicillin-resistant Staphylococcus aureus (MRSA) has widely spread to all parts of the world. For surveillance and effective infection control molecular typing is required. We have evaluated the utility of virulence gene determination as a complementary tool for epidemiological typing of MRSA in r...
Clostridium difficile causes outbreaks of infectious diarrhoea, most commonly occurring in healthcare institutions. Recently, concern has been raised with reports of C. difficile disease in those traditionally thought to be at low risk i.e. community acquired rather than healthcare acquired. This ha...
Mupirocin is the cornerstone of decolonization regimens, a successful strategy to prevent healthcare-associated staphylococcal infections. Several recent studies have reported alarming results: (i) an extending reservoir of mupA, the ancestral mobile resistance gene, among coagulase-negative staphyl...
Invasive listeriosis is a rare, life-threatening foodborne disease. Lombardy, an Italian region accounting for 16% of the total population, reported 55% of all listeriosis cases in the years 2006-2010. The aim of our study was to provide a snapshot of listeriosis epidemiology in this region after th...
During October 2010, Egypt reported an outbreak of acute hemorrhagic conjunctivitis (AHC). A total of 1831 cases were reported from three governorates; 1703 cases in El Daqahliya, 92 cases in Port Said, and 36 in Damietta. The purpose of this study was to identify and characterize the causative agen...
The identification of patients colonized or infected with carbapenemase-producing Enterobacteriaceae (CPE), in order to control and prevent the global spread of multidrug-resistant (MDR) pathogens. From June 1 to June 15, 2012, eight Citrobacter freundii strains with reduced susceptibility to carbap...
Forty two Candida albicans isolates were collected from clinical samples in Israel. Twenty strains were isolated from blood cultures and 22 from superficial candidiasis. Isolates were typed by MLST analysis. Thirty-seven Diploid Sequence Types (DSTs) were identified. Seventeen isolates (40.5%) displ...
An unusually high incidence of aseptic meningitis caused by enteroviruses was noted in Alberta, Canada between March and October 2010. Sequence based typing was performed on the enterovirus positive samples to gain a better understanding of the molecular characteristics of the Coxsackie A9 (CVA-9) s...
Vancomycin-resistant enterococci (VRE) can be associated with serious bacteraemia. The focus of this study was to characterize the molecular epidemiology of VRE from bacteraemia cases that were isolated from 1999 to 2009 as part of Canadian Nosocomial Infection Surveillance Program (CNISP) surveilla...
Epidemiological surveillance of Clostridium difficile infection has gained importance in recent years as a result of the rapid spread of epidemic strains, including hypervirulent strains and strains with reduced susceptibility to antimicrobials. The molecular epidemiology and antimicrobial susceptib...
We developed a new phage-typing method and evaluated its application in combination with XbaI macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) as a useful tool for the long-term epidemiology of Salmonella enterica serovar Infantis. In this study, we investigated 1008 S. Infantis...
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) continue to be a problem for clinicians worldwide. The objective of this study was to determine the changes in antibiograms of MRSA and their genotypic characteristics. The antibiograms of 162 MRSA isolates (52 from 2003 and 110...
The co-existence of carbapenemase, 16S rRNA methylase and mutated quinolone resistance-determining regions (QRDRs) can cause serious difficulty in treating infections with multidrug-resistant Acinetobacter baumannii. In this study, we aimed to determine the mechanisms of imipenem, amikacin and cipro...
Maternal-fetal Escherichia coli infections, such as neonatal bacteremia and meningitis, are important causes of morbidity and mortality. From 2006 to 2010, we studied newborns and their mothers who were colonized with E. coli in a French hospital in order to document (i) the epidemiology and genetic...
The emergence and spread of Vibrio cholerae O1 El Tor variant strains causing severe diarrhea has been witnessed worldwide in recent years. In the state of Odisha, India, the spread of the V. cholerae O1 El Tor variant strains was studied during outbreaks in 2008 and 2009. Analysis of 194 V. cholera...
Infection from fluoroquinolone-resistant Enterobacteriaceae is an increasing health problem worldwide. In the present study, we developed a pyrosequencing-based high-throughput method for analyzing the nucleotide sequence of the quinolone resistance-determining regions (QRDRs) of gyrA and parC. By u...
The aim of this study was to determine the characteristics and shifts in serotype distribution of pneumococcal isolates causing ocular infections in a region of northern Spain in two periods: 1999-2010 for episodes of conjunctivitis (n = 612) and 1980-2010 for uncommon and more severe non-conjunctiv...
Enterococcus faecalis is a member of the mammalian gastrointestinal microbiota but has been considered a leading cause of hospital-acquired infections. In the oral cavity, it is commonly detected from root canals of teeth with failed endodontic treatment. However, little is known about the virulence...
Methicillin-resistant Staphylococcus aureus sequence type 398 (MRSA ST398) has emerged in livestock worldwide. In particular, areas in Europe with high densities of livestock farming are affected. Consequently, the incidence of human colonization and infection with ST398 is rapidly increasing. Disti...
Successful clones of Neisseria gonorrhoeae multiantigen sequence typing sequence type (ST) 1407 and ST1407-related genotypes have been reported to cause cefixime and ceftriaxone treatment failure in many countries. We characterized the 47 isolates of a strain cluster of ST4378, a genotype that diffe...
Theiler's disease is an acute hepatitis in horses that is associated with the administration of equine blood products; its etiologic agent has remained unknown for nearly a century. Here, we used massively parallel sequencing to explore samples from a recent Theiler's disease outbreak. Metatranscrip...
In November through December 2007, the drinking water distribution system in the town of Nokia, Finland, was contaminated with treated sewage effluent that resulted in a large gastroenteritis outbreak in the community. The aim of the present study was to investigate if the contaminated water in this...
In many parts of the world, MRSA are responsible for a high proportion of S. aureus infections in patients in contact with healthcare. Molecular studies have shown this is due to one or more MRSA clones that have become endemic in each hospital or healthcare facility, resulting in hospital- or healt...
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Domestic farm animals (n=145) were sampled for the presence of ectoparasites in northwestern Peru during March, 2008. Ninety domestic animals (62%) were positive for the presence of an ectoparasite(s) and produced a total collection of the following: 728 ticks [Amblyomma maculatum, Anocentor nitens,...
Staphylococcal cassette chromosome (SCC) elements are complex mobile genetic elements that often carry antimicrobial resistance and in some cases virulence-associated genes. In addition to SCCmec, which harbours the methicillin resistance gene mec, many different SCC elements have been identified in...
Staphylococcus epidermidis is a major cause of catheter-related bloodstream infections (CRBSIs). Recent studies suggested the existence of well-adapted, highly resistant, hospital-associated S. epidermidis clones. The molecular epidemiology of S. epidermidis in Belgian hospitals and the Belgian comm...
To establish the possible sources and routes of transmission of a multidrug-resistant Acinetobacter baumannii outbreak involving 22 patients. Descriptive, retrospective study. An environmental investigation was undertaken, monitoring surfaces, air and water. Reconstruction of the spread of the infec...
Peste des petits ruminanats (PPR) is an economically important viral disease affecting goats and sheep. Four genetically distinct lineages of peste des petits ruminants virus (PPRV) have been identified. In Gabon, the virus has not so far been detected. Epidemiological investigations of Aboumi PPR o...
Although Ethiopia ranks seventh among the world's 22 high-burden tuberculosis (TB) countries, little is known about strain diversity and transmission. In this study, we present the first in-depth analysis of the population structure and transmission dynamics of Mycobacterium tuberculosis strains fro...
Extrapulmonary tuberculosis (EPTB) constitutes about 10% to 20% of all cases of tuberculosis in immunocompetent patients and more than 50% of the cases in HIV-positive individuals worldwide. Little information is available on the clonal diversity of Mycobacterium species in Ethiopia from EPTB. This...
Methicillin-resistant Staphylococcus aureus (MRSA) is known to be present in small animal veterinary clinical environments. However, a better understanding of the ecology and dynamics of MRSA in these environments is necessary for the development of effective infectious disease prevention and contro...
VIM-producing Klebsiella pneumoniae (n = 21) isolated from ten Greek hospitals during 2003-2007 were characterized with multilocus sequence typing (MLST), semi-automated repetitive sequence-based PCR (rep-PCR) (Diversilab), plasmid replicon typing, serotyping and screening for multiple resistance de...
In this study, we report the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) among veterinary students and personnel in Malaysia. Nasal and oral swabs were collected from 103 veterinary medicine students and 28 personnel from a veterinary hospital. Antibiotic sensitivity...
A large outbreak of cholera reported during April-July 2009 in the Kendrapada district of Odisha, India was investigated. Forty-one rectal swabs and 41 water samples, collected from diarrhoeal patients and from different villages were bacteriologically analysed for the isolation of bacterial enterio...
We conducted a molecular study of MRSA isolated in Swiss hospitals, including the first five consecutive isolates recovered from blood cultures and the first ten isolates recovered from other sites in newly identified carriers. Among 73 MRSA isolates, 44 different double locus sequence typing (DLST)...
The carbapenem resistance rate of Acinetobacter baumannii in our hospital has increased steadily since 2004. The molecular epidemiology of carbapenem resistant A. baumannii (CRAB) clinical isolates was characterized by multilocus sequence typing (MLST) and rep-PCR in parallel, with pan-drug suscepti...
Exserohilum rostratum was the major cause of an outbreak of fungal infections linked to injections of contaminated methylprednisolone acetate. Because almost 14,000 persons were exposed to product that was possibly contaminated with multiple fungal pathogens, there was unprecedented need for a rapid...
Colibacillosis in different forms is responsible for significant economic losses in the poultry industry worldwide. Escherichia coli strains frequently implicated in poultry disease are designated as avian pathogenic E. coli (APEC). Natural infections and disease due to APEC have been described in w...
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Parthenium hysterophorus L. is an obnoxious weed of the family asteraceae recognized for its detrimental effects and significant economic losses to agriculture. In this study 42 endophytic streptomycetes strains were isolated from its roots and leaves. The isolates were identified by morphological,...
Aedes aegypti (L.) is the principal mosquito vector of dengue fever, the second-most deadly vector-borne disease in the world. In Ae. aegypti and other arthropod disease vectors, genetic markers can be used to inform us about processes relevant to disease spread, such as movement of the vectors acro...
Vancomycin-resistant enterococci (VRE) are primarily opportunistic pathogens with incalculable clinical significance. In addition, the effectiveness of isolation in VRE is often not easily assessed. The goals of this study were to estimate the transmissibility of VRE of patients with VRE bacteraemia...
In this study, we characterized 272 Shiga toxin-producing Escherichia coli (STEC) isolates from humans, food, and cattle in Belgium [O157 (n = 205), O26 (n = 31), O103 (n = 15), O111 (n = 10), O145 (n = 11)] for their virulence profile, whole genome variations and relationships on different genetic...
We characterized Streptococcus pneumoniae serotype 6D from among previously identified S. pneumoniae serotype 6B strains from Jewish and Bedouin children in southern Israel during a decade before vaccination. S. pneumoniae serotype 6D isolates constituted 6.7% of the presumed S. pneumoniae serotype...
The aim of this study was to evaluate the emergence of blaNDM-1 among clinical isolates of Acinetobacter baumannii isolated from a north Indian tertiary care hospital and to assess the gene cassettes and resistance determinants located within them. In total, 74 A. baumannii were screened for MBL pro...
Banana bunchy top virus (BBTV) is the most destructive pathogenic virus of banana plants worldwide. The virus is transmitted in a circulative non-propagative manner by the banana aphid, Pentalonia nigronervosa Coquerel. In this work, we examined the localization, accumulation, and transmission effic...
This study aimed to investigate the genetic association between fluoroquinolone (FQ) and/or cephalosporin (CEP) resistance in Escherichia coli isolates from dogs, and the risk to human health. We characterized E. coli clinical isolates, derived from faecal samples of dogs attending veterinary hospit...
Imported dengue cases originating from the Madeiran outbreak are increasingly reported. In 2012 five Finnish travellers returning from Madeira were diagnosed with dengue fever. Viral sequence data was obtained from two patients. The partial C-preM sequences (399 and 396 bp respectively) were found s...
The aim of this study was to retrospectively assess the value of whole genome sequencing (WGS) compared to conventional typing methods in the investigation and control of an outbreak of Shigella sonnei in the Orthodox Jewish (OJ) community in the UK. The genome sequence analysis showed that the stra...
This paper describes a nosocomial outbreak of tuberculosis in a hospital ward where the number of cases with active tuberculosis among contacts was unexpectedly high. The outbreak was not revealed until the Mycobacterium tuberculosis genotyping results from the first two secondary tuberculosis cases...
Resistance to extended-spectrum β-lactams is increasing worldwide among Escherichia coli and has been linked to a small number of emergent clones (e.g. ST38, ST131 and ST405) recovered from extraintestinal infections in community and hospital settings. There are, however, limited data about the rela...
Typing of methicillin-resistant Staphylococcus aureus (MRSA) remains necessary in order to assess whether transmission of MRSA occurred and to what extent infection prevention measures need to be taken. Raman spectroscopy (SpectraCellRA [SCRA]; RiverD International, Rotterdam, The Netherlands) is a...
The evolution of antibiotic resistance can now be rapidly tracked with high-throughput technologies for bacterial genotyping and phenotyping. Combined with new approaches to evolve resistance in the laboratory and to characterize clinically evolved resistant pathogens, these methods are revealing th...
In November 2008, a study was performed with support from the European Centre for Disease Prevention and Control (ECDC) to obtain an overview of Clostridium difficile infections (CDIs) in European hospitals. A collection of 398 C. difficile isolates obtained from this hospital-based survey was utili...
In humans, Streptococcus agalactiae or group B streptococcus (GBS) is a frequent coloniser of the rectovaginal tract, a major cause of neonatal infectious disease and an emerging cause of disease in non-pregnant adults. In addition, Streptococcus agalactiae causes invasive disease in fish, compromis...
We report a nosocomial outbreak of urinary tract infection by extremely drug resistant Pseudomonas aeruginosa, susceptible only to colistin. Infection in three patients followed urodynamic studies. Two of the three patients were children, one of whom also developed urosepsis. The investigation led t...
Streptococcus pneumoniae is a major cause of mortality and morbidity in young children and the elderly. In the present study we evaluated antimicrobial susceptibilities, serotypes, and sequence types of pneumococcal isolates recovered in New Delhi, India. A total of 126 clinical isolates of Streptoc...
USA300 methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of skin and soft-tissue infection (SSTI) in military personnel. USA300 MRSA has emerged as an important cause of healthcare-associated bloodstream infection (BSI) in metropolitan centers. To determine the prevalence, risk fa...
Outbreaks of invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae serotype 12F were observed in two neighboring regions of rural Alaska in 2003 to 2006 and 2006 to 2008. IPD surveillance data from 1986 to 2009 and carriage survey data from 1998 to 2004 and 2008 to 2009 were reviewe...
Of the 200+ serogroups of Vibrio cholerae, only O1 or O139 strains are reported to cause cholera, and mostly in endemic regions. Cholera outbreaks elsewhere are considered to be via importation of pathogenic strains. Using established animal models, we show that diverse V. cholerae strains indigenou...
To determine prevalence, predictors, and outcomes of infection due to Escherichia coli sequence type ST131. Retrospective cohort. All healthcare settings in Olmsted County, Minnesota (eg, community hospital, tertiary care center, long-term care facilities, and ambulatory clinics). Ambulatory and hos...
The epidemiology of Clostridium difficile infections (CDIs) has dramatically changed over the last decade in both North America and Europe, and it has become more frequent, more severe, more refractory to standard therapy, and more likely to relapse. These changes have been associated with the emerg...
The risk of serious infections caused by Staphylococcus aureus is well-known. However, most studies regarding the distribution of (clinically relevant) S. aureus among humans and animals took place in the western hemisphere and only limited data are available from (Central) Africa. In this context,...
The study aim was to describe the emergence of carbapenem resistance and clonal complexes (CC), defined by multilocus sequence typing (MLST), in Acinetobacter baumannii in a surveillance system for meningitis. Starting in 1996 in an urban setting of Brazil, surveillance detected meningitis by Acinet...
Vampire bats are notorious for being the sole mammals that strictly feed on fresh blood for their survival. While their saliva has been historically associated with anticoagulants, only one antihemostatic (plasminogen activator) has been molecularly and functionally characterized. Here, RNAs from bo...
This study describes the comparison of three methods for genotyping of Mycobacterium tuberculosis, namely MIRU-VNTR (mycobacterial interspersed repetitive units-variable number of tandem repeats), spoligotyping and, for the first time, MLST (Multilocus Sequence Typing). In order to evaluate the disc...
Sequence analysis of dnaE, hlyA, and asd housekeeping genes were used to determine the genetic relatedness of our collection of Vibrio cholerae isolated from patients and surface waters over a 5-year period in Iran. The results showed 41, 17, and 9 variable sites throughout the sequenced fragments o...
In order to determine the occurrence of AbaR-type genomic island in multidrug resistant Acinetobacter baumannii (MDRAb) strains circulating in Argentina, Uruguay, and Chile, we studied 51 MDRAb isolates recovered from several hospitals over 30 years. AbaR-type genomic resistance islands were found i...
There have been increasing reports of bla(OXA-23)-carrying strains of carbapenem-resistant Acinetobacter baumannii (CRAB), which has become a significant public health concern in Taiwan. To determine the origin of these CRAB strains, the prevalence of CRAB and bla(OXA-23)-carrying CRAB in a regional...
This study used multilocus sequence typing (MLST) of total DNA extracted from faecal specimens to genotype Helicobacter pylori to analyse intra-familial transmission. Faecal DNA was extracted and amplified by nested PCR. The products were analysed by direct sequencing and the allele type was determi...
Multidrug-resistant organisms (MDROs) pose significant infection-control challenges in settings with high prevalence and limited isolation facilities. This observational study in an 800-bed hospital determined the prevalence, bacterial density and genetic relatedness of MDROs isolated from ward surf...
An outbreak of dengue fever in Madeira island was reported in 2012. Clinical and laboratory findings of the first two laboratory-confirmed autochthonous cases are reported. Both cases had fever (≥38 °C) and petechial rash. Symptoms also included myalgia, asthenia, nausea, vomiting, anorexia, diffuse...
Urinary tract infections (UTI), which are mostly caused by Escherichia coli, are an important public health problem worldwide. Although men experience diverse UTI syndromes, there have been relatively few molecular-epidemiological studies of UTI pathogenesis in men. We studied the distribution of 22...
Previous studies showed that DENV-1 transmitted from monkeys to humans approximately 125 years ago. However, there is no comprehensive analysis about phylogeography and population dynamics of Asian DENV-1. Here, we adopt a Bayesian phylogeographic approach to investigate the evolutionary history and...
Among 594 Streptococcus pneumoniae serotype 19A invasive pneumococcal disease (IPD) isolates collected from 1993 to 2011, we identified 85 sequence types by multilocus sequence typing. CC320 was associated with multidrug resistance and reduced susceptibility to penicillin and ceftriaxone and still p...
Footrot is a contagious disease of small ruminants which is caused by the bacterium Dichelobacter nodosus. In its virulent form there are severe economic losses and a very significant animal welfare issue. Sheep and goats can be vaccinated for treatment and prevention of the disease. There are 10 di...
No abstract available
Sequence data are well established in the reconstruction of the phylogenetic and demographic scenarios that have given rise to outbreaks of viral pathogens. The application of similar methods to bacteria has been hindered in the main by the lack of high-resolution nucleotide sequence data from quali...
Epidemiological models have highlighted the importance of population structure in the transmission dynamics of infectious diseases. Using HIV-1 as an example of a model evolutionary system, we consider how population structure affects the shape and the structure of a viral phylogeny in the absence o...
Bayesian phylogeographic methods simultaneously integrate geographical and evolutionary modelling, and have demonstrated value in assessing spatial spread patterns of measurably evolving organisms. We improve on existing phylogeographic methods by combining information from multiple phylogeographic...
RNA viruses account for numerous emerging and perennial infectious diseases, and are characterized by rapid rates of molecular evolution. The ecological dynamics of most emerging RNA viruses are still poorly understood and difficult to ascertain. The availability of genome sequence data for many RNA...
To compare demographic and clinical characteristics, and methicillin-resistant Staphylococcus aureus (MRSA) strain characteristics, in patients with early-onset (EO) and late-onset (LO) MRSA nosocomial pneumonia. This was a retrospective analysis of data from a multicenter observational study of nos...
We investigated whether spa typing is useful for indicating the setting of methicillin-resistant Staphylococcus aureus (MRSA) acquisition (community or health care acquired), the clinical relevance (colonization or infection), the type of infection (invasive or noninvasive), and the clinical outcome...
To conduct an etiological molecular epidemiological survey and laboratory test on a foodborne disease epidemic outbreak to make clear of the cause and implement effective prevention and control on it. On May 12th 2012, 135 kindergarten children were sent to Xuzhou City People's Hospital and Children...
Corynebacterium striatum is a potentially pathogenic microorganism with the ability to produce outbreaks of nosocomial infections. Here, we document a nosocomial outbreak caused by multidrug-resistant (MDR) C. striatum in Rio de Janeiro, Brazil. C. striatum identification was confirmed by 16S rRNA a...
Crimean-Congo hemorrhagic fever virus was detected in ticks removed from migratory birds in Morocco. This finding demonstrates the circulation of this virus in northwestern Africa and supports the hypothesis that the virus can be introduced into Europe by infected ticks transported from Africa by mi...
To elucidate whether Rift Valley fever virus (RVFV) diversity in Sudan resulted from multiple introductions or from acquired changes over time from 1 introduction event, we generated complete genome sequences from RVFV strains detected during the 2007 and 2010 outbreaks. Phylogenetic analyses of sma...
Identification of human monkeypox cases during 2005 in southern Sudan (now South Sudan) raised several questions about the natural history of monkeypox virus (MPXV) in Africa. The outbreak area, characterized by seasonally dry riverine grasslands, is not identified as environmentally suitable for MP...
After 25 years of no cases of plague, this disease recurred near Tobruk, Libya, in 2009. An epidemiologic investigation identified 5 confirmed cases. We determined ribotypes, Not1 restriction profiles, and IS100 and IS1541 hybridization patterns of strains isolated during this outbreak. We also anal...
We detected Bartonella quintana in 48.6% of captive rhesus macaques from an animal facility in Beijing, China. Prevalence of infection increased over the period of observation. Our findings suggest that macaques may serve as reservoir hosts for B. quintana and that Pedicinus obtusus lice might act a...
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Vibrio parahaemolyticus is a seafood-borne pathogenic bacterium that is a major cause of gastroenteritis worldwide. We investigated the genetic and evolutionary relationships of 101 V. parahaemolyticus isolates originating from clinical, human carrier, and various environmental and seafood productio...
There is concern that ships' ballasting operations may disseminate Vibrio cholerae to ports throughout the world. Given evidence that the bacterium is indeed transported by ships, we isolated pandemic serotypes O1 and O139 from ballast tanks and characterized them with respect to antibiotic resistan...
Invasive fusariosis (IF) is a rare but often fatal fungal infection in immunosuppressed patients. In 2007, cases of IF above the expected epidemiologic baseline were detected in the hematology ward of a hospital in Rio de Janeiro, Brazil. Possible sources of infection were investigated by performing...
In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a...
There is increasing interest in the presence of Staphylococcus aureus, specifically methicillin-resistant S. aureus (MRSA), on retail meat products. In this study, staphylococci were isolated from retail pork and retail beef in Georgia, and MRSA from the products was compared to human MRSA from the...
Strain-typing technology in support of outbreak identification and resolution has evolved from phenotypic analysis, such as serology and biotypes, to much-more-robust molecular genetic approaches, such as pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. Whole-genome mapping (WGM)...
In low- as well as in high-prevalence settings, healthcare workers (HCWs) may be a substantial, under-recognized, reservoir of meticillin-resistant Staphylococcus aureus (MRSA) and an important potential source of transmission to patients. To report an outbreak of MRSA in a cardiac surgery unit in E...
Methicillin-resistant Staphylococcus aureus (MRSA) represent a serious threat for public health worldwide. Of particular concern is the emergence of community-acquired MRSA, which is often difficult to distinguish from nosocomial MRSA due to a lack of suitable typing methods for early detection. For...
Most studies on Staphylococcus aureus have focused on the molecular epidemiology of methicillin-resistant S. aureus (MRSA) infections. In contrast, little information is available regarding the molecular epidemiology of currently circulating methicillin-susceptible S. aureus (MSSA) isolates in hospi...
With the advent of deep sequencing, genomic surveillance has become a popular method for detection of infectious disease, supplementing information gathered by classic clinical or serological techniques to identify host-determinant markers and trace the origin of transmission. However, two main fact...
Helicobacter pylori is a major gastric bacterial pathogen, presumed to have established itself in the human stomach approximately 100,000 years ago. Helicobacter pylori co-evolved with its host, and human migrations shaped the expansion and the diversity of strains around the world. Here, we investi...
Enteropathogenic Escherichia coli (EPEC) are an important cause of diarrhoea worldwide, particularly in children. Sixty-one EPEC strains isolated from stool specimens of symptomatic persons from 2008 to 2011 were characterised for the prevalence of diarrhoea-associated putative virulence genes. Phyl...
Multi-locus sequence typing (MLST) is a high-resolution genetic typing approach to identify species and strains of pathogens impacting human health, agriculture (animals and plants), and biosafety. In this review, we outline the general concepts behind MLST, molecular approaches for obtaining MLST d...
In the United States, the blaCMY-2 gene contained within incompatibility type A/C (IncA/C) plasmids is frequently identified in extended-spectrum-cephalosporin-resistant (ESC(r)) Escherichia coli strains from both human and cattle sources. Concerns have been raised that therapeutic use of ceftiofur...
Molecular typing is an essential tool to monitor Clostridium difficile infections and outbreaks within healthcare facilities. Molecular typing also plays a key role in defining the regional and global changes in circulating C. difficile types. The patterns of C. difficile types circulating within Eu...
Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, m...
No abstract available
Clostridium perfringens type E is considered a rare toxinotype and an infrequent cause of enterotoxemia of lambs, calves, and rabbits. Until now, only cases of young animal of C. perfringens type E bovine enterotoxemia, characterized by hemorrhagic enteritis and sudden death, have been reported. The...
A panel of seven variable-number tandem-repeat (VNTR) markers was selected for Acinetobacter baumannii typing analysis (MLVA-7). Compared with pulsed-field gel electrophoresis (PFGE), MLVA-7 provided greater discrimination. We modified the criteria for MLVA complex assignments proposed previously, a...
Streptococcus canis is an animal pathogen that occasionally causes human infections. Isolates recovered from infections of animals (n = 78, recovered from 2000 to 2010 in three European countries, mainly from house pets) and humans (n = 7, recovered from 2006 to 2010 in Portugal) were identified by...
Understanding viral transmission is an important factor for the effective prevention one of the most devastating swine diseases, porcine reproductive and respiratory syndrome. Focusing on molecular epidemiology of type 1 PRRSV, this study analysed a large ORF5 dataset collected worldwide from 1991 t...
Aspergillus flavus is the second most important Aspergillus species associated with aspergillosis and the incidence of infections caused by it are increasing in the immunocompromised population. This species is of major epidemiological importance in regions with a dry and hot climate. Despite the gr...
The main objective of this study was to assess the frequency and possible sources of colonization and infection by Acinetobacter in the intensive care unit (ICU) of a university hospital in Rio de Janeiro, Brazil, and characterize the isolates for relatedness to internationally and locally dissemina...
Staphylococcus aureus remains a leading cause of hospital-acquired and community-associated infection worldwide. The burden of disease is exacerbated by the emergence of virulent strains with reduced susceptibility to commonly used antibiotics and their dissemination in healthcare settings and in th...
Mortality related to methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection (BSI) remains high, despite changes in the epidemiology. To analyze the current predictive factors for mortality we conducted a prospective study in a large cohort of patients with MRSA-BSI from 21 Spanish...
Brachyspira pilosicoli is an anaerobic intestinal spirochaete that colonizes the large intestine of various host species, in which it may induce diarrhoea, poor growth rates and a localized colitis known as intestinal (or colonic) spirochaetosis. The spirochaete is considered to be potentially zoono...
Meticillin-resistant Staphylococcus aureus (MRSA) is a significant cause of mortality and morbidity in healthcare and community settings; however, there is a paucity of large-scale, longitudinal studies monitoring the occurrence of MRSA in the care home setting. To determine the molecular epidemiolo...
Molecular-based surveillance of campylobacteriosis in New Zealand contributed to the implementation of interventions that led to a 50% reduction in notified and hospitalised cases of the country's most important zoonosis. From a pre-intervention high of 384 per 100,000 population in 2006, incidence...
Mycobacterial interspersed repetitive-unit-variable-number tandem repeat typing alone was used to investigate the genetic lineages among 361 Mycobacterium tuberculosis strains circulating in Ireland over a two-year period, 2010 and 2011. The majority of isolates, 63% (229/361), belonged to lineage 4...
Treatment of gonorrhoea is threatened by antimicrobial resistance, and decreased susceptibility and resistance to recommended therapies is emerging in Europe. Current associations between resistance and molecular type remain poorly understood. Gonococcal isolates (n=1,066) collected for the 2009 and...
Spoligotyping has shown Mycobacterium tuberculosis strains to be composed of different lineages, and some of them are not just geographically restricted but also affect specific ethnic populations and are associated with outbreaks and drug resistance. We recently described a particular subtype withi...
Cholera, caused by Vibrio cholerae, results in significant morbidity and mortality worldwide, including Thailand. Representative V. cholerae strains associated with endemic cholera (n = 32), including strains (n = 3) from surface water sources, in Khon Kaen, Thailand (2003-2011), were subjected to m...
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After 25 years without any reported cases of rabies in Uruguay, the northern region of the country experienced an epizootic of bovine paralytic rabies in October 2007. The outbreak affected bovines and equines, and the main source of infection was the bat Desmodus rotundus, the only hematophagous sp...
Between January and September 2012, a teacher and four students at a technical college in Marseille, France, developed pulmonary tuberculosis. All Mycobacterium tuberculosis isolates from these cases were identical and belonged to the Beijing strain family, multispacer sequence type 72, a rare genot...
There is debate over the optimal policy for detecting meticillin-resistant Staphylococcus aureus (MRSA) colonization at hospital admission. The emergence of community-associated (CA)-MRSA may compromise targeted screening strategies based on risk factors for healthcare-associated (HA)-MRSA. To deter...
Helicobacter suis is a Gram-negative bacterium colonizing the majority of pigs, in which it causes gastritis and decreased daily weight gain. H. suis is also the most prevalent gastric non-Helicobacter pylori Helicobacter species in humans, capable of causing gastric disorders. To gain insight into...
In October 2010, nearly 10 months after a devastating earthquake, Haiti was stricken by epidemic cholera. Within days after detection, the Ministry of Public Health and Population established a National Cholera Surveillance System (NCSS). The NCSS used a modified World Health Organization case defin...
Multiyear molecular epidemiological surveillance of multidrug-resistant Pseudomonas aeruginosa (MRPA) in a pediatric cystic fibrosis care center identified an endemic MRPA strain (Houston-1). Recent hospitalization was found to be a statistically significant risk factor for acquisition of the endemi...
To determine rates of carriage of fluoroquinolone-resistant Escherichia coli and extraintestinal pathogenic E. coli (ExPEC) among dogs in a specialist referral hospital and to examine the population structure of the isolates. Fluoroquinolone-resistant faecal E. coli isolates (n = 232, from 23 of 123...
As a way to contribute to the assessment of Acinetobacter baumannii clinical population structure, multi-locus sequence typing (MLST) was performed in a collection of 93 isolates from Buenos Aires (1983-2012) and Rosario (2006-2009) hospitals. Sequence types (STs) were achieved by Bartual (B) and In...
To clarify the incidence and prognosis of early-onset (EOD) and late-onset (LOD) GBS disease in Japan. To evaluate the influence of national guidelines issued in 2008 on the epidemiology of GBS disease. Retrospective nationwide questionnaire surveillance on culture-confirmed GBS infections between 2...
Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. Current CPV populations are considered to be spatially structured with relatively little movement of viruses between geographical areas. Here we describe th...
The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that cau...
Certain adenovirus serotypes cause severe infections, especially in children. It is important to monitor temporal changes in serotypes causing clinical disease. The objective of this study was to document circulating respiratory adenovirus serotypes by sequencing adenovirus culture isolates from the...
The spread of MRSA strains at hospitals as well as in the community are of great concern worldwide. We characterized the MRSA clones isolated at Tunisian hospitals and in the community by comparing them to those isolated in other countries. We characterized 69 MRSA strains isolated from two Tunisian...
A female newborn was admitted to our department 15 days after birth for insufficient sucking and jaundice. The patient's blood and urine cultures were both positive for group B streptococcal (GBS) infection. A maternal vaginal sample at 35 weeks' gestation was negative for GBS in culture-based micro...
A total of 31 Vibrio cholerae O1 (4- Inaba and 27- Ogawa serotype) isolates collected during a three-year period (2006-2009) from acute diarrheal cases in Tamil Nadu, India were analyzed for antibiotic resistance profiling, virulence-associated factors, genetic profiling by enterobacterial repetitiv...
Cryptococcus neoformans variety grubii is the major etiological agent of cryptococcal meningitis in both immunocompromised and immunocompetent patients. The current PCR-based molecular methods are not sufficient to discriminate among the different populations of this yeast. Therefore, the aim of the...
The increasing use of chlorhexidine for methicillin-resistant Staphylococcus aureus (MRSA) decolonization raises concerns about reduced susceptibility. We evaluated the carriage of chlorhexidine resistance genes and chlorhexidine susceptibility in MRSA before and after introduction of an institution...
To investigate the duration of faecal carriage of CTX-M-15-producing Klebsiella pneumoniae in infants colonized during a nosocomial neonatal intensive care unit (NICU) outbreak after discharge from hospital, possible risk factors for long-term colonization and transmission to household contacts (HCs...
Fluoroquinolone-resistant Escherichia coli are increasingly prevalent. Their clonal origins--potentially critical for control efforts--remain undefined. Antimicrobial resistance profiles and fine clonal structure were determined for 236 diverse-source historical (1967-2009) E. coli isolates represen...
Dengue fever is re-emerging as a major scourge in south-east Asian countries, affecting about 50-100 million people and causing about 25,000 deaths annually. The Indian population as a whole is at risk of succumbing to this disease. This study genetically characterized viruses causing dengue infecti...
In August 2008 an outbreak of Salmonella Typhimurium DT104 occurred in South West London. Sixteen cases were identified with a particular multilocus variable number tandem repeat analysis (MLVA) pattern. In a matched case-control study 14 primary cases were included. These were defined as individual...
While much is known about the geographic distribution of different clonal types of methicillin-resistant Staphylococcus aureus (MRSA), few studies have assessed the molecular epidemiology of methicillin-susceptible S. aureus (MSSA), despite its continued clinical importance. In each U.S. Census regi...
To compare the population dynamics of HIV-2 and HIV-1, and to characterize ongoing HIV-2 transmission in rural Guinea-Bissau. Phylogenetic and phylodynamic analyses using HIV-2 gag and env, and HIV-1 env sequences, combined with epidemiological data from a community cohort. Samples were obtained fro...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major antimicrobial drug-resistant pathogen causing serious infections. It was first detected in healthcare settings, but in recent years it has also become disseminated in the community. Children and young adults are most susceptible to infect...
Salmonellosis outbreaks related to consumption of raw almonds have encouraged the scientific community to study the inactivation kinetics of pathogens in this dry commodity. However, the low moisture content of the product presents a challenge for thermal control, because the time required to achiev...
An outbreak of Staphylococcus aureus infections occurred in a university with an enrollment of 80 students in the city of Daejon, Republic of Korea. All nine S. aureus isolates from patients (n = 7), staff members (n = 1), and the fried chicken served as the lunch (n = 1) harbored the enterotoxin A...
The recognition of infection clusters via determination of clonal relationships between pathogen isolates represents the major aim of pathogen subtyping during outbreaks. In addition, a continuing and comprehensive subtyping of pathogen isolates is a prerequisite for early recognition of changes wit...
Timely outbreak detection is a major objective of the surveillance of food-borne infections. In this regard molecular subtyping is a very useful tool for several bacterial pathogens, e.g. enterohemorrhagic E. coli (EHEC), Listeria monocytogenes and various serotypes of non-typhoidal Salmonella. The...
We identified a novel serotype 1/2a outbreak strain and 2 novel epidemic clones of Listeria monocytogenes while investigating a foodborne outbreak of listeriosis associated with consumption of cantaloupe during 2011 in the United States. Comparative analyses of strains worldwide are essential to ide...
Although Escherichia albertii is an emerging intestinal pathogen, it has been associated only with sporadic human infections. In this study, we determined that a human gastroenteritis outbreak at a restaurant in Japan had E. albertii as the major causative agent.
Listeria monocytogenes, a bacterial foodborne pathogen, can cause meningitis, bacteremia, and complications during pregnancy. This report summarizes listeriosis outbreaks reported to the Foodborne Disease Outbreak Surveillance System of the Centers for Disease Control and Prevention during 1998-2008...
During 2011, 5 persons in the area of Lazio, Italy were infected with a monophyletic strain of hepatitis E virus that showed high sequence homology with isolates from swine in China. Detection of this genotype in Italy parallels findings in other countries in Europe, signaling the possible spread of...
The increasing prevalence and global spread of carbapenem-resistant Acinetobacter baumannii (A. baumannii) has become a serious problem. The aim of this study was to investigate molecular and epidemiological characteristics of carbapenem-resistant A. baumannii isolates collected from Korean non-tert...
Streptococcus pneumoniae serotype 1 presents a high invasiveness index and is seldom isolated from its niche, the nasopharynx. We report an unusual serotype 1 carriage in a healthy pediatric population at the time of the heptavalent pneumococcal vaccine adoption in Belgium. Our sampling period coinc...
Sequence Type 258 (ST258) together with its allelic single- and double-locus variants have mostly been associated with the dissemination of KPC-producing Klebsiella pneumoniae in Europe. A total of 56 nonreplicate K. pneumoniae isolates with decreased carbapenem-susceptibility, collected at 7 differ...
Hospital associated methicillin-resist Staphylococcus aureus has long been associated to outbreaks in the hospital environment. In this work, we investigated an outbreak of Hospital associated methicillin-resist Staphylococcus aureus carrying the Panton-Valentine leukocidin gene, which occurred in a...
Surveillance of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is generally considered to benefit from molecular techniques like multiple-locus variable-number of tandem repeats analysis (MLVA), which allow earlier detection and confinement of outbreaks. Here, a surveillanc...
Extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) were isolated from infants hospitalized in a neonatal, post-surgery ward during a four-month-long nosocomial outbreak and six-month follow-up period. A multi-locus variable number tandem repeat analysis (MLVA), using 10 loci (GE...
The Bluetongue virus serotype 8 (BTV-8) strain, which emerged in Europe in 2006, had an unusually high ability to cause foetal infection in pregnant ruminants. Other serotypes of BTV had already been present in Europe for more than a decade, but transplacental transmission of these strains had never...
To implement effective control measures, timely outbreak detection is essential. Shigella is the most common cause of bacterial diarrhea in Argentina. Highly resistant clones of Shigella have emerged, and outbreaks have been recognized in closed settings and in whole communities. We hereby report ou...
Coxsackievirus A16 (CVA16) is responsible for nearly 50% of all the confirmed hand, foot, and mouth disease (HFMD) cases in mainland China, sometimes it could also cause severe complications, and even death. To clarify the genetic characteristics and the epidemic patterns of CVA16 in mainland China,...
The large Surinamese migrant population in the Netherlands is a major risk group for urogenital Chlamydia trachomatis infection. Suriname, a former Dutch colony, also has a high prevalence of C. trachomatis. Surinamese migrants travel extensively between the Netherlands and Suriname. Our objective w...
The aim of this study was to use molecular methods to identify selected strains of C. difficile isolated from patients hospitalized at Independent Public Central Teaching Hospital [SP CSK] between 2008 and 2011 in order to demonstrate their toxicgenic character and to determine their epidemic potent...
A large pertussis epidemic occurred between 2008 and 2010 in Japan. To investigate epidemic strains, we analyzed 33 Bordetella pertussis isolates from the epidemic period by sequencing virulence-associated genes (fim3, ptxP, ptxA, and prn) and performing multilocus variable-number tandem repeat anal...
We investigated the changing trend of various toxigenic Clostridium difficile isolates at a 3 500-bed hospital in Taiwan. Genetic relatedness and antimicrobial susceptibility of toxigenic C. difficile isolates were also examined. A total of 110 non-repeat toxigenic C. difficile isolates from differe...
Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory tract infections in young children, but very little is known about its epidemiology and circulating genotypes in Pakistan. This study analyzed the epidemiological and molecular characteristics of RSV genotypes detected i...
The burden of infections caused by community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is increasing among different patient populations globally. As CA-MRSA has become established in healthcare facilities, the range of infections caused by them has also increased. Molecular c...
Carbapenem resistance due to OXA-type carbapenemases seriously limits therapeutic options in nosocomial infections caused by Acinetobacter baumannii. Previous studies have shown the presence of OXA-51, OXA-58, and OXA-23 carbapenemases but not OXA-24/40 in A. baumannii in Turkey. In this study, we i...
The largest known outbreak caused by a rare hybrid strain of Shiga toxin-producing E.coli (STEC) and enteroaggregative E. coli (EAEC) (E.coli O104:H4) of serotype O104:H4 occurred in Germany in 2011. Fenugreek sprouts acted as a transmission vehicle and were widely consumed in the outbreak area at t...
Previous studies have shown that the HIV-1 epidemic in Cuba displayed a complex molecular epidemiologic profile with circulation of several subtypes and circulating recombinant forms (CRF); but the evolutionary and population history of those viral variants remains unknown. HIV-1 pol sequences of th...
The goal of this work was to compare the efficiency of the influenza A and B viruses Isolated during 2010-2011 epidemic season. The clinical samples were taken in the test tubes with the transport medium on the.basis of the medium EMEM and commercial test tubes Sigma-Virocult (M40 Compliant, Sigma V...
Streptococcus uberis is a common cause of dairy cow mastitis throughout the world. The failure to control bovine mastitis caused by S. uberis is largely attributed to the little known about the epidemiology of this bacteria, especially strain differences in the same area. To define the local epidemi...
After the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) in Alaska, the incidence of invasive pneumococcal disease (IPD) due to non-vaccine serotypes, particularly serotype 19A, increased. The aim of this study was to describe the molecular epidemiology of IPD due to serotype 19A...
Limited HIV-1 drug-resistance surveillance has been carried out in Ghana since the implementation of antiretroviral therapy (ART). This study sought to provide data on the profile of HIV-1 drug resistance in ART-experienced and newly diagnosed individuals in Ghana. Samples were collected from 101 HI...
Neisseria meningitidis is a leading etiologic agent of severe invasive disease. The objective of the study was to characterise invasive meningococcal disease (IMD) epidemiology in Poland during the last decade, based on laboratory confirmed cases. The study encompassed all invasive meningococci coll...
We identified 2 poultry workers with conjunctivitis caused by highly pathogenic avian influenza A(H7N3) viruses in Jalisco, Mexico. Genomic and antigenic analyses of 1 isolate indicated relatedness to poultry and wild bird subtype H7N3 viruses from North America. This isolate had a multibasic cleava...
During an investigation of an outbreak of gastroenteritis caused by Salmonella enterica serovar Paratyphi B variant L(+) tartrate(+), we identified unpasteurized tempeh as a novel food vehicle and Rhizopus spp. starter culture as the source of the contamination. Safe handling of uncooked, unpasteuri...
Dengue disease is currently a major health problem in Indonesia and affects all provinces in the country, including Semarang Municipality, Central Java province. While dengue is endemic in this region, only limited data on the disease epidemiology is available. To understand the dynamics of dengue i...
Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification of aphid genes and proteins mediating virus transmission is critical to develop agriculturally sustainable virus management practices and to un...
Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause o...
No abstract available
Here we describe the clinical, microbiological, epidemiological, and molecular characterization of an outbreak of multidrug-resistant Acinetobacter baumannii (MRAB) involving 5 patients admitted to the internal medicine ward of our hospital. Over a 6-week period, 5 MRAB isolates were recovered from...
We have studied the diversity of B. henselae circulating in patients, reservoir hosts and vectors in Spain. In total, we have fully characterized 53 clinical samples from 46 patients, as well as 78 B. henselae isolates obtained from 35 cats from La Rioja and Catalonia (northeastern Spain), four posi...
To gain a more detailed picture of cryptococcosis in Thailand, a retrospective study of 498 C. neoformans and C. gattii isolates has been conducted. Among these, 386, 83 and 29 strains were from clinical, environmental and veterinary sources, respectively. A total of 485 C. neoformans and 13 C. gatt...
Fixed laboratory capacity in Africa may be inadequate; mobile microbiological laboratories may address this issue but their utility has seldom been evaluated. During 2012, the Benin Ministry of Health requested mobile microbiological laboratory (LaboMobil®) support following the failure of polysacch...
Colibacillosis is an economically important syndromic disease of poultry caused by extra-intestinal avian pathogenic Escherichia coli (APEC) but the pathotype remains poorly defined. Combinations of virulence-associated genes (VAGs) have aided APEC identification. The intestinal microbiota is a pote...
Infectious bronchitis is a highly contagious viral disease of poultry caused by infectious bronchitis virus (IBV) and is considered one of the most economically important viral diseases of chickens. Control of IBV has been attempted using live attenuated and inactivated vaccines. Live attenuated vac...
After its emergence in 2003, a livestock-associated (LA-)MRSA clade (CC398) has caused an impressive increase in the number of isolates submitted for the Dutch national MRSA surveillance and now comprises 40% of all isolates. The currently used molecular typing techniques have limited discriminatory...
We investigated the clonal relatedness of seven multi-drug-resistant (MDR) Klebsiella pneumoniae isolates, as well as three susceptible K. pneumoniae isolates collected during hospital outbreaks and outbreak-related microbiological surveillance, respectively. The relatedness among K. pneumoniae isol...
A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging d...
Tuberculosis (TB) remains a global public health problem whose effects have major impact in developing countries like Uganda. This study aimed at investigating genotypic characteristics and drug resistance profiles of Mycobacterium tuberculosis isolated from suspected TB patients. Furthermore, risk...
Salmonella Enteritidis is recognized worldwide as one of the main agents of human gastrointestinal infection. Several reports indicate the presence of isolates with decreased sensitivity to ciprofloxacin that can lead to a delayed response or the development of resistance during treatment. To descri...
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of healthcare-associated infections and significant contributor to healthcare cost. Community-associated-MRSA (CA-MRSA) strains have now invaded healthcare settings. A convenience sample of 97 clinical MRSA isolates was obtained f...
Acinetobacter baumannii is an important pathogen in hospitalized patients, particularly those in the intensive care unit (ICU). A total of 21 A. baumannii (6 from 5 patients and 15 from environmental samples) were isolated in the ICU and the isolation room of a state hospital in June 2011. The possi...
A total of 12 enterohemorrhagic Escherichia coli (EHEC) O157:H7 strains were isolated during a recent outbreak in a nursery school in Ehime Prefecture, Japan. These isolates were considered to be derived from a common strain when analyzed using an IS-printing method and pulsed-field gel electrophore...
Salmonella Typhimurium is an important nontyphoidal Salmonella serovar associated with foodborne diseases in many parts of the world. This organism is the major causative agent of nontyphoidal salmonellosis in Malaysia. We aimed to investigate the genetic profiles of the strains isolated from clinic...
Vibrio parahaemolyticus is a foodborne pathogen that has become a public health concern at the global scale. The epidemiological significance of V. parahaemolyticus infections in Latin America received little attention until the winter of 1997 when cases related to the pandemic clone were detected i...
Acinetobacter baumannii is an increasingly important global nosocomial pathogen. Clonal complex 92 (CC92) has become the most prevalent clonal complex in many regions. We investigated the molecular epidemiology and resistance profile of 52 imipenem-nonsusceptible A. baumannii isolates obtained from...
Disease outbreaks caused by arthropod-borne animal viruses (arboviruses) resulting in significant livestock and economic losses world-wide appear to be increasing. Rift Valley fever (RVF) virus is an important arbovirus that causes lethal disease in cattle, camels, sheep and goats in Sub-Saharan Afr...
Lyme disease Borrelia spp. are transmitted by Ixodes ticks, and more than 10 species of borreliae have been identified around the world. Recently, another Borrelia sp. has been reported in Asia (Japan, Korea, China, Taiwan and Thailand) as Borrelia valaisiana-related sp. In the present study, we obt...
Bacterial whole genome sequencing offers the prospect of rapid and high precision investigation of infectious disease outbreaks. Close genetic relationships between microorganisms isolated from different infected cases suggest transmission is a strong possibility, whereas transmission between cases...
Ticks were collected from the vegetation in the Baltic countries Estonia, Latvia, Lithuania and eastern Poland and analyzed for the presence of tick-borne encephalitis virus (TBEV) by amplification of the partial E and NS3 genes. In Estonia we found statistically significant differences in the TBEV...
The predominant community-associated MRSA strains vary between geographic settings, with ST8-IV USA300 being the commonest clone in North America, and the ST30-IV Southwest Pacific clone established as the dominant clone in New Zealand for the past two decades. Moreover, distinct epidemiological ris...
Molecular typing is an important tool in the investigation of methicillin resistant Staphylococcus aureus (MRSA) outbreaks and in following the evolution of MRSA. The staphylococcal cassette chromosome mec (SCCmec) contains a hypervariable region with a variable number of 40 bp repeats named direct...
To study the molecular characteristics of a long-term, low frequency outbreak of bla KPC-2 in a low prevalence setting involving the hospital environment. KPC-producing bacteria were screened by selective chromogenic agar and Real-Time PCR. The presence of antibiotic resistance genes was ascribed by...
To describe an outbreak of multi-resistant Pseudomonas aeruginosa bloodstream infections (MRPA-BSI) that occurred in the haematology ward of a tertiary academic hospital in Cape Town, South Africa, and determine risk factors for acquisition of MRPA-BSI. The outbreak investigation included a search f...
The incidence of human brucellosis in Kyrgyzstan has been increasing in the last years and was identified as a priority disease needing most urgent control measures in the livestock population. The latest species identification of Brucella isolates in Kyrgyzstan was carried out in the 1960s and inve...
The current millennium has seen a steep rise in the number, size and case-fatalities of cholera outbreaks in many African countries. Over 40,000 cases of cholera were reported from Nigeria in 2010. Variants of Vibrio cholerae O1 El Tor biotype have emerged but very little is known about strains caus...
Influenza A virus is one of world's major uncontrolled pathogen, causing seasonal epidemic as well as global pandemic. This was evidenced by recent emergence and continued prevalent 2009 swine origin pandemic H1N1 Influenza A virus, provoking first true pandemic in the past 40 years. In the course o...
The aim of this study was to examine the link between Campylobacter jejuni isolates obtained from chicken meat (n = 7) and gastroenteritis patients (n = 744). In total, 751 isolates were subjected to Lior serotyping. All the isolates from chicken meats were serotyped as Lior serotype 76 (LIO76). Amo...
Over 3,900 water samples from 688 cooling towers were tested for Legionella in 2008 in New Zealand. Of 80 (2.05% isolation rate) Legionella isolates, 10 (12.5%) were L. pneumophila serogroup 1; 10 (12.5%) were L. anisa; nine (11.2%) were L. pneumophila serogroup 8; and one (1.2%) was L. longbeachae...
Shiga toxin-producing Escherichia coli (STEC) O157:H7 is the causal agent for more than 96,000 cases of diarrheal illness and 3,200 infection-attributable hospitalizations annually in the United States. We defined a confirmed case as a compatible illness in a person with the outbreak strain during 1...
In recent years, the population of men who have sex with men (MSM) have become the most significant increasing group of HIV-1 transmission in China. To identify new recombinant strains and transmission patterns of HIV-1 in Chinese MSM population, a cross-sectional investigation of MSM in Anhui Provi...
The increasing occurrence of livestock-associated (LA) methicillin-resistant Staphylococcus aureus (MRSA) associated with the clonal complex (CC) 398 within the past years shows the importance of standardized and comparable typing methods for the purposes of molecular surveillance and outbreak detec...
Cases of a novel swine-origin influenza A(H3N2) variant (H3N2v) have recently been identified in the US, primarily among children. We estimated potential epidemic attack rates (ARs) based on age-specific estimates of sero-susceptibility and social interactions. A contact network model previously est...
The International Circumpolar Surveillance (ICS) project is a population-based surveillance network. Since 2000, Canada has participated in the ICS Invasive Bacterial Disease Working Group's surveillance of invasive disease due to Haemophilus influenzae (Hi). A standardized case report form containi...
Modern risk control and food safety practices involving food-borne bacterial pathogens are benefiting from new genomic technologies for rapid, yet highly specific, strain characterisations. Within the United States Food and Drug Administration (USFDA) Center for Food Safety and Applied Nutrition (CF...
Contamination with Legionella spp. of hot water system (HWS) in hospitals is a considerable problem and elimination of bacteria poses difficulties. Obligatory control of Legionella spp. in hospital HWS was implemented in Poland in 2008y. After that, Legionella spp. has been isolated repeatedly from...
Staphylococcus aureus is one of the most important etiological factors of both nosocomial and community-acquired infections. Multidrug-resistant S. aureus is frequently isolated nowadays. Antibiotics used on the hospital ward exert a selective pressure on the strains and favor resistant strains. Mul...
Protein function prediction is an important problem in the post-genomic era. Recent advances in experimental biology have enabled the production of vast amounts of protein-protein interaction (PPI) data. Thus, using PPI data to functionally annotate proteins has been extensively studied. However, mo...
Health care workers (HCWs) are at the interface between hospitals and communities. The survey for methicillin-resistant Staphylococcus aureus (MRSA) carriage among HCWs has mostly been conducted to investigate outbreaks or endemics. Community-associated MRSA are prevalent among children in Taiwan. W...
Pseudomonas aeruginosa is one of the primary opportunistic pathogens responsible for nosocomial infections. Recently, sequence type 235 (ST235) has been found internationally in a multidrug-resistant clone and is involved in the dissemination of genes encoding IMP-6 and VIM-2. This study aimed to de...
The Romanian HIV epidemic is characterized by the prevalence of a single particular HIV1 subtype, called F, a minor form, previously reported only in South America and Central Africa. Initially reported in the early '90s by serotyping studies in the large cohort of parenterally infected children, th...
Human genetic studies are rarely conducted for immunological purposes. Instead, they are typically driven by medical and evolutionary goals, such as understanding the predisposition or resistance to infectious or inflammatory diseases, the pathogenesis of such diseases, and human evolution in the co...
The present study was designed to evaluate the molecular epidemiology of CTX-M producing Klebsiella pneumoniae, Enterobacter cloacae and Escherichia coli isolated from bloodstream infections at tertiary care hospitals in the State of Rio de Janeiro, Brazil. A total of 231 nonduplicate Enterobacteria...
Legionella spp. is considered an emerging microorganism involved in aquatic environments contamination and cause of Legionnaires' disease. The aims of the study are to evaluate the level of contamination of Legionella spp. in the water system of the largest Hospital of Apulia region during a 4-year...
Methicillin-resistant Staphylococcus aureus (MRSA) ST398, associated with livestock animals, was described in 2003 as a new lineage infecting or colonizing humans. We evaluated the prevalence and molecular characteristics of MRSA ST398 isolated in the Hospital Universitari de Bellvitge from January...
In order to obtain adequate information for the treatment of methicillin resistant Staphylococcus aureus (MRSA) infections, it is crucial to identify trends in epidemiological and antimicrobial resistance patterns of local S. aureus strains. Community and hospital acquired S. aureus isolates (n=202)...
Acinetobacter baumannii is an important opportunist pathogen, due to severe antibiotic resistance and nosocomial infection. The epidemiology and antibiotic resistance of A.baumannii have been extensively reviewed, but the pathogenesis and virulence remain unclear. Proteomics analysis has been applie...
The prevalence of Methicillin resistant Staphylococcus aureus (MRSA) is progressively increasing globally with significant regional variation. Understanding the Staphylococcus aureus lineages is crucial in controlling nosocomial infections. Recent studies on S. aureus in Uganda have revealed an esca...
Scientific justification of optimization of epidemiologic diagnostic of suppurative-septic infection (SSI) caused by Pseudomonas aeruginosa based on comparability of antibiotic sensitivity and beta-lactamase production. Intraspecies typing of 37 P. aeruginosa strains isolated during microbiological...
Staphylococcus epidermidis is a common cause of nosocomial infections worldwide. This study analyzed the differences in genetic endowment and clonal lineages with pathogenesis and resistance traits of S. epidermidis isolates collected from community and hospital environments (patients and healthcare...
There is a need for a regional assessment of the frequency and diversity of MRSA to determine major circulating clones and the extent to which community and healthcare MRSA reservoirs have mixed. We conducted a prospective cohort study of inpatients in Orange County, California, systematically colle...
To establish the relatedness of methicillin-resistant Staphylococcus aureus (MRSA) isolates in the Maternity Hospital, Kuwait. A total of 22 MRSA were isolated from 20 neonates and 1 mother in the Special Care Unit, Maternity Hospital, Kuwait. They were characterized using antibiogram, pulsed-field...
Bloodstream infections (BSIs) are a prominent clinical problem in patients undergoing hemodialysis. These infections appear to be more common among patients who have a central line as their dialysis access and can be associated with substantial morbidity and mortality. Accurately diagnosing BSIs cle...
According to the EARS-Net surveillance data, Portugal has the highest prevalence of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) in Europe, but the information on MRSA in the community is very scarce and the links between the hospital and community are not known. In this study we ai...
Laboratory methods that can unambiguously fingerprint pathogenic microbes are needed to investigate the transmission of human infectious diseases from diverse sources, such as from the community, from the environment, within hospitals, or from contaminated food or water sources. Public health invest...
Molecular typing of the pneumococcus has played a crucial role in understanding the epidemiology of the organism. However, most of what is known about molecular epidemiology of the pneumococcus pertains to the developed world. The brunt of pneumococcal infections is borne by sub-Saharan African coun...
The genetic diversity and the clinical relevance of the drug-resistant Klebsiella pneumoniae isolates from hospital settings are largely unknown. We thus conducted this prospective study to analyze the molecular epidemiology of K. pneumoniae isolates from patients being treated in the 306 Hospital i...
Until recently, Clostridium difficile infection (CDI) has been mostly diagnosed in hospitalized elderly patients treated with antibacterial agents. The epidemiology of C difficile is changing as the ribotype 027 strain is spreading worldwide, and more infections are diagnosed in patients residing in...
Diseases caused by Streptococcus pyogenes (Group A streptococcus, GAS) range from superficial infections such as pharyngitis and impetigo to potentially fatal rheumatic heart disease and invasive disease. Studies spanning emm-typing surveillance to population genomics are providing new insights into...
As a vast majority of the human listeriosis cases are caused by serotypes 1/2a, 1/2b and 4b strains, it is imperative that strains from clinical as well as from food and environment are further characterised so that accurate and timely epidemiological determination of sources of the contamination ca...
The south-central skunk rabies virus (SCSK) is the most broadly distributed terrestrial viral lineage in North America. Skunk rabies has not been efficiently targeted by oral vaccination campaigns and represents a natural system of pathogen invasion, yielding insights to rabies emergence. In the pre...
Crimean-Congo hemorrhagic fever (CCHF) is a zoonosis mainly transmitted by ticks that causes severe hemorrhagic fever and has a mortality rate of 5-60%. The first outbreak of CCHF occurred in the Crimean peninsula in 1944-45 and it has recently emerged in the Balkans and eastern Mediterranean. In or...
Human Influenza A virus undergoes recurrent changes in the hemagglutinin (HA) surface protein, primarily involved in the human antibody recognition. Relevant antigenic changes, enabling the virus to evade host immune response, have been recognized to occur in parallel to multiple mutations at antige...
The geographic ranges of ticks and tick-borne pathogens are changing due to global and local environmental (including climatic) changes. In this review we explore current knowledge of the drivers for changes in the ranges of ticks and tick-borne pathogen species and strains via effects on their basi...
The circulation of vector-borne zoonotic viruses is largely determined by the overlap in the geographical distributions of virus-competent vectors and reservoir hosts. What is less clear are the factors influencing the distribution of virus-specific lineages. Japanese encephalitis virus (JEV) is the...
Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viralphylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed light...
The epidemiology of chronic viral infections, such as those caused by Hepatitis C Virus (HCV) and Human Immunodeficiency Virus (HIV), is affected by the risk group structure of the infected population. Risk groups are defined by each of their members having acquired infection through a specific beha...
Wolbachia is a symbiont intensively studied due to its ability to interfere with their host's reproduction, and it has been recently proposed as an alternative tool to control insect pests or vectors of diseases. The Asian citrus psyllid Diaphorina citri is an important pest of citrus since it vecto...
In 2006, Bluetongue serotype 8 was notified for the first time in north-western Europe, more specifically in Belgium, the Netherlands, Luxemburg, Germany and France. The disease spread very rapidly, affecting mainly cattle and sheep farms. In this paper, we examined risk factors affecting the spatia...
Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently deve...
The introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) in September 2006 has markedly reduced the burden of invasive pneumococcal disease (IPD) including meningitis in England and Wales. This study examined changes in the molecular epidemiology of pneumococcal isolates causing mening...
Glycopeptide-resistant Staphylococcus epidermidis (GRSE) strains are of increasing concern in bone and joint infections (BJIs). Using multilocus sequence typing and multilocus variable-number tandem repeat analysis, we show that BJI-associated GRSE strains are genetically diverse but arise from rela...
Methicillin-resistant Staphylococcus aureus (MRSA) has become a common cause of skin infections and invasive infections in community dwellers in the United States since the late 1990s. Isolates characterized as USA300 by pulsed-field gel electrophoresis (PFGE) are the predominant strain type in thes...
An increased incidence of Mycoplasma pneumoniae infections was reported in 2011 in two cities in France, Bordeaux and Caen. Two complementary molecular typing methods, PCR-RFLP on adhesin P1 and multilocus variable number tandem repeat analysis (MLVA), were used to determine whether this phenomenon...
We describe an outbreak of spotted fever group (SFG) rickettsiosis that occurred in 2007 in a farming community in southeastern Guatemala. We identified 17 cases of an acute febrile illness, among which 10, including two fatalities, were confirmed or probable cases of rickettsial disease (case-fatal...
Dairy cattle serve as a potential source for Campylobacter infection in humans. Outbreaks associated with consumption of either Campylobacter contaminated raw milk or contaminated milk after treatment were previously recorded in the United States. Further, starlings have been implicated in the sprea...
Newborns are rarely infected by extended-spectrum β-lactamase (ESBL)-producing members of the Enterobacteriaceae. In a neonatal intensive care unit, 14 newborns were infected or colonized by CTX-M-15-producing Enterobacter cloacae. All seven infected patients had underlying medical conditions, and f...
We compared the antibiotic susceptibility, clonal lineages and resistance genes of singleton Acinetobacter baumannii strains to those of isolates representing repeatedly encountered molecular types in five Abu Dhabi hospitals. One hundred and ten clinically relevant, non-repeat strains were typed by...
Methicillin-resistant Staphylococcus aureus (MRSA) infections have changed since certain non-multiresistant MRSA lineages have emerged in hospitals. In this study, 99 MRSA isolates, 77 from a public and 22 from a private hospital, were characterized. Isolates were tested for antimicrobial susceptibi...
The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales - from the individual to the population - are essential for devising effective measures to predict, prevent or co...
To study the molecular epidemiology of Acinetobacter baumannii isolates from Lithuanian hospitals with an emphasis on the characterization of plasmids and antibiotic-resistance genes and their relationship with European clones (ECs) I and II. PFGE, PCR analysis of ECs and resistance genes, plasmid r...
With increasing rates of antibiotic resistance, bacterial infections have become more difficult to treat, elevating the importance of surveillance and prevention. Effective surveillance relies on the availability of rapid, cost-effective, and informative typing methods to monitor bacterial isolates....
An outbreak of multidrug-resistant Pseudomonas aeruginosa (MDRPA) infections in a university hospital is described. Phenotypic and genotypic analysis of 240 isolates revealed that 152 patients, mainly in the intensive care unit (ICU), were colonized or infected with MDRPA, the majority with O11. All...
Long-term typhoid carriers can simultaneously excrete Salmonella enterica serovar Typhi variants with considerable genetic differences, a situation that complicates the interpretation of the subtyping data used in outbreak investigations and disease surveillance.
Neonatal candidemia can occur, however, infections caused by Candida pelliculosa are rare. Here, we describe an outbreak of candidemia caused by C. pelliculosa among babies hospitalized in a neonatal intensive care unit.
From January to December 2011, 24 Pseudomonas aeruginosa strains producing the extended-spectrum β-lactamase SHV-2a were identified in 13 hospitals in France. With one exception, all the strains belonged to the same clone. Double-disk synergy tests with cefepime and clavulanate were able to detect a...
An outbreak of hospital-acquired Acinetobacter baumannii infections, caused by a bla(OXA-23)-positive carbapenem-resistant strain belonging to international clone II/ST2, was detected in Latvia. The strain was partially equipped with the armA gene and the intI1-aacA4-catB8-aadA1-qacEΔ1 class 1 integ...
It is essential in an outbreak investigation that strain characterization of Neisseria meningitidis is performed in a rapid and accurate manner. This study evaluated two new molecular typing methods, multiple-locus variable number tandem repeat analysis (MLVA) and repetitive sequence-based PCR (rep-...
For exhaustive detection of diarrheagenic Escherichia coli, we previously developed a colony-hybridization method using hydrophobic grid-membrane filters in combination with multiplex real-time PCR. To assess the role of domestic animals as the source of atypical enteropathogenic E. coli (aEPEC), a...
After a trend of increasing incidence of gonorrhoea in the 1990s, by 2004 the incidence was declining in England, but continuing to increase in Wales. This prompted an investigation of the epidemiology of gonorrhoea in Wales to inform future prevention and control measures. As an extension to Gonoco...
Methicillin-resistant Staphylococcus aureus (MRSA) has become an important hospital-acquired pathogen, with transfer of the organism from a carrier or infected patient to uninfected patients by the hands or clothing of staff as the main mode of transmission. Investigation of a cluster of new cases o...
Genotypic diversity, antimicrobial susceptibilty, and presence of OXA-genes were assessed in 100 nosocomial Acinetobacter strains from a tertiary-care hospital, Turkey. Ninety-eight isolates were identified by AFLP library identification to Acinetobacter baumannii. Furthermore, the isolates were div...
Enterococcus cecorum was isolated from spondylitis lesions in broilers from two flocks in North Carolina that were experiencing increased mortality. Affected birds showed paresis and paralysis, clinical signs characteristic of enterococcal spondylitis (ES). Affected birds rested on their hocks and c...
Although azithromycin promised to be a safe and effective single-dose oral treatment of early syphilis, azithromycin treatment failure has been documented and is associated with mutations in the 23S rDNA of corresponding Treponema pallidum strains. The prevalence of strains harboring these mutations...
In January 2008, laboratory-based surveillance of Clostridium difficile was initiated as a part of the Finnish National Infectious Disease Register (NIDR) and enhanced surveillance of hospitalized patients with C. difficile-associated infections (CDI) by the Finnish Hospital Infection Programme (SIR...
No abstract available
The most widespread type of carbapenemases among carbapenem-resistant Acinetobacter baumannii (CRAB) belongs to the oxacillinase (OXA) group. A total of 57 CRAB isolates and 20 non-CRAB isolates (i.e., A. baumannii susceptible to carbapenems) were studied to investigate the molecular epidemiology of...
A few lineages of Group A streptococci (GAS) have been associated with a reemergence of severe invasive streptococcal disease in developed countries. However, the majority of the comparisons between invasive and non-invasive GAS isolates have been performed for collections of reduced genetic diversi...
Methicillin-resistant Staphylococcus aureus (MRSA) infection or colonization has become a serious emerging condition in equine hospitals. Following the detection of MRSA in asymptomatic hospitalized horses and in two horses with post-operative wound infections, an investigation was conducted. Twelve...
Sixty-three Brucella isolates from water buffaloes and cattle slaughtered within the Italian national plan for brucellosis control were characterized by multiple-locus variable-number tandem repeat analysis (MLVA). Genotyping indicated a strong influence of geographic origin on the Brucella abortus...
The Burkholderia cepacia complex is a group of Gram-negative bacteria known as respiratory pathogens in cystic fibrosis patients, but also increasingly reported as a cause of healthcare associated infections. We describe an outbreak of B. cepacia bloodstream infections in a referral hospital in Phno...
Implementation of control measures in line with European Commission regulations has led to a decrease in salmonellosis in the European Union since 2004. However, control programmes do not address laying hens whose eggs are produced for personal consumption or local sale. This article reports an inve...
Pertussis remains an important cause of morbimortality despite current vaccination strategies. This study was designed to describe the results and characteristics of close contacts of pertussis cases diagnosed in children less than 16 years in a tertiary hospital in Barcelona. Cross-sectional study....
Comparison of studies evaluating patient-to-patient transmission of organisms is difficult, given the lack of standardized criteria. We used fluoroquinolone-resistant Escherichia coli (FQREC) as a model to characterize variability in definitions of relatedness across studies and to evaluate the resu...
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been evaluated for the identification of multidrug-resistant Acinetobacter baumannii nosocomial outbreaks in comparison with the repetitive sequence-based PCR DiversiLab system. The results suggest that M...
An outbreak of Legionnaires' Disease took place in the Swedish town Lidköping on Lake Vänern in August 2004 and the number of pneumonia cases at the local hospital increased markedly. As soon as the first patients were diagnosed, health care providers were informed and an outbreak investigation was...
Thirteen outbreaks of foot-and-mouth disease (FMD) were reported in pigs and cattle in Korea between 8 April and 4 June 2010. The FMD virus (FMDV) isolates were of serotype O, indicating that they were related to the virus strains of the Southeast Asia topotype that are circulating in East Asian cou...
Remarkable changes in the epidemiology of human nontyphoidal salmonellosis have occurred in the United Kingdom over the last century. Between 1981 and 1991, the incidence of nontyphoidal salmonellosis in the United Kingdom rose by >170%, driven primarily by an epidemic of Salmonella enterica subspec...
To understand epidemiologic patterns of meningococcal disease in Asia, we performed a retrospective molecular analysis of cerebrospinal fluid (CSF) specimens collected in prospective surveillance among children aged < 5 years of age in China, South Korea, and Vietnam. A total of 295 isolates and 2,3...
Staphylococcus aureus remains a leading cause of hospital-acquired infection but weaknesses inherent in currently available typing methods impede effective infection prevention and control. The high resolution offered by whole genome sequencing has the potential to revolutionise our understanding an...
Arthropod-borne viral infections cause several emerging and resurging infectious diseases. Among the diseases caused by arboviruses, chikungunya is responsible for a high level of severe human disease worldwide. The salivary glands of mosquitoes are the last barrier before pathogen transmission. We...
Clostridium difficile infection (CDI) is the most important bacterial cause of hospital-acquired diarrhoea. Although reports of deaths associated with CDI have been decreasing since a peak in 2007 in England and Northern Ireland, it remains a major cause of morbidity and mortality. The Health Protec...
Community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA) is responsible for severe infections in previously healthy people acquired in the community in different areas of the world. To report an outbreak of CA-MRSA in a hospital newborn nursery in northern Italy in September-October 2...
Methicillin-resistant Staphylococcus aureus (MRSA) has been endemic in Hong Kong for three decades. This study evaluated the practical use of high-resolution melting (HRM) real-time PCR analysis on MRSA staphylococcal Protein A (spa) typing on local MRSA isolates. Among 55 clinical MRSA isolates col...
A West Nile virus (WNV) disease outbreak occurred in 2010 in northern Greece with a total of 262 laboratory-confirmed human cases and 35 deaths. A serological and molecular surveillance was conducted on samples of hunter-harvested wild birds prior to and during the outbreak. Serum and tissue samples...
Vector-borne diseases (VBDs) are defined as infectious diseases of humans and animals caused by pathogenic agents such as viruses, protists, bacteria, and helminths transmitted by the bite of blood-feeding arthropod (BFA) vectors. VBDs represent a major public health threat in endemic areas, general...
To study the distribution, diversity and activity of Acinetobacter-derived cephalosporinase (ADC)-, carbapenem-hydrolysing oxacillinase (CHO)- and metallo-β-lactamase (MBL)-encoding genes, and of the most common insertion sequences (ISs), in the genome of nosocomial, epidemic, multidrug-resistant Ac...
In 2006, 0.6% of healthy subjects living in the Paris area had extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in their gut. To assess the evolution of this rate, a study identical to that of 2006 was conducted in 2011. Healthy adults who visited the IPC check-up centre in February-M...
The hospital environment has been suggested as playing an important role in the transmission of hospital-associated (HA) pathogens. However, studies investigating the contamination of the hospital environment with methicillin-resistant Staphylococcus aureus (MRSA) or Clostridium difficile have gener...
An outbreak of foot-and-mouth disease (FMD) in Egypt affected approximately 40,000 cattle and water buffaloes and killed more than 4,600 animals during February-March 2012. To investigate the etiology of the 2012 outbreak, specimens were collected from six governorates and analyzed using universal p...
The anterior nares are the site of choice for the Veterans Administration methicillin-resistant Staphylococcus aureus (MRSA) surveillance program; however, a correlation between nares colonization and concomitant wound infections has not been well established. The purpose of this study was 3-fold: t...
We report a pseudo-outbreak of Tsukamurella due to improperly wrapped scissors used for processing of tissue specimens. A polyphasic approach, involving biochemical, genetic, and metabolomic techniques, was used in the laboratory investigation. This report highlights that early recognition of pseudo...
Since 1995, a methicillin-resistant Staphylococcus aureus (MRSA) clone has spread in southern Germany. The strain was assigned to the Rhine-Hesse pulsed-field gel electrophoresis (PFGE) type by the staphylococcal reference center and was highly similar to epidemic clones known to belong to clonal co...
To study the evolutionary relationship of Mycobacterium tuberculosis isolates from 13 patients in a large outbreak of isoniazid-resistant tuberculosis in London. Genotypic and phenotypic susceptibility tests were performed. Molecular genotyping using restriction fragment length polymorphisms and myc...
An outbreak of acute hemorrhagic conjunctivitis (AHC) occured in India between August and October 2010. Molecular typing by RT-PCR and sequencing of a partial VP1 region identified coxsackievirus A24 variant (CV A24v) as the serotype involved in this outbreak. Phylogenetic analysis based on the VP1...
The rapid expansion of Acinetobacter baumannii clinical isolates exhibiting resistance to carbapenems and most or all available antibiotics during the last decade is a worrying evolution. The apparent predominance of a few successful multidrug-resistant lineages worldwide underlines the importance o...
Surveillance is critical for the prevention and control of infectious disease. China's real-time web-based infectious disease reporting system is a distinguished achievement. However, many aspects of the current China Infectious Disease Surveillance System do not yet meet the demand for timely outbr...
During June 2003, mosquito surveillance was conducted at a US Army installation and a US Military training site 2 km south of the demilitarized zone, Republic of Korea. Mosquitoes were collected using Mosquito Magnets™, sorted to species, and assayed for the presence of arboviruses. From the 3,149 m...
Community-onset bloodstream infections caused by extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC-COBSIs) were investigated over a 7-year-period (2003-2009) in our institution. ESBL-EC-COBSI inclusion criteria were cefotaxime/ceftazidime non-susceptible blood isolates recovered duri...
The staphylococci are implicated in a variety of human infections; however, many clinical microbiology laboratories in Nigeria do not identify staphylococci (in particular coagulase negative staphylococci - CNS) to the species level. Moreover, data from multi-centre assessment on antibiotic resistan...
The phylogenetic analysis of VP1 sequences of the 39 type O foot and mouth virus (FMDV) isolates collected from different regions of India during the year of 2001-12 revealed that all isolates belonged to the Middle East - South Asia (ME-SA) topotype. Based on the amount of divergence among the isol...
Staphylococcus aureus, including meticillin-sensitive and -resistant S. aureus (MSSA and MRSA, respectively), is associated with severe nosocomial human infections. This study aimed to investigate the molecular profile, including the dynamic changes and genotype/phenotype correlation, of S. aureus i...
Clostridium difficile is the most common pathogen causing antibiotic-associated diarrhea. Antibiotic therapy also favors the development and the epidemic spreading of multiresistant strains. In this present retrospective study clinical isolates from the University of Saarland Medical Center and of o...
Nosocomial infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a problem in hospital settings worldwide. The National Reference Centre for Staphylococci performs molecular typing on a representative sample set of MRSA isolates from German hospitals for assessing long-term tre...
Human parechovirus has rarely been shown to cause clinical disease in adults. During June-August 2008, a total of 22 adults sought treatment at Yonezawa City Hospital in Yamagata, Japan, for muscle pain and weakness of all limbs; most also had fever and sore throat. All patients received a clinical...
To assess risk for importation of dengue virus (DENV) into Queensland, Australia, and sources of imported viruses, we sequenced the envelope region of DENV isolates from symptomatic patients with a history of travel during 2002-2010. The number of imported dengue cases greatly increased over the sur...
During a pneumococcal disease outbreak in a pediatric psychiatric unit in a hospital in Rhode Island, USA, 6 (30%) of 20 patients and staff were colonized with Streptococcus pneumoniae serotype 15A, which is not included in pneumococcal vaccines. The outbreak subsided after implementation of antimic...
During an outbreak of severe acute respiratory infections in 2 orphanages, Vietnam, 7/12 hospitalized children died. All hospitalized children and 26/43 children from outbreak orphanages tested positive for rhinovirus versus 9/40 control children (p = 0.0005). Outbreak rhinoviruses formed a distinct...
Pseudomonas aeruginosa is a known opportunistic pathogen frequently causing serious infections in burned patients. To analyze the epidemiological profile of Pseudomonas aeruginosa isolated in a Tunisian burn unit. During a 3-year period (from 01 July 2008 to 30 June 2011), 544 non repetitive strains...
The spread of carbapenemase-producing gram-negative bacteria is one of the major challenges of the present. Since 2009, the National Reference Laboratory for gram-negative nosocomial pathogens has observed the molecular epidemiology of carbapenemases in Germany. In 2011, 1,454 referred bacterial iso...
Enterococci (mainly E. faecalis, E. faecium) are important nosocomial pathogens predominantly affecting older and/or immunocompromised patients. The bacteria possess a broad spectrum of intrinsic and acquired antibiotic resistance properties. Among these, the transferrable glycopeptide resistance of...
Genetic assessment by spoligotyping of 565 Mycobacterium tuberculosis complex strains collected from the Western Region of Cameroon between 2004 and 2005 has confirmed the establishment of the "Cameroon family" as the leading cause of tuberculosis in 45.9% of cases and evidenced the rapid quasi exti...
We describe using major outer membrane protein (MOMP) typing as a screen to compare the Campylobacter jejuni porA gene sequences of clinical outbreak strains from human stool with the porA sequences of dairy farm strains isolated during two milk-borne campylobacteriosis outbreak investigations in Ca...
The aim of our study was to investigate and control an outbreak and identify risk factors for colonization and infection with Serratia marcescens in two departments in Tartu University Hospital. The retrospective case-control study was conducted from July 2005 to December 2006. Molecular typing by p...
Given the emergence of transmissible strains of Pseudomonas aeruginosa, such as the Liverpool epidemic strain (LES), in cystic fibrosis (CF) centres, it is important to carry out regular surveillance of isolates. In a survey of 22 P. aeruginosa isolates, each from a different CF patient identified a...
To determine whether transfer from a long-term care facility (LTCF) is a risk factor for colonization with Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae upon acute care hospital admission. Microbiologic survey and nested case-control study. Four hospitals in a metropolitan a...
The term synanthropic describes organisms that thrive in human-altered habitats. Where synanthropic nonhuman primates (NHP) share an ecological niche with humans, cross-species transmission of infectious agents can occur. In Bangladesh, synanthropic NHP are found in villages, densely populated citie...
Patients are often screened with surveillance cultures to discern transmissions vs transformation of an isolate to vancomycin-resistant Enterococcus faecium. To determine the amount of time between which isolates could be considered genetically similar by pulsed-field gel electrophoresis, isolate ch...
To report an outbreak of extensively drug-resistant (XDR) Acinetobacter baumannii in the neonatal intensive care unit (NICU) of an Italian university hospital. Patient risk profiles for acquisition of A. baumannii and measures used to control the outbreak are described. Antibiotic susceptibility of...
The epidemiology and molecular characteristics of vancomycin-resistant enterococci (VRE) from China deserve further investigation. This study reports on the molecular characterization of 101 unique VRE (96 E. faecium and 5 E. faecalis strains) recovered from diverse samples of 12 hospitals in China....
No abstract available
Streptococcus pneumoniae infections remain a major cause of morbidity and mortality worldwide. The diversity of pneumococci was first evidenced by serotyping of their capsular polysaccharides, responsible of virulence, resolving into more than 93 serotypes. Molecular tools have been developed to tra...
During 9 May 2010-7 May 2011, an outbreak of pertussis-like illness (incidence, 80 cases per 100 000 persons) occurred in Franklin County, Ohio. The majority of cases were identified by IS481-directed polymerase chain reaction (PCR), which does not differentiate among Bordetella species. We sought t...
Epidemiological data on staphylococcal scalded skin syndromes (SSSS), including bullous impetigo (BI) and generalized exfoliative syndrome (GES), are scarce. To better characterize SSSS and associated Staphylococcus aureus strains, we conducted a retrospective study of 349 cases collected in France...
Infections caused by Histoplasma capsulatum are found most often in endemic regions of North, Central, and South America. H. capsulatum has been divided into eight geographic clades by multi-locus sequence typing (MLST). Recently, one isolate and five formalin-fixed paraffin-embedded (FFPE) tissue s...
To perform molecular epidemiology for 113 KPC-producing Klebsiella pneumoniae isolated in 2010 from 12 Brazilian states. The resistance profile was determined by disc diffusion and Etest. Genetic polymorphism was analysed by PFGE and multilocus sequence typing. The genetic environment of the bla(KPC...
Hospital-acquired infections (HAIs) are a global problem. The widespread use of antibiotics continues to exacerbate the problem giving rise to antibiotic-resistant bacteria both in and outside a clinical context. The general hospital environment is an obvious important focus for the selection and sp...
The present study describes the frequency of Foot and Mouth Disease (FMD) virus serotypes (O, A and Asia-1) in major regions (all provinces) of Pakistan using Indirect Sandwich ELISA. Also, spatial distribution of various FMD serotypes and their comparison is discussed. A total of 590 samples (Epith...
Bangladesh has been severely hit by highly pathogenic avian influenza H5N1 (HPAI-H5N1). However, little is known about the genetic diversity and the evolution of the circulating viruses in Bangladesh. In the present study, we analyzed the hemagglutinin gene of 30 Bangladeshi chicken isolates from 20...
The aim of this study was to investigate the genetic background of methicillin-susceptible (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) obtained from clinical specimens of inpatients and outpatients. Methicillin resistance was confirmed by the presence of the mecA gene by PCR. The g...
Recurrent Clostridium difficile infection (CDI) occurs in up to 35% of patients. Recurrences can be due to either relapse with the same strain or reinfection with another strain. In this study, multilocus variable-number tandem-repeat analysis (MLVA) was performed on C. difficile isolates from patie...
Pulsed-field gel electrophoresis (PFGE) was used to type 128 Streptococcus infantarius subsp. coli isolates from sea otters and mussels. Six SmaI PFGE groups were detected, with one predominant group representing 57% of the isolates collected over a wide geographic region. Several sea otter and muss...
Streptococcus pneumoniae is the main pathogen that causes respiratory infections in children younger than five years. The increasing incidence of macrolide- and tetracycline-resistant pneumococci among children has been a serious problem in China for many years. The molecular characteristics of eryt...
Fungemia in preterm infants is associated with high mortality and morbidity. This study reports an outbreak of unusual fungemia in a tertiary neonatal intensive care unit (NICU). Ten Candida pelliculosa bloodstream isolates were identified from six infants hospitalized in the NICU from February to M...
No abstract available
We report on an unusual familial outbreak of a coxsackie virus infection in Switzerland in which five family members were affected. Most of the patients presented with signs of meningitis, and four were hospitalized. In three individuals, the virus was detected in the cerebrospinal fluid, pharynx, a...
During the 1990s, various reports of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections appeared in the literature, caused by novel strains genetically distinct from traditional healthcare-associated MRSA (HA-MRSA). Numerous lineages of CA-MRSA have since emerged o...
The sporadic emergence of New Delhi metallo-β-lactamase-1 (NDM-1)-producing Acinetobacter spp. has been reported in China; however, NDM-1-positive bacteria epidemics are rarely reported in intensive care units (ICUs) in China, or even in the world. During 15 months' surveillance Acinetobacter spp. i...
Despite infection control measures, an important increase in the extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae incidence density occurred in our hospital from 2006 onwards. This study, focusing on the 2005-2007 period, was performed in an attempt to explain this increase. ESBL...
We report on an outbreak caused by Salmonella enteritidis phage type 4 (PT4) among 143 participants at a soccer camp in Austria in August 2010. The outbreak affected 34 persons, including 24 epidemiologically related cases and 10 laboratory-confirmed cases. Food-specific cohort analyses revealed spa...
To investigate the species distribution within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex and the molecular epidemiology of A. baumannii and Acinetobacter nosocomialis, 376 Acinetobacter isolates were collected prospectively from hospitalized patients at 15 medical centres in Ge...
Multilocus sequence typing (MLST) is one of the most reliable methods for typing of Escherichia coli, including extended-spectrum-β-lactamase-producing E. coli (ESBL-EC). We investigated the performance of a new typing method, SpectraCell RA (River Diagnostics, Madison, WI), in comparison on MLST on...
A strain of Escherichia coli O111:H21 recently isolated in the United Kingdom harbored the phage-encoded vtx2c gene and the aggregative adherence plasmid. Although exhibiting the same pathogenic profile as the E. coli O104:H4 strain linked to the outbreak in Germany, there were important differences...
Neisseria lactamica is a true commensal bacterium occupying the same ecological niche as the pathogenic Neisseria meningitidis, which is responsible for outbreaks and large epidemics, especially in sub-Saharan Africa. To better understand the epidemiology of N. lactamica in Africa and its relationsh...
To describe the molecular and population-level characterization of a selected group of OXA-48-like-producing Klebsiella pneumoniae isolates collected in Spain between January 2011 and May 2012. During the study period, 151 OXA-48-like-producing K. pneumoniae isolates were collected from 10 hospitals...
Several outbreaks of cholera have been reported in Chandigarh region during a span of seven years from 2002-2008. The genetic characteristics of Vibrio cholerae isolates obtained during these outbreaks have not been adequately studied. The aim of this study was to do molecular typing of V. cholerae...
Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen that has diverse molecular heterogeneity. Most MRSA strains in the United States are pulsed-field gel electrophoresis USA100 sequence type (ST) 5 and USA300 ST8. Infections with MRSA ST239-III are common and found during health c...
The epidemiology of foot-and-mouth disease (FMD) in North Africa is complicated by the co-circulation of endemic FMD viruses (FMDV), as well as sporadic incursions of exotic viral strains from the Middle East and Sub-Saharan Africa. This report describes the molecular characterization of SAT 2 FMD v...
To characterize Escherichia coli ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients by determining antibioresistance and genotypic characteristics of E. coli isolates responsible for VAP or lung colonization, by comparing them with their oropharyngeal and rectal counterparts...
In this study, using multilocus microsatellite analysis, we report the genetic characterization of 27 Candida parapsilosis isolates recovered in two different periods of time (2007-2009 and 2011-2012) from infants hospitalized in the neonatal intensive care unit of a hospital in Messina, Italy. The...
To report an outbreak due to Providencia stuartii isolates carrying bla(OXA-48), bla(PER-1), bla(CMY-4) and qnrA6 in a Tunisian hospital in 2011. Eight intensive care unit (ICU) patients infected/colonized by extended-spectrum β-lactamase (ESBL)-producing P. stuartii between March and May 2011 were...
Three clinical Acinetobacter baumannii isolates (A-C) were isolated from three separate patients during an outbreak in a hospital in Krakow, Poland. Isolate A was recovered first and was susceptible to carbapenems, whereas isolates B and C were resistant. The aim of this study was to investigate the...
A better understanding of virulence gene profiling and molecular characterization of Staphylococcus aureus isolates associated with bloodstream infection (BSI) may provide further insights related to clinical outcomes with these infections. We analyzed 89 S. aureus isolates including 37 MRSA isolate...
The most efficient method for HIV-1 genetic characterization involves full-genome sequencing, but the associated costs, technical features, and low throughput preclude it from being routinely used for the analysis of large numbers of viral strains. Multiregion hybridization assays (MHA) represent an...
Metallo-β-lactamase (MBL) producers have been reported among the various Acinetobacter species worldwide. In this study, the epidemiology and molecular characteristics of carbapenemase-encoding genes and mobile elements were studied to analyse the regional dissemination of MBL genes in Acinetobacter...
Among 3967 Staphylococcus aureus recovered from a Gran Canaria hospital (2003-2010), 28 strains were Panton-Valentine leukocidin-positive community-associated methicillin-resistant Staphylococcus aureus and were included in this study. Most isolates (89.3%) caused skin and skin-structure infections....
Imipenem-resistant Acinetobacter baumannii (IRAB) poses a great threat to healthcare systems. Production of carbapenem-hydrolyzing class D β-lactamases (CHDLs) is the major mechanism for imipenem resistance. In this study, we found a high prevalence of IRAB carrying a gene encoding CHDL, bla(OxA-23)...
Infection control data from psychiatric units and clinics are limited. This time series study was designed to determine the prevalence and risk factors for methicillin-resistant Staphylococcus aureus (MRSA) colonization and/or infection among 500 men and women on admission to psychiatric units at Th...
Group A Streptococcus (GAS) causes human diseases ranging in severity from uncomplicated pharyngitis to life-threatening necrotizing fasciitis and shows high rates of macrolide resistance in several countries. Our goal is to identify antimicrobial resistance in Spanish GAS isolates collected between...
In 1988, the World Health Assembly resolved to eradicate poliomyelitis worldwide. One of the main tools used in polio eradication efforts has been the live, attenuated oral poliovirus vaccine (OPV). This inexpensive vaccine is administered easily by mouth, makes recent recipients resistant to infect...
A cluster of time-linked cases and the identification of a clonal strain suggest the occurrence of an outbreak of listeriosis in Belgium in 2011, presumably due to the consumption of hard cheese made with pasteurised milk and produced by a Belgium manufacturer. The outbreak clone was identified as L...
Community acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is a major global problem. This study attempted to investigate the prevalence of nasal carriage of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) strains among 360 healthy university students at An...
Human campylobacteriosis exhibits a distinctive seasonality in temperate regions. This paper aims to identify the origins of this seasonality. Clinical isolates [typed by multi-locus sequence typing (MLST)] and epidemiological data were collected from Scotland. Young rural children were found to hav...
No abstract available
The aim of the two studies reported here was to investigate the distribution of stx genes in human faecal samples from volunteers and in faecal samples submitted to a regional microbiology hospital laboratory, and to isolate and characterize STEC from stx-positive samples. In total, faecal samples f...
Foot-and-mouth disease virus (FMDV) is the causative agent of the most important disease of domestic cattle, foot-and-mouth disease. In Ecuador, FMDV is maintained at an endemic state, with sporadic outbreaks. To unravel the tempo and mode of FMDV spread within the country we conducted a Bayesian ph...
The population structure of 111 methicillin-susceptible Staphylococcus aureus (MSSA), recovered in Spain from healthy and risk-free carriers was investigated using pulsed-field gel electrophoresis (PFGE), spa (staphylococcal protein A) typing, multi locus sequence typing (MLST) and the accessory gen...
This study was carried out on 189 methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates collected in a third-level hospital in Valladolid, Spain, between 2005 and 2008 in order to investigate the changes in molecular epidemiology and genetic backgrounds associated with the changes in...
A 52-year-old male Japanese businessman with massive cerebral bleeding was transferred from India to Japan and was admitted to our hospital. Multidrug-resistant Acinetobacter baumannii was isolated from his sputum. The minimum inhibitory concentrations for this strain were as follows: imipenem, 64 μ...
Previously, a small study showed that 14f was the predominant subtype of Treponema pallidum in Shanghai, China. The result was quite different from the genotype distribution in other areas of China. This study aimed to identify the strain types of Treponema pallidum in samples collected over a 5-yea...
In 1991, multiresistant Escherichia coli O78:H10 strains caused an outbreak of urinary tract infections in Copenhagen, Denmark. The phylogenetic origin, clonal background, and virulence characteristics of the outbreak isolates, and their relationship to nonoutbreak O78:H10 strains according to these...
From August 1999 through July 2002, hyperinvasive Neisseria meningitidis serogroup B (MenB) clonal complexes (CCs), namely, ST-32/ET-5 (CC32) and ST-41/44/lineage 3 (CC41/44), were predominant in the Western Cape Province of South Africa. This study analyzed MenB invasive isolates from a national la...
The main goal of this study was to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA), particularly livestock-associated MRSA (LA-MRSA) in pigs and pork. The genotypic relatedness of isolates on the farm, at slaughter, and at the retail level was assessed. Paired nasal an...
A total of 434 methicillin-resistant Staphylococcus aureus (MRSA) baseline isolates were collected from subjects enrolled in a prospective, double-blind randomized trial comparing linezolid versus vancomycin for the treatment of nosocomial pneumonia. Isolates were susceptibility tested by broth micr...
No abstract available
A longitudinal study combining multilocus sequence typing with molecular evolutionary analysis determined the distribution, population structure, and evolution of antibiotic resistance in Neisseria gonorrhoeae isolates in Saskatchewan that were collected between 2005 and 2008. Of 195 gonococcal isol...
Increasing resistance due to the production of ESBL in Escherichia coli (ESBL-E. coli) has become a major threat to public health. Our aims were to study the incidence of ESBL-E. coli acquisition during hospitalization and the transmission rates of different ESBL-E. coli clones. This was a prospecti...
Between March and May of 2011, a cluster of three fatal cases of meningococcal sepsis occurred in Andalusia, Spain, in a municipality with a population of around 20,000 inhabitants. The cases were in their mid-teens to early thirties and were notified to the epidemiological surveillance system of An...
The global emergence of vancomycin-resistant Enterococcus faecium (VREfm) has been characterized by a clonal spread of strains belonging to clonal complex 17 (CC17). Genetic features and clonal relationships of 53 VREfm isolated from patients in 2 hospitals in Ribeirao Preto, São Paulo, Brazil, duri...
Neisseria meningitidis serogroup C has emerged as a cause of epidemic disease in Hefei. The establishment of serogroup C as the predominant cause of endemic disease has not been described. We conducted national laboratory-based surveillance for invasive meningococcal disease during 2000-2010. Isolat...
The recent outbreak caused by Schmallenberg virus, which affected sheep, goats and cattle in Europe, highlighted the importance of having a robust surveillance plan capable of monitoring abortions and malformations in the livestock offspring. In this context, bluetongue viruses (BTVs) represented an...
The Netherlands is one of the most densely populated countries in the world, with extensive livestock of pigs. In 2005, the emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) was a fact, with a relatively high MRSA colonisation among pig farmers. These MRSA isola...
Listeria monocytogenes is an intracellular, opportunistic pathogen which can cause severe infections such as meningitis, encephalitis and bacteremia. It can also cause abortions in human beings. Foods are the vehicle for infection of the host. Serotypification has discriminated 13 serotypes: 1/2a,1/...
Investigate the molecular epidemiological characteristics of bloodstream infections (BSI) due to Candida albicans (C. albicans) in the intensive care unit (ICU) of West China Hospital, Sichuan University. C. albicans isolates recovered from blood cultures in West China Hospital, Sichuan University b...
In 2011, an outbreak of illness caused by Yersinia enterocolitica O:9 in Norway was linked to ready-to-eat salad mix, an unusual vehicle for this pathogen. The outbreak illustrates the need to characterize isolates of this organism, and reinforces the need for international traceback mechanisms for...
Rotavirus (RV) and norovirus (NoV) are considered the most common causes of viral gastroenteritis in children. In this study, the prevalence of RV and NoV infection in 55 children with diarrhea from the rural community Akinlalu in Southwestern Nigeria was investigated using real-time PCR assays. The...
Noroviruses are the most common cause of acute non-bacterial gastroenteritis outbreaks worldwide, including New Zealand. New Zealand has a population of 4.4 million, which allows for centralized outbreak surveillance and a Norovirus Reference Laboratory, which facilitates efficient diagnosis, survei...
GI noroviruses are relatively rare and systematic studies of the molecular epidemiology of GI norovirus outbreaks are lacking. The current study examined the molecular virology of GI norovirus outbreaks in Victoria, Australia (2002-2010). Of 1,617 norovirus outbreaks identified, 69 (4.3%) were assoc...
The lipooligosaccharide (LOS) locus class was determined using polymerase chain reaction (PCR) in 335 Finnish Campylobacter jejuni strains isolated from humans, poultry and bovines with known multilocus sequence types. The results revealed an association between clonal complexes/sequence types (STs)...
No abstract available
In November 2009, we initiated a multistate investigation of Salmonella Montevideo infections with pulsed-field gel electrophoresis pattern JIXX01.0011. We identified 272 cases in 44 states with illness onset dates ranging from 1 July 2009 to 14 April 2010. To help generate hypotheses, warehouse sto...
The purpose of this retrospective study was to evaluate the pathogenic role of Corynebacterium species in lower respiratory tract infections as well as their routine laboratory investigation. From April 2007 to August 2009, 27 clinical isolates were significantly recovered from respiratory specimens...
We report the first case of peritonitis caused by Roseomonas mucosa which led to technique failure in an adolescent patient with HIV receiving peritoneal dialysis. Identification of the causative organism by 16S rRNA gene sequencing and phylogenetic analysis is described.
The rate of new emerging infectious diseases entering the human population has increased over the past century, with pathogens originating from animals or from products of animal origin accounting for the vast majority. Primary risk factors for the emergence and spread of emerging zoonoses include e...
Understanding the epidemiological dynamics of influenza virus is central to surveillance and vaccine strain selection. It has been suggested that tropical and subtropical regions represent the global source of influenza epidemics. However, our understanding of the epidemiological dynamics of influen...
In the spring of 2009, swine-origin influenza H1N1pdm09 viruses caused the first influenza pandemic of this century. We characterized the influenza viruses that circulated early during the outbreak in Mexico, including one newly sequenced swine H1N1pdm09 virus and three newly sequenced human H1N1pdm...
In April 2012, a cluster of two cases of meningococcal disease caused by rifampicin-resistant C meningococci was reported in the Champagne-Ardenne region, France. The two cases occurred in a student population living in the same town but studying at different schools. Bacteriological and epidemiolog...
High-resolution genotyping of Chlamydia trachomatis improves the characterization of strains infecting different patient groups and sexual networks. In this study, multilocus sequence typing (MLST) and ompA sequence determination were used for an analysis of C. trachomatis strains from 203 men who h...
The prevalence of asymptomatic carriers of methicillin-resistant Staphylococcus aureus (MRSA) in the general population is increasing and now is estimated to be 5%-10%. Although the overall prevalence of MRSA infections in hospitals may be decreasing, it remains important, as asymptomatic carriers a...
A major outbreak of methicillin-resistant Staphylococcus aureus (MRSA) occurred in locations C and Z of our hospital and lasted for several years. It affected 1,230 patients and 153 personnel. Outbreak management was installed according to the Dutch "search and destroy" policy. A rapid, high-through...
In central area of Argentina, the epidemiologic and molecular characteristics of Chlamydophila psittaci infections are still unknown. Nested polymerase chain reaction of domains II, III, and IV of the omp A gene was used to detect Chlamydophila in 43 pharyngeal swab samples from patients with suspec...
Although there has been a worldwide emergence and spread of methicillin-resistant Staphylococcus aureus (MRSA), little is known about the molecular epidemiology of MRSA in Tanzania. In this study, we characterized MRSA strains isolated from clinical specimens at the Bugando Medical Centre, Tanzania,...
Methicillin resistant Staphylococcus aureus (MRSA) infection can cause significant morbidity and mortality in neonates. We investigated a nosocomial MRSA outbreak in a neonatal intensive care unit (NICU), using a novel typing method. Following two fatal cases, in May 2011, a prospective outbreak inv...
Cryptococcosis is primarily caused by two Cryptococcus species, i.e., Cryptococcus neoformans and C. gattii. Both include several genetically diverse subgroups that can be differentiated using various molecular strain typing methods. Since little is known about the molecular epidemiology of the C. n...
No abstract available
We describe polyclonal spread of colistin-resistant Klebsiella pneumoniae in an acute general hospital in Italy. Between June and December 2011, 58 colistin-resistant K. pneumoniae isolates were recovered from 28 patients admitted to different wards, but mainly in the intensive care units. All isola...
In settings of high methicillin-resistant Staphylococcus aureus (MRSA) prevalence, detection of nosocomial transmission events can be difficult without strain typing. Prospective typing of all MRSA isolates could potentially identify transmission in a timely fashion, making infection control respons...
Using a repetitive-sequence-based (rep)-PCR (DiversiLab), we have molecularly typed Acinetobacter nosocomial bloodstream isolates (Acinetobacter baumannii [n = 187], Acinetobacter pittii [n = 23], and Acinetobacter nosocomialis [n = 61]) obtained from patients hospitalized in U.S. hospitals over a 1...
Introduction of the Haemophilus influenzae type b (Hib) conjugate vaccine has resulted in a dramatic reduction of Hib disease in the U.S. and an increase in the relative importance of infections caused by nontypeable strains. The current project describes the characteristics and clinical outcomes of...
A molecular epidemiological survey was conducted on an extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBLKp) infection in our neonatal intensive care unit (NICU) from February to June 2008. Cultures of clinical samples from neonates in the NICU, the hands of healthcare workers an...
In this study, 116 multidrug-resistant Acinetobacter baumannii (MDR-Ab) isolates recovered in various regions of Portugal were studied. All isolates were non-susceptible to tigecycline; one isolate was also non-susceptible to colistin, making it a step closer to pandrug resistance. Among 72 isolates...
An important virulence factor of Klebsiella pneumoniae is the production of capsular polysaccharide (CPS), a thick mucus layer that allows for evasion of the host's defense and creates a barrier against antibacterial peptides. CPS production is driven mostly by the expression of genes located in a l...
Salmonella enterica subsp. enterica serovar Typhimurium is responsible for the majority of salmonellosis cases worldwide. This Salmonella serovar is also responsible for die-offs in songbird populations. In 2009, there was an S. Typhimurium epizootic reported in pine siskins in the eastern United St...
A novel targeted massive parallel sequencing approach identified genetic variation in eight known or predicted fimbrial adhesins for 46 Salmonella strains. The results highlight associations between specific adhesin alleles, host species, and antimicrobial resistance. The differentiation of allelic...
In this study, the population structure, incidence, and potential sources of human infection caused by the d-tartrate-fermenting variant of Salmonella enterica serovar Paratyphi B [S. Paratyphi B (dT+)] was investigated. In Germany, the serovar is frequently isolated from broilers. Therefore, a sele...
Recent molecular-typing studies suggest cross-infection as one of the potential acquisition pathways for Pseudomonas aeruginosa in patients with cystic fibrosis (CF). In Australia, there is only limited evidence of unrelated patients sharing indistinguishable P. aeruginosa strains. We therefore exam...
Fourteen cases of Legionnaires’ disease were confirmed in residents from England and Wales with history of travel to Corfu, Greece, in the 14 days before symptom onset. These cases were reported to the Health Protection Agency national surveillance scheme for Legionnaires’ disease in residents of En...
Candida parapsilosis has become a significant cause of invasive fungal infections in seriously ill patients. Nosocomial outbreaks through direct and indirect contact have been described. The aim of this study was the molecular characterization of what appeared to be an ongoing C. parapsilosis outbre...
Buruli ulcer (BU) is a necrotizing infection of skin and soft tissue caused by Mycobacterium ulcerans. In Australia, most cases of BU are linked to temperate, coastal Victoria and tropical, northern Queensland, and strains from these regions are distinguishable by variable-number tandem repeat (VNTR...
Campylobacter jejuni, the most leading cause for bacterial gastroenteritis worldwide, shows a high genetic diversity among its isolates. Recently, we demonstrated the existence of six C. jejuni-groups by combining MLST with six genetic markers. These groups were further characterized by the detectio...
The objective of this study was to identify patient symptoms and case outcomes that were more likely to occur as a result of Salmonella infections caused by bovine-associated subtypes (isolates that matched contemporary bovine isolates from New York by serovar and pulsed-field gel electrophoresis pa...
Evidence is accumulating that active surveillance, when combined with appropriate infection control, is a successful measure for controlling hospital-acquired meticillin-resistant Staphylococcus aureus (MRSA). In this study, the impacts of a long-term control strategy of this type, including the use...
Seven metallo-β-lactamase-positive isolates of Serratia marcescens were recovered from three patients hospitalized in a neonatal ward in an Argentinean hospital during the period July-September 2011. All the isolates were multidrug-resistant, they belonged to a single clone, and carried a blaVIM-16...
Streptococcus agalactiae (Group B Streptococcus, GBS), Streptococcus dysgalactiae subsp. dysgalactiae (Group C Streptococcus, GCS) and Streptococcus uberis are relevant mastitis pathogens, a highly prevalent and costly disease in dairy industry due to antibiotherapy and loss in milk production. The...
Nosocomial infections caused by Pseudomonas aeruginosa presenting resistance to beta-lactam drugs are one of the most challenging targets for antimicrobial therapy, leading to substantial increase in mortality rates in hospitals worldwide. In this context, P. aeruginosa harboring acquired mechanisms...
Burkholderia spp. strains collected in Spain over a 13-year period from patients with cystic fibrosis (CF) (n = 148), non-CF patients (n = 103) and from environmental sources (n = 64) were characterised. One hundred and forty-one of the examined strains were involved in seven suspected nosocomial di...
No abstract available
Feline calicivirus (FCV) is an important pathogen of domestic cats and a frequently used model of human caliciviruses. Here we use an epidemiologically rigorous sampling framework to describe for the first time the phylodynamics of a calicivirus at regional and national scales. A large number of FCV...
Gram-negative bloodstream infections are an important cause of neonatal mortality. In October 2009, we investigated a Klebsiella spp outbreak in a neonatal intensive care unit in Guatemala. Probable cases were defined as a Klebsiella spp isolated from blood in neonates aged <28 days in the neonatal...
A total of 183 patients were colonized or infected with multidrug-resistant Pseudomonas aeruginosa isolates at a hospital in Spain during 2007-2010; prevalence increased over this period from 2.8% to 15.3%. To characterize these isolates, we performed molecular epidemiologic and drug resistance anal...
During the 1990s, an epidemic of B:4 Neisseria meningitidis infections affected Brazil. Subsequent increase in C:4 disease suggested B → C capsular switching. This study identified B → C switches within the sequence type 32 complex. Substantial disease related to capsular switching emphasizes the ne...
To determine the origin of >4,000 suspected diarrheagenic Escherichia coli strains isolated during 2004-2011 in South Africa, we identified 7 isolates as serotype O104; 5 as enteroaggregative E. coli O104:H4, and 2 as enteropathogenic E. coli O104:non-H4. Pulsed-field gel electrophoresis showed that...
Methicillin-resistant Staphylococcus aureus (MRSA) strains are the major causative agents of numerous hospital- and community-acquired infections. Increasing prevalence of MRSA in cystic fibrosis (CF) populations is reported all over the world. Although there are papers reporting the prevalence and...
Clostridium difficile is a spore-forming Gram-positive bacterium that causes chronic diarrhea and sometimes life-threatening disease mainly in elderly and hospitalized patients. The reported incidence of C. difficile infection has changed dramatically over the last decade and has been related to the...
No abstract available
Since the mid-1980s, rice cultivation has expanded rapidly in Burundi to reach approximately 50,000 ha in 2011. In 2007, leaf mottling, reduced tillering, and stunting symptoms were observed on rice at Gatumba near Bujumbura, causing small patches in less than 10% of the fields. Rice yellow mottle v...
After community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) was identified, new community-onset, healthcare-associated MRSA (HA-MRSA-CO) infections have been noticed as MRSA infection in patients with community-onset infection who have underlying conditions resulting in frequent...
This report describes a risk assessment and subsequent actions following isolation of Legionella pneumophila serogroup 1 in the water supply to a birthing pool during a planned maintenance programme. A literature search for cases of neonatal legionellosis identified 24 reports of cases among babies...
In December 2009, a 76-year-old male patient developed pneumonia due to Burkholderia cepacia whilst in an intensive care unit at a Japanese university hospital. During the subsequent environmental investigation to find the source, B. cepacia with an identical DNA type was found in his denture storag...
Shigella sonnei has become the dominant serotype causing shigellosis in Asian countries in recent years. In this study, we characterize the increasing trend of antibiotic resistance profiles and genotypes of S. sonnei isolates in the Beijing area. From January 2002 to December 2007, a total of 1108...
The purpose of this study was to examine the carbapenemase-encoding resistance genes and analyze homologous of multidrug-resistant Acinetobacter baumannii (MRAB) isolates from nosocomial infections. Seventy-six A. baumannii strains were collected from inpatients and object surface of devices in inte...
Multidrug-resistant Pseudomonas aeruginosa (MDR-P) expressing VIM-metallo-beta-lactamase is an emerging infection control problem. The source of many such infections is unclear, though there are reports of hospital outbreaks of P. aeruginosa related to environmental contamination, including tap wate...
Microsatellites (or short tandem repeats, STRs) are the genetic markers of choice for studying Aspergillus fumigatus molecular epidemiology due to its reproducibility and high discrimination power. However, the specificity of these markers must be investigated in a group of isolates from closely rel...
Pseudomonas aeruginosa is an opportunistic pathogen which has the potential to become extremely harmful in the nosocomial environment, especially for cystic fibrosis (CF) patients, who are easily affected by chronic lung infections. For epidemiological purposes, discriminating P.aeruginosa isolates...
The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been associated with the emergence of the CTX-M-producing sequence type 131 (ST131) pandemic clonal group, a member of the O25b serogroup and the B2 phylogenetic group. To assess the clonal spread of ESB...
Clostridium difficile is an emerging threat in hospital environments. To analyse possible transmission and to distinguish between relapse and reinfection a collection of C. difficile isolates, sampled from 162 consecutive episodes of C. difficile infection, were PCR ribotyped. Two ribotypes (001 and...
We aimed to determine whether additional molecular and microbiological evaluations of methicillin-resistant Staphylococcus aureus (MRSA) isolated from patients newly identified as nasal carriers were useful for control strategies and whether longitudinal testing during the same or repeat hospitaliza...
The early identification of outbreaks is crucial for the control of Clostridium difficile infection. This study aimed to determine if the number of hospital-acquired C. difficile infections could be reduced by rapidly typing C. difficile strains using multiple-locus variable-number tandem-repeat ana...
Potato virus Y (PVY) is an important plant pathogen with a wide host range that includes, among others, potato, tobacco, tomato and pepper. The coat protein (CP) of PVY has been commonly used in phylogenetic studies for strain classification. In this study, we used a pool of 292 CP sequences from is...
While Staphylococcus epidermidis is commonly isolated from healthy human skin, it is also the most frequent cause of nosocomial infections on indwelling medical devices. Despite its importance, few genome sequences existed and the most frequent hospital-associated lineage, ST2, had not been fully se...
This is a retrospective study of the outbreaks of foot-and-mouth disease (FMD) in Peninsular Malaysia between 2001 and May 2007. In total, 270 outbreaks of FMD were recorded. Serotype O virus (89.95 %) and serotype A (7.7 %) had caused the outbreaks. Significant differences on the occurrence of FMD...
Described in detail is the molecular epidemiology of wild-type 1 poliovirus circulation in Ghana between 1995-2008, following the implementation of a surveillance system for cases of acute flaccid paralysis and poliovirus infection. Molecular phylogenetic analysis combined with a detailed evaluation...
No abstract available
Nasal colonisation with Staphylococcus aureus is a risk factor for invasive infection in human immunodeficiency virus (HIV)-positive individuals. This study aimed to characterise colonising S. aureus from regions with a high HIV prevalence. Single nasal swabs were taken from a total of 374 HIV-posit...
Methicillin-resistant Staphylococcus aureus (MRSA) is spreading worldwide and poses a serious public health problem, being present in hospital settings and communities. However, from the Middle East and the Arabian Peninsula few molecular typing data on MRSA strains are currently available. In order...
The transmission of meticillin-resistant Staphylococcus aureus (MRSA) between individual patients is difficult to track in institutions where MRSA is endemic. We investigated the transmission of MRSA where ST22-MRSA-IV is endemic on four wards using demographic data, patient and environmental screen...
In June 2010, a bla(KPC)-negative, ertapenem-resistant ST-258 Klebsiella pneumoniae strain was isolated from a patient in the Laniado Medical Center (LMC). Our aims were (i) to describe its molecular characteristics and resistance mechanisms and (ii) to assess whether the bla(KPC)-negative ST-258 K....
Temporal and seasonal trends in Campylobacter genotypes causing human gastroenteritis were investigated in a 6-year study of 3,300 recent isolates from Oxfordshire, United Kingdom. Genotypes (sequence types [ST]) were defined using multilocus sequence typing and assigned to a clonal complex (a clust...
Methicillin-resistant Staphylococcus aureus (MRSA) originated from the health care setting but is now emerging in communities without health care contact (CA-MRSA) or in livestock (LA-MRSA). The impact on the whole MRSA population was assessed in a German prospective multicenter study. Thirty-three...
Twenty-three strains of Staphylococcus aureus with borderline resistance to oxacillin were studied. These strains were not detected by the cefoxitin test, tests for penicillin-binding protein 2a (PBP2a), mecA, and mecA(LGA251) were negative, and the strains were genetically unrelated. To detect all...
An outbreak of salmonellosis (Salmonella Typhimurium, phage type DT120) occurred from 26 January to 15 March 2011, in Denmark, with 22 laboratory confirmed cases. Hypothesis-generating patient interviews gave rise to the suspicion that smoked pork tenderloin was the source of infection. The primary...
In this prospective, observational study of 618 consecutive adult patients with skin and soft tissue infections (SSTI) caused by methicillin-resistant Staphylococcus aureus (MRSA), the clinical characteristics, molecular epidemiology, and outcome of patients with clindamycin-resistant MRSA (n = 64)...
Data on the prevalence of Pneumocystis jirovecii (P. jirovecii) dihydropteroate synthase (DHPS) mutants in France are still limited. In this study, mutant prevalence in the Brest region (western France) was determined. Archival pulmonary specimens from 85 patients infected with P. jirovecii and admi...
Enterococcus faecalis is a nosocomial opportunistic pathogen, but is also found in fermented food products where it plays a fundamental role in the fermentation process. Previously, we have described the non-starter E. faecalis cheese isolate QA29b as harboring virulence genes and proven to be virul...
To characterize isolates of Staphylococcus aureus that were associated with staphylococcal food poisoning between 2006 and 2009 in Shenzhen, Southern China, a total of 52 Staphylococcus aureus isolates from 11 outbreaks were analyzed by using multilocus sequence typing (MLST), spa typing, and pulsed...
Recently, the first outbreak of clonally related VIM-2 metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa in a Dutch tertiary-care centre was described. Subsequently, a nationwide surveillance study was performed in 2010-2011, which identified the presence of VIM-2 MBL-producing P. aeruginos...
Escherichia coli clonal group A (CgA) causes disease in humans. This is the first study investigating the prevalence of CgA among E. coli from non-urine, extraintestinal infections in a northern European country. E. coli blood (n = 196) and paired urine (n = 195) isolates from the same patients with...
We investigated the molecular characteristics of ESBL-producing Escherichia coli in Japan. A total of 101 clinical isolates of ESBL-positive E. coli collected in Japan between June 2008 and November 2009 were studied. Among the 101 strains, 97 were positive for CTX-M, while 47 and two were positive...
We analyzed 353 Staphylococcus aureus bloodstream isolates from 2004 to 2009 to identify dominant genotypes, changes over time, and associations between genotype, phenotype, and clinical parameters. The isolates were genotyped with regard to spa type and presence of Panton-Valentine leukocidin and t...
Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdu...
The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans, an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (CF)....
The increase in the capacity and reduction in cost of whole-genome sequencing methods present the imminent prospect of such data being used routinely in real time for investigations of bacterial disease outbreaks. For this to be realized, however, it is necessary that generic, portable, and robust a...
Mycobacterium orygis, previously called the oryx bacillus, is a member of the Mycobacterium tuberculosis complex and has been reported only recently as a cause of human tuberculosis in patients of South Asian origin. We present the first case documenting the transmission of this organism from a huma...
No abstract available
Marked increases in Clostridium difficile infection (CDI) incidence, driven by epidemic strain spread, is a global phenomenon. The Clostridium difficile Ribotyping Network (CDRN) was established in 2007 as part of enhanced CDI surveillance in England, to facilitate the recognition and control of epi...
Biological differences, including vector competence for the protozoan parasite Theileria parva have been reported among populations of Rhipicephalus appendiculatus (Acari: Ixodidae) from different geographic regions. However, the genetic diversity and population structure of this important tick vect...
Hospital-associated infections are an increasing cause of morbidity and mortality in veterinary patients. With the emergence of multi-drug resistant bacteria, these infections can be particularly difficult to eradicate. Sources of hospital-associated infections can include the patients own flora, me...
Environmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (Bison bison) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park. Bacillus anthracis spores were isolated from these samples...
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the main bacterial pathogens responsible for nosocomial infections leading to pneumonia, bloodstream, skin, and soft tissue infections. The objective of this study was to investigate the genomic changes of MRSA in a tertiary hospital betwe...
A variable-number tandem-repeat (VNTR) typing assay for the differentiation of Mycobacterium abscessus strains was developed. This assay showed complete reproducibility, locus stability, and a discriminatory power (Hunter-Gaston discriminatory index [HGDI] of 0.9563) that is superior to that of mult...
Escherichia coli is the species most frequently associated with clinical infections by extended-spectrum-β-lactamase (ESBL)-producing isolates, with the CTX-M ESBL enzymes being predominant and found in genetically diverse E. coli isolates. The main objective of this study was to compare, on the bas...
To examine temporal dynamics of corneal infection (keratitis)-associated Pseudomonas aeruginosa, we compared the genetic characteristics of isolates collected during two different time periods (2003-2004 and 2009-2010) using an ArrayTube genotyping system. The distribution of keratitis-associated is...
The majority of HA-MRSA infections are caused by endogenous infection and by only a small number of clones. The reasons for the success of some clones over others are unknown. We investigated the evolution of an MRSA population from a large, acute-care teaching hospital in London, UK over a 10 year...
No abstract available
A cholera outbreak in Terengganu, Malaysia, in November 2009 was caused by 2 El Tor Vibrio cholerae variants resistant to typical antimicrobial drugs. Evidence of replacement of treatable V. cholerae infection in the region with antimicrobial-resistant strains calls for increased surveillance and pr...
Species of the Enterobacter cloacae complex are widely encountered in nature, but they can act as pathogens. The biochemical and molecular studies on E. cloacae have shown genomic heterogeneity, comprising six species: Enterobacter cloacae, Enterobacter asburiae, Enterobacter hormaechei, Enterobacte...
Epidemic disease caused by Neisseria meningitidis, the meningococcus, has been recognized for two centuries, but remains incompletely controlled and understood. There have been dramatic reductions in serogroup A and C meningococcal disease following the introduction of protein-polysaccharide conjuga...
Hetero-resistant vancomycin intermediate Staphylococcus aureus (hVISA) emerges worldwide in recent decade. The purpose of this study was to investigate the glycopeptide usage trend, the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) with reduced vancomycin susceptibility, the susce...
The prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been increased not only in the hospital but also in the community worldwide. This study was aimed to characterize ESBL- producing E. coli isolates and to investigate the molecular epidemiology of community isolates...
Carbapenem-resistant Acinetobacter baumannii infections are a worldwide endemic nosocomial threat. Between December 2010 and April 2011, an increase of carbapenem-resistant A. baumannii infections occurred in several Marseille University Hospitals. The aim of this study was to investigate the increa...
To describe an outbreak of KPC-2-producing Klebsiella pneumoniae with inter-hospital spread and measures taken to control transmission. Between January and March 2011, 13 K. pneumoniae isolates were collected from nine patients at hospital A and two patients at hospital B. Meropenem, imipenem and er...
The dengue virus serotype 3 (DENV-3) Indian subcontinent strain emerged in Puerto Rico in 1998 after a 21-year absence. The rapid expansion of DENV-3 on the island correlated with the withdrawal of the other serotypes for 7 years. The DENV-3 prevalence declined in 2008 and remains undetected. We seq...
We analyse the diversity of extended-spectrum beta-lactamases (ESBLs), antibiotic resistance genes, and plasmid content among Escherichia coli from a community and a hospital setting in Rio de Janeiro, Brazil. ESBL producers (CTX-M-2, CTX-M-9, CTX-M-59) belonged to different phylogroups/sequence typ...
Gentamicin is important in synergistic bactericidal therapy with cell wall agents for severe enterococcal infections. During 2003-2008, a 10-fold increase in the prevalence of high-level gentamicin resistance (HLGR), to above 50%, in blood culture isolates of Enterococcus faecium, was reported by th...
Extended-spectrum beta-lactamases (ESBLs) are an increasingly important cause of resistance in Gram-negative bacteria throughout the world. We investigated the clinical and molecular epidemiology of infections caused by ESBL-producing Enterobacteriaceae in a UK hospital, to identify the types of ESB...
Some molecular features of meticillin-resistant Staphylococcus aureus (MRSA) isolates causing invasive infections have been shown to have clinical implications. There is a need to monitor the situation using a combination of molecular and clinical data because, although MRSA clones tend to predomina...
Anthrax is a serious disease caused by Bacillus anthracis. Humans can become infected by handling products from infected animals, by breathing spores and rarely by eating undercooked meat from infected animals. The genome of B. anthracis is highly monomorphic and thus shows very low DNA sequence var...
Understanding the spread of infectious diseases is crucial for implementing effective control measures. For this, it is important to obtain information on the contemporary population structure of a disease agent and to infer the evolutionary processes that may have shaped it. Here, we investigate on...
Listeria monocytogenes can cause invasive diseases in humans and farm animals and is frequently isolated from dairy products and poultry. Listeriosis is uncommon in China but L. monocytogenes has been isolated from foods and food processing environments in China. However little is known of genetic d...
No abstract available
Multidrug-resistant Acinetobacter baumannii (MRAB) is a serious nosocomial pathogen characterized by its survival on inanimate surfaces for long periods, making control of outbreaks difficult. To analyse two hospital outbreaks caused by MRAB, determine their epidemiology, carbapenem-resistance mecha...
The contribution of horizontal gene transmission (HGT) in the emergence and spread of extended-spectrum beta-lactamase (ESBL)-producing Gram-negative bacteria during periods of endemicity is unclear. Over a 12-month period, rectal colonization with SHV-5- and SHV-12-producing Escherichia coli and Kl...
Widespread emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has changed the epidemiology of S. aureus infections. We examined the molecular types and antibiotic susceptibility of CA-MRSA and health care-associated MRSA (HA-MRSA) among Korean children. MRSA isol...
Limited comprehensive molecular typing data exist currently for Panton-Valentine leucocidin (PVL)-positive, methicillin-sensitive Staphylococcus aureus (PVL-MSSA) clinical isolates. Characterization of PVL-MSSA isolates by multilocus sequence typing (MLST) and spa typing in this study showed a genet...
We investigated the use of whole-genome mapping and pulsed-field gel electrophoresis (PFGE) with isolates from an outbreak of Salmonella enterica serotype Saintpaul. PFGE and whole-genome mapping were concordant with 22 of 23 isolates. Whole-genome mapping is a viable alternative tool for the epidem...
Studies about transmission rates of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in hospitals and households are scarce. Eighty-two index patients with new carriage of ESBL-producing Escherichia coli (ESBL-Ec; n = 72) or ESBL-producing Klebsiella pneumoniae (ESBL-Kp; n = 10) and...
To survey healthcare-associated Clostridium difficile infection (HA-CDI) in a 900-bed tertiary-care hospital, we prospectively investigated the epidemiology of CDI and distribution of PCR-ribotypes. From February 2009 through January 2010, all patients with HA-CDI were enrolled. Epidemiological info...
Tuberculosis (TB) remains a major global health problem. To investigate the genotypes of Mycobacterium tuberculosis (MTB) and the distribution of Beijing family strains, molecular epidemiology technologies have been used widely. From June 2010 to June 2011, 55 M. tuberculosis isolates from patients...
Foot-and-mouth disease virus serotype O accounts for around 80 % of the outbreaks in India. Although Indian serotype O isolates belongs to the ME-SA topotype, circulation of different lineages has been noted. After its emergence in the year 2001, the 'Ind2001' lineage outcompeted the PanAsia lineage...
We aim to characterise multiple ertapenem-resistant (ERT-R, n = 15) Enterobacteriaceae isolates identified as presumptive carbapenemase producers in a Portuguese hospital in a short period of time (March-July 2010). Antibiotic susceptibility patterns, β-lactamases, genetic relatedness [pulsed-field...
Colonized or infected patients pose a significant risk to noncolonized patients occupying the same room. The aim of this study was to investigate how far Enterococcus spp can spread from isolated and nonisolated patients. Conventional microbiological methods were used to recover enterococci from the...
The molecular fingerprints of 878 isolates of Mycobacterium bovis collected from cattle between 2009 and 2010 in different regions of Mexico were used in this study. One hundred and ninety-four spoligotypes were observed in total with a high degree of heterogeneity. Sixty-four percent of the isolate...
Molecular typing was used to elucidate Neisseria gonorrhoeae transmission networks among men who have sex with men (MSM) in Amsterdam, the Netherlands. We determined whether clusters of patients infected with specific N. gonorrhoeae genotypes were related to various epidemiological characteristics....
Methicillin-resistant Staphylococcus aureus (MRSA) pulsed-field type (PFT) USA300 causes skin and soft tissue infections in military recruits and invasive disease in hospitals. Chlorhexidine gluconate (CHG) is used to reduce MRSA colonization and infection. The impact of CHG on the molecular epidemi...
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has recently emerged as an important pathogen in neonatal intensive care units (NICUs). The purposes of this study were to characterize methicillin-resistant isolates from an outbreak in a NICU, to examine the genetic traits...
The World Health Organization (WHO) declared human tuberculosis (TB) a global health emergency and launched the "Global Plan to Stop Tuberculosis" which aims to save a million lives by 2015. Global control of TB is increasingly dependent on rapid and accurate genetic typing of species of the Mycobac...
A polyphasic analysis was carried out on Yersinia ruckeri strains isolated from recently outbreaks in vaccinated fish using a combination of different phenotypic and molecular typing methods in order to study their variability and epidemiological relationships. Eighty strains were subjected to bioty...
Molecular genotyping of Mycobacterium tuberculosis has proved to be a powerful tool in tuberculosis surveillance, epidemiology, and control. Based on results obtained through 15 years of nationwide IS6110 restriction fragment length polymorphism (RFLP) genotyping of M. tuberculosis cases in Denmark,...
Since its emergence in 2000, epidemic spread of the methicillin-resistant Staphylococcus aureus (MRSA) clone USA300 has led to a high burden of skin and soft tissue infections (SSTIs) in the United States, yet its impact on MRSA bloodstream infections (BSIs) is poorly characterized. To assess clonal...
Despite the importance of the Enterobacter cloacae complex as a nosocomial pathogen, little is known about the relative contribution of its single species and genotypes to its pathogenicity. We studied here the relationship between phylogenetically related strains and clinical infection sites. A tot...
Avibacterium paragallinarum causes infectious coryza in chickens, an acute respiratory disease that has worldwide economic significance. The objectives of this study were to determine the serovars, antimicrobial resistance, and pathogenicity of A. paragallinarum isolated from chickens in Thailand. E...
Coxiella burnetii is a highly clonal microorganism which is difficult to culture, requiring BSL3 conditions for its propagation. This leads to a scarce availability of isolates worldwide. On the other hand, published methods of characterization have delineated up to 8 different genomic groups and 36...
Numerous outbreaks of cholera have occurred in Kenya since 1971. To more fully understand the epidemiology of cholera in Kenya, we analyzed the genetic relationships among 170 Vibrio cholerae O1 isolates at 5 loci containing variable tandem repeats. The isolates were collected during January 2009-Ma...
Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are found with increasing the frequency, both in healthy individuals in the community and in hospitalized patients. In Colombia and the Andean region, CA-MRSA isolates have a genetic background that is related to the...
Despite South Africa being one of the high-burden multidrug-resistant tuberculosis (MDR-TB) countries, information regarding the population structure of drug-resistant Mycobacterium tuberculosis strains is limited from many regions of South Africa. This study investigated the population structure an...
Recent studies on outbreaks of Candida showed an increased incidence of bloodstream infections in neonatal intensive care units (NICUs) caused by C. parapsilosis species, highlighting the need for the proper identification and epidemiology of these species. Several systems are available for molecula...
Community-associated meticillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as an important pathogen worldwide in a continent-specific manner. Clinical characteristics of infections caused by CA-MRSA other than USA300, especially in healthcare settings, have not been well established. To c...
Molecular typing of Mycobacterium tuberculosis can be used to elucidate the epidemiology of tuberculosis, including the rates of clustering, the frequency of polyclonal disease, and the distribution of genotypic families. We performed IS6110 typing and spoligotyping on M. tuberculosis strains isolat...
There was a high percentage of macrolide resistance in Mycoplasma pneumoniae clinical isolates in China. The genetic relatedness of macrolide-resistant M. pneunomiae strains was investigated using the multilocus variable-number tandem-repeat assay (MLVA). Among 152 M. pneunomiae isolates, the 137 ma...
The recent emergence of carbapenemase-producing Enterobacteriaceae strains represents a major threat for hospitalized patients. We document the dissemination and control of carbapenemase-producing Klebsiella pneumoniae clones in a Greek hospital. During a 3-year study period (January 2009 to Decembe...
Nosocomial outbreaks of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae are an increasing concern in neonatal intensive care units (NICUs). We describe an outbreak of ESBL-producing K. pneumoniae that lasted 5 months and affected 23 neonates in our NICU. Proton pump inhibitor an...
The usefulness and performance of repetitive-sequence-based polymerase chain reaction (rep-PCR), the DiversiLab system, in the epidemiological surveillance for methicillin-resistant Staphylococcus aureus (MRSA) strain typing was assessed. MRSA isolates from five distinct outbreaks with precise epide...
The Aboriginal communities in Canada are challenged by a disproportionate burden of TB infection and disease. Contact investigation (CI) guidelines exist but these strategies do not take into account the unique social structure of different populations. Because of the limitations of traditional CI,...
Cholera occurs in sporadic cases and outbreaks in Nepal each year. Vibrio cholerae O1 (n = 522) isolated during 2007-2010 from diarrheal patients at 10 different hospital laboratories in Nepal were characterized. Biochemical and serologic identifications showed that all the isolates belonged to sero...
Once the outbreak with Burkholderia cenocepacia ST32 was identified in the Prague cystic fibrosis (CF) centre, molecular tools were implemented into diagnostic routine in order to complement infection control measures with as accurate as possible microbiological service. In addition, genotyping tech...
Vancomycin-resistant enterococci (VRE), particularly vancomycin-resistant Enterococcus faecium (VREfm), have emerged among the leading pathogens causing hospital-acquired infections worldwide. We aimed to examine whether there were newly introduced clones contributing to this increase and to assess...
New distinct strains of community-associated meticillin-resistant Staphylococcus aureus (CA-MRSA) have emerged as a cause of infection in previously healthy individuals in community settings. It is important to identify CA-MRSA for clinical management, epidemiological analysis, infection prevention...
In this study, dengue virus (DENV) isolates from a localized, small-scale, non-seasonal dengue outbreak were genetically characterized. The outbreak occurred during the pre-monsoon months (April-May) in a medical college campus in Kerala, South India in 2009 affecting 76 people. Analysis of 39 viral...
A scarlet fever outbreak occurred in Hong Kong in 2011. The majority of cases resulted in the isolation of Streptococcus pyogenes emm12 with multiple antibiotic resistances. Phylogenetic analysis of 22 emm12 scarlet fever outbreak isolates, 7 temporally and geographically matched emm12 non-scarlet f...
Shigellosis is a major public health concern worldwide, especially in developing countries. It is an acute intestinal infection caused by bacteria of the genus Shigella, with a minimum infective dose as low as 10-100 bacterial cells. Increasing prevalence of Shigella sonnei as the etiologic agent of...
Clostridium difficile is a gram positive, spore forming, toxin producing, anaerobic bacteria and an opportunistic pathogen for Man and many animal species, causing diarrhea in young piglets. Piglets probably become colonized from the environment. To investigate the possible spread and transmission o...
Streptococci are one among the major mastitis pathogens which have a considerable impact on cow health, milk quality, and productivity. The aim of the present study was to investigate the occurrence and virulence characteristics of streptococci from bovine milk and to assess the molecular epidemiolo...
Helicobacter cinaedi colonizes the colons of human and animals and can cause colitis, cellulitis, and sepsis in humans, with infections in immunocompromised patients being increasingly recognized. However, methods for analyzing the molecular epidemiology of H. cinaedi are not yet established. A geno...
Using polymerase chain reaction (PCR) to detect faecal hepatitis A virus (HAV) can be a useful tool for investigating HAV outbreaks, especially in low-endemic countries. We describe the use of faecal HAV PCR as a non-invasive tool for screening. Two Dutch children visiting different daycare centres...
Thailand was a hyper-endemic country for dengue with co-circulation of four serotypes and tens of thousands of infected cases annually. Taking into consideration the large number of local dengue virus (DENV) sequences available in GenBank, Thailand was the most ideal locality to study co-evolution o...
Carbapenem-resistant Acinetobacter baumannii has been known as an opportunistic pathogen that causes a variety of illness worldwide. In this study, we characterize the molecular epidemiology of 174 non-repetitive clinical isolates of A. baumannii collected from January to June 2009 from Xiangya Hosp...
Hypermucoviscous (HV) isolates of Klebsiella pneumoniae have been linked to virulence potential in experimental infections. We examined 33 isolates of K. pneumoniae from patients with bacteraemia for the HV phenotype on agar culture, and determined their virulence potential by screening for capsular...
Non-typhoidal Salmonella (NTS) contamination in poultry and poultry products is a major cause of food-borne disease in humans. This study presents the molecular epidemiology of NTS isolated from poultry in Senegal. A total of 261 NTS recovered from broiler farms, chicken carcasses and street vendors...
Mycoplasma agalactiae causes chronic infections in small ruminants and remains endemic in many regions of the world, despite intensive and costly eradication programs. In this study, the innate genomic plasticity of M. agalactiae was exploited to design and assess a combination of molecular epidemio...
The main perspective of this study was to determine cross-transmissions amongst anthrax cases and provide detailed information regarding the genotypes of Bacillus anthracis isolates circulating in Turkey. A total of 251 B. anthracis isolates were obtained from human (93 isolates), animal (155 isolat...
Understanding how pathogens invade and become established in novel host populations is central to the ecology and evolution of infectious disease. Influenza viruses provide unique opportunities to study these processes in nature because of their rapid evolution, extensive surveillance, large data se...
In this study, the association between antimicrobial susceptibility, PCR ribotype and presence of the ermB gene in clinical isolates of Clostridium difficile was investigated. PCR ribotyping and ermB gene PCR were performed on 131 C. difficile isolates. The susceptibility of these isolates to metron...
Methicillin-resistant Staphylococcus aureus (MRSA) infections represent a serious challenge for health care institutions, which is inherent in the combination of prevalence, transmission rates and costs. Furthermore, performing an MRSA screening requires information on the complex system of effectiv...
This study investigated the prevalence of vancomycin-resistant enterococci (VRE) in the broiler production environment after the avoparcin ban and their epidemiological relationship with human clinical VRE from the same geographical regions in Greece. Caecal contents from broilers (n = 500) from eig...
No abstract available
Tuberculosis (TB) is endemic in Taiwan and usually affects the lung, spinal TB accounting for 1-3% of all TB infections. The manifestations of spinal TB are different from those of pulmonary TB. The purpose of this study was to define the epidemiological molecular types of mycobacterial strains caus...
Enteropathogenic Escherichia coli (EPEC) is the most important cause of persistent diarrhea in children, particularly in developing countries. Animals serve as pathogenic E. coli reservoirs, and compelling evidence for cross-species EPEC transmission exists. In this report, enzootic EPEC infection a...
The detection of outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) infections and a rapid and accurate identification of sources and routes of transmission should be conducted in hospital settings as early and swiftly as possible. In this study, we investigated the application potentia...
The aim of this study was to describe the epidemiology of enterococci isolated from infections at an Algerian university hospital, and to evaluate the prevalence of vancomycin-resistant enterococci (VRE) and the clonal cluster present in this country. Patients who presented at Annaba University Hosp...
Bacillus species have caused healthcare-associated outbreaks of invasive disease as well as pseudo-outbreaks. We report an outbreak investigation of blood cultures positive for Bacillus cereus associated with alcohol prep pads (APPs) contaminated with B. cereus and Bacillus species resulting in a ra...
The aim of this study was to characterize the first two extended-spectrum cephalosporin-resistant and multidrug-resistant (MDR) Neisseria gonorrhoeae isolates collected from two sexually related patients (men who have sex with men) in Spain. Antimicrobial susceptibility was studied by Etest. Genes i...
On October 20, 2010, an outbreak of cholera was confirmed in Haiti for the first time in more than a century. As of April 10, 2012, a total of 534,647 cases, 287,656 hospitalizations, and 7,091 deaths have been reported in Haiti as a result of the outbreak. The Vibrio cholerae strain that caused the...
This study aimed to determine the aetiology of community-acquired pneumonia (CAP) by adding polymerase chain reaction (PCR) to conventional methods and to describe the clinical and laboratory features between patients with bacterial pneumonia (BP) and viral pneumonia (VP). Adults with CAP admitted f...
Comparison of genome-wide, high-resolution restriction maps of Klebsiella pneumoniae clinical isolates, including an NDM-1 producer, and in silico-generated restriction maps of sequenced genomes revealed a highly heterogeneous region we designated the 'high heterogeneity zone' (HHZ). The HHZ consist...
The analytical studies used to investigate foodborne outbreak are mostly case-control or retrospective cohort studies. However, these studies can be complex to perform and susceptible to biases. This article addresses basic principles of epidemiology, probability, and the use of case-case design to...
Diseases from Staphylococcus aureus are a major problem in Indian hospitals and recent studies point to infiltration of community associated methicillin resistant S. aureus (CA-MRSA) into hospitals. Although CA-MRSA are genetically different from nosocomial MRSA, the distinction between the two grou...
In Canada before 2005, large outbreaks of pneumococcal disease, including invasive pneumococcal disease caused by serotype 5, were rare. Since then, an epidemic of serotype 5 invasive pneumococcal disease was reported: 52 cases during 2005, 393 during 2006, 457 during 2007, 104 during 2008, and 42 d...
Dengue outbreaks and epidemics have been reported in all regions of Africa, and it is believed that all four dengue virus serotypes are in circulation. Available data suggest that dengue is endemic to 34 African countries and that Aedes aegypti mosquitoes--the primary vector for dengue transmission-...
Irruptive forest insect pests cause considerable ecological and economic damage, and their outbreaks have been increasing in frequency and severity. We use a phylogeographic approach to understand the location and progression of an outbreak by the MPB (Dendroctonus ponderosae Hopkins), an irruptive...
Vibrio parahaemolyticus has been one of the most important foodborne pathogens in Japan since the 1960s, and a large epidemic was caused by the pandemic serotype O3:K6 from 1997 to 2001. V. parahaemolyticus infections, however, have sharply declined since that time. Data on serotypes isolated from 9...
This paper describes the isolation and molecular identification of a novel paramyxovirus found during an investigation of an outbreak of neurorespiratory disease in a collection of Australian pythons. Using Illumina® high-throughput sequencing, a 17,187 nucleotide sequence was assembled from RNA ext...
Clostridium difficile infections (CDIs) are traditionally seen in elderly and hospitalized patients who have used antibiotic therapy. In the community, CDIs requiring a visit to a general practitioner are increasingly occurring among young and relatively healthy individuals without known predisposin...
This paper shows that control of foodborne disease outbreaks may be challenging even after establishing the source of infection. An outbreak of Salmonella Typhimurium U323 infections occurred in Denmark from March to September 2010, involving 172 cases. Before the detection of human cases, several p...
Candida albicans and Candida glabrata are the most common causative agents of both vulvovaginal candidiasis (VVC) and recurrent vulvovaginal candidiasis (RVVC). Studying the population structure and genotype differentiation of Candida species that cause RVVC may lead to a significant improvement in...
This study was conducted to investigate the molecular characteristics and genetic relatedness of vancomycin-resistant Enterococcus faecium (VREF) isolates obtained from humans and poultry in Korea. A total of 147 VREF isolates from humans (71 clinical isolates) and poultry (76 isolates) in Korea wer...
We describe an outbreak of methicillin-resistant Staphylococcus aureus (MRSA) ST398 in a nursing home in the Netherlands. Seven residents and 4 healthcare workers were identified with MRSA ST398, but 2 of the healthcare workers carried other strains. This study demonstrates that MRSA ST398 can sprea...
Outbreaks caused by linezolid-resistant (LR) enterococci remain rare. We report the epidemiological and molecular characteristics of the multiclonal dissemination of LR enterococci in the intensive care unit (ICU) of a Greek hospital. All LR enterococcal isolates recovered from patients hospitalized...
No abstract available
The global spread of New Delhi metallo-β-lactamase (NDM) is of significant public health concern. This study sought to determine whether bla(NDM) was present in Enterobacteriaceae isolates displaying resistance to carbapenems that were submitted to the National Antibiotic Reference Laboratory, Insti...
The emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has changed the epidemiology of MRSA infections worldwide. In contrast to hospital-associated MRSA (HA-MRSA), CA-MRSA more frequently affects healthy individuals, both with and without recent healthcare expos...
A cohort study on a barbecue-associated Salmonella outbreak was conducted to describe the burden of disease and to identify the outbreak vehicle. Dose-response relationships were tested with Fisher's exact and Wilcoxon rank sum tests (alpha = 0·05). S. Enteritidis isolates were cultured and phage-ty...
Patients receiving hemodialysis infected with methicillin-resistant Staphylococcus aureus (MRSA) have been considered to have healthcare-associated (HA) infections, but strains with community-associated (CA) characteristics have also been identified in this population. The authors compared infection...
Lymphogranuloma venereum (LGV) infections caused by Chlamydia trachomatis L types have recently emerged in Europe among HIV-positive men having sex with men. Our aim was to introduce a genotyping strategy suitable for a diagnostic laboratory using nucleic acid amplification tests (NAATs) for detecti...
To evaluate the antimicrobial susceptibility and genetic relatedness of 11 Stenotrophomonas maltophilia isolates from an outbreak of bovine clinical mastitis in one herd and two isolates from two separate mastitis cases in two other herds. Thirteen S. maltophilia isolates were obtained from milk sam...
The implementation of nationwide pneumococcal vaccination may lead to alterations in the pneumococcal population due to selective pressure induced by the vaccine. To monitor such changes, pneumococcal isolates causing invasive pneumococcal disease (IPD) before (2004-2005, n=1154) and after (2008-200...
Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clin...
Bluetongue virus (BTV) is transmitted by biting midges (Culicoides spp.). It causes disease mainly in sheep and occasionally in cattle and other species. BTV has spread into northern Europe, causing disease in sheep and cattle. The introduction of new serotypes, changes in vector species, and climat...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of infections that are becoming increasingly difficult to combat because of emerging resistance. In this study, 103 S. aureus, 41 MRSA and 62 methicillin-sensitive Staphylococcus aureus isolates, were collected from children in Jord...
Studies of macrolide resistance mutations and molecular typing using the newly proposed enhanced typing system for Treponema pallidum isolates obtained from HIV-infected patients in the Asia-Pacific region are scarce. Between September 2009 and December 2011, we conducted a survey to detect T. palli...
Between June and November 2010, a concerning rise in the number of cases of puerperal sepsis, a postpartum pelvic bacterial infection contracted by women after childbirth, was observed in the New South Wales, Australia, hospital system. Group A streptococcus (GAS; Streptococcus pyogenes) isolates PS...
In 2011, Germany experienced the largest outbreak with a Shiga toxin-producing Escherichia coli (STEC) strain ever recorded. A series of environmental and trace-back and trace-forward investigations linked sprout consumption with the disease, but fecal-oral transmission was also documented. The geno...
The genetic diversity and antibiotic resistance profiles of 38 Streptococcus equi subsp. zooepidemicus isolates were determined from a kennelled canine population during two outbreaks of hemorrhagic pneumonia (1999 to 2002 and 2007 to 2010). Analysis of the szp gene hypervariable region and the 16S-...
A refractory epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) emerged in the adult population at our hospital in 2005, as in most Israeli hospitals. Contemporaneously, a different clone of CRKP caused an easily contained outbreak in a paediatric long-term care facility (LTCF) in Jerusal...
The emergence of multidrug-resistant (MDR) Pseudomonas aeruginosa isolates producing IMP-type metallo-β-lactamases (MBLs) and aminoglycoside 6'-N-acetyltransferase [AAC(6')-Iae] has become a serious problem in medical settings in Japan. A total of 217 MDR P. aeruginosa isolates were obtained from Au...
We describe an outbreak of Nocardia cyriacigeorgica soft-tissue infections attributable to unlicensed cosmetic injections and the first report using multilocus sequence typing sequence data for determining Nocardia strain relatedness in an outbreak. All 8 cases identified had a common source exposur...
Bluetongue (BT) is a disease of ruminants caused by bluetongue virus (BTV), which is spread between its hosts by Culicoides midges. Vaccination is the most effective way to protect susceptible animals against BTV and was used reactively to control the recent northern European outbreak. To assess the...
The phylogenetic and epidemic relationships of 104 clinical isolates of Clostridium difficile from three hospitals of different geographical and population sources in China were investigated by multilocus sequence typing. Twenty-two sequence types (STs) were identified, four of which, ST117, ST118,...
A cluster of methicillin-resistant Staphylococcus aureus (MRSA) breast abscesses in women who had given birth at a hospital in Mumbai, India was investigated retrospectively. Nineteen of 20 cases were caused by a single clone: pvl-positive, spa type 648 (Ridom t852), ccrB:dru subtype 3:0, ST22-MRSA-...
Specific single-nucleotide polymorphisms (SNPs) are recognized as important DNA sequence variations influencing the pathogenesis of Pneumocystis jirovecii and the clinical outcome of Pneumocystis pneumonia, which is a major worldwide cause of illness among immunocompromised patients. Genotyping plat...
Seven Enterobacter cloacae isolates and seven Klebsiella pneumoniae isolates harbouring a phenotype compatible with the production of a metallo-β-lactamase were recovered between 2009 and 2011 in three Intensive Care Units of Hospital Vall d'Hebron (Barcelona, Spain). The presence of bla(VIM), bla(I...
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae has become endemic in many US hospitals. On the other hand, KPC-producing Escherichia coli remains rare. We studied infection or colonization due to KPC-producing E. coli identified at our hospital between September 2008 and February...
Human immunodeficiency virus (HIV) is one of the most genetically variable human viruses as it is characterized by high rates of mutation, viral replication, and recombination. Phylodynamics is a powerful means of describing the behavior of an infection as a combination of evolutionary and ecologica...
Genital herpes, usually caused by herpes simplex virus type 2 (HSV-2), is one of the most common sexually transmitted diseases in humans. By contrast, intrauterine HSV-2 infections have been described rarely in the literature. Our report describes a case of neonate who was delivered after 30+2 gesta...
Rickettsial infections remain under-diagnosed due to lack of diagnostic facilities in developing world. Here we present our experience at National Centre for Disease Control, Delhi, about a serosurvey done in Delhi for rickettsial disease with easy to perform low cost, low expertise Weil Felix test....
The rapid emergence of KPC-producing Klebsiella pneumoniae has become a serious problem in health-care settings, increasing in frequency worldwide. These infections are worrisome, since the antimicrobial treatment options for infections due to multidrug-resistant strains are very limited, and outbre...
Salmonella Chester infection has rarely been reported in the literature. In 2010, 33 case patients were reported in 2 months in four Canadian provinces. We conducted an outbreak investigation in collaboration with public health agencies, food safety specialists, regulatory agencies, grocery store ch...
Genetic typing data are a potentially powerful resource for determining how infection is acquired. In this paper MLST typing was used to distinguish the routes and risks of infection of humans with Campylobacter jejuni from poultry and ruminant sources C. jejuni samples from animal and environmental...
Salmonella enterica serovar Paratyphi A infection has caused public health problems in some countries in recent years. Pulsed-field gel electrophoresis (PFGE) has been used for the subtyping and epidemiological investigations of some serotypes of Salmonella, mainly in outbreaks caused by non-typhoid...
In the present study, nonduplicate, clinical isolates of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, Klebsiella spp, and Proteus mirabilis were collected during a 10-year period from 2000 to 2009 at several hospitals in the Kinki region, Japan. The detection rate of E coli marke...
The study objective was to define the risk factors and the route of Staphylococcus aureus transmission between mother and newborn. Women at late pregnancy were screened for nasal and vaginal S. aureus colonization. Newborns were screened for nasal, auricular, umbilical, and rectal colonization at bi...
The annual incidence of invasive Kingella kingae infection in children younger than 4 years of age was significantly higher in westernized Jews than in indigent Bedouins living side by side in southern Israel (12.21/100,000 and 5.83/100,000, respectively, (P < 0.05). One K. kingae clone was overrepr...
The aim of this study was to detect extended-spectrum beta-lactamases (ESBL) in Enterobacteriaceae isolates in the intensive care unit (ICU) of Tlemcen hospital in north-western Algeria. Antimicrobial susceptibility testing, molecular typing, characterization of ESBL-encoding genes and the genetic e...
Prospective typing of Salmonella enterica serovar Typhimurium (STM) by multiple-locus variable-number tandem-repeat analysis (MLVA) can assist in identifying clusters of STM cases that might otherwise have gone unrecognised, as well as sources of sporadic and outbreak cases. This paper describes the...
Phylogenetic analysis has become a powerful tool for the investigation of evolution at a molecular level. During the last three decades, statistical phylogenetics has increasingly been applied to the study of microbial pathogens. The new field of phylodynamics was formally introduced in 2004 and enc...
This study was performed to describe the epidemiological traits of ceftazidime-resistant Acinetobacter baumannii clinical isolates from Korea. Antimicrobial susceptibilities were determined by disk diffusion assay. PCR experiments were performed to detect genes encoding extended-spectrum β-lactamase...
Outbreaks caused by Klebsiella pneumoniae producing carbapenemases and other β-lactamases have been reported. Four neonates admitted to a neonatal intensive care unit (NICU) in a Chinese hospital developed respiratory infection while receiving intensive care. In all four cases, multidrug-resistant K...
Diagnoses of Shigella flexneri in the United Kingdom (UK) are usually travel-related. However, since 2009, there has been an overall increase in UK-acquired cases. The Health Protection Agency has been investigating a national outbreak of S. flexneri detected in 2011 and which is still ongoing. Case...
Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers, and adolescents worldwide. DNA sequence-based typing, including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens, has become the standard f...
On 22 June 2011, 8 patients with hemolytic uremic syndrome (HUS) or bloody diarrhea were reported in France. All 8 were attendees of a community center event on 8 June near Bordeaux. Three Escherichia coli cases were confirmed by isolation of Shiga toxin-producing E. coli O104:H4 stx2 aggR producing...
In this review, based on my Garrod Lecture to the British Society for Antimicrobial Chemotherapy, I have given a brief outline of my career over the past 40 years, starting with research in the 1970s into the properties and functions of penicillin-binding proteins (PBPs), leading to the identificati...
No abstract available
The epidemic of USA300-0114 methicillin-resistant Staphylococcus aureus (MRSA) in the USA has been remarkable for its virulence and for its ability to cause infections in both the community and healthcare settings. Although it has mainly been associated with skin and soft tissue infections, particul...
Acinetobacter baumannii presents a clinical challenge when it is non-susceptible to carbapenems. The prevalence of carbapenem-non-susceptible A. baumannii in Japan is unclear, as previous studies have been limited in scope. We investigated the spread of carbapenem-non-susceptible A. baumannii in Jap...
Throughout history, technologic advancements have fueled the engine of innovation, which, in turn, has driven discovery. Accordingly, recent advancements in DNA sequencing technology are revolutionizing bacterial genomics. To review important developments from the literature. The current state of ba...
Little is known about the dynamics of colonizing Enterococcus faecium clones during hospitalization, invasive infection and after discharge. In a prospective observational study we compared intestinal E. faecium colonization in three patient cohorts: 1) Patients from the Hematology Unit at the Unive...
No abstract available
Clostridium difficile infection (CDI) is an important cause of morbidity and mortality internationally, yet there are important regional differences in the epidemiology and microbiology of disease. Most reports have come from North America and Europe, with limited information from other regions, inc...
A set of 300 Dutch Cryptococcus neoformans isolates, obtained from 237 patients during 1977 to 2007, was investigated by determining the mating type, serotype, and AFLP and microsatellite genotype and susceptibility to seven antifungal compounds. Almost half of the studied cases were from HIV-infect...
We report the molecular epidemiology of 27 clinical multidrug-resistant Staphylococcus epidermidis (MDRSE) isolates collected between 2003 and 2007 in an Australian teaching hospital. The dominant genotype (sequence type 2 [ST2]) accounted for 85% of the isolates tested and was indistinguishable fro...
We determined the population genetic structures of feline and canine Staphylococcus aureus strains in Japan by multilocus sequence typing (MLST). Ecological analyses suggested that multiple feline-related S. aureus clones, including ST133, naturally occur as commensals and can cause endogenous infec...
There have been numerous reports of clustered outbreaks of Pneumocystis pneumonia (PCP) at renal transplant centers over the past 2 decades. It has been unclear whether these outbreaks were linked epidemiologically to 1 or several unique strains, which could have implications for transmission patter...
Passive reporting and laboratory testing delays may limit gastrointestinal (GI) disease outbreak detection. Healthcare systems routinely collect clinical data in electronic medical records (EMRs) that could be used for surveillance. This study's primary objective was to identify data streams from EM...
Human migration caused by political unrest, wars and poverty is a major topic in international health. Infectious diseases like tuberculosis follow their host, with potential impact on both the migrants and the population in the recipient countries. In this study, we evaluate Mycobacterium tuberculo...
Bluetongue (BT) is an economically important disease of ruminants caused by bluetongue virus (BTV) and transmitted by Culicoides biting midges. The most practical and effective way to protect susceptible animals against BTV is by vaccination. Data from challenge studies in calves and sheep conducted...
A variable-number tandem repeat (VNTR) protocol targeting 10 loci in the Brucella abortus genome was used to assess genetic diversity among 366 field isolates recovered from cattle, bison, and elk in the Greater Yellowstone Area (GYA) and Texas during 1998 to 2011. Minimum spanning tree (MST) and un...
Staphylococcus epidermidis is a harmless commensal, but it can become a human pathogen, mainly in the hospital environment. In order to clarify strategies used by these bacteria to adapt to the hospital environment, we compared the population structure and staphylococcal cassette chromosome mec (SCC...
This study investigated the correlation between bla(OXA-51) variants and Acinetobacter baumannii worldwide clonal lineages 1 to 8 (WW1 to -8). The bla(OXA-51-like) genes of 102 A. baumannii isolates were sequenced. Using DiversiLab repetitive-sequence-based PCR (rep-PCR) typing, 92 of these isolates...
No abstract available
No abstract available
In Ethiopia where there is no strong surveillance system and state of the art diagnostic facilities are limited, the real burden of tuberculosis (TB) is not well known. We conducted a community based survey to estimate the prevalence of pulmonary TB and spoligotype pattern of the Mycobacterium tuber...
Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core...
HIV-1 subtype B is predominant in Europe except in some countries from Eastern Europe which are characterized by a high prevalence of non-B subtypes and circulating recombinant forms (CRFs). Romania is a particular case: the HIV-1 epidemic started with subtype F1 which is still the most prevalent. P...
Pneumocystis jirovecii pneumonia (PCP) and cytomegalovirus (CMV) infection represent possible complications of medical immunosuppression. Between 2005 and 2010, non-human immunodeficiency virus (HIV) PCP patients admitted to a nephrology unit were analyzed for outcome, CMV comorbidity, and patient-t...
The objective of the present study was to characterize Erysipelothrix sp. strains from recent erysipelas outbreaks in Japan. Eighty-three (100%) strains were identified as E. rhusiopathiae, based on serotyping and spaA PCR. Fifty (60.3%), 5 (6.0%), and 28 (33.7%) strains were isolated from animals w...
The demographic characteristics of the population of Madrid, with a steady increase in immigrants, from 4.7% in 1998 to 17.4% in 2007, provide an opportunity to study in depth the transmission of TB. Our aim was to compare two 3-year longitudinal molecular studies of TB to define transmission patter...
To characterize Neisseria meningitidis isolates collected from cerebrospinal fluid of meningitis cases in Egypt (1998-2003) as part of surveillance studies, 67 isolates were serogrouped, tested for antibiotic sensitivity and analyzed using multilocus sequence typing (MLST). Results show that isolate...
Chamois (Rupicapra spp.) are mountain ungulates from Southern and Central Europe and the Near East. A newly reported border disease virus (BDV) has affected the easternmost populations of Pyrenean chamois, leading to a dramatic population decrease that may drive to genetic variability loss. The Majo...
Surveillance is integral for the monitoring and control of infectious diseases. We conducted prospective laboratory surveillance of methicillin-resistant Staphylococcus aureus (MRSA) in five Singaporean public-sector hospitals from 2006 to 2010, using WHONET 5.6 for data compilation and analysis. Mo...
To investigate the prevalence and molecular epidemiology of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) nasal carriage in children. We collected nasal and nasopharyngeal swabs from 2211 children aged 2-5 years attending 79 day care centers (DCCs) and 113 kindergartens (KGs) in a...
To investigate the occurrence and molecular mechanisms associated with carbapenemases in carbapenem-resistant Gram-negative isolates from Canadian cases. Twenty hospital sites across Canada submitted isolates for a 1 year period starting 1 September 2009. All Enterobacteriaceae with MICs ≥ 2 mg/L an...
The molecular epidemiology of third-generation cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in developing countries is poorly documented. From February 2007 to March 2008, we collected 135 3GC-R K. pneumoniae isolates from seven major towns in Maghreb (Morocco), West Africa (Senegal, Côte d...
The increased prevalence of hypervirulent ribotype 027 Clostridium difficile requires rapid identification of isolates in order to implement timely infection control strategies. High resolution melt (HRM) analysis of PCR products can identify strain variation amongst genera of bacteria. The intergen...
This study aimed to estimate the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carriage upon hospital admission and to study the molecular epidemiology of MRSA in order to assess the proportion of Panton-Valentine leukocidin (PVL)-positive community-associated (CA) and livestock-a...
Surveillance is very important for preventing the nosocomial spread of methicillin-resistant Staphylococcus aureus (MRSA), and the pulsed-field gel electrophoresis (PFGE) method has long been used to identify the infection source and route as a molecular and epidemiological genotyping method. Howeve...
Foot-and-mouth disease (FMD) outbreaks recently affected 2 countries (Japan and South Korea) in eastern Asia that were free of FMD without vaccination. Analysis of viral protein 1 nucleotide sequences indicated that FMD serotype A and O viruses that caused these outbreaks originated in mainland Sout...
The genetic diversity of Chikungunya virus (CHIKV) causing recurring outbreaks in India since 2006 was studied. The 2006 epidemic was caused by a virus strain of the East, Central and South African (ECSA) genotype with 226A in the E1 glycoprotein. The variant strain with E1-A226V mutation caused out...
Increasing international migration has changed the epidemiology of tuberculosis (TB) in Europe. Little is published on clinical manifestations and epidemiology in children in this new era. Clinical and laboratory data on all children with TB in Stockholm between 2000 and 2009 were entered into a dat...
No abstract available
Staphylococcus aureus is a major pathogen responsible for severe nosocomial and community-associated infections of humans and infections of economically important livestock species. In recent years, studies into livestock-associated S. aureus including methicillin-resistant (MRSA) strains have provi...
We applied MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing) to directly analyze the bacilli present in 61 stain-positive specimens from tuberculosis patients. A complete MIRU type (24 loci) was obtained for all but one (no amplification in one locus) of the...
Denmark and several other countries experienced the first epidemic of methicillin-resistant Staphylococcus aureus (MRSA) during the period 1965-75, which was caused by multiresistant isolates of phage complex 83A. In Denmark these MRSA isolates disappeared almost completely, being replaced by other...
We sought to explain seasonality and other aspects of Campylobacter jejuni epidemiology by integrating population genetic and epidemiological analysis in a large 3-year longitudinal, two-centre, population-based study. Epidemiological information was collected for 1505 isolates, which were multilocu...
Outbreaks of human salmonellosis associated with live poultry contact have been reported since 1955. Multiple Salmonella serotypes have been associated with these outbreaks, and specific outbreak strains have been repeatedly linked to single hatcheries over multiple years. During 2009, four multista...
One hundred and forty-eight colonizing isolates from adult Romanian women were conventionally serotyped and screened for antibiotic resistance. Capsular type assignment by multiplex polymerase chain reaction (PCR) was performed for nonserotypeable isolates. Tetracycline and macrolide resistance gene...
The lack of epidemiologic data on invasive Streptococcus pyogenes infections in many developing countries is concerning, as S. pyogenes infections are commonly endemic in these areas. Here we present the results of the first prospective surveillance study of invasive Streptococcus pyogenes infection...
With the recent detection of MRSA (methicillin-resistant Staphylococcus aureus) infections in patients lacking health care-related risk factors, the term community-acquired MRSA (CA-MRSA) has been become widely recognised. Many cases of CA-MRSA spreading to the community have been described worldwid...
Panton-Valentine leucocidin-positive meticillin-resistant Staphylococcus aureus (PVL-MRSA) has become a globally common cause of community-acquired infections. We report an outbreak of PVL-MRSA in a regional neonatal unit in the UK involving three babies and three staff members. Quinolone susceptibi...
Salmonella enterica serovar Typhi (Salmonella Typhi) causes an estimated 22 million typhoid fever cases and 216 000 deaths annually worldwide. In Africa, the lack of laboratory diagnostic capacity limits the ability to recognize endemic typhoid fever and to detect outbreaks. We report a large labora...
Salmonella enterica serovar Typhi causes an estimated 22 million cases of typhoid fever and 216 000 deaths annually worldwide. We investigated an outbreak of unexplained febrile illnesses with neurologic findings, determined to be typhoid fever, along the Malawi-Mozambique border. The investigation...
Salmonella is one of the most common foodborne pathogens in humans. Laboratory-based surveillance for non-typhoidal Salmonella infection was conducted in Guangdong Province, China to improve understanding about the disease burden and detection of dispersed outbreaks. Salmonella isolated from patient...
Escherichia coli sequence type ST131 (from phylogenetic group B2), often carrying the extended-spectrum-β-lactamase (ESBL) gene bla(CTX-M-15), is an emerging globally disseminated pathogen that has received comparatively little attention in the United States. Accordingly, a convenience sample of 351...
Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a major concern worldwide. In the United States, ST8 CA-MRSA with SCCmecIVa (USA300) has been predominant, affecting the entire United States. In this study, we investigated Japanese ST8 CA-MRSA with new SCCmecIVl (d...
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We describe the isolation of an NDM-1-producing Acinetobacter baumannii in a Czech patient repatriated in July 2011 from Egypt. The infection spread to another patient on the same ward. Both isolates showed the same resistance pattern and were susceptible only to colistin. They had an identical PFGE...
In the era after the introduction of the meningococcal serogroup C conjugate vaccine, from 1 January 2003 to 31 December 2010, serogroup B meningococci were the major cause of invasive meningococcal disease in the province of Québec, Canada, being responsible for 72% of all meningococcal disease cas...
Human listeriosis outbreaks in Canada have been predominantly caused by serotype 1/2a isolates with highly similar pulsed-field gel electrophoresis (PFGE) patterns. Multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MVLST) each identified a diverse population of Listeria mo...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial pneumonia. To characterize pathogen-derived and host-related factors in intensive care unit (ICU) patients with MRSA pneumonia, we evaluated the Improving Medicine through Pathway Assessment of Critical Therapy in Hosp...
The objective of our study was to provide a genotype analysis of H7N7 and H7N9 influenza A viruses (IAV) and infer their relationships to co-circulating non-H7 IAV genomes. The H7N7 strains were collected in central Europe (Hungary-1, Czech Republic-1, Slovenia-1 and Poland-4) and the H7N9 in the Cz...
A study was designed to investigate the molecular epidemiology of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae isolated in a centralized region over a 10 year period (2000-09). Molecular characterization was done using isoelectric focusing, PCR and sequencing for bla(CTX-M),...
No abstract available
We conducted an epidemiological study concerning carbapenem-non-susceptible clinical isolates of Acinetobacter spp. in Japan by molecular procedures including carbapenemase gene identification and amplified ribosomal DNA restriction analysis. Among 598 clinically isolated Acinetobacter spp. in 2007,...
Eighteen renal transplant recipients (RTRs) developed Pneumocystis jirovecii infections at the renal transplantation unit of Brest University Hospital (Brest, Brittany, France) from May 2008 through April 2010, whereas no cases of P. jirovecii infection had been diagnosed in this unit since 2002. Th...
Multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) has been shown to provide a high level of information for epidemiological investigations and the follow-up of Pseudomonas aeruginosa chronic infection. In the present study, an automatized MLVA assay has been developed for the a...
Co-colonization of patients with carbapenem-resistant Enterobacteriaceae (CRE) and Acinetobacter baumannii (AB) or Pseudomonas aeruginosa (PA) is reported to be associated with increased antibiotic resistance and mortality. CREs isolated between September 2008 and September 2009 were analyzed at Det...
No abstract available
In October 2011, two primary cases of hepatitis A virus (HAV) infection with identical HAV genotype IB strains to those seen in other outbreaks associated with semi-dried tomatoes were reported in England. Both cases had consumed semi-dried tomatoes. Epidemiological investigations revealed two addit...
The risk posed to the United Kingdom by West Nile virus (WNV) has previously been considered low, due to the absence or scarcity of the main Culex sp. bridge vectors. The mosquito Culex modestus is widespread in southern Europe, where it acts as the principle bridge vector of WNV. This species was n...
The present study aimed to describe the prevalence and molecular epidemiology of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa isolates obtained from non-tertiary care hospitals and geriatric hospitals in South Korea. Of the 644 isolates, 224 were carbapenem-resistant, amongst which 41...
Clostridium difficile infection (CDI) is a leading cause of antibiotic-associated diarrhoea and is endemic in hospitals, hindering the identification of sources and routes of transmission based on shared time and space alone. This may compromise rational control despite costly prevention strategies....
Bat flies are obligate ectoparasites of bats and it has been hypothesized that they may be involved in the transmission of Bartonella species between bats. A survey was conducted to identify whether Cyclopodia greefi greefi (Diptera: Nycteribiidae) collected from Ghana and 2 islands in the Gulf of G...
The incidence of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infection has been increasing; however, the sources of infection remain unclear. Therefore, we investigated the involvement of meat as a possible mediator of CA-MRSA infection. We examined the distribution of M...
To study the origin and spread of Yersinia enterocolitica among pigs, fecal and blood samples were repeatedly taken on a fattening farm. A few piglets were found to be already infected on breeding farms. After the piglets were mixed, the infection spread through the whole unit. Eventually, all the p...
This study aimed to investigate the possible influence of bacterial intra- and interspecies interactions on the ability of Listeria monocytogenes and Salmonella enterica to develop mixed-culture biofilms on an abiotic substratum, as well as on the subsequent resistance of sessile cells to chemical d...
The objective of the current study was to determine whether the antimicrobial susceptibility profile or genotype of hospital-acquired isolates of Clostridium difficile differed from isolates causing community-acquired disease. Five hundred diarrhoeal stool samples (one >2 ml sample per patient) from...
An outbreak of the monophasic variant of Salmonella enterica serotype 4,[5],12:i:- occurred in November and December 2011 in France. Epidemiological investigation and food investigation with the help of supermarket loyalty cards suggested dried pork sausage from one producer as the most likely sourc...
Salmonella is a leading cause of foodborne illness in the United States. It is a zoonotic pathogen found in many species of food animals, and contamination of foodstuffs by strains of Salmonella found on farms is an important source of human exposure. Here we describe a long-term (2004-2010) study o...
The introduction of molecular typing methods in the 1990s to study the epidemiology of tuberculosis (TB) has significantly improved the possibilities of quantifying transmission of Mycobacterium tuberculosis in different human settings. The purpose of this study was to investigate transmission of TB...
We describe virus isolation, full genome sequence analysis, and clinical pathology in ferrets experimentally inoculated with pandemic (H1N1) 2009 virus recovered from a clinically ill captive cheetah that had minimal human contact. Evidence of reverse zoonotic transmission by fomites underscores the...
We investigated an outbreak of non-O157 Shiga toxin-producing Escherichia coli at a high school in Minnesota, USA, in November 2010. Consuming undercooked venison and not washing hands after handling raw venison were associated with illness. E. coli O103:H2 and non-Shiga toxin-producing E. coli O145...
Nipah virus (NiV) is a highly pathogenic paramyxovirus that causes fatal encephalitis in humans. The initial outbreak of NiV infection occurred in Malaysia and Singapore in 1998-1999; relatively small, sporadic outbreaks among humans have occurred in Bangladesh since 2001. We characterized the compl...
Nontypeable Haemophilus influenzae (NTHi) causes otitis media, sinusitis, and likely lower respiratory tract infections in children. Colonization, strain diversity, transmission, and antimicrobial susceptibility have implications for both children and their caregivers. For 13 months, we conducted a...
Serratia marcescens can cause health care-associated infections. We herewith report the investigation and control of an outbreak of S marcescens bloodstream infections (BSI) in a general pediatric department. From April to May 2009, temporally related cases of S marcescens BSI occurred in a 40-bed g...
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To investigate the molecular basis for serotype variation in Vibrio cholerae O1 and the genetic relatedness amongst different serotypes isolated from 2004 to 2008 in Iran. Despite the presence of all three serotypes of V.cholerae O1 (Ogawa, Inaba and Hikojima) in Iran in the last decade, the Inaba s...
Aspergillus flavus is one of the most common fungal eukaryotes on the planet. It is notorious for production of aflatoxins, for causing aspergillosis in humans and animals, and as an opportunistic pathogen of animals and plants. Its role in marine habitats is unclear. Until now, little phylogeograph...
The identification of Pseudomonas stutzeri clinical isolates through conventional phenotypic methods was compared with identification through partial rpoD gene sequencing. We observed that commercial phenotypic systems easily confuse P. stutzeri with other Pseudomonas species. We also demonstrated t...
A child's death due to pneumococcal meningitis after contracting the disease in an after-school programme prompted an investigation to assess nasopharyngeal (NP) carriage among her contacts. The serotype of the meningitis case isolate was determined, together with the serotypes of the NP specimens o...
Salmonella enterica serovar Enteritidis (S. Enteritidis) is a major serovar associated with human salmonellosis. A total of 425 clinical S. Enteritidis isolates of human origin were collected between June 2009 and September 2010 from North Carolina. The isolates were further characterized for antimi...
Acinetobacter baumannii is a Gram-negative organism reported worldwide as a cause of health-care-associated infections, particularly in intensive care units (ICUs). The aim of this study is to describe the emergence and spread of carbapenem-resistant A. baumannii (CRAB) isolates in hospitalized pati...
The detection of Legionella pneumophila DNA in clinical specimens using quantitative real-time polymerase chain reaction (qPCR) combined with direct sequence-based typing (SBT) offers rapid confirmation and timely intervention in the investigation of cases of Legionnaires' disease (LD). We assessed...
Global dissemination of imipenem-resistant (IR) clones of Acinetobacter baumannii - A. calcoaceticus complex (ABC) have been frequently reported but the molecular epidemiological features of IR-ABC in military treatment facilities (MTFs) have not been described. We characterized 46 IR-ABC strains fr...
No abstract available
To develop an optimized random amplified polymorphic DNA (RAPD) protocol for fingerprinting clinical isolates of Klebsiella pneumoniae. Employing factorial design of experiments, repeatable amplification patterns were obtained for 54 nosocomial isolates using 1 μmol 1(-1) primer, 4 mmol 1(-1) MgCl(2...
Recognizing the uniqueness of secondary dengue virus (DENV)-1/3 dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS) cases at an interval of 24 years, we sought to estimate DENV infections as well as the ratios between mild disease and DHF/DSS by DENV infection sequence in Playa District (Havana...
This report describes 3 consecutive outbreaks caused by genetically unrelated Serratia marcescens clones that occurred in a neonatal intensive care unit (NICU) over a 35-month period. Carriage testing in neonates and health care workers and environmental investigation were performed. An unmatched ca...
To evaluate the prevalence of maternal and neonatal colonization with group B streptococcus (GBS) and Escherichia coli, and examine GBS serotypes and susceptibility to antibiotics. A prospective cross-sectional study was carried out in Lithuania between October 2006 and June 2007. Lower vaginal/rect...
Staphylococcus aureus is a pathogen that can be the cause of nosocomial infections, community-acquired diseases and food-borne disease outbreaks. A number of variable number tandem repeat loci have been reported by various groups for use in epidemiological studies and outbreak investigations. The ai...
Rates of resistance to macrolide antibiotics in Streptococcus pneumoniae are rising around the world due to the spread of mobile genetic elements harboring mef(E) and erm(B) genes and post-vaccine clonal expansion of strains that carry them. Characterization of 592 clinical isolates collected in Ari...
In November 2010, NDM-1-producing Klebsiella pneumoniae (NDMKP) was identified for the first time in South Korea from four patients with no history of traveling abroad who stayed for 21 to 205 days in a tertiary care hospital. All were sequence type (ST) 340 and had nearly identical XbaI pulsed-fiel...
This study is a nationwide survey of all clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates, including community-acquired MRSA (CA-MRSA), in Japan. A total of 857 MRSA clinical isolates were collected from the 16 institutions throughout Japan that participated in the survey (2008-2...
Propionibacterium acnes, a commensal of human skin, is also an opportunistic pathogen of common acne and certain infectious diseases. However, it is still not obvious which strain is pathogenic for a certain infectious disease, and investigations to characterize pathogenic strains using molecular ty...
Variation of sclB gene sequences in group A Streptococcus (GAS) strains was evaluated for its potential use in subtyping the most common serotypes of Streptococcus pyogenes encountered in the UK. We sequenced a total of 188 strains, including randomly selected invasive GAS and outbreak-related strai...
Chronic infection with Helicobacter pylori strains expressing the bacterial oncoprotein CagA confers an increased risk of gastric cancer. While much is known about the ancestry and molecular evolution of Western, East Asian, and Amerindian cagA sequences, relatively little is understood about a four...
We describe an outbreak investigation of Pantoea agglomerans bacteraemia associated with anticoagulant citrate-dextrose 46% (ACD) solution prepared in-house. A healthy man presented with septic shock during plasmapheresis for granulocyte donation. The solution used for priming and blood samples were...
The purpose of this investigation was to describe the first documented carbapenem-resistant Klebsiella pneumoniae (CRKP) outbreak in a tertiary care facility in Saudi Arabia. We initiated a prospective study to follow all cases of CRKP as well as the active surveillance of patients in areas where ca...
No abstract available
Endemic strains of Legionella pneumophila sequence type 1 (ST1), in particular the ST1/Paris pulsotype, are dispersed worldwide and represent about 10% of culture-proven clinical cases of Legionnaires' disease in France. The high rate of isolation of this strain from both clinical and environmental...
Studies of U.S. epidemics of community- and health care-associated methicillin-resistant Staphylococcus aureus (MRSA) suggested differences in MRSA strains in adults and those in children. Comprehensive population-based studies exploring these differences are lacking. We conducted a prospective coho...
The impact of Panton-Valentine leukocidin (PVL) on the outcome in Staphylococcus aureus pneumonia is controversial. We genotyped S. aureus isolates from patients with hospital-acquired pneumonia (HAP) enrolled in two registrational multinational clinical trials for the genetic elements carrying pvl...
A study published in 1998 linking MMR vaccine and autism was recently retracted by the Lancet because the data were falsified. The impressive reduction of invasive pneumococcal diseases with the 7-valent pneumococcal conjugate vaccine is due to a more than 90% reduction in rates of infections due to...
Hepatitis A virus is one of the most prominent causes of fecally transmitted acute hepatitis worldwide. In order to characterize the viral agents causing an outbreak in Korea (comprising North and South Korea) from June 2007 to May 2009, we collected specimens and performed genotyping of the VP1/P2A...
Enterobacteriaceae are important pathogens of both nosocomial and community-acquired infections. In particular, strains with broad-spectrum beta-lactamases increasingly cause problems in health care settings. Rapid and reliable typing systems are key tools to identify transmission, so that targeted...
This article reviews recent findings on the global epidemiology of healthcare-acquired/associated (HA), community-acquired/associated (CA) and livestock-associated (LA) meticillin-resistant Staphylococcus aureus (MRSA) and aims to reach a consensus regarding the harmonisation of typing methods for M...
Bluetongue (BT) is an important viral disease of ruminants that is transmitted by hematophagous Culicoides midges. We examined the seasonal patterns of abundance and infection of Culicoides sonorensis at four dairy farms in the northern Central Valley of California to develop estimates of risk for b...
Multilocus sequence typing (MLST) is usually based on the sequencing of 5 to 8 housekeeping loci in the bacterial chromosome and has provided detailed descriptions of the population structure of bacterial species important to human health. However, even strains with identical MLST profiles (known as...
Various combinations of antibiotics are reported to show synergy in treating nosocomial infections with multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii). Here, we studied hospital-acquired outbreak strains of MDR A. baumannii to evaluate optimal combinations of antibiotics. One hundr...
Chikungunya virus (CHIKV) is an arthropod-borne virus of the Alphavirus genus, which is transmitted to humans by Aedes spp. mosquitoes and was firstly identified in Tanzania in the mid 1950s. In this article, the findings of a phylogenetic and phylogeographic analysis of the recent CHIKV pandemic ar...
Changes in Dengue virus (DENV) disease patterns in the Americas over recent decades have been attributed, at least in part, to repeated introduction of DENV strains from other regions, resulting in a shift from hypoendemicity to hyperendemicity. Using newly sequenced DENV-1 and DENV-3 envelope (E) g...
Ixodes ricinus horizontal movement within a humidity gradient and the influence of infection by Borrelia burgdorferi sensu lato (s.l.) on tick walking were investigated. Nymphs were placed within an arena containing a humidity gradient ranging from 45 to 95% relative humidity (RH). After 1 h of accl...
Travel is a risk factor for Legionnaires' disease. In 2008, two cases were reported in condominium guests where we investigated a 2001 outbreak. We reinvestigated to identify additional cases and determine whether ongoing transmission resulted from persistent colonization of potable water. Exposures...
By the end of May 2010, an increase in the number of urine specimens that were culture positive for extremely drug-resistant (XDR) Pseudomonas aeruginosa was observed in our 800-bed university hospital. This led to an infection control alert. No epidemiological link between the patients and no incre...
We report a food-related outbreak of salmonellosis in humans caused by a nonmotile variant of Salmonella enterica serotype Typhimurium in France in 2009. This nonmotile variant had been circulating in laying hens but was not considered as Typhimurium and consequently escaped European poultry flock r...
The role that wildlife may play in the transmission of Mycobacterium avium subspecies paratuberculosis (Map), the causative agent of Johne's disease (JD), and the potential consequences of infection in these populations are being given increasing consideration. A yearling male Rocky Mountain bighorn...
There have been limited data on molecular epidemiology of syphilis in China. This study aimed to analyze strain type distribution of Treponema pallidum causing early syphilis across geographic areas in China using an enhanced method. Genital samples were collected from patients in East, South, and N...
During August to November 2010, a dengue (DEN) outbreak occurred, and several cities of Pakistan were affected. In this study, serum samples from 317 patients, based on clinical symptoms and blood test, were included from Lahore, Sheikhpura and Gujranwala cities for further diagnosis of different ge...
Bartonella spp. are facultative intracellular pathogens that employ a unique stealth infection strategy comprising immune evasion and modulation, intimate interaction with nucleated cells, and intraerythrocytic persistence. Infections with Bartonella are ubiquitous among mammals, and many species ca...
We investigated an increase of human cases of Salmonella Enteritidis occurring from August until November 2010 in Belgium, Luxembourg and Germany involving an estimated three hundred laboratory confirmed cases. Molecular typing indicated that the increase in Luxembourg and Belgium was due a particul...
Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that cause mild or serious diseases and can lead to people death. This study reports the prevalence and characteristics of STEC O157 and non-O157 in commercial ground beef and environmental samples, including meat table, knife, me...
Coxsackieviruses A10 (CV-A10) and A6 (CV-A6) have been associated with increasingly occurred sporadic hand-foot-mouth disease (HFMD) cases and outbreak events globally. However, our understanding of epidemiological and genetic characteristics of these new agents remains far from complete. This study...
This study was carried out to identify predominant spoligotypes responsible for transmission and prevalence of tuberculosis in central India since there is no data available about the genetic biodiversity of Mycobacterium tuberculosis isolates from patients with tuberculosis in this region. 35 strai...
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is mainly associated with swine and is capable of causing zoonotic infections. The methicillin-resistant S. aureus (MRSA) multilocus sequence type (ST) 398 of swine origin is predominant in Europe and North America, whereas S...
Sado Island in Japan is an area with low antimicrobial pressure. A total of 41 community-onset methicillin-resistant Staphylococcus aureus (MRSA) isolates were obtained from pediatric outpatients and healthy children between August 2009 and January 2012, and genotyping and antimicrobial susceptibili...
Carrying out analysis of epizootologic-epidemiologic situation on anthrax that had emerged in Omsk region in 2010 when horse meat from epizootic focus of anthrax was used in production of meat semi-finished products. Study of samples for detection of anthrax causative agents and strain identificatio...
PCR-genotyping of Vibrio parahaemolyticus strains that had caused sporadic diseases in Novorossiysk from 1973 to 1976. 24 clinical strains of V. parahaemolyticus isolated in Novorossiysk, most of which belonged to serogroups O4:K12 and O4:K8; 10 O3:K6 strains--causative agents of gastroenteritis out...
Dengue is a mosquito-borne infectious disease that constitutes a growing global threat with the habitat expansion of its vectors Aedes aegyti and A. albopictus and increasing urbanization. With no effective treatment and limited success of vector control, dengue vaccines constitute the best control...
It has been suggested that the probability of dengue epidemics could increase because of climate change. The probability of epidemics is most commonly evaluated by the basic reproductive number (R(0)), and in mosquito-borne diseases, mosquito density (the number of female mosquitoes per person [MPP]...
The aims of this study were to determine the occurrence of Listeria monocytogenes in cattle feces and ground beef, to characterize these strains by pulsed-field gel electrophoresis and to compare them to three listeria strains found in humans. Cattle from different origins (n = 250) and ground beef...
Legionella, the causative agent for Legionnaires' disease, is ubiquitous in both natural and man-made aquatic environments. The distribution of Legionella genotypes within clinical strains is significantly different from that found in environmental strains. Developing novel genotypic methods that of...
To determine the role of the pandemic influenza A/H1N1 2009 (A/H1N1 2009pdm) in acute respiratory tract infections (ARTIs) and its impact on the epidemic of seasonal influenza viruses and other common respiratory viruses, nasal and throat swabs taken from 7,776 patients with suspected viral ARTIs fr...
Infections caused by multidrug-resistant bacteria are a major concern in hospitals. Current infection-control practices legitimately focus on hygiene and appropriate use of antibiotics. However, little is known about the intrinsic abilities of some bacterial strains to cause outbreaks. They can be m...
The aim of this study was elimination of false positive results obtained by the Chlamylege kit. Two serological kits (IgM ELISA L. pneumophila sgs1-7; ImmuView(TM) L. pneumophila sg1/sg3) and pre-absorption tests (with L. pneumophila sg1 and sg3 reference strains antigens) were used. 153 sera (79 pa...
We aimed to evaluate the stability of the Chlamydia trachomatis multi locus VNTR analysis (MLVA-ompA) and multi sequence typing (MST) systems through multiple passages in tissue culture. Firstly, we analyzed the stability of these markers through adaptation of C. trachomatis to tissue culture and se...
Tracking of sources of sporadic cases of campylobacteriosis remains challenging, as commonly used molecular typing methods have limited ability to unambiguously link genetically related strains. Genomics has become increasingly prominent in the public health response to enteric pathogens as methods...
In Australia the PVL-positive ST93-IV [2B], colloquially known as "Queensland CA-MRSA" has become the dominant CA-MRSA clone. First described in the early 2000s, ST93-IV [2B] is associated with skin and severe invasive infections including necrotizing pneumonia. A singleton by multilocus sequence ty...
A molecular epidemiology survey was performed in order to establish and document the respiratory adenovirus pathogen profiles among children in Southern Palestine. Three hundred and thirty-eight hospitalized pediatric cases with adenovirus-associated respiratory tract infections were analyzed. Forty...
We examine a mathematical model for the transmission of Streptococcus Pneumoniae amongst young children when the carriage transmission coefficient depends on the serotype. Carriage means pneumococcal colonization. There are two sequence types (STs) spreading in a population each of which can be expr...
Leafhoppers (HEmiptera: Cicadellidae) are plant-phloem feeders that are known for their ability to vector plant pathogens. The black-faced leafhopper (Graminella nigrifrons) has been identified as the only known vector for the Maize fine streak virus (MFSV), an emerging plant pathogen in the Rhabdov...
Streptococcus pneumoniae (S. pneumoniae) is one of the most common bacterial pathogens in community‑acquired pneumonia. However, nosocomial pneumococcal infections are more and more widely observed. The aim of the study was to analyze nosocomial outbreak in one of the Polish hospitals and to charac...
In developed countries invasive listeriosis is an infection of great concern to public health to due its clinical severity and high fatality rate, despite its low incidence. In Europe, statistically significant increasing trends in listeriosis notification rates from 2005 to 2009 were noted in Austr...
Mycoplasma pneumoniae infections occur both endemically and epidemically, and macrolide resistance has been spreading for 10 years worldwide. A substantial increased incidence of M. pneumoniae infections has been reported in several countries since 2010. Whether this increased incidence is attribute...
The investigation of cases of acute intestinal infections in the Sakhalin region of Russia in August, 2010 is described. Epidemiological and molecular biological studies were conducted. After initial PCR screening and determining the nucleotide sequences of the positive samples the following enterov...
To characterise and classify clinical isolates collected from tuberculosis (TB) patients in rural Bangladesh and to investigate the mode of transmission. An epidemiological study using a combination of conventional and molecular methods was performed in a rural population of Bangladesh. A total of 1...
A microbial strain harboring the eae gene, which is known as the virulence gene of enteropathogenic Escherichia coli (EPEC) and most enterohemorrhagic E. coli, was isolated from a patient in a gastroenteritis outbreak that occurred in 22 patients in Akita Prefecture, Japan, in November 2011. The bio...
The serotype, Shiga toxin (Stx) type, and antimicrobial resistance patterns of 138 Stx-producing Escherichia coli (STEC) strains isolated from humans between 2003 and 2007 in Shizuoka Prefecture, Japan were characterized. The predominant O serogroups of the STEC isolates were O157, O26, and O111. An...
Rabies is a fatal infection of the central nervous system primarily transmitted by rabid animal bites. Rabies virus (RABV) circulates through two different epidemiological cycles: terrestrial and aerial, where dogs, foxes or skunks and bats, respectively, act as the most relevant reservoirs and/or v...
Publications worldwide have reported on the re-occurrence of human enterovirus 68 (EV68), a rarely detected pathogen usually causing respiratory illness. However, epidemiological data regarding this virus in particular on the Asian continent has so far been limited. We investigated the epidemiology...
Dengue hemorrhagic fever (DHF) is a severe form of dengue, characterized by bleeding and plasma leakage. A number of DHF risk factors had been suggested. However, these risk factors may not be generalized to all populations and epidemics for screening and clinical management of patients at risk of d...
Cross-sectional serosurveys using IgG antibody to pertussis toxin (IgG-PT) are increasingly being used to estimate trends in recent infection independent of reporting biases. We compared the age-specific seroprevalence of various levels of IgG-PT in cross-sectional surveys using systematic collectio...
Enterovirus 68 (EV68) was first isolated in 1962. Very few cases of EV68 infection were described over the ensuing 40 years. However, in the past few years, an increase in severe respiratory tract infections associated with EV68 has been reported. We identified two clusters of EV68 infection in Sout...
Genotyping methods are essential to understand the transmission dynamics of Acinetobacter baumannii. We examined the representative genotypes of A. baumannii at different time periods in select locations in Ohio, using two rapid automated typing methods: PCR coupled with electrospray ionization mass...
Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electr...
Knowledge about molecular epidemiology of B. henselae is important for recognizing the geographical distribution of strains and identification of isolates virulent for humans. Eleven Polish feline B. henselae isolates were typed, using 2 different techniques: pulse-field gel electrophoresis (PFGE) a...
Between January 2004 and December 2004, an outbreak of imipenem-resistant Acinetobacter baumannii (IRAB) in 2 intensive care units (ICU) of Chosun University Hospital, Korea affected 77 patients. A case-control study revealed that the time spent in the hospital and mechanical ventilation practices w...
Neisseria meningitidis serogroup B has been predominant in Brazil, but no broadly effective vaccine is available to prevent endemic meningococcal disease. To understand genetic diversity among serogroup B strains in Brazil, we selected a nationally representative sample of clinical disease isolates...
On December 19, 2010, 57 cases of gastroenteritis were reported in the community health center of Lalpur town. A rapid response team was sent to investigate the outbreak on December 21, 2010. To identify the source, to institute control and prevention measures. The outbreak was confirmed using the p...
We describe an outbreak of bullous impetigo (BI) that occurred in a maternity unit and show phenotypic and genotypic properties and relatedness of isolated Staphylococcus aureus strains. Clinical material was obtained from 11 affected neonates. Additionally, nasal swabs from 67 healthy care workers...
Vibrio cholerae O1 El Tor dominated the seventh cholera pandemic which occurred in the 1960s. For two decades, variants of V. cholerae O1 El Tor that produce classical cholera toxin have emerged and spread globally, replacing the prototypic El Tor biotype. This study aims to characterize V. cholerae...
The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by com...
Community-associated methicillin-resistant Staphylococcus aureus-(CA-MRSA) strains have emerged in Argentina. We investigated the clinical and molecular evolution of community-onset MRSA infections (CO-MRSA) in children of Córdoba, Argentina, 2005-2008. Additionally, data from 2007 were compared wit...
This paper describes the new microbiological hazards in food. For protecting human health, nowadays food safety authorities face with many challenges, that years ago were largely unheard. In 2011 verocytotoxigenic Escherichia coli O104:H4 has been isolated in Germany. Strain came from fenugreek spro...
Sequencing of bacterial genomes became an essential approach to study pathogen virulence and the phylogenetic relationship among close related strains. Bacterium Enterococcus faecium emerged as an important nosocomial pathogen that were often associated with resistance to common antibiotics in hospi...
Dengue is a vector-borne disease recognized as the major arbovirose with four immunologically distant dengue serotypes coexisting in many endemic areas. Several mathematical models have been developed to understand the transmission dynamics of dengue, including the role of cross-reactive antibodies...
Disease outbreak investigation is a key aspect of public health. Whole-genome sequencing of bacterial pathogen based on new generation high-throughput sequencing technologies has facilitated outbreak investigations recently. Whilst the approach has become more affordable and accessible to research a...
Study genetic diversity of P. aeruginosa strains persisting in patients of Federal Scientific Center of Transplantology and Artificial Organs, and main factors facilitating persistence of strains in the hospital. 136 P. aeruginosa strains isolated from patients of the center for 3 years 6 months wer...
Coxiella burnetii, the causative agent of Q fever, has remained a public health concern since the identification of this organism in 1935 by E. H. Derrick in Australia and at the Rocky Mountain Laboratory in the USA by H.R. Cox and G. Davis. Human Q fever has been described in most countries where C...
Methicillin-resistant Staphylococcus aureus (MRSA) strains are leading causes of hospital-acquired infections in the United States, and clonal cluster 5 (CC5) is the predominant lineage responsible for these infections. Since 2002, there have been 12 cases of vancomycin-resistant S. aureus (VRSA) in...
Effective contact investigations are paramount to the success of tuberculosis (TB) control in high-risk communities in low TB prevalence countries. National and international guidelines on TB contact investigations are available and vary widely on recommendations. Because of the limitations of tradi...
A key priority in infectious disease research is to understand the ecological and evolutionary drivers of viral diseases from data on disease incidence as well as viral genetic and antigenic variation. We propose using a simulation-based, Bayesian method known as Approximate Bayesian Computation (AB...
Viral infections by sexual and droplet transmission routes typically spread through a complex host-to-host contact network. Clarifying the transmission network and epidemiological parameters affecting the variations and dynamics of a specific pathogen is a major issue in the control of infectious di...
Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamic...
Serially-sampled nucleotide sequences can be used to infer demographic history of evolving viral populations. The shape of a phylogenetic tree often reflects the interplay between evolutionary and ecological processes. Several approaches exist to analyze the topology and traits of a phylogenetic tre...
Potato virus Y (PVY) is an important plant pathogen, whose host range includes economically important crops such as potato, tobacco, tomato, and pepper. PVY presents three main strains (PVY(O), PVY(N) and PVY(C)) and several recombinant forms. PVY has a worldwide distribution, yet the mechanisms tha...
Although evolution is a multifactorial process, theory posits that the speed of molecular evolution should be directly determined by the rate at which spontaneous mutations appear. To what extent these two biochemical and population-scale processes are related in nature, however, is largely unknown....
Recent years have seen a rapid increase in the number of rabies cases in China and an expansion in the geographic distribution of the virus. In spite of the seriousness of the outbreak and increasing number of fatalities, little is known about the phylogeography of the disease in China. In this stud...
Rift Valley Fever (RVF) virus (Family Bunyaviridae) is an arthropod-borne RNA virus that infects primarily domestic ruminants and occasionally humans. RVF epizootics are characterized by numerous abortions and mortality among young animals. In humans, the illness is usually characterized by a mild s...
Human metapneumovirus (hMPV) is a respiratory viral pathogen in children worldwide. hMPV is divided into four subtypes: hMPV_A1, hMPV_A2, hMPV_B1, and hMPV_B2. hMPV_A2 can be further divided into hMPV_A2a and A2b based on phylogenetic analysis. The typical prevalence pattern of hMPV involves a shift...
To investigate antimicrobial susceptibility and clonal relatedness of Enterococcus faecalis human isolates recovered recently (2006-09) in six European countries. Antimicrobial susceptibility of 386 isolates from Denmark, Germany, Norway, Poland, Spain and The Netherlands, from hospital infections (...
Multiple group B Streptococcus (GBS) isolates with reduced penicillin susceptibility (PRGBS) were recovered from several patients, hence a probable nosocomial transmission of PRGBS in a hospital setting was suspected. Ten PRGBS recovered from eight patients in a general hospital were characterized....
Acinetobacter baumannii has emerged as a serious problem in the hospital environment at a global scale. Previous results from our laboratory showed a high frequency of class 2 integrons in A. baumannii strains from Argentina regarding the low rate of this element in A. baumannii isolates from the re...
Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have sho...
Of 109 clinical Escherichia coli isolates from two major tertiary hospitals in Lagos (University Teaching Hospital and the National Orthopaedic Hospital Igbobi), 14 (12.8%) extended-spectrum beta-lactamse (ESBL) producers were characterized using PCR and sequencing, ERIC-PCR and multilocus sequence...
Campylobacter jejuni is a major zoonotic pathogen. A highly virulent, tetracycline-resistant C. jejuni clone (clone SA) has recently emerged in ruminant reservoirs and has become the predominant cause of sheep abortion in the United States. To determine whether clone SA is associated with human dise...
Sequence type 22 (ST22) methicillin-resistant Staphylococcus aureus (MRSA) harboring staphylococcal cassette chromosome mec (SCCmec) IV (ST22-MRSA-IV) has predominated in Irish hospitals since the late 1990s. Six distinct clones of community-associated MRSA (CA-MRSA) have also been identified in Ire...
The genotypic diversity of Coxiella burnetii in clinical samples obtained from the Dutch Q fever outbreak episodes of 2007-2010 was determined by using a 6-locus variable-number tandem repeat analysis panel. The results are consistent with the introduction of one founder genotype that is gradually d...
No abstract available
In July 2010, we identified an outbreak of vancomycin-resistant enterococci (VRE) in our 26-bed neonatal intensive care unit. We performed an epidemiological investigation after clinical cultures of 2 neonates were positive for VRE. Identification, susceptibility testing, and molecular characterizat...
For this study, ten complex class 1 integron was characterized in Escherichia coli (E. coli) isolates from Zhenjiang. Among the ten isolates, five included the bla ( CTX-M-1 ) gene between orf513 and the IS 3000. Analysis the five isolates by PFGE showed that zj102 and zj562 had same patterns profil...
No abstract available
Multitarget genotyping of the etiologic agent Mycobacterium avium subsp. paratuberculosis is necessary for epidemiological tracing of paratuberculosis (Johne's disease). The study was undertaken to assess the informative value of different typing techniques and individual genome markers by investiga...
Seventy-five individuals with Salmonella infection were identified in the Portsmouth area during August and September 2009, predominantly Salmonella Enteritidis phage type 8. Five patients were admitted to hospital. A case-case comparison study showed that a local restaurant was the most likely sour...
Prior to the recent outbreak of equine encephalosis in Israel in 2009, equine encephalosis virus (EEV) had only been isolated from equids in South Africa. In this study we show the first evidence for the circulation of EEV beyond South Africa in Ethiopia, Ghana and The Gambia, indicating that EEV is...
To investigate the characteristics of main Streptococcus pneumoniae clones of serotype 6D (ST282 and ST3171) in South Korea, antimicrobial susceptibility testing was performed, and 11 genes around the cps locus were sequenced on ST282(6D), ST3171(6D), and ST81(6A) isolates. The antimicrobial suscept...
Genotyping of multidrug-resistant (MDR) Mycobacterium tuberculosis strains isolated from tuberculosis (TB) patients in four South African provinces (Western Cape, Eastern Cape, KwaZulu-Natal, and Gauteng) revealed a distinct population structure of the MDR strains in all four regions, despite the ev...
Whole-genome analysis by 62-strain microarray showed variation in resistance and virulence genes on mobile genetic elements (MGEs) between 40 isolates of methicillin-resistant Staphylococcus aureus (MRSA) strain CC22-SCCmecIV but also showed (i) detection of two previously unrecognized MRSA transmis...
Campylobacter spp. are a leading cause of bacterial gastroenteritis worldwide. The need for molecular subtyping methods with enhanced discrimination in the context of surveillance- and outbreak-based epidemiologic investigations of Campylobacter spp. is critical to our understanding of sources and r...
To establish the molecular epidemiology and antimicrobial resistance pattern of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae harbouring bla(CTX-M) in Glasgow, Scotland. During a 12 week period, Enterobacteriaceae isolates obtained from urine samples were collected and susceptibi...
We evaluated Clostridium difficile prevalence rates in 2,807 clinically indicated stool specimens stratified by inpatient (IP), nursing home patient (NH), outpatient (OP), age, gender, and specimen consistency using bacterial culture, toxin detection, and polymerase chain reaction (PCR) ribotyping....
To investigate the clinical and molecular epidemiology of the imipenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii (IRAcb) complex during an outbreak in an intensive care unit (ICU). Forty-six clinical and 11 environmental isolates of the IRAcb complex were collected from the ICU o...
Extended-spectrum beta-lactamase- (ESBL)-producing Escherichia coli are an increasingly significant cause of community-acquired infection worldwide. The aim of this study was to assess the prevalence of ESBL-producing E. coli in a community, to analyze the relationship between strains studied, and t...
The increasing prevalence of uropathogenic Escherichia coli (UPEC) strains resistant to multiple antibiotics complicates the treatment of urinary tract infections (UTIs). This study aimed to analyze the antimicrobial resistance, serotypes, and phylogenetic groups among strains of E. coli isolated fr...
Aimed at assessing the circulation of Mycobacterium tuberculosis in a highly endemic prison, this 13-month prospective study was performed on strains isolated from tuberculosis (TB) cases detected passively and actively. We used X-ray screening of newly admitted inmates and mass screening at the beg...
During a 2-year period in 2005 and 2006, 64 multidrug-resistant Providencia stuartii isolates, including 58 strains from 58 patients and 6 strains obtained from the same tracheal aspirator, were collected in a burn unit of a Tunisian hospital. They divided into four antibiotypes (ATB1 to ATB4) and t...
A total of 299 nares and 194 blood isolates of methicillin-resistant Staphylococcus aureus (MRSA), each recovered from a unique patient, were collected from 23 U.S. hospitals from May 2009 to March 2010. All isolates underwent spa and staphylococcal cassette chromosome mec element (SCCmec) typing an...
Adenovirus keratoconjunctivitis outbreaks have rarely been reported in preterm infants. An outbreak of adenovirus conjunctivitis occurred between 15 January and 25 February at a neonatal intensive care unit of a university hospital in Turkey. To describe the evolution, investigation and management o...
The aims of this study were to assess the prevalence of isolates of Beijing lineage in childhood tuberculosis (TB) and the association between strain family and clinical characteristics. A total of 105 children aged less than 18 years with culture-confirmed TB were evaluated by spoligotyping and the...
The prevalence of ampicillin-resistant Moraxella catarrhalis has been higher in Taiwan than in other countries, with reports of 97.7% in the 1990s. The aims of this study were to assess resistance trends for M. catarrhalis, which causes respiratory tract infections, against several classes of oral a...
Escherichia coli O157:H7 is a Shiga toxin-producing E. coli (STEC) associated with numerous foodborne outbreaks in the United States and is an important cause of bacterial gastrointestinal illness. In May 2009, we investigated a multistate outbreak of E. coli O157:H7 infections. Outbreak-associated...
This study was conducted to investigate the molecular epidemiology and antimicrobial susceptibility of multidrug-resistant (MDR) Acinetobacter baumannii to three types of antibiotics. One hundred and thirty-four specimens of MDR A baumannii were collected from three branches (Taipei, Dalin, and Hual...
Molecular epidemiological features of Mycobacterium tuberculosis strains among different patient groups in Russia have not been studied well. The aim of our study was to compare the genotypes of M. tuberculosis strains circulating among tuberculosis (TB) patients from different groups: homeless, hum...
Campylobacter spp. may be responsible for unreported outbreaks of food-borne disease. The detection of these outbreaks is made more difficult by the fact that appropriate methods for detecting clusters of Campylobacter have not been well defined. We have compared the characteristics of five molecula...
A study was designed to assess the importance of sequence types among extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates causing bacteremia over an 11-year period (2000 to 2010) in a centralized Canadian region. A total of 197 patients with incident infections were identified;...
To characterize methicillin-resistant Staphylococcus aureus (MRSA) clinical strains from cats and dogs in France, and to compare the clones identified with the distribution of French human MRSA. Susceptibilities to antimicrobials were assessed by disc diffusion. Resistance and virulence genes were s...
There has been increasing interest in Clostridium difficile infection (CDI) due its association with healthcare and its impact on morbidity and mortality in the elderly. During the last few years there has been a growing increase in the number of published studies on the incidence, changes on the cl...
To understand the etiological and molecular-epidemiological characteristics of Vibrio parahaemolyticus in Beijing. Stool specimens from sporadic diarrheal patients were collected during April to December, 2010. Culture and serotyping were used to detect the Vibrio parahaemolyticus from the 2118 spec...
To study the serotypes, virulence features and molecular characteristics of Vibrio parahaemolyticus isolated in food poisoning cases and surveillance program on diarrhea patients in Guangdong, 2009. 95 Vibrio parahaemolyticus strains from food poisoning cases and 15 strains from surveillance program...
The carbapenemase OXA-48 has been reported from different Mediterranean countries. It is mostly encoded on a single plasmid in various Enterobacteriaceae species. We characterized the epidemiological and molecular features of OXA-48-producing Enterobacteriaceae (OPE) in Israel. Epidemiological inves...
The non-O157 Shiga toxin-producing Escherichia coli (STEC) contamination in carcasses and feces of 811 bovines in nine beef abattoirs from Argentina was analyzed during a period of 17 months. The feces of 181 (22.3%) bovines were positive for non-O157 STEC, while 73 (9.0%) of the carcasses showed no...
To investigate the possible presence of H. pylori in subgingival dental plaque of children with upper gastrointestinal symptoms, as well as of their parents' and to detect any association between the presence of H. pylori and oral hygiene together with the periodontal status of children and their pa...
Streptococcus agalactiae, also known as group B streptococcus (GBS), is the most common cause of neonatal sepsis and meningitis. To improve our understanding of the pathogenesis of neonatal GBS sepsis, better knowledge of clonal relatedness and diversity among invasive and noninvasive GBS isolates i...
No abstract available
Seventeen cases of Acinetobacter baumannii infection in a neonatal intensive care unit (NICU) were evaluated. The strains were characterized as resistant to carbapenems. The aim of the present study was therefore to investigate the clinical and molecular epidemiological characteristics of the 17 car...
Rapidly growing mycobacteria (RGM) are ubiquitous in nature and widely distributed in water, soil and animals. During the past three decades we have observed a notable increment of infections caused by RGM, both localized and disseminated, as well as nosocomial outbreaks of contaminated medical equi...
The clonal lineages, resistance mechanisms and virulence traits of tetracycline-resistant (Tet(R)) methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in a Spanish hospital during 2009 and 2010 were investigated. Fifty-two Tet(R) MRSA strains from unrelated patients were included in...
We conducted population-based surveillance for pneumococcal bacteremia within a 5-county region surrounding Philadelphia from October 2001 through September 2008, the period following introduction of the seven-valent pneumococcal conjugate vaccine. Erythromycin resistance increased from 14.7% in 200...
In April 2008, foot-and-mouth disease (FMD) outbreaks were reported in Kamuli district of the eastern region of Uganda. Soon after lifting the quarantines in this area, further FMD outbreaks were reported in northern Uganda, which spread to more than 10 districts. The aim of this study was to identi...
The purpose of this investigation was to analyse Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected in Italy from vaginal and urine samples in respect to their clonality, distribution of virulence factors and antimicrobial resistance determinants. Three hundred and eighty-eight...
The objective of this study was to investigate the genetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC) 398 using pulsed-field gel electrophoresis (PFGE). Dust and pigs at five age groups were sampled in six Danish MRSA-positive pig farms. MRSA CC398 was isolat...
Clostridium difficile-associated disease (CDAD) is caused by a spore-forming bacterium and can result in highly variable disease, ranging from mild diarrhoea to severe clinical manifestations. Infections are most commonly seen in hospital settings and are often associated with on-going antibiotic th...
Between July and October 2010, a national outbreak comprising 136 cases of Salmonella Java phage type 3b variant 9 was identified by the Health Protection Agency. Most cases were female. Cases had a median age of 39.5 years and lived in London, the South East and East of England. Parallel case–contr...
Pulsed-field gel electrophoresis (PFGE) analysis demonstrated that while 76% of patients had only one genotype of campylobacter, 10% carried two different but related genotypes (Dice coefficients > 0.78), and 14% carried at least two unrelated genotypes (Dice coefficients < 0.65). This supports the...
Immigrants from high-burden countries and HIV-coinfected individuals are risk groups for tuberculosis (TB) in countries with low TB incidence. Therefore, we studied their role in transmission of Mycobacterium tuberculosis in Switzerland. We included all TB patients from the Swiss HIV Cohort and a sa...
A Stx2a-producing Escherichia coli (STEC) strain belonging to serotype O104:H4, with virulence features common to the enteroaggregative E. coli pathotype, was reported as the cause of the recent 2011 outbreak in Germany. In addition, the German outbreak strain was found to possess several virulence...
Since 1950, Brucella melitensis has been the predominant strain associated with human brucellosis in China. In this study we investigated the genotypic characteristics of B. melitensis isolates from China using a multiple-locus variable-number tandem-repeat analysis (MLVA) and evaluated the utility...
No abstract available
Total enterococci and vancomycin-resistant enterococci (VRE) were enumerated in samples of effluent (n = 50) and water (n = 167) from a number of sources. VRE were detected in the outflow of a wastewater treatment plant and in a single rural drinking water supply, suggesting potential for transmissi...
The genus Weissella contains 14 bacterial species that usually occur in nutrient-rich environments and in fermented foods and beverages. Outbreaks of hemorrhagic septicemia were reported in three commercial rainbow trout (Oncorhynchus mykiss) farms in Brazil in 2008 and 2009. Seventy-seven Gram-posi...
We report a nosocomial outbreak of urinary tract infection caused by Myroides odoratimimus, previously called Flavobacterium odoratum, in the urology unit of a Tunisian hospital. From May to November 2010, seven isolates of M. odoratimimus were recovered from urine. Pulsed-field gel electrophoresis...
Neisseria meningitidis is a leading pathogen of epidemic bacterial meningitis and fulminant sepsis worldwide. Twelve different N. meningitidis serogroups have been identified to date based on antigenic differences in the capsular polysaccharide. However, more than 90% of human cases of N. meningitid...
In 2006, a large outbreak of Escherichia coli O157:H7 was linked to the consumption of ready-to-eat bagged baby spinach in the United States. The likely sources of preharvest spinach contamination were soil and water that became contaminated via cattle or feral pigs in the proximity of the spinach f...
Beta-Hemolytic group G streptococci cause a considerable invasive disease burden and sometimes disease outbreaks. Little is known about the critical epidemiologic parameter of genetic relatedness between isolates. We determined the emm types of 65 Streptococcus dysgalactiae subsp. equisimilis isolat...
Eighty methicillin-resistant Staphylococcus aureus (MRSA) isolates from three hospitals in Trinidad and Tobago were collected and genotyped using microarray hybridisation. They were found to belong to three distinct MRSA strains. Of the 80 isolates, 76 were assigned to ST239-MRSA-III. They were larg...
The performance characteristics of Neisseria gonorrhoeae multilocus variable-number tandem-repeat analysis were evaluated, by comparison with N. gonorrhoeae multiantigen sequence typing and full-length porB sequence typing. Assessment of the relatedness of intra- and interpatient isolates showed tha...
Isolates from consecutive Clostridium difficile infection (CDI) fecal samples underwent multilocus sequence typing. Potential reinfections with different genotypes were identified in 88/560 (16%) sample pairs taken 1 to 1,414 days (median, 24; interquartile range [IQR], 1 to 52 days) apart; odds of...
Variable-number tandem repeat (VNTR) and spoligotyping analyses were used to assess transmission of Mycobacterium bovis between humans. VNTR was more discriminatory than spoligotyping. Low case numbers, despite a substantial animal reservoir, and resolution of all isolates provided no evidence of re...
The genetic diversity and population structure of Escherichia coli isolates from small-scale dairy farms were used to assess the ability of E. coli to spread within the farm environment and between neighboring farms. A total of 164 E. coli isolates were obtained from bovine feces, bedding, cow teats...
The four dengue virus serotypes (DENV1-4) cause the most prevalent mosquito-borne viral disease affecting humans worldwide. In 2009, Nicaragua experienced the largest dengue epidemic in over a decade, marked by unusual clinical presentation, as observed in two prospective studies of pediatric dengue...
Syphilis is resurgent in many regions of the world. Molecular typing is a robust tool for investigating strain diversity and epidemiology. This study aimed to review original research on molecular typing of Treponema pallidum (T. pallidum) with three objectives: (1) to determine specimen types most...
It has been speculated that ticks may serve as vectors of Bartonella species. Circumstantial, clinical, epidemiological and serological evidence suggest that B. vinsonii subspecies berkhoffii (B. v. berkhoffii) might be transmitted by Rhipicephalus sanguineus. The purpose of the present study was to...
Genitourinary candidiasis, which is most frequently caused by Candida albicans, is a common problem worldwide. The pathogenesis of the infection, especially recurrence of the infection, remains to be elucidated. This study analyzed 199 independent Chinese C. albicans isolates using multilocus sequen...
To study the prevalence of the Panton-Valentine leucocidin (PVL) gene in methicillin-susceptible (MSSA) and methicillin-resistant (MRSA) Staphylococcus aureus obtained in Gipuzkoa, northeastern area of the Basque Country, north-central Spain, and perform the molecular characterization of PVL-positiv...
Development of carbapenem resistance in Enterobacteriaceae has impacted Clinical and Laboratory Standards Institute (CLSI) guidelines, infection control approaches and treatment strategies. The clinical, phenotypic and genotypic characteristics of carbapenem-resistant Enterobacteriaceae (CRE) infect...
In October 2010, the US Centers for Disease Control and Prevention received reports of cases of severe watery diarrhea in Haiti. The cause was confirmed to be toxigenic Vibrio cholerae, serogroup O1, serotype Ogawa, biotype El Tor. We characterized 122 isolates from Haiti and compared them with isol...
We used multilocus sequence typing and variable number tandem repeat analysis to determine the clonal origins of Vibrio cholerae O1 El Tor strains from an outbreak of cholera that began in 2009 in Papua New Guinea. The epidemic is ongoing, and transmission risk is elevated within the Pacific region.
A cholera outbreak in Laos in July 2010 involved 237 cases, including 4 deaths. Molecular subtyping indicated relatedness between the Vibrio cholerae isolates in this and in a 2007 outbreak, uncovering a clonal group of V. cholerae circulating in the Mekong basin. Our finding suggests the subtyping...
The aim of the present study was to develop and validate a multitarget pyrosequencing-based protocol for basic Chlamydia trachomatis genotyping directly from clinical samples and to characterize the distribution of genotypes among Slovenian sexually active population. The newly developed combination...
Multidrug-resistant (MDR) Acinetobacter baumannii (MDR-AB) is an important nosocomial pathogen associated with significant morbidity and mortality. We conducted a prospective cohort study of intensive care unit patients colonized or infected with MDR-AB at a tertiary care hospital from October 2008...
Six long-term care facilities were surveyed for methicillin-resistant Staphylcoccus aureus (MRSA). Among 191 residents, 14% were carriers; 1 strain predominated (ST5-SCCmec II). Among 132 staff members, 11% were positive; 2 strains predominated (ST5-SCCmec II, ST8-SCCmec IV). All strains were Panton...
Adenovirus infections are usually mild or even asymptomatic, but infections with the virus are being recognized increasingly as a major cause of mortality and morbidity in the immunocompromised, particularly hematological stem cell transplant patients where infections can be life threatening and mor...
Adenoviruses cause a variety of clinical symptoms, involving the respiratory, gastrointestinal, urogenital, and neurologic systems. Only a few of the 55 known serotypes of adenovirus that affect humans can cause outbreaks of respiratory tract infection. To describe the characteristics and clinical m...
Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a prevalent pathogen of necrotizing fasciitis (NF) in Taiwan. A four-year NF cases and clinical and genetic differences between hospital acquired (HA)- and community-acquired (CA)-MRSA infection and isolates were investigated. A retro...
Due to the need to track and monitor genetic diversity, the genome of the infectious hypodermal and hematopoietic necrosis virus (IHHNV) strain KLV-2010-01 in cultured Litopenaeus vannamei shrimp that originated from the first Korean outbreak in 2010 was sequenced and analyzed. The genome, with a le...
Meticillin-resistant Staphylococcus aureus (MRSA) strains isolated in Tawam Hospital, a tertiary care hospital in the United Arab Emirates, were examined in order to understand the reasons for a doubling of its incidence between 2003 and 2008 while maintaining the same infection control measures. Al...
In 2008, a vancomycin-resistant enterococci outbreak occurred across 2 intensive care units in our hospital. This outbreak prompted us to implement intensified control measures. We describe the molecular epidemiology of the outbreak, as well as the intervention strategies that resulted in successful...
Recently, it has been suggested that the Escherichia coli causing urinary tract infection (UTI) may come from meat and animals. The purpose was to investigate if a clonal link existed between E. coli from animals, meat and UTI patients. Twenty-two geographically and temporally matched B2 E. coli fro...
Surveillance of Clostridium difficile infection (CDI) is compulsory in Belgian hospitals. Our objectives were to compare incidence and case characteristics of nosocomial infections (Nc-CDI) with onset of diarrhoea more than two days after hospital admission, with non-nosocomial cases (Nnc-CDI). The...
From 2006 to 2009, 315 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates were collected from 5 hospitals across Israel. Most isolates (64%) were related to the global clones spa types t001-SCCmec-I (SCCmec-I stands for staphylococcal cassette chromosome mec type I) (n = 99; 31%),...
Globally, China is the second place with high burden of tuberculosis (TB). To explore the characteristics of the pathogens of Mycobacterium tuberculosis (MTB) circulating in this area is helpful for understanding and controlling the spread of the strains. Recent developments in molecular biology hav...
Aedes (Stegomyia) aegypti, the main vector of Dengue and Yellow Fever viruses, is present in all the northern and central provinces of Argentina. During 2009, a Dengue outbreak spread broadly throughout the country, causing 27,752 infections in 13 provinces. In Argentina, little is known about the d...
Next-generation sequencing has ushered in a new era of microbial genomics, enabling the detailed historical and geographical tracing of bacteria. This is helping to shape our understanding of bacterial evolution.
Studies on transmission of Enterococcus faecalis among chickens during hatch have not been carried out so far. Information about vertical transmission and subsequent spreading and colonization of the cloacal mucosa through cloacal 'drinking' during hatch are important to understand the epidemiology...
The asymptomatic oropharyngeal colonization rate by Streptococcus pyogenes was 10.7% in children (901 among 8,405 children 0-16 years old) and 3.3% in adults (37 among 1,126 households of children) in the Lisbon area during 2000-2006. Macrolide-resistant S. pyogenes from children (n = 149) was varia...
Viral encephalopathy and retinopathy (VER) is one of the most devastating diseases for marine aquaculture, and similarly represents a threat to wild fish populations because of its high infectivity and broad host range. Betanodavirus, the causative agent of VER, is a small non-enveloped virus with a...
We investigated the relatedness of multidrug-resistant Acinetobacter baumannii isolates from a burn intensive care unit (BICU) outbreak, control isolates, and isolates from a previous 2007 outbreak by 3 molecular typing methods (repetitive sequence-based polymerase chain reaction [rep-PCR], broad-ra...
Methicillin-resistant Staphylococcus aureus (MRSA) infections have been the most common cause of nosocomial infections in Japan, but their genetic characteristics related to bloodstream infections have not been well studied. The aim of this study was to investigate a comprehensive molecular characte...
Cryptococcus gattii (Cg) has caused increasing infections in the US Pacific Northwest (PNW) since 2004. We describe this outbreak and compare clinical aspects of infection in the United States among patients infected with different Cg genotypes. Beginning in 2005, PNW state health departments conduc...
Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of...
Melioidosis is caused by Burkholderia pseudomallei, a Gram-negative bacillus, primarily found in soils in Southeast Asia and northern Australia. A recent case of melioidosis in non-endemic Arizona was determined to be the result of locally acquired infection, as the patient had no travel history to...
We study the epidemiology, molecular basis, clinical risk factors, and outcome involved in the clonal dissemination of VIM-1-producing Klebsiella pneumoniae isolates in the hospital setting. All patients infected/colonized by carbapenem-nonsusceptible K. pneumoniae (CNSKP) in 2009 were included. Mol...
Our study describes the emm type distributions of invasive and non-invasive group A streptococci (GAS) and group G streptococci (GGS) strains in one of the biggest Health Districts in Finland. A total of 571 GAS or GGS were recovered from patients with invasive or non-invasive infections during a 1-...
Two isolates of enterohemorrhagic Escherichia coli (EHEC) O104:H4 were isolated in France in 2004 and 2009. Both were characterized and compared to the strain which caused the German outbreak in 2011 and to other O104:H4 strains. This suggests that different O104:H4 EHEC strains were present several...
We evaluated 11 variable number tandem repeat (VNTR) markers for the epidemiological investigation of Salmonella enterica serovar Typhi (S. Typhi) infection and compared the results to those obtained by PFGE. PFGE, using one or two restriction enzymes (XbaI and BlnI), was insufficient to differentia...
Staphylococcus epidermidis is a pathogen associated with nosocomial infection in neonatal intensive care units (NICU). This study investigates an outbreak of methicillin resistant S. epidermidis in an NICU in a hospital in Saudi Arabia. A total of 41 isolates identified as Gram-positive cocci were o...
Studies of recent hospital outbreaks caused by multiresistant P.aeruginosa (MRPA) have often failed to identify a specific environmental reservoir. We describe an outbreak due to a single clone of multiresistant (MR) Pseudomonas aeruginosa (PA) and evaluate the effectiveness of the surveillance proc...
In this brief report, we provide a portrait of the CEM-NET initiative and review studies that highlight contributions of this molecular epidemiological network to the understanding of the molecular mechanisms of drug resistance in Staphylococcus aureus and Streptococcus pneumoniae clones as well as...
The ongoing change in the relationship between humans and companion animals is hallmarked by the increasing intensive care provided to companion animals in veterinary medicine, resulting in growing numbers of high-risk animal patients. The emergence of nosocomial infections in small animal clinics i...
Mycobacterium porcinum is a rarely encountered rapidly growing Mycobacterium (RGM). We identified M. porcinum from 24 patients at a Galveston university hospital (University of Texas Medical Branch) over a 5-year period. M. porcinum was considered a pathogen in 11 (46%) of 24 infected patients, incl...
Neisseria meningitidis causes life-threatening disease in infants, toddlers, and adolescents. Besides representative case notification, public health management of the disease requires bacterial typing information. European reference laboratories and state epidemiologists in collaboration with Europ...
To characterize the complete sequence, horizontal spread and stability of the CTX-M-15-encoding multiresistance plasmid of a Klebsiella pneumoniae strain involved in a large nosocomial outbreak. The 220 kbp plasmid pUUH239.2 was completely sequenced using 454 technology. The conjugational host range...
Little information is available about pediatric infections caused by extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli. We characterized an outbreak caused by a CTX-M-14-producing E. coli isolate in a neonatal intensive care unit (NICU) and studied other infections caused by ESBL-produ...
No abstract available
Tracing the spatial spread of pathogens is a key objective of molecular infectious disease epidemiology. Accordingly, a wide range of genotyping approaches have been used to monitor the dissemination of Staphylococcus aureus strains, from localized outbreaks to global spread. We provide a critical r...
Molecular identification methods based on the staphylococcal cassette chromosome mec (SCCmec) genotype are more reliable than clinical risk factors and demographic data for differentiating community-acquired and healthcare-associated (HCA) meticillin-resistant Staphylococcus aureus (MRSA). However,...
Listeriosis is caused by Listeria monocytogenes, a gram-positive bacillus common in the environment and acquired by humans primarily through consumption of contaminated food. Infection causes a spectrum of illness, ranging from febrile gastroenteritis to invasive disease, including sepsis and mening...
No abstract available
Since 18 August 2011, 17 cases of travel-associated Legionnaires' disease have been reported. They were tourists from five European countries who had stayed in five accommodation sites in Lazise, Italy. The dates of symptom onset ranged from 18 July to 25 August 2011. Control measures were implement...
The aim of this study was to investigate the genetic relatedness between Candida albicans isolates and to assess their nosocomial origin and the likeliness of cross-transmission between health care workers (HCWs) and hospitalized neonates in a neonatal intensive care unit (NICU). We retrospectively...
Human rhinoviruses (HRVs) are an important cause of respiratory tract infections. We questioned whether the high prevalence rates of HRVs found in epidemiological studies is due to long-term individual continuity or a result of frequent infections with different HRV subtypes. In a 6-month winter per...
A Klebsiella pneumoniae isolate with decreased susceptibility to carbapenems was isolated in April 2011 in a hospital in Amsterdam (the Netherlands) and later found to be the source of an important outbreak in a Rotterdam hospital. The strain, belonging to sequence type (ST) 395, carried the bla(OXA...
Phenotypic and molecular methods were used to characterize the antibiotic resistance of 64 clinical isolates of Staphylococcus haemolyticus. By PCR of the mecA gene, 87% were found to be methicillin resistant. Approximately 55% harbored staphylococcal cassette chromosome mec element (SCCmec) type V,...
Molecular typing was used to examine surveillance definitions for recurrent Clostridium difficile-associated diarrhea. Among 102 patients, 85 had a second episode within 8 weeks, 88% of which were relapses. Of 49 second episodes occurring after > 8 weeks, 65% were relapses. Categorization of a recur...
Invasive group A streptococcal (GAS) infections cause significant morbidity and mortality. A national survey was initiated to assess the burden of invasive GAS infections in France, describe their clinical characteristics, and assess the molecular characteristics of GAS strains responsible for these...
Despite the rapid spread of antibiotic resistance among gonococci worldwide, limited reports are available from Brazilian locations. In the present study, 25 quinolone-resistant Neisseria gonorrhoeae (QRNG) strains isolated in Rio de Janeiro, Brazil, were characterized by phenotypic and molecular me...
The purpose of this investigation was to control the post-outbreak prevalence of vancomycin-resistant enterococci (VRE) in the affected Kyoto region. The study period was from 2005 to 2010. Faecal samples were subjected to VRE screening, and vancomycin resistance genes were detected by polymerase ch...
In the 1950s an unusually virulent and transmissible penicillin-resistant Staphylococcus aureus clone harbouring Panton-Valentine leukocidin (PVL) genes, known as phage type 80/81 and subsequently identified as multilocus sequence type (ST) 30, emerged and caused serious infections in hospitals and...
In Norway the Norwegian Institute of Public Health (NIPH) is the primary facility for nationwide surveillance of foodborne infections, and it is vital that we can perform rapid and high resolution identification of foodborne bacteria at the strain level. During the last decade a rapid introduction o...
The Netherlands is known for its low methicillin-resistant Staphylococcus aureus (MRSA) prevalence. Yet MRSA with no link to established Dutch risk factors for acquisition, MRSA of unknown origin (MUO), has now emerged and hampers early detection and control by active screening upon hospital admitta...
Although a whole-cell pertussis vaccine was introduced in Pakistan in 1980, little is known about the pertussis prevalence and circulating strains in Pakistan. The aim of this study was to analyze Bordetella parapertussis isolates circulating between 2005 and 2009 in Pakistan and to compare them wit...
The rate of mupirocin resistance in meticillin-resistant Staphylococcus aureus (MRSA) in Besançon University Hospital is low with a decreasing trend, from 10% in 2004 to 3% in 2009. This trend in resistance paralleled mupirocin consumption. Genotyping results showed that this decrease was not linked...
Slovenia is one of the few countries where IS6110 RFLP is applied for genotyping M. tuberculosis at a nationwide level, which has been in effect since 2000. Based on S6110 RFLP clustering, typical risk factors and routes of M. tuberculosis transmission were identified, such as alcohol abuse, homeles...
Vancomycin-resistant enterococci (VRE) frequently cause therapeutic problems and provide information about the epidemiological condition of the ward. VRE isolated from patients on transplantation wards in 2007-2008 were compared using 2 molecular methods: RFLP-PFGE (restriction fragment length polym...
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Bacteroides fragilis represents an early infant colonizer with important host interactions. Our knowledge about the diversity, transmission, and persistence of this bacterium, however, is limited. Here, we addressed these questions using a combination of multilocus sequence typing (MLST) and variabl...
Of 53 potential Clostridium difficile infection (CDI) case clusters/outbreaks, affecting 2 to 41 patients in 27 institutions, 19% comprised unrelated isolates and 34% had highly related and distinct isolates as shown by multilocus variable-number tandem-repeat analysis, despite sharing a common ribo...
Sequence-based typing (SBT) is the internationally recognized standard method for genotyping Legionella pneumophila. To date all strains of serogroup 1 (SG1) and some of SGs 2 to 14 yield a seven-allele profile and can be assigned a sequence type (ST). However, for some strains belonging to SGs 2 to...
Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described....
This report describes an outbreak involving vancomycin-resistant Enterococcus faecium colonization in 2 separate intensive care units (ICUs). Outbreak investigation including pulsed-field gel electrophoresis demonstrated that transfer of a vancomycin-resistant Enterococcus faecium colonized patient...
Risk of exposure to nymphal Ixodes pacificus Cooley and Kohls ticks was investigated at 7 picnic areas in Tilden Regional Park, a heavily used recreation area of over 2000 acres in northwestern California, east of San Francisco Bay. Wooden picnic tables, tree trunks, logs, leaf litter, surrounding v...
Japanese encephalitis virus (JEV) genotype V reemerged in Asia (China) in 2009 after a 57-year hiatus from the continent, thereby emphasizing a need to increase regional surveillance efforts. Genotypic characterization was performed on 19 JEV-positive mosquito pools (18 pools of Culex tritaeniorhync...
Salmonellosis is a frequently diagnosed infectious disease of passerine birds in garden habitats within Great Britain with potential implications for human and domestic animal health. Postmortem examinations were performed on 1,477 garden bird carcasses of circa 50 species from England and Wales, 19...
The aims of this study were to determine the ability of amplified fragment length polymorphism (AFLP) to differentiate Salmonella isolates from different units of swine production and to demonstrate the relatedness of Salmonella between farms and abattoirs by AFLP. Twenty-four farms in the midwester...
Genotypes of two different loci of the Pneumocystis jirovecii mitochondrial gene were studied in specimens from a total of 75 Pneumocystis pneumonia patients in Spain, France and Cuba. A new genotype of the mitochondrial small subunit rRNA gene of P. jirovecii (160A/196T) was identified, which was r...
Molecular analysis of Clostridium difficile (28 isolates) from children (n = 128) in Oxfordshire, United Kingdom, identified eight toxigenic genotypes. Six of these were isolated from 27% of concurrent adult C. difficile-associated infections studied (n = 83). No children carried hypervirulent PCR r...
Under certain circumstances, it is possible to identify clonal variants of Mycobacterium tuberculosis infecting a single patient, probably as a result of subtle genetic rearrangements in part of the bacillary population. We systematically searched for these microevolution events in a different conte...
In this study 45 isolates of Acinetobacter baumannii identified from patients in intensive care units of three different hospitals and from pressure ulcers in home care patients in Palermo, Italy, during a 3-month period in 2010, were characterized. All isolates were resistant to at least three clas...
Given the unpredictability of Neisseria meningitidis outbreaks and the increased prevalence of serogroup C strains following the introduction of serogroup A-based vaccines, we conducted an analysis of serogroups and sequence types (STs) in disease-associated and carrier N. meningitidis isolates that...
To investigate the epidemiological traits of Pseudomonas aeruginosa clinical isolates producing metallo-β-lactamases (MBLs) in Korea. A total of 386 non-duplicate P. aeruginosa clinical isolates were collected from Korea in 2009. Detection of MBL genes was performed by PCR. The genetic organization...
To analyse the evolution and genetic relatedness of Acinetobacter baumannii clonal lineages in Greece during a 10 year period. The study included 94 randomly selected A. baumannii clinical isolates recovered from 2000 to 2009 in eight tertiary Greek hospitals. Carbapenem MICs were determined by agar...
The consequences of the clonality of the Mycobacterium tuberculosis complex are described and, in particular, the identification of clonal complexes. Clonal complexes are groups of strains all descended from a single cell that was the most recent common ancestor (MRCA) of the clonal complex and all...
Many studies of sexual behavior have shown that individuals vary greatly in their number of sexual partners over time, but it has proved difficult to obtain parameter estimates relating to the dynamics of human immunodeficiency virus (HIV) transmission except in small-scale contact tracing studies....
Mycobacterium tuberculosis (MTB) strains were isolated from cerebrospinal fluids collected from individual tuberculous meningitis (TBM) patients from 1996 to 2007 (n = 184) and characterised based on IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, Mycobacterium interspersed re...
Gentamicin-susceptible methicillin-resistant Staphylococcus aureus (GS-MRSA) clones have gradually replaced gentamicin-resistant MRSA (GR-MRSA) clones in many European countries. We studied molecular and epidemiological aspects of MRSA strain replacement in individual patients. All patients from who...
Acinetobacter baumannii is emerging as an important nosocomial pathogen worldwide. We report molecular epidemiology of 65 carbapenem-nonsusceptible A. baumannii isolates identified from hospitals in New York, Pennsylvania, Florida, Missouri, Nevada, and California between 2008 and 2009. All isolates...
The aim of this study was to investigate the intraspecific diversity of Trichophyton rubrum clinical isolates. Thirty clinical isolates of T. rubrum were selected for molecular typing by PCR amplification of two tandemly repetitive elements (TRS-1 and TRS-2) of the rDNA and randomly amplified polymo...
Clostridium difficile infection (CDI) due to polymerase chain reaction (PCR) ribotype 027 (type 027) has been described worldwide. In some countries, an increase was reported of toxin A-negative PCR ribotype 017 (type 017). We encountered an outbreak due to these 2 types occurring simultaneously in...
Since the first reported outbreak of dengue hemorrhagic fever in Pakistan, several mini outbreaks have erupted in the region. Dengue virus serotype 3 (DEN-3) was first documented in 2005 outbreak in Karachi. Reports show that serotype 3 is prevalent in Lahore since 2008. Serotype 2 (DEN-2) is the ma...
During the years 2009 and 2010 relevant epidemic waves of foot-and-mouth disease (FMD) serotype O occurred in Ecuador, representing a great drawback for the last stages of the ongoing eradication program in South America. This study describes the molecular and antigenic characterizations of 29 isola...
From 1994 to 2009, the incidence of invasive serotype 19A pneumococci isolated from adults in Barcelona and San Sebastian almost doubled every 4 years. Genotyping of the 167 invasive isolates studied showed serotype 19A to be highly heterogeneous, with 35 different sequence types (STs) and a differe...
On October 29th 2009 the health authorities in the city of Trondheim, Norway were alerted about a case of Shiga toxin-positive E. coli (STEC) O145 in a child with bloody diarrhoea attending a day-care centre. Symptomatic children in this day-care centre were sampled, thereby identifying three more c...
No abstract available
Since early May 2011, a large outbreak of enterohemorrhagic gastroenteritis and hemolytic uremic syndrome (HUS) related to infections with Shiga toxin-producing Escherichia coli O104:H4 (STEC O104:H4) had been reported in Germany, which marks one of the largest outbreaks ever described of the HUS wo...
Triatomines are hemipteran bugs acting as vectors of the protozoan parasite Trypanosoma cruzi. This parasite causes Chagas disease, one of the major parasitic diseases in the Americas. Studies of triatomine genetics and evolution have been particularly useful in the design of rational vector control...
From March 2009 to May 2009, 24 carbapenem-resistant Klebsiella pneumoniae isolates were recovered from 16 patients hospitalized in an Italian intensive care unit (ICU). All isolates contained KPC-3 carbapenemase and belonged to a single pulsed-field gel electrophoresis (PFGE) clone of multilocus se...
An increased incidence of nosocomial and community-acquired infections caused by methicillin-resistant Staphylococcus aureus (MRSA) has been observed worldwide. The molecular characterization of MRSA has played an important role in demonstrating the existence of internationally disseminated clones....
To understand the genetic polymorphism of Salmonella and Staphylococcus aureus in Guangdong province, as well as to explore methods for identifying and tracing the source of these two foodborne pathogens. Using the automated ribotyping system, two foodborne pathogens were tested with either EcoR I o...
Mycobacterium tuberculosis is one of the most dangerous human pathogens. Molecular typing of M. tuberculosis has allowed better control of tuberculosis and, among other benefits, identification of genetic lineages among strains. To test the potential of polymerase chain reaction (PCR) based methods...
In 2010, we observed isolates with matching pulsed-field gel electrophoresis patterns from 13 cases of ciprofloxacin-resistant Shigella sonnei in Montréal. We report on the emergence of this resistance type and a study of resistance mechanisms. The investigation suggested local transmission among me...
Cholera has been a significant public health challenge in many communities. An outbreak of acute diarrheal illness occurred among participants in a wedding ceremony in a village in Qazvin, Iran, in 2008. We conducted an epidemiological, environmental and microbiological investigation to determine th...
Exposure network analysis and molecular epidemiologic methods were used to analyze the emergence and regional spread of Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae over a 1-year period. Although 40 patients and 26 health care facilities were affected, 1 long-term acute care hosp...
A Shiga-toxin-producing Escherichia coli (STEC) strain belonging to serotype O104:H4, phylogenetic group B1 and sequence type ST678, with virulence features common to the enteroaggregative E. coli (EAEC) pathotype, was reported as the cause of the recent 2011 outbreak in Germany. The outbreak strain...
No abstract available
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An increase in prevalence of multidrug-resistant Acinetobacter spp. in hospitalized animals was observed at the Justus-Liebig-University (Germany). Genotypic analysis of 56 isolates during 2000-2008 showed 3 clusters that corresponded to European clones I-III. Results indicate spread of genotypicall...
A total of 70 Staphylococcus aureus isolates from postoperative infections in hospitalized horses were isolated between January 2005 and January 2011. Among them, 12 isolates were methicillin-susceptible S. aureus (MSSA), 18 were borderline-oxacillin-resistant S. aureus (BORSA), and 40 were methicil...
To describe the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) carriage and transmission in an ambulatory hemodialysis population. Prospective cohort study. Outpatient hemodialysis facility affiliated with a large academic medical center. Of the 170 facility patients, 103 (61%) p...
Multilocus sequence typing (MLST) was used to examine the clonal relationship and genetic diversity of 71 Vibrio parahaemolyticus isolates from clinical and seafood-related sources in southeastern Chinese coast between 2002 and 2009. The tested isolates fell into 61 sequence types (STs). Of 17 clini...
Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal re...
During the incursion of bluetongue virus (BTV) serotype 8 in France in 2007, an increase in the number of abortions in cattle was observed, but the cause was not clearly established. A survey of all the reported cases of abortion in cattle from November 2008 to April 2009 was conducted in the Nièvre...
The molecular epidemiology of VIM-producing Enterobacteriaceae isolated at the beginning of an epidemic in the Intensive Care Unit (ICU) of a university hospital in Athens, Greece, was studied. All Gram-negative organisms isolated from March 2004 to November 2005 positive for metallo-β-lactamase (MB...
Until recently New Zealand had one of the highest rates of human campylobacteriosis reported by industrialized countries. Since the introduction of a range of control measures in the poultry production chain a reduction in human cases of around 50% has been observed nationwide. To inform risk manage...
At least four outbreaks of invasive disease caused by serotype 12F, clonal complex 218 Streptococcus pneumoniae have occurred in the United States over the past two decades. We studied the population structure of this clonal complex using a sample of 203 outbreak and surveillance isolates that were...
No abstract available
In Germany the number of new tuberculosis incidents continues to decline slightly. Cases of illnesses are often diagnosed late, due to the uncharacteristic course of tuberculosis. The success in environment investigations by health authorities in finding incidents within one infection chain depends...
Diarrhoea-associated haemolytic uraemic syndrome in adults is a life-threatening, but rare multisystem disorder that is characterised by acute haemolytic anaemia, thrombocytopenia, and renal insufficiency. We aimed to assess the success of management of this disorder with plasma exchange therapy. Pa...
No abstract available
Ninety-five colonizing isolates and 74 invasive isolates of Streptococcus agalactiae from Kenyan adults were characterized by using capsular serotyping and multilocus sequence typing. Twenty-two sequence types clustering into five clonal complexes were found. Data support the view that S. agalactiae...
This report describes an outbreak of Clostridium difficile infection (CDI) in a vascular surgery ward in 2009 caused by a high-level clindamycin-resistant ribotype 106. A case of CDI was defined as a patient with diarrhoea, positive for C. difficile toxin and negative for other enteric pathogens. Cu...
To assess the molecular epidemiology and prevalence of antibiotic resistance in Escherichia coli causing urinary tract infections of elderly patients from community and hospital settings. Also, to determine whether the possession of antibiotic resistance and virulence-associated genes can be linked...
In Europe, the Lyme borreliosis (LB) agents like Borrelia burgdorferi sensu stricto (ss), B. afzelii, and B. garinii are maintained in nature by enzoonotic transmission cycles between vertebrate hosts and Ixodes ricinus ticks. The outer surface protein C is a highly antigenic protein expressed by sp...
To assess the in vitro susceptibility of Francisella tularensis subsp. holarctica biovar II strains to 24 antimicrobial agents. Thirty-nine F. tularensis strains isolated from humans in the Central Anatolia region of Turkey were examined. Each isolate was identified by conventional and molecular tec...
PCR ribotyping is currently used in many countries for epidemiological investigation to track transmission and to identify emerging variants of Clostridium difficile. Although PCR ribotyping differentiates over 300 types, it is not always sufficiently discriminatory for epidemiological investigation...
More than 1,500 perirectal swab cultures and 552 environmental and equipment cultures were collected during the study period. Enterococcus faecium was the most frequent species isolated, being responsible for 71% of the positive cultures. Fifty infections were documented, with bloodstream infections...
The third-generation cephalosporins recommended in national guidelines are amongst the last remaining effective agents for treatment of gonorrhoea. This study characterizes gonococcal isolates with decreased cefixime susceptibility from England and Wales. A total of 96 isolates of Neisseria gonorrho...
Microsatellite typing of 25 Candida parapsilosis isolates from a described outbreak in a neonatal intensive care showed 2 large groups of blood isolates that were related to hand isolates from specific hospital staff, not infant-colonizing isolates. These results demonstrate the power of this typing...
Between December 2007 and July 2008, three neonates in a neonatal intensive care unit (NICU) in Salford, UK, were diagnosed with primary cutaneous aspergillosis (PCA) due to Aspergillus fumigatus. The first PCA case, in December 2007, developed multi-organ failure leading to death within a short tim...
Acinetobacter species are well-known causes of health care-associated infections. The longitudinal epidemiology of this species in the hospital setting is poorly understood. A sudden, persistent increase in multidrug-resistant (MDR) A baumannii infections occurred beginning in June 2006 at Temple Un...
Salmonella enterica serovar (S.) Enteritidis is an important cause of food-borne infection in Europe and the United States. Further subtyping of isolates is necessary to support epidemiological data for the detection of outbreaks and identification of the vehicle of infection. Multilocus variable-nu...
We recently reported an outbreak of invasive aspergillosis in the major heart surgery unit of Hospital Gregorio Marañón, Madrid, Spain (T. Peláez, P. Muñoz, J. Guinea, M. Valerio, M. Giannella, C. H. W. Klaassen, and E. Bouza, Clin. Infect. Dis., in press). Aspergillus fumigatus was isolated from cl...
Clostridium difficile is considered to be a leading cause of hospital-acquired diarrhea. C. difficile (CDI) infection shows a high rate of recurrence. There would have to be a predominantly monoclonal mechanism of CDI within individual patients in order for molecular epidemiologic tools such as poly...
Bloodstream infections due to Staphylococcus aureus (BSI) are serious infections both in hospitals and in the community, possibly leading to infective endocarditis (IE). The use of glycopeptides has been recently challenged by various forms of low-level resistance. This study evaluated the distribut...
Staphylococcus haemolyticus is one of the most clinically relevant coagulase-negative staphylococci (CoNS), particularly in immunocompromised patients; however, little is known regarding its molecular epidemiology. In this work, we characterized the genetic background and the SCCmec region of 36 met...
A laboratory-based surveillance study was conducted from January 2007 to May 2010 in San Martino Tertiary Referral Hospital in Genoa, Italy in which the molecular epidemiology of multidrug-resistant Acinetobacter baumannii was investigated in the five intensive care units (ICUs). A total of 53 A. ba...
In order to understand the population structure and dynamics of bacterial microorganisms, typing systems that accurately reflect the phylogenetic and evolutionary relationship of the agents are required. Over the past 15 years multilocus sequence typing schemes have replaced single locus approaches,...
To provide molecular epidemiological evidence of avian transmission of Escherichia coli O157:H7 between dairy farms in Ohio, this study was designed to identify genetic relatedness between isolates originating from bovine faecal samples and intestinal contents of European starlings captured on these...
During the recent outbreak of Shiga toxin-producing Escherichia coli (STEC) O104:H4 in Germany most cases notified in the State of Hesse (6 million inhabitants) were linked to satellite clusters or had travelled to the outbreak area in northern Germany. Intensified surveillance was introduced to rap...
Fast, reliable, and versatile typing tools are essential to differentiate among related bacterial strains for epidemiological investigation and surveillance of health care-associated infection with multidrug-resistant (MDR) pathogens. The DiversiLab (DL) system is a semiautomated repetitive-sequence...
Foot-and-mouth disease (FMD) is endemic in Pakistan and Afghanistan. Three different serotypes of the virus, namely O, A and Asia-1, are responsible for the outbreaks of this disease in these countries. In the present study, the nucleotide-coding sequences for the VP1 capsid protein (69 samples) or...
To characterize the genetic background of multidrug-resistant Acinetobacter baumannii (A. baumannii) from China, and the population structure of this pathogen. A previously reported MLST scheme was applied to a collection of 33 multidrug-resistant strains of A. baumannii from China, and the data of...
Hepatitis B infection causes a wide spectrum of liver diseases. Previous analyses of hepatitis B virus (HBV) genome have revealed eight HBV genotypes (A-H), with distinct geographical distribution worldwide. The epidemiology of HBV genotypes and their implications for natural history of disease prog...
Antimicrobial resistance in Neisseria gonorrhoeae (NG) is a public health concern globally, and azithromycin-resistant NG isolates have been identified in many countries. This study aimed to investigate azithromycin susceptibility in NG and to genetically characterize the azithromycin-resistant isol...
To determine the source of Burkholderia cepacia complex associated with a hospital outbreak and describe the measures taken to identify and confirm the source. A 250-bed, tertiary care pediatric hospital in Denver, Colorado. An epidemiologic investigation was used to identify possible causes for an...
An outbreak of multidrug-resistant (MDR) Pseudomonas aeruginosa occurred in an acute care hospital in Japan, which lasted for more than three years. During January 2006 to June 2009, 59 hospitalised patients with MDR P. aeruginosa were mainly detected by urine culture in the first half, whereas isol...
We report two patients with multidrug-resistant KPC-carbapenemase-producing Klebsiella pneumoniae urinary tract infections. A bla(KPC-2) gene was detected in both of the isolates by polymerase chain reaction and sequencing. The isolates had identical pulsed-field gel electrophoresis patterns and bel...
Both methicillin-resistant Staphylococcus aureus (MRSA) and penicillin-resistant Streptococcus pneumoniae have become significant causes of disease, both in health care and community settings. All patients admitted to our pediatric intensive care unit (PICU) currently had a rapid test for methicilli...
Drug-resistant Acinetobacter baumannii-calcoaceticus complex, Klebsiella pneumoniae, and methicillin-resistant Staphylococcus aureus colonize and infect combat casualties from Iraq and Afghanistan. We retrospectively evaluated relatedness, by pulsed-field gel electrophoresis and antibiotic susceptib...
Phycodnaviruses have a significant role in modulating the dynamics of phytoplankton, thereby influencing community structure and succession, nutrient cycles and potentially atmospheric composition because phytoplankton fix about half the carbon dioxide (CO(2)) on the planet, and some algae release d...
Although Ixodes scapularis is the most important vector of Borrelia burgdorferi sensu stricto, the causative agent of Lyme disease in North America, little is known of the genetic diversity in this tick species within the recently established populations in Canada. In the present study, 153 I. scapu...
No abstract available
Yersinia enterocolitica 1A strains are generally considered apathogenic. However, besides environmental sources, foods and animals, they are repeatedly isolated from patients with gastrointestinal symptoms typical to those evoked by Yersinia of the virulent 1B and 2-4 biotypes. Also, at least 2 gast...
No abstract available
We report an outbreak of linezolid-resistant Staphylococcus haemolyticus strains (MIC 32 mg/L) in patients admitted to the Verona University Hospital Intensive Care Unit. The strains proved to be clonally related at pulsed field gel electrophoresis. All the strains showed the G2576T mutation respons...
A multiple-locus variable-number tandem-repeat analysis (MLVA) was applied to investigate the epidemiological relationship and genetic diversity among 162 human Brucella isolates collected from all geographic regions of Turkey in an 8-year period (2001 to 2008). The isolates were genotyped by using...
Vibrio (V.) parahaemolyticus has endemically established in Chilean sea shores, causing outbreaks every year, with an important number of cases. In order to know the genetic relationship, genotype dominance and antibiotic resistance of isolates obtained from two outbreaks, this study characterized 1...
A large outbreak of diarrhea and the hemolytic-uremic syndrome caused by an unusual serotype of Shiga-toxin-producing Escherichia coli (O104:H4) began in Germany in May 2011. As of July 22, a large number of cases of diarrhea caused by Shiga-toxin-producing E. coli have been reported--3167 without t...
The goal of this study was to delineate the molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) in Taiwan. Ninety-six MRSA isolates were collected from the blood cultures of different patients during the period July to December of 2008. The spa typing, staphylococcal chro...
Staphylococcus aureus infections continue to pose a global public health problem. Frequently, this epidemic is driven by the successful spread of single S. aureus clones within a geographic region, but international travel has been recognized as a potential risk factor for S. aureus infections. To s...
An outbreak of gastrointestinal illness was identified among attendees at a large community barbeque at a Sydney sports club on 30 January 2009. A retrospective cohort study was initiated, and attendees were identified through hospital emergency department gastroenteritis presentations, snowball rec...
Most published data on multidrug-resistant Acinetobacter baumanii (MDR Ab) are derived from outbreaks. We report incidence trends on health care-acquired infections due to MDR Ab over a 12-month period in the city of Porto Alegre in southern Brazil. Clinical and epidemiologic data were obtained from...
No abstract available
Two devastating cases of multidrug-resistant Pseudomonas aeruginosa endophthalmitis after keratoplasty as the result of transmission from the same donor were confirmed by pulsed-field gel electrophoresis. Strategies for preventing donor-to-host transmission, such as the use of antimicrobial agents o...
Bartonella bacilliformis is the aetiological agent of human bartonellosis, a potentially life threatening infection of significant public health concern in the Andean region of South America. Human bartonellosis has long been recognised in the region but a recent upsurge in the number of cases of th...
To examine the pathogenesis of USA300 MRSA infection in long-term care residents, we performed a retrospective cohort study of 1691 adult residents of two extended-care facilities from 2003 to 2007 to assess whether the risk of subsequent MRSA infection is higher in USA300 MRSA-colonized residents c...
Staphylococcus aureus represents an organism of striking versatility. While asymptomatic nasal colonization is widespread, it can also cause serious infections, toxinoses and life-threatening illnesses in humans and animals. Staphylococcal food poisoning (SFP), one of the most prevalent causes of fo...
Aspergillosis remains a major cause of infection-related avian mortality in birds that are debilitated and undergoing rehabilitation for release into the wild. This study was designed to understand the source of avian aspergillosis in seabirds undergoing rehabilitation at selected northern Californi...
Enterotoxigenic Escherichia coli (ETEC) caused 131 outbreaks in Tokyo, Japan, between 1966 and 2009. The major serogroups were O6, O27, O148, and O159. The incidence of serogroups O25 and O169 recently increased. Heat-stable enterotoxin (ST) subtyping revealed that E. coli of serogroups O6, O15, O25...
This study describes the attempt to trace the first Mycobacterium bovis outbreak in alpacas (Lama pacos) in Spain by spoligotyping and variable-number tandem-repeat (VNTR) analysis. Due to high genotype diversity, no matching source was identified, but local expansion of a clonal group was found and...
Enterobacter hormaechei and Cronobacter sakazakii are amongst the most important causes of outbreaks of neonatal sepsis associated with powdered milk. In this study, we report for the first time an outbreak of a novel Enterobacter sp. harbouring bla(CTX-M-15) in a neonatal unit in Tanzania. Seventee...
Since 2004, an increasing number of multidrug-resistant Salmonella serovar Concord infections have been isolated in Belgium among children adopted from Ethiopia. The patients or their family were interviewed and the isolates were subtyped. Between 2004 and 2009, a total of 39 Salmonella Concord infe...
We report the results of a three-year surveillance program of Klebsiella spp. in six hospitals in Florence (Italy). A total of 172 Klebsiella isolates were identified and typed by AFLP: 122 were K. pneumoniae and 50 were K. oxytoca. Most K. pneumoniae (80%) and K. oxytoca (93%) showed unrelated AFLP...
We determined the fecal carriage rate of serotype K1 Klebsiella pneumoniae in healthy Koreans and studied their genetic relationship with liver abscess isolates. We compared the carriage according to the country of residence. The stool specimens were collected through health promotion programs in Ko...
Staphylococcus aureus is a major agent of bovine mastitis. The concomitant emergence of pig-associated methicillin-resistant S. aureus (MRSA) in human carriage and infection requires a reexamination of the host range and specificity of human- and cow-associated S. aureus strains, something which has...
Seventy-five clinical isolates of Pseudomonas aeruginosa collected in a tertiary teaching hospital in Thailand were investigated for susceptibility to antimicrobials including imipenem. Metallo-β-lactamase (MBL) enzymes were detected by E-test MBL assay and PCR; class 1 integron genes were also dete...
In June 2010, a severe outbreak of 13 cases of post-cataract surgery endophthalmitis caused by multidrug-resistant Pseudomonas aeruginosa occurred. Pulse-field gel electrophoresis in eye isolates found 95% genetic similarity; however, extensive environmental and carriage investigation revealed no so...
Candidaemia is associated with high patient mortality. Among those who survive an initial episode of candidaemia, the incidence of recurrent episodes has been incompletely defined. All patients in Iceland with candidaemia in 1980-2008 were identified, and clinical information was reviewed. Episodes...
Enterococci have been implicated in severe human infections as a consequence of associated determinants of virulence and antimicrobial resistance. The majority of vancomycin-resistant Enterococcus faecium (VRE(fm)) connected to outbreaks worldwide pertains to the clonal complex 17 (CC17). In Brazil,...
According to molecular epidemiology theory, two isolates belong to the same chain of transmission if they are similar according to a highly discriminatory molecular typing method. This has been demonstrated in outbreaks, but is rarely studied in endemic situations. Person-to-person transmission cann...
We describe six patients with hospital-acquired bacteremia caused by Methylobacterium species, including M. radiotolerans (n = 2), M. thiocyanatum (n = 2), M. aminovorans (n = 1), and M. lusitanum (n = 1), which were confirmed to species level by 16S rRNA gene sequence analysis. Among these patients...
No abstract available
Candida parapsilosis, which was previously considered to be a complex of three genetically distinct groups, has emerged as a significant agent of nosocomial infections. Recently, this complex was separated into three species: C. parapsilosis sensu stricto, C. orthopsilosis and C. metapsilosis. In Ch...
At the beginning of May an outbreak of bloody diarrhoea and haemolytic uraemic syndrome (HUS) began in Germany. During the succeeding months following the initial outbreak in Germany, thousands of infections occurred resulting in 877 cases of haemolytic uraemic syndrome (HUS) with 32 deaths and 3,04...
This study was aimed at tracing the molecular characteristics of carbapenem-resistant Acinetobacter baumannii (CRAB) clinical isolates in Italy with both pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Two hundred and two CRAB isolates were collected during 2004-2009,...
Listeria monocytogenes is a foodborne pathogen associated with severe diseases in humans and animals. The genotypic analysis of 17 L. monocytogenes isolates recovered from humans in India during 2006-2009 using multiplex serotyping PCR allowing serovar predictions, conventional serology and by pulse...
No abstract available
With more than 250,000 cases and 4,000 deaths in the first 6 months, the cholera epidemic in Haiti has been one of the most explosive and deadly in recent history. It is also one of the best documented, with detailed surveillance information available from the beginning of the epidemic, which allowe...
We confirm a natural infection of dromedaries with glanders. Multilocus variable number tandem repeat analysis of a Burkholderia mallei strain isolated from a diseased dromedary in Bahrain revealed close genetic proximity to strain Dubai 7, which caused an outbreak of glanders in horses in the Unite...
Interest in peste des petits ruminants virus (PPRV) has been stimulated by recent changes in its host and geographic distribution. For this study, biological specimens were collected from camels, sheep, and goats clinically suspected of having PPRV infection in Sudan during 2000-2009 and from sheep...
In 1988, the World Health Assembly resolved to eradicate poliomyelitis worldwide. The live, attenuated oral poliovirus vaccine (OPV) has many advantages favoring its use in polio eradication: it is administered easily by mouth; confers intestinal immunity, making recent OPV recipients resistant to i...
Bacillus cereus is becoming an important nomosomial pathogen because of frequent isolation from blood cultures and from severe systemic infections. To differentiate highly pathogenic outbreak strain of B. cereus from other sources of the Bacillus cereus, we attempted to analyze their dnaJ sequences....
Among Coxsackie B viruses, Coxsckievirus B5 is one of the most predominant serotypes in human, it is frequently associated with cases of neurological diseases, epidemics of meningitis and is a common cause of cardiomyopathy and diabetes. In the present study 27 isolates of Coxsackievirus B5 from Nor...
Pandemic influenza A/H1N1 2009 (A/H1N1pdm) virus caused significant outbreaks worldwide last year (2009). A number of oseltamivir-resistant A/H1N1pdm viruses possessing an H275Y substitution in the neuraminidase (NA) protein were reported sporadically in several countries, including Japan, but they...
Molecular fingerprinting techniques that have the potential to identify or subtype bacteria at the strain level are needed for improving diagnosis and understanding of the epidemiology of pathogens such as Xanthomonas citri pv. mangiferaeindicae, which causes mango bacterial canker disease. We devel...
No abstract available
During an area-based study, 75 group B streptococcus (GBS) strains isolated both from early-onset disease (EOD, 37 strains) and from late-onset disease (LOD, 38 strains) were analysed for serotype, pulsed field gel electrophoresis (PFGE) and multilocus sequence typing profiles, protein markers and a...
The genome sequences of two Escherichia coli O104:H4 strains derived from two different patients of the 2011 German E. coli outbreak were determined. The two analyzed strains were designated E. coli GOS1 and GOS2 (German outbreak strain). Both isolates comprise one chromosome of approximately 5.31 M...
During 2007, a study of pneumococcal carriage in children was performed in two towns (Trinidad and Riberalta) in the Beni region of the Bolivian Amazon basin. Little has previously been reported regarding the epidemiology of pneumococcal carriage in Bolivia, and no multilocus sequence typing (MLST)...
Multidrug-resistant Acinetobacter baumannii (MDRAB) is an important cause of hospital acquired infection. We describe a 7-month outbreak of a MDRAB infection involving various wards of an Italian hospital and an investigation of the possible source of the infection was conducted. A baumannii was iso...
We examined the detection and spread of carbapenem-resistant Citrobacter freundii in Huashan Hospital, Shanghai, China between 2005 and 2008. Twenty-three isolates of carbapenem-resistant C freundii collected in our hospital underwent resistant gene amplification by polymerase chain reaction, follow...
Sporotrichosis has significantly increased in Brazil in the last decade, particularly in the state of Rio de Janeiro, with the occurrence of an epidemic related to zoonotic transmission from cats to humans. Recently, four new phylogenetic species were incorporated into the Sporothrix species complex...
This study investigated the transmission dynamics of meticillin-resistant Staphylococcus aureus (MRSA) in a tertiary referral surgical unit with 300 beds. All adult patients were actively screened for MRSA by culture at hospital admission and twice weekly thereafter during hospitalisation from 1 Oct...
In an ongoing outbreak of haemolytic uraemic syndrome and bloody diarrhoea caused by a virulent Escherichia coli strain O104:H4 in Germany (with some cases elsewhere in Europe and North America), 810 cases of the syndrome and 39 deaths have occurred since the beginning of May, 2011. We analysed viru...
We analyzed 212 group B streptococci (GBS) from newborns with invasive infections in the area of Barcelona, Spain, between 1992 and 2009, with the aim of documenting changes in the prevalences of serotypes, antimicrobial resistance, and genetic lineages and evaluating their associations with either...
During the COMParative Activity of Carbapenems Testing (COMPACT) surveillance study, 448 Pseudomonas aeruginosa clinical isolates were obtained from 16 Spanish hospitals. Nonsusceptibility (EUCAST breakpoints) to imipenem (35%), meropenem (33%), and/or doripenem (33%) was observed with 175 isolates...
Typing of Chlamydia trachomatis is important to understanding its epidemiology. Currently used methods such as DNA sequencing of the ompA gene and multilocus sequence typing (MLST) either offer limited epidemiological resolution or are laborious and expensive, or both. DNA microarray technology usin...
This study was performed to determine the prevalence, distribution of specimen sources, and antimicrobial susceptibility of the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) species complex in Singapore. One hundred and ninety-three non-replicate Acb species complex clinical isolates wer...
To investigate the genetic environment of the metallo-β-lactamase gene bla(NDM-1) in an Acinetobacter baumannii isolated in 2007 in a German hospital. Antimicrobial susceptibility testing was performed and resistance genes were characterized by PCR amplification and sequencing. Transferability of β-...
Bovine tuberculosis (BTB), a chronic disease of mammals caused by Mycobacterium bovis, is a threat to South African wildlife. It has been reported that African buffaloes (Syncerus caffer) are reservoir hosts of BTB in South African wildlife populations. This study reports on the molecular identifica...
The genetic diversity of Campylobacter jejuni strains isolated from Finnish patients was studied by typing 508 strains by pulsed-field gel electrophoresis: 311 were isolated from domestically acquired infections and 197 from travel-related infections. The strains were systematically selected from a...
Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) was responsible for a worldwide pandemic during the 1980s and 1990s; however, changes in the dominant lineage before and after this event remain unknown. This study determined S. Enteritidis lineages before and after this pande...
Wolbachia are endocellular bacteria known for manipulating the reproductive systems of many of their invertebrate hosts. Wolbachia are transmitted vertically from mother to offspring. In addition, new infections result from horizontal transmission between different host species. However, to what ext...
To evaluate the impact of an 'intervention' consisting of revised antibiotic guidelines for empirical treatment of common infections and enhanced stewardship on reducing broad-spectrum antibiotic usage and its effect on incidence of Clostridium difficile infection (CDI). This was a retrospective, qu...
The global accumulation of Escherichia coli with CTX-M extended-spectrum β-lactamases partly reflects the dissemination of clonal lineages, notably ST131 and ST405. More recently, E. coli have emerged that produce NDM carbapenemase. We sought to determine the clonal diversity of E. coli with this en...
V. cholerae is the etiological agent of cholera, a major public health concern in most developing countries. Virulence of V. cholerae relies on the powerful cholera toxin, encoded by the CTX prophage. The emergence of new pathogenic variants in the recent years has been mostly associated with new CT...
We investigated a cluster of Burkholderia cepacia complex colonization in ventilated pediatric patients. Isolates from 15 patients, 2 sink drains, and several ventilator components were found to belong to a single B cenocepacia clone. Hospital tap water used during oral and tracheostomy care was ide...
Our retrospective investigation of methicillin-resistant Staphylococcus aureus (MRSA) infection at a hospital in Japan around 2007 suggested dissemination of community-associated MRSA (CA-MRSA) strains among healthy students in a Japanese boarding school, which frequently caused skin disease and exh...
Plasmid-mediated 16S rRNA methylases such as ArmA, which confer high levels of resistance to aminoglycosides, are increasingly reported in Enterobacteriaceae. This study investigated the molecular mechanism of β-lactam and aminoglycoside resistance in extended-spectrum β-lactamase (ESBL)-producing S...
We report the first outbreak caused by colistin-resistant Klebsiella pneumoniae producing KPC-3 carbapenamase in two Italian hospitals. This spread occurred in 1 month, and was caused by eight colistin-resistant and carbapenem-resistant Klebsiella pneumoniae isolates from eight patients. A further t...
The multidrug-resistant tuberculosis (MDR-TB) epidemic in Eastern Europe bordering Finland has raised worries concerning the risk of disease in near-frontier contacts. Our aim was to find out the amount of multidrug resistance, characterise the resistance profiles and evaluate the outcome of treatme...
Vibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emergence of a pandemic. Other serovariants of this strain emerged during its dissemination a...
No abstract available
The rate of infection with Clostridium difficile colitis and its associated mortality have been increasing in the last decade. The molecular epidemiology of C. difficile in Israel has not been studied. To screen for the existence of the 027 and 078 ribotypes and determine the longitudinal molecular...
Despite the prevalence of Streptococcus pneumoniae serotype 19A, the molecular characteristics of this serotype are yet to be fully elucidated. The aim of this study was therefore to determine the homology of the serotype 19A in China. Pulsed-field gel electrophoresis and multilocus sequence typing...
Due to the inability to cultivate Mycobacterium leprae in vitro and most cases being paucibacillary, it has been difficult to apply classical genotyping methods to this organism. The objective of this study was therefore, to analyze the diversity among M. leprae strains from Uttar Pradesh, north Ind...
A nationwide outbreak of Salmonella enterica serotypes Newport and Reading occurred between 17 October and 28 November 2008 in Finland. A total of 77 culture-confirmed Salmonella Newport and 30 Salmonella Reading cases, including one case with a double infection, were reported. All strains isolated...
The domestic pig is an important source of human salmonellosis, and houseflies are potential mechanical vectors of foodborne Salmonella pathogens. In 2005, we recovered 144 Salmonella isolates from flies and swine stool samples from 11 farms in Taoyuan County and Hsin Chu County (northwestern Taiwan...
Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are vectored by aphids. The identification of vector proteins mediating virus transmission is critical to develop sustainable virus management practices and to understand viral strategies for circ...
We used molecular typing methods to investigate an outbreak of methicillin-resistant Staphylococcus aureus (MRSA) infections in a respiratory care ward in Taiwan. From March to June 2006, the incidence of MRSA infection increased 3.75-fold. The overall carrier rates among the health care workers (HC...
Serological techniques play a critical role in various aspects of influenza surveillance, vaccine development and evaluation, and sometimes in diagnosis, particularly for novel influenza virus infections of humans. Because individuals are repeatedly exposed to antigenically and genetically diverse i...
Genotyping of Mycobacterium tuberculosis has been extensively used for investigating epidemics of multidrug-resistant strains of M. tuberculosis, in order to identify the factors involved in the transmission of such strains and determine effective control programmes to limit their expansion at both...
Automated repetitive PCR (rep-PCR; DiversiLab) was compared to PCR ribotyping of the 16S-23S RNA intergenic spacer of Clostridium difficile (CD) as the "gold standard" method for CD typing. PCR products were separated on DiversiLab LabChips (bioMérieux, St. Laurent, Quebec, Canada) utilizing a 2100...
The introduction of the seven-valent pneumococcal conjugate vaccine (PCV7) in Portugal led to extensive serotype replacement among carriers of pneumococci, with a marked decrease of PCV7 types. Although antimicrobial resistance was traditionally associated with PCV7 types, no significant changes in...
Although elimination of measles virus (MV) by 2010 was a revised target, a new epidemic has been ongoing in Greece and other European countries. The purpose of this study was the molecular and phylogenetic analysis of the Greek MV circulating strain. Twenty-four MV strains isolated from clinical sam...
We illustrate how genotyping of mycobacterial strains contributed to the discovery of an undetected outbreak of tuberculosis in a hospital ward, ruling out misleading assumptions of transmission chains. Genotyping should be taken into account in routine tests for the control of tuberculosis.
Borrelia burgdorferi sensu lato (s.l.) complex is a diverse group of worldwide distributed bacteria that includes 18 named spirochete species and a still not named group proposed as genomospecies 2. Descriptions of new species and variants continue to be recognized, so the current number of describe...
The Babesia bovis and B. bigemina apicomplexan protozoa in conjunction with the rickettsia Anaplasma marginale are intraerythrocytic pathogens that are responsible for the most prevalent and costly tick borne diseases (TBD's) of cattle worldwide. These organisms are historically associated as they c...
Extra-intestinal pathogenic Escherichia coli (ExPEC) causing urinary tract infections (UTIs) most often belong to phylogenetic group B2 and stem from the patient's own faecal flora. It has been hypothesized that the external reservoir for these uropathogenic E. coli in the human intestine may be mea...
To assess the prevalence of faecal coliform bacteria and multiple drug resistance among Escherichia coli and Salmonella serotypes from Vembanadu Lake. Systematic microbiological testing. Monthly collection of water samples were made from ten stations on the southern and northern parts of a salt wate...
Invasive disease caused by the encapsulated bacteria Neisseria meningitidis, Haemophilus influenzae and Streptococcus pneumoniae remains an important cause of morbidity and mortality worldwide, despite the introduction of successful conjugate polysaccharide vaccines that target disease-associated st...
From June 2003 to December 2009, 98 isolates of vancomycin-resistant enterococci (VRE) were cultured from clinical specimens taken from patients admitted to a 1,500-bed tertiary-care teaching hospital in Beijing, China. Isolates were characterized by pulsed-field gel electrophoresis and multilocus s...
We report on a coinfection of Mycobacterium avium subsp. avium and Salmonella enterica serotype Typhimurium var. Copenhagen phage type DT2 in pigeons from one flock, from which squabs were occasionally consumed by humans. Triplex quantitative real-time PCR and culture methods were used for M. a. avi...
In Osaka Prefecture, Japan, three foodborne outbreaks were caused by Salmonella enterica serotype Montevideo in rapid succession between September 2007 and May 2008. Further, Salmonella Montevideo was also isolated from several sporadic diarrhea patients and asymptomatic carriers examined during app...
Pasteurella multocida causes disease in many host species throughout the world. In bovids, it contributes to bovine respiratory disease (BRD) and causes haemorrhagic septicaemia (HS). Previous studies have suggested that BRD-associated P. multocida isolates are of limited diversity. A multilocus seq...
A wide range of blood-sucking arthropods have either been confirmed or are suspected as important vectors in Bartonella transmission to mammals, including humans. Overall, it appears that the diversity of Bartonella species DNA identified in ectoparasites is much broader than the species detected in...
No abstract available
The characteristics of 218 Klebsiella pneumoniae isolates from patients with hospital-acquired pneumonia in nine Asian countries were investigated. In total, 92 isolates (42.2%) produced extended-spectrum β-lactamases (ESBLs), amongst which 67 (72.8%) possessed CTX-M ESBL genes; CTX-M-15 was the maj...
VIM-producing Klebsiella pneumoniae (VPKP) has been identified as a source of hospital outbreaks and is prevalent particularly in the Mediterranean region. In this study we have characterized eight VPKP isolates identified in Scandinavia during 2005-2008. With the exception of one isolate, all were...
The molecular epidemiology of 32 non-duplicate, CTX-M-15 extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains, isolated from clinical samples, was investigated. Multilocus sequence typing revealed multiple sequence type clonal complexes: ST131 (12), ST405 (4), ST638 (3), ST38 (...
Human enteroviruses (HEVs) are responsible for a wide spectrum of clinical diseases. Even though usually associated with non-specific febrile illness, they are the most common cause of viral meningitis and pose a serious public-health problem, especially during outbreaks. Rapid detection and identif...
No abstract available
The purpose of this study was to investigate if multiresistant methicillin-susceptible Staphylococcus aureus (MR-MSSA) causing a clonal outbreak in Östergötland County, Sweden, were derived from methicillin-resistant S. aureus (MRSA) by carrying remnants of SCCmec, and, if so, to characterise this e...
This study aimed to determine the genetic diversity of clinical multidrug-resistant Pseudomonas aeruginosa. We used pulsed-field gel electrophoresis and multilocus sequence typing to analyze 187 strains isolated in different French hospitals. To illustrate the diversity of resistance mechanisms to a...
To examine the distribution and context of aminoglycoside resistance genes in multiply antibiotic-resistant Acinetobacter baumannii isolates from Australia that are members of the global clone 2 and carry the bla(OXA-23) gene conferring resistance to carbapenems. Sixty-one multiply antibiotic-resist...
Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis r...
Salmonella enterica serotype Bovismorbificans is a rare serotype in Finland. In June 2009, a nationwide outbreak of S. Bovismorbificans infections occurred, and 42 clinical isolates were identified. We conducted a case-control study enrolling 28 cases and 48 matched controls, and found ready-to-eat...
There is a notable dearth of data about Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) prevalence in Afghanistan. Awareness program and research capacity in the field of hepatitis are very limited in Afghanistan. Number of vulnerabilities and patterns of risk behaviors signal the need to take a...
Multilocus sequence typing (MLST) has been successfully applied to the epidemiology of Candida albicans isolates not only within the hospital setting but also in multiple locations nationwide. We performed MLST to investigate the genetic relatedness among bloodstream infection (BSI) isolates of C. a...
This study shows the benefit of spoligotyping coupled to mycobacterial interspersed repetitive-unit (MIRU) typing to pinpoint circulating Mycobacterium tuberculosis genotypes in Guadeloupe, Martinique, and French Guiana. We hereby propose reduced 4-locus and 6-locus subsets for LAM and Haarlem linea...
To evaluate colonization, transmission rate and serotype distribution of group B streptococci (GBS) in pregnant women and infants born in a single University Center in Germany. In a prospective study we collected cultures from pregnant women and ear cultures from newborns. We performed serotyping an...
Shewanella xiamenensis, a newly established species originally from sea sediments, was repeatedly recovered from peripancreatic drainages in a patient and was the probable pathogen of hospital-acquired peripancreatic infection. A commercially available system misidentified it as Shewanella putrefaci...
Staphylococcus aureus is an important pathogen causing a wide range of infections in the hospital and community setting. In order to have adequate information for treatment of S. aureus infections, it is crucial to understand the trends in the antibiotic-resistance patterns. In addition, the occurre...
Evolutionary analyses have revealed an origin of pandemic HIV-1 group M in the Congo River basin in the first part of the XX century, but the patterns of historical viral spread in or around its epicentre remain largely unexplored. Here, we combine epidemiologic and molecular sequence data to invest...
Bluetongue (BT) is a vector-borne disease of ruminants caused by bluetongue virus that is transmitted by biting midges (Culicoides spp.). In 2006, the introduction of BTV serotype 8 (BTV-8) caused a severe epidemic in Western and Central Europe. The principal effective veterinary measure in response...
The recently determined serotypes 6C and 6D Streptococcus pneumoniae, as well as subtypes 6B-I and 6B-II, were not reported in China. Among the 171 invasive isolates, 19 were identified as serogroup 6. There were equal distribution (42.1%) of 6B-I and 6B-II, 15.8% of 6A and lack of 6C and 6D. Among...
To follow the epidemic of KPC-2-producing Klebsiella pneumoniae in Greece. KPC-2-producing isolates (n = 378) were collected during January 2009-April 2010 in 40 Greek hospitals. bla(KPC) and bla(VIM) were detected by PCR. Carbapenemase production was confirmed by spectrophotometry. Sequences flanki...
Thirty-four Vibrio cholerae isolates collected from a cholera outbreak in Hyderabad, South India were found to belong to serogroup Ol biotype El Tor serotype Ogawa. The genotype of all the isolates was confirmed by PCR assays. All the isolates were found PCR positive for ctxAB, ompW, rflOl, rtxC, an...
The incidence of Clostridium (C.) difficile infection (CDI) was on the rise from 2001 to 2006 in Singapore. Recent unpublished data suggests that its incidence had remained stable or decreased in most local public hospitals between 2006 and 2010. It is, however, not known if the polymerase chain rea...
The aim of present study was to determine the prevalence of O serogroups of Escherichia coli (E. coli) strains that cause community-acquired urinary tract infections (UTI) in children. In this study, 96 children with UTI referred to two Jahrom University-affiliated Hospitals in Iran were enrolled, d...
To examine associations between clinical features of Streptococcus suis serotype 2 infections in humans in Thailand and genotypic profiles of isolates, we conducted a retrospective study during 2006-2008. Of 165 patients for whom bacterial cultures of blood, cerebrospinal fluid, or both were positiv...
In view of the increasing use of pneumococcal vaccines, especially in the developing world, there is a need for appropriate diagnostics to understand the aetiology of pneumonia, to define the burden of pneumococcal disease, and to monitor vaccine efficacy and effectiveness. This article summarizes a...
To define the molecular epidemiology of colonization and disease-associated isolates of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA). Laboratory-based comparative study of clinical staphylococcal isolates. We analyzed 255 pediatric CA-MRSA isolates for molecular charact...
No abstract available
Pan-European surveillance of bacteraemia caused by methicillin-resistant Staphylococcus aureus (MRSA) shows it to be a problem affecting all European countries, although there is marked geographical variation in prevalence. Although the proportion of S. aureus bacteraemia due to MRSA is declining in...
No abstract available
The incidence of pleural infection continues to rise worldwide. Identifying the causative organism(s) is important to guide antimicrobial therapy. The bacteriology of pleural infection is complex and has changed over time. Recent data suggest that the bacterial causes of empyema are significantly di...
The Indian Subcontinent has emerged as a scene of many mosquito-borne infectious diseases, including malaria and dengue fever. After the 1990s, the rate of malaria declined owing largely to preventive measures, but at the same time dengue fever (DF) and dengue hemorrhagic fever (DHF) were increasing...
During 2005-2007, we experienced sporadic isolations of multidrug-resistant (MDRP) Pseudomonas aeruginosa from wards in a general hospital in Hiroshima. The objective of this study was to analyze epidemiology relationships and the mode of spread of the strains. Clonality was assessed using pulsed-fi...
Continued rapid evolution of the influenza A virus is responsible for annual epidemics and occasional pandemics in the Shanghai area. In the present study, the representative strains of A/H1N1 and A/H3N2 influenza viruses isolated in the Shanghai area from 2005 to 2008 were antigenically and genetic...
Current knowledge of plant virus diversity is biased towards agents of visible and economically important diseases. Less is known about viruses that have not caused major diseases in crops, or viruses from native vegetation, which are a reservoir of biodiversity that can contribute to viral emergenc...
Epidemiological investigations of Clostridium difficile often focus on differences between separate geographical areas. In this investigation, two populations of C. difficile recovered from separate tertiary referral Trusts within the West Midlands, UK, were characterized using both PCR ribotyping a...
We investigated molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) isolated at 10 intensive care units (ICUs) in Korea. MRSA isolates from bacteremia and nasal colonization were collected prospectively from October 2008 through May 2009 at 10 University-affiliated hospital...
The incidence, clinical manifestations, and circulating clones involved in Streptococcus pyogenes invasive disease was analyzed in two regions of Spain between 1998 and 2009. The annual average incidence of invasive disease was 2 episodes per 100,000 inhabitants (3.1 for children and 1.9 for adults)...
No abstract available
The aim of this study was to provide baseline information on the molecular epidemiology and the antimicrobial susceptibility of Clostridium difficile (C. difficile) clinical isolates from patients throughout New Zealand. Faecal specimens that were C. difficile-toxin positive by EIA assay were cultur...
This study was designed to investigate the prevalence and characteristics of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa in a tertiary care centre in The Netherlands, a country that is considered to have a low prevalence of antibiotic-resistant bacteria. Imipenem-resistant P. aerugino...
Capsule-forming Klebsiella pneumoniae K1 caused primary liver abscess in two household members of a family. The causative isolates had identical pulsed-field gel electrophoresis patterns and were determined to be sequence type 23. An additional member of the family was found to carry the same strain...
Staphylococcal cassette chromosome mec (SCCmec) typing is essential for investigating the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA). Published assays were often found to be limited in their ability to characterize isolates that were not collected locally. We aimed...
The usefulness of mec-associated dru typing in the epidemiological analysis of methicillin-resistant Staphylococcus aureus (MRSA) isolated in Malaysia was investigated and compared with pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and spa and SCCmec typing. The isolate...
No abstract available
Enterovirus environmental surveillance on sewage from the city of Jinan, Shandong Province, China, was initiated in 2008. Thirty echovirus 6 (E6) strains-1 in 2008 and 29 in 2010-were isolated and identified. Most E6 isolates (n = 21) came from the sewage collected on August 2010, revealing high loc...
Streptococcus agalactiae is a major pathogen of neonates and immunocompromised adults. Prior studies have demonstrated that, beyond the neonatal period, S. agalactiae rarely causes invasive infections in children. However, during 2004-2005, S. agalactiae was the causative agent of 60 meningitis epis...
No abstract available
PFGE is currently the North American standard for surveillance for Clostridium difficile but lacks discriminatory power to aid outbreak investigation. A further limitation to PFGE is the high baseline rate of the epidemic North American pulsotype (NAP) 1 strain in hospitals. Multilocus variable-numb...
This paper details the phenotypic, genotypic, and antibiotic sensitivity patterns of 88 Vibrio cholerae strains from Zimbabwe. Of the 88 strains, 83 were classified as "altered El Tor" and 5 as "hybrid El Tor" strains. All of the strains were susceptible to tetracycline, doxycycline, ciprofloxacin,...
Bartonella henselae is one of the most common zoonotic agents acquired from companion animals (cats) in industrialized countries. Nonetheless, although the prevalence of infections in cats is high, the number of human cases reported is relatively low. One hypothesis for this discrepancy is that B. h...
Intestinal carriage of extended-spectrum beta-lactamase (ESBL) -producing bacteria in food-producing animals and contamination of retail meat may contribute to increased incidences of infections with ESBL-producing bacteria in humans. Therefore, distribution of ESBL genes, plasmids and strain genoty...
Mycobacterium bovis and, more rarely, Mycobacterium caprae, may cause zoonotic bovine tuberculosis (bTB) in an extensive range of animal species. In Portugal, during 2009, a remarkable raise of bTB incidence was registered in cattle along with an increase of new cases in wildlife. In this work, we r...
Our purpose was to evaluate the natural epidemiological history of circulating Bordetella pertussis clinical isolates in Turkey, comparing isolates by means of pulsed-field gel electrophoresis (PFGE) profiles according to years, geographic regions, vaccination status, and demographic characteristics...
Differentiation of the growing nosocomial infectious threats, Ralstonia pickettii and Ralstonia insidiosa, based on nitrate reduction, desferrioxamine susceptibility, arabinose, N-acetyl-glucosamine and phenylacetate assimilation is described. These tests can be used for preliminary identification o...
From 1980 onwards, an increasing number of outbreaks of Pneumocystis pneumonia (PCP) among kidney transplant recipients have been reported. The cause of these outbreaks is unclear and different explanations have been provided. We performed a systematic review to provide a comprehensive overview of t...
El Tor Vibrio cholerae O1 carrying ctxB C trait, so-called El Tor variant that causes more severe symptoms than the prototype El Tor strain, first detected in Bangladesh was later shown to have emerged in India in 1992. Subsequently, similar V. cholerae strains were isolated in other countries in As...
Q fever is a zoonosis caused by the bacterium Coxiella burnetii. One of the largest reported outbreaks of Q fever in humans occurred in the Netherlands starting in 2007; epidemiologic investigations identified small ruminants as the source. To determine the genetic background of C. burnetii in domes...
The natural history of contemporary Staphylococcus aureus nasal colonization was evaluated in community children during a 1-year period. Methicillin-susceptible S. aureus nasal carriage was more persistent than methicillin-resistant S. aureus nasal carriage, which was usually self-limited. Children...
The molecular genotyping of Mycobacterium tuberculosis is expected to lead to a better understanding of M. tuberculosis transmission in Xi'an, one of the largest cities in Western China. To characterize the population of M. tuberculosis strains circulating in Xi'an and to evaluate the feasibility of...
The epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) in Africa is poorly documented. From January 2007 to March 2008, 555 S. aureus isolates were collected from five African towns in Cameroon, Madagascar, Morocco, Niger, and Senegal; among these, 456 unique isolates were suscepti...
Escherichia coli is one of the major pathogens responsible for bactaeremia. Empirical antibiotherapy of these infections usually relies on third-generation cephalosporins (3GCs). Thus, the occurrence and epidemiology of 3GC-resistant strains have to be monitored. The French prospective multicentre s...
No abstract available
USA300 is an epidemic community-acquired methicillin-resistant Staphylococcus aureus (C-MRSA) clone in the USA, whereas the European C-MRSA clone ST80-IV has mainly a sporadic diffusion in Europe. The prevalence of European clone ST80-IV in Algeria is poorly documented. We prospectively studied S. a...
No abstract available
Hospital strains of Enterococcus faecium could be characterized and typed by various molecular methods (MLST, AFLP, MLVA) and allocated to a distinct clonal complex known as MLST CC17. However, these techniques are laborious, time-consuming and cost-intensive. Our aim was to identify hospital E. fae...
Streptococcus pneumoniae serotype 6C, which was described in 2007, causes invasive disease in adults and children. We investigated the prevalence of 6C among pediatric isolates obtained from eight children's hospitals in the United States. S. pneumoniae isolates were identified from a prospective mu...
Pseudomonas infections are an important cause of morbidity and mortality in immunocompromised patients. We present here data for the spread of Pseudomonas fluorescens caused by a contaminated drinking water dispenser in a bone marrow transplant unit. Over a 1-month period we observed a sharp increas...
Acinetobacter spp. increasingly have been wreaking havoc in hospitals and communities worldwide. Although much has been reported regarding Acinetobacter isolates responsible for nosocomial infections, little is known about these organisms in correctional facilities. In this study, we performed speci...
The aim of this study was to provide molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) spa type t127, sequence type (ST) 1 isolates, detected in a European baseline survey in holdings of breeding pigs, to determine phenotypic and genotypic drug resistance and to compar...
Argentina suffered an extensive foot-and-mouth disease (FMD) epidemic between July 2000 and January 2002, 3 months after obtaining the official FMD-free without vaccination status conferred by the World Organization for Animal Health. This is one of the largest FMD epidemics controlled by implementa...
A collection of 20 multidrug-resistant Providencia stuartii isolates recovered from 2005 to 2009 at the Military Hospital of Tunis, Tunisia, was analysed. They all expressed the extended-spectrum β-lactamase (ESBL) VEB-1a. The bla (VEB-1a) gene was plasmid-located and it was associated with complex...
A significant increase in adenovirus detection among patients at the Children's Mercy Hospital, Kansas City was observed between June 2007 and January 2008. To molecularly characterize the human adenoviruses and describe their association with clinical illness in children. One hundred adenovirus-pos...
The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal sw...
Different strains of Listeria monocytogenes are well known to persist in individual food processing plants and to contaminate foods for many years; however, the specific genotypic and phenotypic mechanisms responsible for persistence of these unique strains remain largely unknown. Based on sequences...
Brucellosis, a zoonosis caused by the genus Brucella, has been eradicated in Northern Europe, Australia, the USA and Canada, but remains endemic in most areas of the world. The strain and biovar typing of Brucella field samples isolated in outbreaks is useful for tracing back source of infection and...
Due to an increase in bovine tuberculosis in cattle in the United Kingdom, we investigated the characteristics of Mycobacterium bovis infection in humans and assessed whether extensive transmission of M. bovis between humans has occurred. A cross-sectional study linking demographic, clinical, and DN...
Varieties of Salmonella enterica are the second most commonly notified causes of gastroenteritis in Australia. Outbreaks of Salmonella infection are commonly linked to food, particularly foods containing chicken meat and eggs. A number of European countries have introduced interventions based on Sal...
The swine influenza (SI) is an infectious disease of swine and human. The novel swine-origin influenza A (H1N1) that emerged from April 2009 in Mexico spread rapidly and caused a human pandemic globally. To determine whether the tremendous virus had existed in or transmitted to pigs in southern Chin...
Human enteroviruses (HEV) are frequent human pathogens and, associated in particular with large outbreaks of aseptic meningitis. Here, we have compiled a database of clinical HEV isolates from the Public Hospitals of Marseille, from 1985 to 2005. Amongst 654 isolates that could be characterized by c...
The purpose of this study was to investigate the molecular epidemiology of CTX-M-14-producing Escherichia coli clinical isolates from Korea. A total of 138 non-duplicate E. coli clinical isolates showing reduced susceptibility or resistance to ceftazidime and/or cefotaxime were included in the study...
A modified multiple-locus variable-number tandem-repeat analysis (MMLVA) method was validated on Clostridium difficile-infected stool specimens from institutional outbreaks. The method allows simultaneous detection of toxin genes, deletions, and tandem repeats from cultured isolates or stool specime...
We used several molecular typing methods to analyze 196 methicillin-resistant Staphylococcus aureus (MRSA) and 139 methicillin-susceptible S. aureus (MSSA) isolates collected between 1996 and 2005. The sequence type 72 MRSA has increased in frequency in the community in the Republic of Korea and in...
We describe a foodborne nosocomial outbreak due to extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae. An outbreak of ESBL K. pneumoniae was detected in March 2008. Initial control measures included contact isolation and a protocol for routine detection and reinforcement in hand hy...
This study examined Klebsiella pneumoniae clinical isolates and their bla(KPC) plasmids to determine potential relatedness of the isolates and their plasmids harbouring carbapenem resistance mechanisms. K. pneumoniae carbapenemase (KPC)-producing K. pneumoniae from New York City (NYC) (n = 19) and T...
To estimate the global and regional distribution of HIV-1 subtypes and recombinants between 2000 and 2007. Country-specific HIV-1 molecular epidemiology data were combined with estimates of the number of HIV-infected people in each country. Cross-sectional HIV-1 subtyping data were collected from 65...
Most rotavirus gastroenteritis is caused by G1P[8] strains. When G2 infections are encountered, the P type has most often been reported to be P[4]. The purpose of our study was to describe an unusual outbreak of G2P[6] cases. Children presenting to The Children's Hospital of Philadelphia with acute...
Bacillus sporothermodurans is an industrially important micro-organism because of its ability to produce endospores which resist ultra-high temperature (UHT) and industrial sterilization processes. It was described by Pettersson et al. (1996) [Pettersson, B., Lembke, F., Hammer, P., Stackebrandt, E....
Drug resistance and molecular epidemiology of tuberculosis (TB) in the Murmansk region was investigated in a 2-year, population-based surveillance of the civilian population. During 2003 and 2004, isolates from all culture-positive cases were collected (n = 1,226). Prevalence of multi-drug resistanc...
Following 7-valent conjugate vaccine introduction in the United States in 2000, invasive serotype (sero19A) pneumococcal disease (IPD) emerged rapidly. Sero19A IPD incidence increased slightly during 2005-2008 (from 2.3 cases to 2.5 cases per 100,000 population), whereas sero19A penicillin resistanc...
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The aim of this study was to investigate the genetic relatedness of 57 KPC-2-producing Klebsiella pneumoniae isolates from 5 states in Brazil, during 2006-2009. Pulse-field gel electrophoresis analysis identified 10 pulsotypes. The pulsotype designated as Kp-RJ (Klebsiella pneumoniae-Rio de Janeiro)...
We report the results of two nationwide surveillance studies of Clostridium difficile infection conducted during 2008 and 2009 in Sweden. The first study aimed to identify and quantify the proportion of C. difficile isolates with decreased susceptibility to moxifloxacin, particularly those of PCR-ri...
Reports of vancomycin treatment failure for infections caused by susceptible methicillin-resistant Staphylococcus aureus (MRSA) strains with elevated minimum inhibitory concentration (MIC) has prompted use of high-dose therapy, but nephrotoxicity is a concern. We determined whether clinical and mole...
Accurate strain typing is critical for understanding the changing epidemiology of Clostridium difficile infections. We typed 350 isolates of toxigenic C. difficile from 2008 to 2009 from seven laboratories in the United States and Canada. Typing was performed by PCR-ribotyping, pulsed-field gel elec...
From around year 2000, impetigo caused by fusidic acid-resistant Staphylococcus aureus was observed in countries of Northern Europe. The bacteria were found to represent a clone, the epidemic European fusidic acid-resistant impetigo clone (EEFIC). This study reports longitudinal data on the incidenc...
The purpose of this study was to investigate a cohort of patients with Burkholderia cepacia bacteremia in the intensive care unit (ICU) at our institution. A large outbreak of B. cepacia bacteremia involving 95 patients lasted for 4 years in an ICU in northern Taiwan. The clinical characteristics an...
The increased prevalence of isoniazid (INH)-resistant tuberculosis (TB) has become a significant challenge for TB control in the last 10 years. It has been reported that INH resistance is most frequently associated with katG 315 and inhA-15 mutations. The relative significance of these mutations in...
Salmonella enterica serotype Enteritidis is a universally recognized cause of foodborne disease. In South Africa, outbreaks of foodborne disease are generally under reported. We investigated the etiology of acute gastroenteritis in 216 patients who presented to a rural hospital in KwaZulu-Natal, Sou...
Three large clusters of Salmonella Typhimurium infections in Denmark in 2008 and 2009 were defined by multilocus variable number of tandem repeat analysis (MLVA). One of these proved to be the hereto largest Danish cluster of salmonellosis with 1446 cases. Two smaller clusters with a total of 197 an...
Several vomiting episodes were reported in December 2007 by the management of a beach club in Calvià. The subsequent case investigation confirmed tuna fish consumption a few hours before onset of emesis in all cases. Microbiological analyses detected high bacterial levels in ready-to-eat fish sample...
Infant colonization by Staphylococcus aureus has not been adequately investigated. In this study, we aimed to define determinants associated with the carriage of S. aureus in early infancy. Serial nasal swabs were collected from 128 infants and their mothers at months 0, 6, and 12 postpartum. S. aur...
Brucella suis biovar 2 is the most common aetiological agent of porcine brucellosis in Europe. B. suis biovar 2 is considered to have low zoonotic potential, but is a causative agent of reproductive losses in pigs, and it is thus economically important. The multilocus variable-number of tandem repea...
Tuberculosis (TB) transmission is associated with patient-related risk factors. However, DNA fingerprint analysis has provided anecdotal evidence suggesting a role for bacteriological factors. To examine the importance of the bacteriological component in TB transmission, we investigated the number o...
Mycoplasma agalactiae is the main cause of contagious agalactia, a serious disease of sheep and goats, which has major clinical and economic impacts. We have developed a multilocus sequence typing (MLST) scheme using the sequenced genomes of the M. agalactiae strains PG2 and 5632. An MLST scheme bas...
Aspergillus flavus is the second most important Aspergillus species causing human infections. The importance of this fungus increases in regions with a dry and hot climate. Small phylogenetic studies in Aspergillus flavus indicate that the morphological species contains several genetically isolated...
From 2006 to December 2009, 45 out of the 513 strains isolated from patients with invasive meningococcal disease in Belgium, were identified as Neisseria meningitidis serogroup B, non-serotypeable, subtype P1.14 (B:NT:P1.14). Most cases were geographically clustered in the northern part of the count...
Multilocus sequence typing reveals that many bacterial species have a clonal structure and that some clones are widespread. This underlying phylogeny was not revealed by pulsed-field gel electrophoresis, a method better suited to short-term outbreak investigation. Some global clones are multiresista...
The genotypes of dengue viruses (DENV) isolated from patients with dengue in Jamaica during 2007 were determined using DNA sequencing and phylogenetic analysis of the C-prM gene junction. The 17 DENV analysed included strains of DENVserotypes 1 (DENV-1, n = 3), DENV-2 (n = 7) and DENV-4 (n = 7). All...
There are only a few reported cases of Salmonella enterica serotype Brandenburg foodborne outbreaks in the literature. In Italy Brandenburg is consistently present among the top ten serotypes from human source, but at low prevalences. Fifty-five S. Brandenburg isolates from human, animal, environmen...
To describe outbreaks of nosocomial influenza infection with molecular methods and to elucidate the viral linkages among outbreak case patients including both inpatients and healthcare workers (HCWs). A 180-bed acute and long-term care hospital in Japan. Retrospective observational study of nosocomi...
To report a large outbreak of Clostridium difficile infection (CDI; ribotype 027) between June 2007 and August 2008, describe infection control measures, and evaluate the impact of restricting the use of fluoroquinolones in controlling the outbreak. Outbreak investigation in 3 acute care hospitals o...
Methicillin-resistant Staphylococcus aureus (MRSA), particularly the multidrug-resistant clones, is an increasing worldwide problem. The average incidence rate of MRSA in Tehran was found to be over 40%. A total of 140 MRSA isolates obtained from patients attending a teaching hospital in Tehran, fro...
Mycobacterium caprae is a pathogen that can infect animals and humans. To better understand the epidemiology of M. caprae, we spoligotyped 791 animal isolates. Results suggest infection is widespread in Spain, affecting 6 domestic and wild animal species. The epidemiology is driven by infections in...
The rapid increase of HIV-1 prevalence among Chinese men who have sex with men (MSM) provides an impetus for the acquisition of molecular epidemiologic information from this population. We conducted four serial cross-sectional surveys during year 2005-2009 and observed that the composition of HIV-1...
Nosocomial infections by methicillin-resistant Staphylococcus aureus (MRSA) are an increasing cause of morbidity and mortality. Recently, a worldwide increase of community-acquired MRSA infections has also been recorded. The purpose of this study was to assess the frequency of MRSA isolation from in...
Human metapneumovirus (hMPV) is responsible for respiratory tract disease, particularly in the young and elderly population. An epidemiological and phylogenic study was performed on children admitted to hospital with an acute lower respiratory tract infection (LRI). Data were obtained and analyzed o...
The application of genotyping tools to the analysis of tuberculosis (TB) has allowed us to identify clinical isolates of Mycobacterium tuberculosis to strain level. M. tuberculosis fingerprinting has been applied at different levels: a) in the laboratory, to optimize identification of cross-contamin...
The aim of this study was to determine the prevalence of the bla (SHV) gene in Klebsiella pneumoniae isolates from hospital and community infections and from the normal microbiota of healthy individuals in Recife, PE, Brazil. Fifty-two K. pneumoniae isolates were analyzed regarding the presence of t...
We assessed the potential of multilocus variable-number tandem-repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility testing for discriminating 104 sporadic and outbreak-related Yersinia enterocolitica (YE) bio/serotype 3-4/O:3 and 2/O:9 isolates. MLVA usi...
Nevirapine resistance mutations arise commonly following single or extended-dose nevirapine (ED-NVP) prophylaxis to prevent mother-to-child transmission (PMTCT) of human immunodeficiency virus (HIV), but decay within 6-12 months of single-dose exposure. Use of ED-NVP prophylaxis in infants is expect...
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Restriction fragment length polymorphism (RFLP) genotyping was employed to analyze the population genetics of Mycobacterium bovis in Iran. One hundred and twenty-three isolates collected from slaughtered tuberculosis-suspect cattle and one clinically asymptomatic buffalo were subjected to RFLP analy...
From 2005 to 2007, Mycobacterium tuberculosis complex (MTC) strains were isolated from cattle, goats and pigs samples collected at the Bodija abattoir and from human samples from tuberculosis patients and livestock traders at the Akinyele cattle market in Ibadan, Southwestern Nigeria. Seventy four i...
Tuberculosis remains a major public health problem in Nigeria. While human to human transmission of Mycobacterium tuberculosis is clearly of major importance in driving the tuberculosis epidemic in Nigeria, the impact of Mycobacterium bovis transmission from infected cattle is largely unknown. Molec...
Raw produce is an increasingly recognized vehicle for salmonellosis. We investigated a nationwide outbreak that occurred in the United States in 2008. We defined a case as diarrhea in a person with laboratory-confirmed infection with the outbreak strain of Salmonella enterica serotype Saintpaul. Epi...
In May 2008, PulseNet detected a multistate outbreak of Salmonella enterica serotype Saintpaul infections. Initial investigations identified an epidemiologic association between illness and consumption of raw tomatoes, yet cases continued. In mid-June, we investigated two clusters of outbreak strain...
In addition to the large virulence plasmid pO157, a novel 38-kb conjugative plasmid, pO157_Sal, was identified and sequenced from an Escherichia coli O157:H7 outbreak-associated Chinese isolate that shares high similarity with a plasmid in Salmonella enterica serovar Agona. The plasmid was found in...
The aim of the present study was to assess the usefulness of insertion element IS1395 for differentiation of Mycobacterium xenopi, an increasingly common opportunistic human pathogen. Fifty-two isolates obtained from 51 patients in Poland in 1996, 1997, and 1999, were analyzed by IS1395 restriction...
The objective of this study was to characterise the epidemiology of Clostridium difficile in Scotland by determining the distribution of PCR ribotypes and antimicrobial susceptibility in 1613 isolates collected from all healthboard areas of Scotland in the period November 2007-December 2009. Three P...
Methicillin-resistant Staphylococcus aureus (MRSA) is highly prevalent in hospitals in many Asian countries. Recent emergence of community-associated (CA) MRSA worldwide has added another serious concern to the epidemiology of S. aureus infections. To understand the changing epidemiology of S. aureu...
To describe clinical features, complications, serotypes and antibiotic resistance in pneumococcal pneumonia in our environment after the generalization of the heptavalent conjugate vaccine (PCV-7) in paediatrics. Prospective study of episodes of pneumococcal pneumonia, with positive cultures in pati...
In Brazil, the spread of an endemic clone of SPM-1-producing Pseudomonas aeruginosa has been reported. Recently, a higher genomic variety has been observed among the SPM-1-producing P. aeruginosa isolates. The principal aim of this study was to analyze through multilocus sequence typing (MLST) analy...
Mycobacterium tuberculosis may survive for decades in the human body in a state termed latent tuberculosis infection (LTBI). We investigated the occurrence during LTBI of insertion/deletion events in a selected set of mononucleotide simple sequence repeats, DNA sequence changes in four M. tuberculos...
Penicillium marneffei is an opportunistic fungus that may cause fatal disease, and usually infects acquired immune deficiency syndrome (AIDS) patients. The molecular epidemiology of this fungus remains enigmatic. A multilocus microsatellite typing (MLMT) system based on 11 microsatellite loci was ap...
Streptococcus pneumoniae remains a leading cause of serious paediatric disease. However, there are few published epidemiological data regarding invasive pneumococcal disease (IPD) in many countries in South East Asia, including Singapore. Baseline data for IPD are essential to inform policy regardin...
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Clostridium difficile is the main cause of antibiotic-associated disease, a disease of high socio-economical importance that has recently been compounded by the global spread of the 027 (BI/NAP1/027) ribotype. C. difficile cases attributed to ribotype 027 strains have high recurrence rates (up to 36...
For the last decade China has occupied second place, after India, among the top five countries with high burdens of tuberculosis (TB). Heilongjiang Province is located in northeastern China. The prevalence of drug-resistant TB in Heilongjiang Province is higher than the average level in China. To de...
The "Harlingen" IS6110 restriction fragment length polymorphism (RFLP) cluster has linked over 100 tuberculosis cases in The Netherlands since 1993. Four Mycobacterium tuberculosis isolates that were epidemiologically linked to this cluster had different spoligotype patterns, as well as slightly div...
Outbreaks of vancomycin-resistant Enterococcus faecium (VRE) strains is an emerging problem worldwide. Even if still relatively uncommon in European hospitals, infections caused by VRE have also been increasing recently in this continent. In this study, we characterized 50 consecutive VRE and 23 van...
The aim of this work was to investigate the molecular epidemiology and mechanisms responsible for reduced susceptibility to amoxicillin/clavulanic acid (AMC) amongst cefazolin-susceptible Klebsiella pneumoniae isolates from patients admitted to a chronic care institution. In total, 51 (29.8%) of 171...
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We report here on the identification of the first meningococcal meningitis case in Slovenia caused by Neisseria meningitidis serogroup Z’ in December 2010. The 19-year-old patient had not left the country during the incubation period. The patient was hospitalised and given the antibiotic treatment w...
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has become an increasing problem worldwide in recent decades. Molecular typing methods have been developed to identify clonality of strains and monitor spread of MRSA. We compared a new commercially available DiversiLab (DL) repetit...
In the present study, clinical isolates of Bordetella pertussis collected in Poland from 1960 to 2005 were analyzed by pulsed-field gel electrophoresis (PFGE) according to protocols recommended in previous studies. Among the 110 isolates from 1995 to 2005, 59 PFGE patterns were found, most of which...
We report an MRSA outbreak in our 25-bed tertiary neonatal intensive care unit (NICU), which was successfully contained. Methods include a retrospective review of patient files, microbiology records and meeting protocols. During the seven months of outbreak, 27 patients and seven health care workers...
South Western islands of the Indian Ocean are permanently threatened by dengue fever outbreaks. On the Reunion Island, two dengue outbreaks were biologically documented (1977-1978 and 2004). And since July 2004 there has been an inter-epidemic period for the island with sporadic cases and clusters....
A total of 29 meticillin-resistant Staphylococcus aureus (MRSA) isolates were obtained from 15 neonates and three healthcare workers (HCWs) in a neonatal intensive care unit (NICU) and special care baby unit (SCBU) and four patients in a medical ward of a Kuwait hospital between 10 and 30 April 2007...
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Yersinia enterocolitica and Yersinia pseudotuberculosis strains isolated from wild boars and fattening pigs were characterized and compared with each other. In wild boars, ail-positive Y. enterocolitica strains belonged to bioserotypes 4/O:3 (36%, 5/14), 2/O:9 (29%, 4/14), and 2/O:5,27 (21%, 3/14)....
Outbreak strains of Acinetobacter baumannii are highly clonal, and cross-infection investigations can be difficult. We sought targets based on AbaR resistance islands and on other genes found in some, but not all, sequenced isolates of A. baumannii among a set of clinical isolates (n = 70) that incl...
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To analyze 67 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolated from pediatric hospital infections, we used multilocus variable-number tandem-repeat DNA sequence-based techniques, targeting the protein A polymorphic X region and the clumping factor B complete R domain. We define a...
We quantified nosocomial transmission rates of sequence type (ST) 398 methicillin-resistant Staphylococcus aureus (MRSA) (an emerging livestock-associated MRSA clone) and non-ST398 MRSA isolates in patients hospitalized without infection control measures in 51 Dutch hospitals. Identification of 174...
Thirty-five multidrug-resistant Acinetobacter baumannii strains, representative of 28 outbreaks involving 484 patients from 20 hospitals in Greece, Italy, Lebanon and Turkey from 1999 to 2009, were analysed by multilocus sequence typing. Sequence type (ST)2, ST1, ST25, ST78 and ST20 caused 12, four,...
Clostridium difficile infection is most often induced by antibiotic treatment. Recently, morbidity and mortality resulting especially from C. difficile PCR ribotype 027 have increased significantly. In addition, more severe disease has been associated with C. difficile PCR ribotype 078 strains. Thus...
Candida krusei has been documented as an emerging pathogen causing nosocomial outbreaks. The consecutive isolation of C. krusei strains in three patients admitted to the same hospital department within 2 months lead us to consider the possibility of an outbreak. Additionally, C. krusei isolates were...
The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in Africa is poorly documented. From January 2007 to March 2008, we collected 86 MRSA isolates from five African towns, one each in Cameroon, Madagascar, Morocco, Niger and Senegal. Although one or two major clones, defined by th...
Genotyping is used to track specific isolates of Mycobacterium tuberculosis in a community. It has been successfully used in epidemiologic research (termed 'molecular epidemiology') to study the transmission dynamics of TB. In this article, we review the genetic markers used in molecular epidemiolog...
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The emergence of metallo-β-lactamase (MBL)-producing Enterobacteriaceae is a serious public health concern. Producers have been repeatedly isolated from patients and long-term care facility (LTCF) residents around Bolzano, and we sought to assess their prevalence and clinical impact. All routine Ent...
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The application of a rapid and direct proteotyping approach with which to identify the gene origin of viral antigens in a reassortant influenza strain is demonstrated. The reassortant strain, constructed for a vaccine against type A 2009 H1N1 pandemic influenza, contains genes derived from a wild-ty...
Mycoplasma pneumoniae is a frequent cause of human lower respiratory tract infections (LRTIs) for which macrolides are the treatment of choice. The aim of this study was to determine the rate of macrolide resistance and to subtype M. pneumoniae strains in Italy. During an outbreak of M. pneumoniae i...
To evaluate a novel sequence-based coa typing method in classification for nosocomial methicillin-resistant Staphylococcus aureus. D1 and D2 regions of coa gene were used to discriminate methicillin-resistant Staphylococcus aureus and compared with other classical sequence-based methods with discrim...
Streptococcus pneumoniae resides on mucosal surfaces in the nasopharynx, where selection for horizontal transfer of antimicrobial resistance genes and virulence factors may provide a survival advantage. We investigated the distribution of genes for pneumococcal cell surface proteins and their correl...
Unprecedented outbreaks of vancomycin-resistant enterococci (VRE) have occurred in French hospitals since 2004. The aim of this study was to provide a picture of the spread and control of VRE in France and to characterize the isolates. Notification of VRE cases to Institut de Veille Sanitaire has be...
In this study, multilocus sequence typing (MLST) was combined with the genetic detection of six genetic markers, ansB, dmsA, ggt, cj1585c, cjj81176-1367/71 (cj1365c), and the two-gene marker tlp7 (cj0951c plus cj0952c), to assess if their presence correlated with different C. jejuni clonal groups. U...
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Laboratory-based surveillance of methicillin-resistant Staphylococcus aureus (MRSA) monitors the baseline occurrence of different genotypes and identifies strains and transmission chains responsible for outbreaks. The consequences of substituting pulsed-field gel electrophoresis (PFGE) with spa typi...
In an asylum seeker centre in Schleswig-Holstein, a resident was diagnosed with furuncle caused by a Panton-Valentine leukocidine (PVL)-positive community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA). As a result of active case finding, 232 of 427 persons (54% of all residents) were...
To identify outbreak episodes of either carriage or infection due to extended spectrum beta-lactamases producing aerobic Gram-negative bacilli (AGNB-ESBL); to establish whether AGNB-ESBL, sensitive to tobramycin, become resistant over time; and to evaluate the impact of selective decontamination of...
Integrative conjugative elements (ICEs) of the SXT/R391 family are self-transmissible mobile elements mainly involved in antibiotic resistance spread among γ-Proteobacteria, including Vibrio cholerae. We demonstrated that the recently described ICEVchInd5 is prevailing in V. cholerae O1 clinical str...
We report two cases of bacteremia caused by the Salmonella enterica serotype Gambia in our children's hospital, with one fatal outcome. The isolates showed indistinguishable genotypes and infrequent resistance markers: CTX-M-3 extended-spectrum β-lactamase and armA methyltransferase. This is the fir...
In March 2008, the Health Protection Agency in England conducted a retrospective case-control study to investigate the cause of 179 cases of the newly recognized, fully antimicrobial-sensitive Salmonella Typhimurium PT U320. Forty-three symptomatic laboratory-confirmed case-patients and 84 asymptoma...
The antimicrobial susceptibility and virulence factors of Clostridium difficile clinical isolates in Taiwan have not previously been reported. One hundred and thirteen isolates were collected from two major teaching hospitals in Taiwan from 2001 to 2009. Molecular typing was performed by an automate...
The role of wildlife in the epidemiology of Salmonella sp.-induced diseases is a matter of increasing concern to public health. However, to date, reports on the occurrence of Salmonella sp. in game hunted for human consumption are very limited. The current study was designed to evaluate the prevalen...
O3:K6 pandemic clone of Vibrio parahaemolyticus has caused outbreaks in coastal countries since 1996. Mutilocus sequence typing (MLST) is an important tool to trace the source and analysis the evolution of bacteria. Based on MLST, the first pandemic clonal complex (CC) of V. parahaemolyticus has bee...
Rapid molecular typing methods can be a valuable aid in the investigation of suspected outbreaks. We used a semi-automated repetitive sequence-based polymerase chain reaction (Rep-PCR) typing assay and pulsed field gel electrophoresis (PFGE) to investigate the relationship between local Klebsiella p...
The 2009 meningitis season in Niger was characterized by an early onset, beginning in the very first weeks of the year and peaking from the 12th to the 15th week with 5655 clinical cases over the 4 weeks. From 1 January 2009 to 28 June 2009 (week 26), a total of 13,733 clinical cases of meningitis w...
Staphylococcus aureus is the major nosocomial pathogen and rapid detection of colonized patients with subsequent precaution is needed to prevent transmission. A new assay, the BD GeneOhm™ SaphSR assay (BD GeneOhm™, San Diego, CA, USA), is a multiplex real-time polymerase chain reaction (PCR) for rap...
The prevalence of quinolone-resistant Neisseria gonorrhoeae (QRNG) in Greece remained low from 1997 to 2003 but increased dramatically from 11% to 56% between 2004 and 2007. N. gonorrhoeae multiantigen sequence typing (NG-MAST) and multilocus sequence typing (MLST) were used to investigate trends in...
Pneumonia caused by adenovirus infection is usually severe especially with adenovirus serotype 7 commonly associated with lower respiratory tract disease outbreaks. We reported an outbreak of 70 cases of severe pneumonia with one death of infants in Shaanxi Province, China. Sampling showed adenoviru...
Serratia marcescens is a well-known but relatively uncommon cause of nosocomial infections, particularly in neonatal intensive care unit (NICU) patients. We investigated an outbreak of S marcescens in the NICU at the Farabi Hospital of Karadeniz Technical University in Trabzon, Turkey. Between March...
Primary pneumonic plague (PPP) caused by Yersinia pestis is the most threatening clinical form of plague. An outbreak was reported in July 2009 in Qinghai Province, China. This outbreak was investigated by clinical, epidemiological, bacteriological, and immunological methods. Multilocus variable num...
The molecular epidemiology of 545 Salmonella enterica serovar Typhimurium isolates collected between 1977 and 2009 from cattle in Hokkaido, Japan, was investigated using pulsed-field gel electrophoresis (PFGE). Nine main clusters were identified from 116 PFGE patterns. Cluster I comprised 248 isolat...
A total of 128 isolates associated with catheter-related infections was recovered from 101 intensive care unit patients in a Spanish hospital during March 2008 to August 2009, and 27 of these isolates (from 21 patients) were typed as methicillin- and linezolid-resistant Staphylococcus epidermidis. T...
The aim of this study was to assess the vancomycin MIC distribution for MRSA blood culture isolates over a period of six years in Germany. The study examined 287 MRSA isolates from blood cultures collected at several hospitals in two German cities between 2004 and 2009. The vancomycin MIC was determ...
Molecular typing of Mycobacterium tuberculosis isolates has greatly facilitated the understanding of tuberculosis epidemiology. This study was done to characterize prevalent M. tuberculosis genotypes in a defined area of Kanpur district, North India by spoligotyping and IS6110-Restriction Fragment L...
VRE isolates from pigs (n = 29) and healthy persons (n = 12) recovered during wide surveillance studies performed in Portugal, Denmark, Spain, Switzerland, and the United States (1995 to 2008) were compared with outbreak/prevalent VRE clinical strains (n = 190; 23 countries; 1986 to 2009). Thirty cl...
Between February 2006 and October 2009, 38 patients in different wards at the A Coruña University Hospital (northwest Spain) were either infected with or colonized by an epidemic, multidrug-resistant (MDR), and extended-spectrum-β-lactamase (ESBL)-producing strain of Enterobacter cloacae (EbSF), whi...
The distribution and characterization of OXA-type carbapenemases in Acinetobacter sp in Taiwan has less been reported. The aim of the study was to investigate the molecular epidemiology and OXA-type carbapenemase genes in a regional hospital in Taiwan. Imipenem-resistant Acinetobacter sp were collec...
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Escherichia coli O157:H7, an important food-borne pathogen, has become a major public health concern worldwide. The aim of this study was to investigate the molecular epidemiologic feature of E. coli O157:H7 strains in China. 105 E. coli O157:H7 isolates were collected from various hosts and places...
The changing pattern in hepatitis C virus (HCV) clades overtime is not well known in Pakistan. To find out the changing pattern of different HCV clades over time in this country 22,125 patients were genotyped and tracked for a period of 11 years (2000-2010). A changing pattern in HCV clades was seen...
Skin infection associated with methicillin-resistant Staphylococcus aureus (MRSA)-ST398 was detected in a pig-farmer, and MRSA-ST398 isolates were also detected in nasal samples of the patient and of 11/12 pigs on his farm. Twelve MRSA isolates were obtained from skin lesions (n = 6) and nasal sampl...
The objective of this study was to evaluate whether cows that were low shedders of Mycobacterium avium subsp. paratuberculosis were passively shedding or truly infected with M. avium subsp. paratuberculosis. We also investigated whether it is possible that these M. avium subsp. paratuberculosis-infe...
Twenty-four Vibrio cholerae O139 strains isolated from Kerala, southern India were characterized by PCR, CTX typing and ribotyping; all of which, except three strains, carried the core of the CTX genetic element, colonization-toxin co-regulated pilus, the adherence outer membrane protein, haemolysin...
Enterococci rank among the leading causes of nosocomial infections. The failure to identify pathogen-specific genes in Enterococcus faecalis has led to a hypothesis where the virulence of different strains may be linked to strain-specific genes, and where the combined endeavor of the different gene-...
In Canada, the incidence of candidemia, the bloodstream infection caused by Candida species, varied from 1.2-5.1 cases/100,000, representing the third most common type of bloodstream infections in intensive care unit patients. However, the relative contributions of nosocomial transmission in candide...
A listeriosis outbreak, in dairy cattle, with a high case mortality and acute death after onset of symptoms was investigated using gross pathology and bacteriologic approaches, including molecular characterization of a clinical Listeria monocytogenes isolate. In a herd of 315 animals, 9 animals show...
Automated repetitive polymerase chain reaction (PCR) (DiversiLab, bioMérieux, St. Laurent, Quebec, Canada) and single locus sequence typing of the Staphylococcus protein A (spa) gene with spa-type assignment by StaphType RIDOM software were compared to pulsed-field gel electrophoresis (PFGE) as the...
Pseudomonas aeruginosa is one of the leading nosocomial pathogens in intensive care units (ICUs). The source of this microorganism can be either endogenous or exogenous. The proportion of cases as a result of transmission is still debated, and its elucidation is important for implementing appropriat...
Sporothrix schenckii, now named the S. schenckii species complex, has largely been known as the etiological agent of sporotrichosis, which is an acute or chronic subcutaneous mycosis of humans and other mammals. Gene sequencing has revealed the following species in the S. schenckii complex: Sporothr...
Streptococcus pneumoniae is the leading cause of vaccine-preventable deaths among children younger than 5 years of age worldwide. The 7-valent pneumococcal conjugate vaccine (PCV7) is currently licensed in more than 90 countries and has contributed to significant declines in the incidence of invasiv...
In 2008, an increase in the prevalence of carbapenem-resistant Klebsiella pneumoniae was noted in a 286-bed tertiary case hospital in Colombia, where 84 patients (32 infected and 52 colonized) had positive cultures. The identified index patient came from Israel for a liver transplantation. High leve...
In this study, the BOX-PCR fingerprinting technique was evaluated for the discrimination of clinical Pseudomonas aeruginosa isolates. All isolates were typeable and nearly half showed unique banding patterns. According to our results, BOX-PCR fingerprinting is applicable for typing of Pseudomonas ae...
To determine potential links between the clinical isolate to animal products and their geographic origin, we genotyped (MLVA-8, MVLA-15, and canSNP analysis) 80 environmental and 12 clinical isolates and 2 clinical specimens from five cases of anthrax (California in 1976 [n = 1], New York in 2006 [n...
Epidemic keratoconjunctivitis (EKC) is a contagious acute conjunctivitis associated with community-acquired infection. Human adenovirus type 8 (HAdV-8) is one of the major serotypes isolated from patients with EKC. DNA restriction enzyme analyses were performed to investigate the genetic characteris...
This study aimed to identify the sources and routes of transmission of Campylobacter in intensively reared poultry farms in the Republic of Ireland. Breeder flocks and their corresponding broilers housed in three growing facilities were screened for the presence of Campylobacter species from Novembe...
Genotype characteristic and determination of serological properties of Vibrio cholerae nonO1/nonO139 strains that caused diseases in population of Rostov region from 2000 to 2009. 15 clinical strains of V. cholerae nonO1/nonO139 were studied. Serotyping was performed by using a kit of monospecific t...
Biotyping of Vibrio cholerae eltor isolated during epidemic complications of cholera in Syberia and Far East by phenotypic and genotypic properties complex. 45 strains of V. cholerae were studied. Phenotypic analysis was performed by using a complex ofbiovar determining tests. Genotyping was perform...
Trichophyton tonsurans has been isolated among judo practitioners, wrestlers, and sumo wrestlers during an epidemic of tinea corporis and tinea capitis in Japan. A previous study using restriction fragment length polymorphism (RFLP) analysis of the non-transcribed spacer (NTS) region of the ribosoma...
Little is known about the viruses infecting most species. Even in groups as well-studied as Drosophila, only a handful of viruses have been well-characterized. A viral metagenomic approach was used to explore viral diversity in 83 wild-caught Drosophila innubila, a mushroom feeding member of the qui...
Several studies in recent years have provided evidence that Pseudomonas aeruginosa has a non-clonal population structure punctuated by highly successful epidemic clones or clonal complexes. The role of recombination in the diversification of P. aeruginosa clones has been suggested, but not yet demon...
The mosquito gut represents an ecosystem that accommodates a complex, intimately associated microbiome. It is increasingly clear that the gut microbiome influences a wide variety of host traits, such as fitness and immunity. Understanding the microbial community structure and its dynamics across mos...
Mycobacterium tuberculosis (MTB) has been classified into 4 main lineages. Some reports have associated certain lineages with particular clinical phenotypes, but there is still insufficient information regarding the clinical and epidemiologic implications of MTB lineage variation. Using large sequen...
The epidemiological situation of human salmonellosis in Poland in the successive years (between 1995 and 2007), presented in this study, was illustrated by using the notification rates expressed as the number of confirmed cases (of total human Salmonella infections and infections associated with cho...
Determination of genetic and molecular features of pathogens circulating in Russia, in the northwest of the country and in St. Petersburg to resolve the problems of spread of diseases caused by these pathogens. Complete and limited gene sequencing, DNA restriction fragment length polymorphism analys...
during the Cuban epidemic that occurred in Santiago de Cuba in 1997, there was observed increasing severity in the course of time, in terms of proportion of serious dengue haemorrhagic cases and deaths that could be due to the emergence of escape mutants to neutralization with greater virulent poten...
An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with...
No abstract available
Cholera has been a prevalent disease worldwide since the early 19th century. Vibrio cholerae O1 and O139 are the two serogroups that have been mainly implicated in causing cholera. This study reports the results of biotyping, serotyping and phage typing of V. cholerae O1 and O139 (1998-2007) strains...
The authors describe a large outbreak of canine salmonellosis in a municipal kennel in Tuscany. During the outbreak, 174 samples of 'diarrhetic' and 'normal' faeces and two batches of commercial dehydrated dog food were cultured for pathogenic bacteria. The results of 25, out of a total of 41 dogs (...
Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provi...
Non-Typhoidal Salmonella (NTS) is an important cause of invasive bacterial disease and associated with mortality in Africa. However, little is known about the environmental reservoirs and predominant modes of transmission. Our study aimed to study the role of domestic animals in the transmission of...
This study reports an outbreak of Klebsiella pneumoniae infections in 14 patients during a 2-month period (August-September, 2008) in the intensive care unit (ICU) of a teaching hospital in Kuwait. The clinical sources were blood (9), urine (3) and respiratory secretions (2) identified by the automa...
Serogroup X meningococci (NmX) historically have caused sporadic and clustered meningitis cases in sub-Saharan Africa. To study recent NmX epidemiology, we analyzed data from population-based, sentinel and passive surveillance, and outbreak investigations of bacterial meningitis in Togo and Burkina...
No abstract available
The objective of this study was to characterize the off-seasonal influenza virus A subtype H3N2, which caused an outbreak in an elderly hospital in Niigata, Japan. Virus isolates were subtyped by the hemagglutination-inhibition test and screened for antiviral drug sensitivity by real-time PCR using...
We investigated the molecular epidemiology, antibiotic susceptibility, and antimicrobial resistant gene determinants of 23 multidrug-resistant (MDR) Acinetobacter baumannii samples that were collected from 5 proximal hospitals in Taiwan during April and May 2009. Major antibiotic resistance varied f...
Characteristic of West Nile fever (WNF) virus strains circulating in southern Russia. WNF RNA was amplified directly from clinical samples, mosquitoes and bird tissues by PCR, nucleotides were sequenced directly and analyzed comparatively. Related but different genovariants of WNF lineage 1a--"Volgo...
Genetic and antigenic characterization of Neisseria meningitidis strains isolated during meningococcal infection outbreaks from individuals in contact with patients with generalized form of meningococcal infection. Strains obtained in 2007 - 2009 in Moscow during examination of individuals that were...
Vibrio cholerae, the causative agent of cholera, is endemic in many parts of the world, especially in countries poor in resources. Molecular subtyping of V. cholerae is useful to trace the regional spread of a clone or multidrug-resistant strains during outbreaks of cholera. Current available PCR-ba...
Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping of over 3300 Mycobacterium tuberculosis isolates from the north of England has identified large clusters of strains which share common profiles. However, many apparent clusters identified when typed using...
This study has evaluated the clinical applicability of a single-tube multiplex RT-PCR as compared with a two-step nested RT-PCR for the diagnosis as well as serotyping of dengue virus in patient's samples. Seventy-six acute phase blood samples collected from clinically suspected dengue patients duri...
Invasive group B streptococcus (GBS) disease is a leading cause of neonatal death. There is no UK national screening programme for GBS in pregnancy, hence colonisation rates are unknown. Intrapartum antibiotic prophylaxis is given during labour to colonised women to reduce neonatal GBS transmission...
A total of 18 strains of EHEC O157:H7 were isolated from distinct cases in Akita Prefecture, Japan from July to September 2007. The genetic relatedness of these isolates was investigated by performing a multilocus variable number of tandem repeats analysis (MLVA) and a pulsed-field gel electrophores...
Recurrence and reinfection of tuberculosis have quite different implications for prevention. We identified 267 spoligotypes of Mycobacterium tuberculosis from consecutive tuberculosis patients in Acapulco, Mexico, to assess the level of clustering and risk factors for clustered strains. Point cluste...
Hospitals around the world have presented multiresistant Acinetobacter sp. outbreaks. The spread of these isolates that harbor an increasing variety of resistance genes makes the treatment of these infections and their control within the hospital environment more difficult. This study aimed to evalu...
Development of Staphylococcus haemolyticus strain typing method based on multilocus sequencing for resolving problems of molecular epidemiology. 102 strains of coagulase negative staphylococci (CNS) isolated in hospitals of various specialization in N. Novgorod and Moscow were studied. Species ident...
No abstract available
The aim of our study was to determine the changes in antibiotic resistance and O serogroup dependence of P. aeruginosa strains isolated from lower respiratory tract specimens of patients in 2003 and 2008; the patients were treated in intensive care units of the biggest treatment facility in Lithuani...
Helicobacter pylori is a major human pathogen and its transmission and epidemiology have been extensively studied; it has been found that H. pylori's prevalence and infection outcome is characterized by marked differences between the developing and the developed worlds. Recent data on genomic analys...
Meticillin-resistant Staphylococcus aureus (MRSA) is one of the main causes of hospital-acquired infections, but since late 1990s also the community-acquired. For better understanding of the S.aureus epidemiology there is an urgent need for creation of new typing method for SCCmec element. The molec...
Pandemic, epidemic and endemic infectious diseases are united by a common problem: how do we rapidly and cost-effectively identify potential pharmacological interventions to treat infections? Given the large number of emerging and neglected infectious diseases and the fact that they disproportionate...
Despite the association of methicillin-susceptible S. aureus (MSSA) with several life-threatening diseases, relatively little is known about their clinical epidemiology in Malaysia. We characterized MSSA isolates (n=252) obtained from clinical and community (carriage) sources based on spa sequencing...
Children attending child care centers (CCCs) are at increased risk for infections, including those caused by methicillin-resistant Staphylococcus aureus (MRSA). Nasal colonization often precedes infection, and MRSA colonization has been associated with increased infection risk. Community-associated...
Taylorella equigenitalis is the etiologic agent of contagious equine metritis (CEM), a venereal disease of horses. A total of 82 strains of T. equigenitalis isolated in the United States were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of genomic DNA with restriction enzyme A...
To establish the prevalence and diversity of clinically significant extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae harbouring bla(CTX-M) in the West Midlands region of the UK. During a 2 month period, 370 consecutive, non-duplicate isolates were collected from 13 laboratories. Iso...
Inadequate potable water supply and poor sanitation predispose to food- and water-borne diseases associated with Salmonella enterica serovars in developing countries. In this study the possible source of an unprecedented upsurge of Salmonella-associated community gastroenteritis was traced using bot...
No abstract available
Acinetobacter baumannii is one of the major pathogens involved in nosocomial outbreaks. The clonal diversity of 729 epidemic strains isolated from 19 Spanish hospitals (mainly from intensive care units) was analyzed over an 11-year period. Pulsed-field gel electrophoresis (PFGE) identified 58 PFGE t...
To broaden knowledge of the molecular bases and genetics of multidrug resistance in clinical isolates of Salmonella enterica serotype 4,5,12:i:- belonging to the Spanish clone. The relatedness of the isolates was determined by phage typing and XbaI-PFGE. Resistance genes, integrons and transposable...
No abstract available
In September-October 2007, a mixed-serotype outbreak of verocytotoxin-producing Escherichia coli (VTEC) O145:H28 and O26:H11 occurred in the province of Antwerp, Belgium. Five girls aged between 2 and 11 years developed hemolytic uremic syndrome, and seven other coexposed persons with bloody diarrhe...
This study was designed to investigate the molecular epidemiology and antibiotic-resistance characteristics of 11 carbapenem-resistant clinical isolates of Acinetobacter baumannii obtained in Norway between 2004 and 2009. Interestingly, all the isolates were linked with recent hospitalization outsid...
While foreign-born persons constitute only 11% of the population in the state of Rhode Island, they account for more than 65% of incident tuberculosis (TB) annually. We investigated the molecular-epidemiological differences between foreign-born and U.S.-born TB patients to estimate the degree of rec...
Knowledge of vector population genetic structure is critical for vector-borne disease control and prevention strategies. Advances in both molecular genotyping technology and theoretical developments have contributed to the growing impact of such approaches on medical entomology. The pattern of genet...
We examined associations of serotypes with multilocus sequence typing (MLST) data for 7 housekeeping genes and the genotype concerning penicillin resistance based on penicillin-binding protein (PBP) alterations in Streptococcus pneumoniae isolates from children with meningitis. From throughout Japan...
Nosocomial norovirus (NoV) infection is common and may lead to complications in vulnerable hospitalized patients. Understanding sources and modes of transmission of noroviruses within health care settings will support the design of evidence-based strategies for reducing introduction and further spre...
Methicillin-resistant Staphylococcus aureus (MRSA) strains are commonly classified as hospital-acquired (HA) or community-acquired (CA). Typical HA-MRSA isolates are characterized by multidrug resistance and the SCCmec type II cassette, while CA-MRSA isolates are generally susceptible to more drug c...
Enteroviruses, members of the Picornaviridae family, are common viruses associated with clinical manifestations ranging from mild respiratory symptoms to serious conditions, including aseptic meningitis, encephalitis, neonatal sepsis, and acute flaccid paralysis. Approximately 100 serotypes of nonpo...
Many studies using DNA fingerprinting to differentiate Mycobacterium tuberculosis (MTB) strains reveal single strains in cultures, suggesting that most disease is caused by infection with a single strain. However, recent studies using molecular epidemiological tools that amplify multiple targets hav...
Molecular typing of methicillin-resistant Staphylococcus aureus (MRSA) has documented the diversity of the genetic background of strains associated with healthcare (HA-MRSA), community (CA-MRSA) and livestock (LA-MRSA). The accessory and core-variable genomes of those strains however remain largely...
Although cholera has been present in Latin America since 1991, it had not been epidemic in Haiti for at least 100 years. Recently, however, there has been a severe outbreak of cholera in Haiti. We used third-generation single-molecule real-time DNA sequencing to determine the genome sequences of 2 c...
Multi-locus sequence typing was performed on 1003 Campylobacter jejuni isolates collected in a 2-year longitudinal study of 15 dairy farms and four sheep farms in Lancashire, UK. There was considerable farm-level variation in occurrence and prevalence of clonal complexes (CC). Clonal complexes ST61,...
Over a 6-year period (March 2000-February 2006), there were 60 vancomycin-resistant Enterococcus faecium (VREF) bloodstream infections (BSIs) in a hematology unit, accounting for 83.3% of all VREF BSIs in the hospital. We investigated 49 VREF isolates causing BSIs in patients with neutropenia to und...
In Egypt, little is known about the genetic background of Escherichia coli isolates harboring extended-spectrum β-lactamase (ESBL). Five hundred twenty Enterobacteriaceae were prospectively collected (May 2007-August 2008) at the Theodor Bilharz Research Institute (Cairo). Among the collected Entero...
The emergence of Clostridium difficile ribotype 027 raised the question of sporicidal surface disinfectants are also effective against spores of C. difficile ribotype 027. Three surface disinfectants based on magnesium monoperoxyphthalate hexahydrate (Dismozon pur), a combination of (ethylenedioxy)d...
Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae has spread rapidly in China. In this study, we aimed to investigate the molecular epidemiology of KPC-producing K. pneumoniae isolates in China. Ninety-five carbapenem-resistant K. pneumoniae isolates from 13 hospitals in nine...
Between January 2004 and May 2006 Escherichia coli producing extended-spectrum β-lactamases (ESBLs) were isolated from the faeces of 118/294 residents from 16 nursing homes in Belfast. Of these, 58 isolates belonged to UK strain A, a variant of the international ST131 clone. Here we investigated the...
Peripartum women are at risk for Clostridium difficile infection (CDI), but the risk magnitude and clinical disease spectrum are unknown. We determined the incidence and clinical features of CDI in peripartum women in the Loyola University Medical Center system and describe typing of C difficile iso...
The antibiotic susceptibility of Acinetobacter calcoaceticus-Acinetobacter baumannii complex strains recovered from the intensive care unit (ICU) of West China Hospital, Sichuan, PR China, from 2006 to 2009 was investigated. The identification of A. baumannii and analysis of carbapenemase-encoding g...
Outbreaks of white spot syndrome virus (WSSV) in shrimp culture and the relationship between the virus and virulence are not well understood. Here, we provide evidence showing that WSSV mixed-genotype infections correlate with lower outbreak incidence and that disease outbreaks correlate with single...
In 2007, recommendations were proposed for the molecular typing of meningococci. Multilocus sequence typing (MLST) was recommended to guide national and international disease management and facilitate studies of population biology and evolution. Sequencing of porA variable regions (VRs) 1 and 2 and...
Melioidosis is an infectious disease caused by Burkholderia pseudomallei and endemic in Southeast Asia. One hundred and forty six clinical isolates of B. pseudomallei from different states in Malaysia were obtained and molecular typing was carried out using pulsed-field gel electrophoresis (PFGE). O...
A total of 480 samples, comprising 429 faecal samples from healthy adult birds and 51 tissue samples from dead birds, were collected from four government poultry farms in the Kashmir valley from September 2007 to April 2008. In all, 33 Salmonella isolates were obtained. Of these, 28 (84.85%) isolate...
To analyze the molecular characteristics and genetic correlations of Vibrio cholerae isolates in Hainan in 2008, so as to provide pathogenic proof to diagnose the plague. Seventy six cholera strains were isolated from this cholera epidemic.69 strains were obtained from patients, 7 were isolated from...
No abstract available
The MLVA assay is known to have a high ability to identify and discriminate Brucella species, so that it can be used as an epidemiological tool to discriminate Brucella isolates originating from restricted geographic sources. In this study, the genetic profiles of 38 B. abortus isolates from humans...
Using multilocus sequence analyses (MLSA), we investigated the phylogenetic relationship of spirochaete strains from North America previously assigned to the genospecies Borrelia bissettii. We amplified internal fragments of 8 housekeeping genes (clpA, clpX, nifS, pepX, pyrG, recG, rplB, and uvrA) l...
Studies of meningococcal carriage are essential in improving knowledge of the epidemiology of meningococcal disease. The aim of this study is to ascertain the carrier rate and the serogroups of Neisseria Meningitidis circulating in a sample of students from the University of Bari. The population con...
Surveillance of the serotypes causing invasive pneumococcal diseases in the UK has indicated increasing incidence of serotype 1- and serotype 3-related disease in recent years. The introduction of a pneumococcal conjugate vaccine to the paediatric vaccination schedule in 2006, which did not cover th...
To determine genotypic distribution of and relationship between human and cat strains of Bartonella henselae,we characterized 56 specimens using multispacer typing (MST). Of 13 MST genotypes identified, 12 were grouped into cluster 1. In Japan, human infections can be caused by B. henselae strains i...
The introduction of bluetongue virus serotype 8 into northern Europe at the end of summer 2006 initiated one of the most widespread epizootics of bluetongue infection ever to occur. In winter 2007-2008, a cross-sectional serologic study was conducted in France along a transect perpendicular to the e...
In 2007, three strains of Salmonella enterica serotype Rissen (S. Rissen) were isolated in the laboratory of diagnostic microbiology of the General Hospital of Prato, Tuscany, Italy, over a 1 month and half interval of time. The first isolate was recovered on January 26 from an outpatient with enter...
No abstract available
Verotoxin-producing Escherichia coli (VTEC) is annually incriminated in more than 100,000 cases of enteric foodborne human disease and in losses amounting to $US 2.5 billion every year. A number of genotyping methods have been developed to track VTEC infections and determine diversity and evolutiona...
Campylobacter jejuni ICDCCJ07001 (HS:41, ST2993) was isolated from a Guillain-Barré syndrome (GBS) patient during a 36-case GBS outbreak triggered by C. jejuni infections in north China in 2007. Sequence analysis revealed that the ICDCCJ07001 genome consisted of 1,664,840 base pairs (bp) and one tet...
With improved measles virus (MV) control, the genetic variability of the MV-nucleoprotein hypervariable region (NP-HVR) decreases. Thus, it becomes increasingly difficult to determine the origin of a virus using only this part of the genome. During outbreaks in Europe and Africa, we found MV strains...
to determine the prevalence of extended-spectrum β-lactamases (ESBLs) in Escherichia coli from poultry in Great Britain (GB). E. coli was isolated from 388 broiler chicken caecal samples from 22 abattoirs and from boot swabs from 442 turkey flocks over successive 1 year periods. CHROMagar ECC with a...
A new tospovirus isolated from naturally infected tomato plants grown in Nakhon Pathom province (Thailand) was characterized. Infected plants showed symptoms consisting of necrotic spots, necrotic ringspots and stem necrosis. This virus was detected using general antibodies that could recognize wate...
Molecular typing of Vibrio cholerae strains is a powerful tool for the surveillance of cholera. Amplified fragment length polymorphism (AFLP) is considered to be a powerful subtyping technique to distinguish bacterial strains at the genetic level. Optimization and standardization of AFLP protocol is...
Helicobacter pullorum represents a potential food-borne pathogen, and avian species appear to be a relevant reservoir of this organism. In this study, the prevalence of H. pullorum was investigated at 30 conventional farms where 169 ceca from 34 flocks were tested, at eight organic farms where 39 ce...
Foot-and-mouth disease (FMD) is endemic in the countries of mainland Southeast Asia where it represents a major obstacle to the development of productive animal industries. The aim of this study was to use genetic data to determine the distribution of FMD virus (FMDV) lineages in the Southeast Asia...
infections caused by multidrug-resistant (MDR) Acinetobacter baumannii are a challenging problem worldwide. Here, the molecular epidemiology and the genetic basis of antibiotic resistance in 111 MDR A. baumannii strains isolated from June 2005 to March 2009 from infected patients in 10 intensive car...
The prevalence of Neisseria gonorrhoeae in the Netherlands has increased in recent years. A multiple-locus variable-number tandem repeat analysis (MLVA) was developed to assess the molecular epidemiology of N. gonorrhoeae and to elucidate transmission networks in high-risk groups in Amsterdam. The M...
Monitoring the emergence and transmission of Pseudomonas aeruginosa strains among cystic fibrosis (CF) patients is important for infection control in CF centers internationally. A recently developed multilocus sequence typing (MLST) scheme is used for epidemiologic analyses of P. aeruginosa outbreak...
Escherichia coli sequence type 131 (ST131) is a worldwide pandemic clone, causing predominantly community-onset antimicrobial-resistant infection. Its pandemic spread was identified in 2008 by utilizing multilocus sequence typing (MLST) of CTX-M-15 extended-spectrum β-lactamase-producing E. coli fro...
This study was undertaken to compare the epidemiological characteristics of the 2007 foot-and-mouth disease outbreak in two districts of Sarpang and Zhemgang in Bhutan. Zhemgang district recorded a significantly higher cumulative incidence in all species (26.9%) as well as for cattle (29.3%) compare...
Rodents are a potential source of pathogenic Yersinia enterocolitica and Y. pseudotuberculosis. In order to study this, 190 rodents were captured and sampled on seven pig farms (n=110), five chicken farms (n=55) and six other locations (n=25) in Sweden. Pigs from three of the pig farms were also sam...
CTX-M enzymes, mainly CTX-M-14 and CTX-M-15, have emerged as the most prevalent extended-spectrum β-lactamase (ESBL) type produced by Escherichia coli in Spain, with successful dissemination of clonal group O25b:H4-B2-ST131 producing CTX-M-15 within the hospital and community settings. However, unti...
Enterobacter cloacae is a major nosocomial pathogen that causes serious infections, including bloodstream infections (BSIs). The clinical significance of extended-spectrum β-lactamase (ESBL) production in E. cloacae is not well established. A multicentre, retrospective, cohort study was conducted to...
Colonisation and infection with extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) is an emerging problem. The aim of this study was to investigate whether colistin, which is reported to be effective against multiresistant enterobacteria, prevents ESBL-E colonisation in neonates. Fo...
No abstract available
There is currently limited information available on the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in South Africa. A molecular characterization of 100 MRSA from five hospitals in Cape Town was carried out in this study. The strains were separated into six clusters...
Johne's disease is chronic granulomatous infectious enteritis of animals caused by Mycobacterium avium subspecies paratuberculosis. A total of 153 animals from 19 dairy farms, 2 gaushalas (unproductive-animal rehabilitation centers), 2 goat and 2 sheep farms from different districts of the Punjab re...
Since 2000, the epidemiology of C. difficile infections (CDI) has changed in the US and Europe. Few population-based assessments of both incidence and case fatality of CDI have been performed. In this study, the Finnish nationwide laboratory-based surveillance data from the year 2008 were analysed t...
We characterized all of the Panton-Valentine leukocidin (PVL)-positive Staphylococcus aureus isolates collected between 2005 and 2008 in the Bilbao, Spain, area. For the first time, the USA300 clone is reported as predominant among PVL-positive clones in a European autochthonous population, requirin...
As a novel antibiotic resistance determinant, investigation of the occurrence and characteristics of class 1 integron was performed on nosocomial methicillin-resistant Staphylococcus aureus (MRSA) strains sampled during 2001-2006. Seventy-six out of 179 (42.5%) of the tested strains were found to ca...
Between 2006 and 2009, all MRSA isolates recovered from human patients in Upper Austria were subjected to molecular biological analysis. Whereas the isolate number decreased from year to year, the proportion of the most common sequence types (ST5, ST8 and ST22) as well as the frequency of associated...
No abstract available
An outbreak of cholera is ongoing in Haiti. On October 21, 2010, toxigenic Vibrio cholerae O1, serotype Ogawa, biotype El Tor was identified by the National Laboratory of Public Health of the Ministry of Public Health and Population in Haiti. Identification of the isolate was confirmed by CDC. Antim...
Between October and December 2009, 23 cases of Salmonella Typhimurium (Dutch) phage type 132, each with an identical multiple-locus variable-number tandem-repeat analysis (MLVA) profile (02-20-08-11-212), were reported from across the Netherlands. A case–control study was conducted using the food-co...
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a global healthcare problem. The purpose of this study was to characterize CA-MRSA clones and their distribution in Kuwait hospitals. In total, 135 CA-MRSA isolates, carrying the SCCmec IV or V genetic elements, isolated i...
to investigate the epidemiological traits of carbapenem-non-susceptible Acinetobacter baumannii (CNSAB) and the usefulness of phylogenetic grouping based on partial rpoB gene sequencing in defining the epidemiological traits of CNSAB. a total of 547 non-duplicate clinical isolates of Acinetobacter s...
this study focused on the population structure of OXA-23-producing Acinetobacter baumannii clinical isolates from Rio de Janeiro, Brazil. the analysis included several genomic typing methods, including PFGE, two multilocus sequence typing (MLST) schemes, sequence group (SG) determination and bla(OXA...
We ran a comparative analysis of all patients for whom a positive culture of Mycobacterium tuberculosis complex was available between April 2004 and October 2005 and whose HIV serology results were known, with spoligotyping results (n = 163) split into 49 HIV-positive patients and 114 HIV-negative p...
The investigation was carried out to elucidate the molecular characteristics and resistant mechanisms of imipenem-resistant Acinetobacter baumannii. Thirty-seven isolates were collected from January 2007 to December 2007. The homology of the isolates was analyzed by both pulsed field gel electrophor...
The molecular typing of 202 Legionella pneumophila sg 1 isolates obtained from environmental water sources and clinical specimens from 1985 to 2007 was conducted using pulsed-field gel electrophoresis (PFGE). In this study, a total of 212 isolates were grouped into 35 different PFGE types and Type 1...
No abstract available
We determined characteristics of Salmonella enterica pulsed-field gel electrophoresis clusters that predict their being solved (i.e., that result in identification of a confirmed outbreak). Clusters were investigated by the Minnesota Department of Health by using a dynamic iterative model. During 20...
Strain typing is a tool for determining the diversity and epidemiology of infections. Treponema pallidum DNA was isolated from 158 patients with syphilis from the United States, China, Ireland, and Madagascar and from 15 T. pallidum isolates. Six typing targets were assessed: (1) the number of 60‐bp...
The effects that immigration might have on the epidemiology of tuberculosis (TB) in a low-incidence area of Italy was investigated by determining, in autochthonous and immigrant TB patients, the molecular characteristics of the Mycobacterium tuberculosis complex (MTBC) isolates, which may provide in...
We present 2 cases of methicillin-resistant Staphylococcus aureus (MRSA) acalculous cholecystitis and review the literature. We performed pulsed field gel electrophoresis, typing of the staphylococcal cassette chromosome mec element, and Panton-Valentine leukocidin testing on the isolates. One each...
Solar disinfection (SODIS) is a simple drinking water treatment method that improves microbiological water quality where other means are unavailable. It makes use of the deleterious effect of solar irradiation on pathogenic microbes and viruses. A positive impact on health has been documented in sev...
Salmonella is a key human pathogen worldwide, most often associated with food poisoning incidences. There is a small number of predominant serotypes found in human cases. The role of exposure in the epidemiology of Salmonella can be explained using dose-response assessment both for infection and acu...
Improved understanding of the ecology and epidemiology of Campylobacter in the poultry farm environment is key to developing appropriate farm-based strategies for preventing flock colonization. The sources of Campylobacter causing broiler flock colonization were investigated on one poultry farm and...
From 2004 to 2005, 60%-72% of invasive Staphylococcus aureus isolates from Romanian hospitals were resistant to methicillin (methicillin-resistant S. aureus [MRSA]), the highest frequency for any European nation. Few reports, however, have addressed the molecular characteristics of S. aureus in Roma...
to assess the frequency and diversity of extended-spectrum β-lactamases (ESBLs) in Enterobacteriaceae isolates in Belgium. during 2006 and 2008, non-duplicate clinical isolates of Enterobacteriaceae resistant to ceftazidime and/or cefotaxime were collected in 100 Belgian hospitals. ESBL production w...
This study was conducted to determine the genetic characterization of extended-spectrum beta-lactamase (ESBL) producing strains of Klebsiella pneumoniae isolated from Iranian patients in hospitals in Tehran. Antibiotic susceptibility of 104 isolates was determined using the disk diffusion test. The...
The causative agent of legionellosis, Legionella pneumophila, colonizes all natural and human-made water networks, thus constituting the source of contaminated aerosols responsible for airborne human infections. Efficient control of infections, especially during epidemics, necessitates the fastest a...
Mycobacterium tuberculosis strains from 349 patients were isolated in western Sweden during the years 2001-2005. Only 26% of the tuberculosis (TB) patients were born in Sweden. All the others were born in any of 42 different countries; 17% in other European countries, 28% in Africa, 16% in Asia, 11%...
Thirty-six children (27 boys, nine girls) that fulfilled CDC criteria for community-acquired infections were diagnosed with bacteraemia and/or osteomyelitis caused by Staphylococcus aureus during an 18-month period (2006-2008). Antibiotic susceptibility was determined by an agar dilution method. SCC...
We have investigated the distribution of integrons among 752 multidrug-resistant Salmonella isolates from human febrile and/or diarrheal patients during 1992-2007 and analyzed their genetic characteristics. Here, we report extensive integron analysis results within human isolates during the last 16...
During August and September 2010, an outbreak comprising 22 cases of Legionnaires' disease was identified by the public health service in Wales. The cases are distributed over a wide geographical area in South East Wales. There are two space-time clusters centred on the upper Rhymney Valley and the...
We investigated an international outbreak of Salmonella Agona with a distinct PFGE pattern associated with an Irish Food company (company X) producing pre-cooked meat products sold in various food outlet chains in Europe. The outbreak was first detected in Ireland. We undertook national and internat...
Adenovirus serotype 4a is a respiratory virus that occasionally causes conjunctivitis. This paper describes an outbreak of follicular conjunctivitis that occurred in a geriatric centre. Outbreak description and epidemiological research through a survey. For the microbiological study conjunctival swa...
A significant increase in the rate of vancomycin-resistant Enterococcus faecium (VREfm) bacteremia at our health service, despite improved infection control, prompted us to investigate the cause. E. faecium bacteremia (including VREfm) over a 12-year period (1998-2009) was investigated using multilo...
Three outbreaks of Legionnaires' disease were reported in the Fredrikstad/Sarpsborg community, Norway, in 2005 and 2008 caused by the L. pneumophila ST15 and ST462 strains determined by sequence based typing. In this retrospective study, we suggest that the aeration ponds, a part of the biological t...
Drugs of abuse serve as cofactors to susceptibility to HIV infection and disease progression. Although clinical reports indicate association between HIV/AIDS and drug use, the molecular mechanism of infection susceptibility and disease progression remains unclear. Drugs such as cocaine exert their a...
Tomato yellow leaf curl virus (TYLCV) is a member of the genus Begomovirus of the family Geminiviridae, members of which are characterized by closed circular single-stranded DNA genomes of 2.7-2.8 kb in length, and include viruses transmitted by the Bemisia tabaci whitefly. No reports of TYLCV in Ko...
The present study investigates epidemiological diversity and multidrug resistance spreading among Mycobacterium tuberculosis strains circulating in Moscow, Russian Federation. Among 115 M. tuberculosis strains selected randomly from the sputum of epidemiologically unrelated tuberculosis (TB) patient...
We describe an outbreak of Bacillus cereus bacteremia that occurred at Jichi Medical University Hospital in 2006. This study aimed to identify the source of this outbreak and to implement appropriate control measures. We reviewed the charts of patients with blood cultures positive for B. cereus, and...
Clostridium difficile is the most common cause of health care-associated diarrhea. Accurate and rapid diagnosis is essential to improve patient outcome and prevent disease spread. We compared our two-step diagnostic algorithm, an enzyme immunoassay for glutamate dehydrogenase (GDH) followed by the c...
No abstract available
Our objective was to analyse phenotypic and genetic data of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae, Enterobacter cloacae, Escherichia coli and Serratia marcescens that cause infections in our hospital. Over a 3 year period, 342 randomly selected clinical Enterobacteriac...
The detection of Enterobacteriaceae carrying the carbapenemase KPC has been problematic. Thirty isolates of KPC-possessing Escherichia coli were gathered from hospitals in New York City and Connecticut. The imipenem, meropenem, doripenem, and ertapenem MIC50 values were 4, 2, 1, and 4 μg/ml, respect...
The incidence of and risk factors for acquiring community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) among patients staying in intensive care units (ICUs) remain unclear. We enrolled patients staying in two ICUs at the Far Eastern Memorial Hospital during the period of 1 Septem...
To perform molecular typing of vancomycin resistant Enterococcus spp. (VRE) strains endemic in various hospitals of Karachi, to characterize the mechanism of glycopeptide resistance and assess the genetic relatedness, for understanding its transmission locally. This was a cross sectional study condu...
The objective of this project was to develop and implement an active surveillance program for the early and rapid detection of equine influenza viruses in Ontario. For this purpose, from October 2003 to October 2005, nasopharyngeal swabs and acute and convalescent serum samples were collected from 1...
The objectives of this study were to report an outbreak of highly drug-resistant Salmonella enterica serotype Oranienburg in dairy calves, and conduct an epidemiological investigation of Oranienburg identified on a dairy herd during a study to determine whether discontinuing feeding medicated milk r...
Recent studies have suggested that Salmonella Typhimurium strains associated with mortality in UK garden birds are significantly different from strains that cause disease in humans and livestock and that wild bird strains may be host adapted. However, without further genomic characterization of thes...
We report a multicity outbreak of cfr-containing linezolid-resistant Staphylococcus epidermidis in Ohio. Thirty-nine isolates were obtained from 2 hospitals. Two clones with different mechanisms of linezolid resistance were circulating in hospital A. One of these contained the cfr gene, and the othe...
Quinolone and β-lactam resistance mechanisms and clonal relationships were characterized among Escherichia coli isolates resistant to ciprofloxacin and extended-spectrum cephalosporins associated with human extra-intestinal infections in Rome. The E. coli. ST131 clone was found to be prevalent. This...
No abstract available
Meticillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen in Pakistan and is emerging in the community. This is one of the first reports of the prevalent genotypes of MRSA in both hospital and community settings in Pakistan. Isolates collected in 2006-2007 were characterized b...
We conducted a prospective study to evaluate the prevalence and epidemiology of CDI in Kuwait government hospitals over a 3-year period, January 2003 to December 2005, to determine the ribotypes responsible for CDI and to estimate the prevalence of ribotype 027. We also conducted a case-control stud...
The aim of this study was to investigate Clostridium difficile-associated diarrhea (CDAD) in an intensive care unit (ICU) of a tertiary hospital in Rio de Janeiro, Brazil, and to characterize epidemiologically C. difficile strains obtained from an outbreak of CDAD. Within almost a 4-year surveillanc...
One-hundred sixty-eight group B streptococcal (GBS) isolates from a Brazilian hospital were phenotypically and genotypically characterized. Isolates were recovered from human sources from April 2006 to May 2008 and classified as either invasive, noninvasive, or colonizing isolates. Classical methods...
Eighty-two percent of 320 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates from various infection sites collected throughout South Africa were separated into five major globally prevalent clusters by SmaI pulsed-field gel electrophoresis, spa, and SCCmec typing. Only one Panton-V...
Shiga toxin-producing Escherichia coli (STEC), an important foodborne pathogen, can cause mild to severe bloody diarrhoea (BD), sometimes followed by life-threatening complications such as haemolytic uraemic syndrome (HUS). A total of 44 O157 strains isolated from different patients from 2000 throug...
In 2005, over 600 clinically diagnosed typhoid fever cases occurred in South Africa, where an outbreak had been previously described in 1993. Case-control and molecular investigations, including Salmonella enterica serovar Typhi (S. Typhi) isolates from that area from 1993, 2005 and later, were unde...
In September 2008, bluetongue virus serotype 8 (BTV-8) infection was detected for the first time in Sweden, in a dairy herd on the west coast. Two different previously published operational atmospheric dispersion models indicate that midges from infected regions in Europe are likely to have reached...
The difference in the outcomes of nosocomial bloodstream infection (BSI) caused by community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains and healthcare-associated MRSA (HA-MRSA) strains remains unclear. From January 1, 2006 to December 31, 2008, all adult patients hospit...
Salmonella enterica subsp. enterica serovar identification is of great importance with respect to outbreak monitoring and case verification. Therefore rapid, sensitive and cost efficient detection of Salmonella spp. is indispensable within microbiology labs. To amalgamate single tube isolate identif...
Bordetella isolates in the Saint Petersburg region have been monitored since 1998. Over the past ten years, concomitant with the increase in pertussis whole-cell vaccine coverage, the incidence of whooping cough has decreased. However, this decrease exists only for Bordetella pertussis infections, a...
No abstract available
One hundred and three Streptococcus pyogenes isolates recovered mainly from streptococcal throat infections in Lebanon were characterized by emm and PFGE typing. Thirty-three emm types and subtypes were detected among the isolates. PFGE was more discriminatory as a typing method. The prevalent emm t...
The detection rates of extended-spectrum β-lactamase (ESBL)-producing bacteria in Japan are very low (∼5%) compared with those obtained worldwide. Further, the current trend of these bacteria in Japan is not known, and few studies with longitudinal observations have been reported. To obtain epidemio...
Many bacterial typing methods are specific for one species only, time-consuming, or poorly reproducible. DiversiLab (DL; bioMérieux) potentially overcomes these limitations. In this study, we evaluated the DL system for the identification of hospital outbreaks of a number bacterial species. Appropri...
In this study, we investigated the risk factors for and carbapenem resistance mechanisms of extensively drug-resistant Acinetobacter baumannii (XDR-AB). Isolates of XDR-AB were collected from seven tertiary care hospitals in South Korea. A case-control study for risk factor analysis was performed an...
Vibrio cholera, the causal agent of cholera, also occupies an autochthonous aquatic inhabitant. The current, seventh cholera pandemic is linked to O1 El Tor biotype and O139 serogroups. In the last decades, we have witnessed a shift involving genetically and phenotypically varied pandemic clones in...
The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) is continuously changing. Iceland has a low incidence of MRSA. A "search and destroy" policy (screening patients with defined risk factors and attempting eradication in carriers) has been implemented since 1991. Clinical and micr...
We describe the development of a multilocus sequence typing (MLST) scheme for Corynebacterium diphtheriae, the causative agent of the potentially fatal upper respiratory disease diphtheria. Global changes in diphtheria epidemiology are highlighted by the recent epidemic in the former Soviet Union (F...
No abstract available
No abstract available
A case-control and a case-crossover study were performed to investigate a Campylobacter jejuni outbreak in Crete in 2009. Most cases originated from rural areas, served by a different water-supply system from that of the adjacent town. Thirty-seven cases and 79 controls were interviewed; cases were...
In September 2007 an increase of severe Clostridium difficile-associated infections (CDI) was noticed in a hospital in the city of Trier, Germany. It was assumed that a new, possibly hypervirulent strain (PCR ribotype 027) was related to these events. An outbreak investigation was initiated by the l...
To investigate an increase in Salmonella typhimurium phage type 1 (STM1) cases identified in the Gisborne region (eastern North Island, New Zealand) in January 2009. Initial investigations found that ham and watermelon were both consumed by a high proportion of cases. A case control study was conduc...
The discriminatory power of multiple-locus variable-number tandem-repeat analysis (MLVA) needs to be evaluated for all Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) phage types so that the power of this methodology is understood and results can be interpreted correctly...
A total of 20 Vibrio cholerae isolates were recovered for investigation from a cholera outbreak in Kelantan, Malaysia, that occurred between November and December 2009. All isolates were biochemically characterized as V. cholerae serogroup O1 Ogawa of the El Tor biotype. They were found to be resist...
No abstract available
This report describes the first outbreak of methicillin-resistant Staphylococcus aureus USA300 in a general hospital ward in Japan, involving 6 health care workers and 4 patients. This report emphasizes the need for health care personnel to be alert that methicillin-resistant Staphylococcus aureus h...
In September 2009, the Connecticut Department of Public Health (DPH) identified an outbreak of Salmonella gastroenteritis among attendees at a reception. A case-control study and environmental and laboratory investigations were conducted. Nine case-patients and 14 control subjects were identified. P...
This study aimed to compare strains of Staphylococcus aureus and E. coli isolated from food workers and enteral diet samples obtained from 2 public hospitals (H1/H2) in Goiania, Goias, Brazil, by the means of antibiogram and pulsed field gel electrophoresis (PFGE). In the H1, strains of S. aureus we...
The isolation and identification of Avibacterium paragallinarum serovar B-1 from severe infectious coryza outbreaks in broiler breeders in Panama is reported for the first time. Infectious coryza was absent for over a decade in the breeder farms area. Disease outbreaks were characterized by an up to...
On June 16 and 17, 2007, the medical clinic of a prison in Isfahan, Iran received multiple reports of gastrointestinal illness among prisoners. A cross-sectional study was therefore undertaken to determine the extent, causative agent and possible source of the outbreak. A case-patient was defined an...
To determine the prevalence of invasive nontyphoid salmonellosis and typhoid fever in Malawi and South Africa, we compared case frequency and patient age distribution. Invasive nontyphoid salmonellosis showed a clear bimodal age distribution; the infection developed in women at a younger age than in...
This study describes the clinical and molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) isolates that emerged after an index case in a tertiary-care oncology hospital in Mexico City and identifies whether these isolates were related with the index case. All MRSA strains...
Resurgence of syphilis in Canada and worldwide requires laboratories to update their methods for molecular epidemiology investigation and surveillance. This study utilizes polymerase chain reaction diagnostic tests for syphilis, identifies macrolide resistance, and uses a molecular typing system to...
We performed an 11-year retrospective analysis of consecutive nonduplicate methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates in two neighbouring hospitals in the Paris area. MRSA isolates were classified according to resistance (R) to fluoroquinolones (Fq), kanamycin (K), tobramyc...
The present study reports the epidemiological investigations undertaken in one of Krakow's city hospitals regarding the source of infection and the routes of transmission of a group A streptococcus (Streptococcus pyogenes), using fluorescent in situ hybridization as a rapid method for detecting S. p...
Pseudomonas aeruginosa is well adapted to the hospital setting and can cause a wide array of nosocomial infections that occasionally culminate in recalcitrant outbreaks. In the present study, we describe the first nosocomial outbreak of infection caused by bla(VIM-2)-positive P. aeruginosa in German...
Bovine tuberculosis is caused by Mycobacterium bovis, a mycobacterium highly similar to M. tuberculosis that belongs to the M. tuberculosis complex. The main host of M. bovis is cattle but it also affects many other mammalians including humans. Tuberculosis in humans caused by either M. bovis or M....
Tuberculosis remains a major public health concern in Russia and worldwide. Given the great geographical, ethnic, and socio-economic heterogeneities between Russian regions, epidemiological data cannot be generalized from a regional to a country-wide level. We present data on the epidemiology of tub...
Knowledge of the epidemiology of Streptococcus agalactiae in Portugal is limited: therefore, the present study aimed to investigate the carriage rate of S. agalactiae among Portuguese women of reproductive age and the prevalence of antibiotic resistance, as well as to perform a molecular characteriz...
Nasal carriage of Staphylococcus aureus contributes to an increased risk of developing an infection with the same bacterial strain. Genetic regulatory elements and toxin-expressing genes are virulence factors associated with the pathogenic potential of S. aureus. We undertook an extensive molecular...
To investigate the outbreak of acinetobacter baumannii in the ICU, and to explore the antimicrobial resistance characteristics of pathogens, and therefore to determine the optimal prevention strategies. From May to June 2007, most of the cases of infection by acinetobacter baumannii in our ICU were...
Influenza A virus (H1N1) 2009, a new swine-origin influenza A virus, has been spread worldwidely and caused great public fear. High-throughput transcriptomics and proteomics methods are now being used to identify H1N1 and H1N1-host interaction. This article reviews recent transcriptomics and proteom...
Influenza A viruses of 16 serologically different hemagglutinin (HA) subtypes have been identified in waterfowl reservoirs, and the introduction of a novel HA subtype of avian viruses into the human population has the potential to generate the next pandemic strains. Both humoral and cellular immunit...
Non-O157 Shiga toxin-producing Escherichia coli (STEC) strains have been linked to outbreaks and sporadic cases of illness worldwide. Illnesses linked to STEC serotypes other than O157:H7 appear to be on the rise in the United States and worldwide, indicating that some of these organisms may be emer...
No abstract available
Widespread global use of rifampin for 2 decades preceded the emergence of clinically significant multidrug-resistant tuberculosis (MDR-TB) in the early 1990s. The prevalence of MDR-TB has gradually increased such that it accounts for approximately 5% of the global case burden of disease (approximate...
We determined the mutation frequencies of 59 nosocomial isolates of Enterobacter cloacae, and investigated their association with antimicrobial susceptibility, genotype, and history of exposure to antimicrobials. The frequencies of mutations leading to rifampicin resistance ranged from 5.8 × 10(-9)...
Multilocus sequence typing (MLST) was applied to all unique serotype 6C and 6D isolates and a random selection of serotype 6B and 6A isolates from nasopharyngeal swabs from Fijian children enrolled in a recent vaccine trial. The results suggest that Fijian serotype 6D has arisen independently from b...
The spoligotyping-based population structure of multidrug-resistant (MDR) Mycobacterium tuberculosis strains isolated in Poland (n = 46), representing all culture-positive MDR tuberculosis (MDR-TB) cases, was compared to that of isoniazid (INH)-monoresistant strains (n = 71) isolated in 2004. The la...
A prospective study to assess fungaemia was conducted for 12 months at a Portuguese University Hospital. A total of 35 Candida albicans isolates obtained from 12 patients with fungaemia were compared by a multiplex PCR system using four microsatellite loci. Blood isolates were evaluated against conc...
Multidrug-resistant Acinetobacter baumannii is a worldwide nosocomial menace. We sought to better understand its behavior through studying the molecular epidemiology of this organism at the Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia, over a 10-year period. Multilocus sequen...
A total of 2,346 Mycobacterium tuberculosis isolates from 13 provinces in China were genotyped by spoligotyping. Two hundred seventy-eight spoligotypes were identified: 2,153 isolates were grouped into 85 clusters, and the remaining 193 isolates were orphans. Comparison with the SpolDB4.0 database r...
Pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem-repeat analysis (MLVA) are used to assess genetic similarity between bacterial strains. There are cases, however, when neither of these methods quantifies genetic variation at a level of resolution that is well suited...
The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) has dramatically changed over the past 10 y with the emergence of community-associated MRSA (CA-MRSA). Recent studies have reported a frequent association of these strains with hospital outbreaks, and an incidence varying over ti...
Pontiac fever and Legionnaires' disease are regarded as clinically and epidemiologically distinct diseases, caused by bacteria of the genus Legionella. Although several outbreaks of either Pontiac fever or Legionnaires' disease have been reported, they are rarely seen simultaneously. In this report...
Infection is a recognized complication of endoscopic retrograde cholangiopancreatography (ERCP). We describe the epidemiologic and molecular investigations of an outbreak of ERCP-related severe nosocomial infection due to KLEBSIELLA PNEUMONIAE producing extended-spectrum beta-lactamase (ESBL). We co...
The study was conducted in three regional states of Ethiopia: Amhara, Oromia, and Addis Ababa from August 2008 to April 2009 with the objectives of identifying the genetic diversity of serotypes and topotypes in Ethiopia, and determining the attack rate and associations of potential risk factors wit...
We performed spoligotyping of Mycobacterium tuberculosis isolates from 833 systematically sampled pulmonary tuberculosis (TB) patients in urban Mumbai, India (723 patients), and adjacent rural areas in western India (110 patients). The urban cohort consisted of two groups of patients, new cases (646...
The aim of this study was to characterize Erysipelothrix sp. isolates from clinically affected pigs and their environment and compare them to the Erysipelothrix sp. vaccines used at the sites. Samples were collected during swine erysipelas outbreaks in vaccinated pigs in six Midwest United States sw...
A 30-probe assay was developed for simultaneous classification of Listeria monocytogenes isolates by lineage (I to IV), major serogroup (4b, 1/2b, 1/2a, and 1/2c), and epidemic clone (EC) type (ECI, ECIa, ECII, and ECIII). The assay was designed to facilitate rapid strain characterization and the in...
In the United Kingdom, EMRSA-15 and EMRSA-16 account for the majority (∼90%) of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections. Currently, the standard typing technique, pulsed-field gel electrophoresis (PFGE), is laborious and insufficient for discriminating between closel...
A variable-number tandem-repeat genotyping method for Mycobacterium tuberculosis was converted to run in a multiplex PCR format on a 12-well microfluidic laboratory chip. Epidemiologically and genotypically distinct isolate clusters of M. tuberculosis were identified. This rapid genotyping method ha...
The aim of this study was to assess the incidence and molecular epidemiology of multidrug-resistant (MDR) Pseudomonas aeruginosa in our university hospital. Analysis included antimicrobial susceptibility profiling, bla gene identification and pulsed-field gel electrophoresis (PFGE). During the one-y...
Hyaluronic acid capsule plays a key role in Streptococcus pyogenes virulence. Circulation of mucoid or highly encapsulated strains has been related to rheumatic fever epidemics and invasive disease in several countries. In 2009, an outbreak of mucoid S. pyogenes isolates was detected in northern Spa...
Staphylococcal cassette chromosome mec (SCCmec) is a large mobile genetic element which is used frequently for subtyping of methicillin-resistant Staphylococcus aureus (MRSA) strains. MRSA SCCmec type IV not only predominates among community-acquired MRSA (CA-MRSA) strains but also is associated wit...
To determine the possible genetic background and the source of our hospital's 43 clinical isolates of multidrug-resistant Acinetobacter baumannii, and the category of gene cassettes in type 1 integrons of all strains. Restriction enzyme Apa I was chosen for all strains in pulsed-field gel electropho...
During 2003-2005, an outbreak of meningitis due to Neisseria meningitidis serogroup C occurred in China. With the aim to find strain clues result in the final epidemics, the ancestral strain 053442, a clinical isolate, and a carrier strain 053426 with different gene type were analyzed. Clinical stra...
The transmission rate of enteroviruses in young children remains unclear. Therefore, we carried out active surveillance in preschool children to investigate the transmission rate and clinical manifestation of enteroviruses. From September 2006 to December 2008, we monitored infectious diseases in ch...
The molecular epidemiology of 33 Escherichia coli and 81 Klebsiella pneumoniae extended-spectrum beta-lactamase-producing healthcare-associated and community-acquired isolates collected in the Helsinki district during 2000-2004 was investigated. Clonality studies, antimicrobial susceptibility and ge...
Escherichia coli sequence type ST131 (O25:H4), associated with the CTX-M-15 extended-spectrum beta-lactamase, has emerged internationally as a multidrug-resistant pathogen but has received little attention in the United States. From the SENTRY and Meropenem Yearly Susceptibility Test Information Col...
Salmonella is the most common bacterial cause of foodborne outbreaks in the United States. Starting in June 2007, investigation of a cluster of Salmonella Montevideo cases with indistinguishable pulsed-field gel electrophoresis (PFGE) patterns resulted in the identification of an outbreak associated...
From June to July 2007, 36 cases of Guillain-Barre syndrome (GBS) occurred in a township in north China. Serological study and bacteria culture were performed to investigate the association between preceding Campylobacter jejuni infection and this GBS outbreak. Anti-C. jejuni antibodies were found i...
To determine the epidemiology of invasive pneumococcal disease (IPD) and the antibiotic susceptibility and serotype distribution of S. pneumoniae in pediatric patients in Lima, Peru. A 2-year, multicenter, passive surveillance study conducted from May 2006- April 2008 in 11 public hospitals and five...
On September 6, 2008, bluetongue was detected for the first time in Sweden. Intensified active surveillance in cattle and vector surveillance, prompted by the situation in northern Europe, preceded the detection. A vaccination campaign and intensive surveillance activities were initiated nationally,...
Dengue is an emerging arboviral disease and currently poses the greatest arboviral threat to human health. In recent decades, there has been a substantial increase in dengue outbreaks in many parts of the world including India. We performed an in-depth investigation of a major dengue outbreak in And...
Between June 2007 and January 2008, 26 Klebsiella pneumoniae isolates carrying bla(DHA-1) on an IncL/M plasmid were obtained from clinical samples at Granollers Hospital, Barcelona, Spain. Three of the isolates also carried a bla(CTX-M-15) gene. The 26 isolates showed 11 pulsed-field gel electrophor...
Vibrio cholerae O1 biotype El Tor (ET), the cause of the current 7th pandemic, has recently been replaced in Asia and Africa by an altered ET biotype possessing cholera toxin (CTX) of the classical (CL) biotype that originally caused the first six pandemics before becoming extinct in the 1980s. Unti...
Contamination of locally produced, ready-to-eat meats by Listeria spp. has been previously reported at one processing plant in Trinidad. However, the status of this pathogen in locally produced products sold at retail outlets is unknown. This study was conducted to establish whether there is a risk...
To obtain the genotype and antimicrobial susceptibility profiles of Campylobacter jejuni isolates from north China, 93 C. jejuni isolates (56 isolates from patients with diarrhoea, 7 isolates from Guillain-Barré syndrome patients and 30 isolates from chicken stools) were selected for multilocus sequ...
No abstract available
Drug-resistant tuberculosis (TB) presents a major challenge to global TB control. To gain a better understanding of drug-resistant TB epidemiology in Malatya, Turkey, we conducted the present study using 397 Mycobacterium tuberculosis clinical isolates collected from Malatya, Turkey, in recent years...
The choice of adequate methods for epidemiological purposes remains a challenging problem in Neisseria gonorrhoeae molecular monitoring. In this study, the collection of geographically unrelated gonococci (n = 103) isolated in Russian clinics was comparably tested by (i) a traditional serotyping sch...
The frequency of transfer of genes encoding resistance to antimicrobial agents was determined by conjugation in ESBL-producing and/or fluoroquinolone or aminoglycoside resistant Enterobacteriaceae clinical isolates at a tertiary care center in Lebanon. In addition, the role of tra genes encoding tra...
A systematic review of outbreak and non-outbreak studies of infections caused by extraintestinal pathogenic Escherichia coli (ExPEC) was conducted. This review examines the epidemiology, seasonality, source or mode of transmission, and temporal changes, based on E. coli serogroup, in ExPEC causing s...
Tuberculosis has had significant effects on Ireland over the past two centuries, causing persistently higher morbidity and mortality than in neighbouring countries until the last decade. This study describes the results of genotyping and drug susceptibility testing of 171 strains of Mycobacterium tu...
In September 2008, an outbreak of pneumonia associated with an emerging human adenovirus (human adenovirus serotype 14 [HAdV-14]) occurred on a rural Southeast Alaska island. Nine patients required hospitalization, and 1 patient died. To investigate the outbreak, pneumonia case patients were matched...
Worldwide increasing rates of Clostridium difficile infections (CDI) with severe courses and outbreaks have been reported. This change in CDI epidemiology has on one hand been related to the spread of specific PCR ribotypes (e.g. 027) and on the other hand to increased prevalence of resistant C. dif...
The objective of the study was to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) contamination of retail meat and to determine the level of contamination. Pork (pork chops and ground pork), ground beef and chicken (legs, wings and thighs) were purchased at retail outl...
We have recently found a high prevalence of non-typeable pneumococcal isolates (NTPn) circulating in day-care centers in Central Brazil, besides serotype 14 isolates. We therefore examined the genetic relationship among NTPn and serotype 14 from carriage and invasive pneumococcal isolates obtained f...
Clostridium difficile is an important nosocomial enteric pathogen and is the etiological agent of pseudomembranous colites. Recently, the rates of C. difficile infection (CDI) have increased worldwide, but in Brazil few data about this situation and the incidence of clonal types of C. difficile exis...
Salmonella I 4,[5],12:i:- is an emerging serotype, and little information regarding attribution or risk factors for infection has been documented. We investigated an outbreak of Salmonella I 4,[5],12:i:- infections in a rural community and identified the community's private water system as the sourc...
The aim of this study was to investigate the high level of pulmonary Mycobacterium abscessus infections and implement a surveillance programme among 43 ventilator-dependent patients, 15 with pulmonary M. abscessus infections, in a hospital long-term respiratory care ward (RCW) in central Taiwan. M....
Amongst the SAT serotypes of foot-and-mouth disease virus (FMDV), the SAT 2 serotype is the most widely distributed throughout sub-Saharan Africa. Kenyan serotype SAT 2 viruses have been reported to display the highest genetic diversity for the serotype globally. This complicates diagnosis and contr...
Extended-spectrum beta-lactamases, plasmid-mediated AmpC beta-lactamases (PABLs), and plasmid-mediated metallo-beta-lactamases confer resistance to many beta-lactams. In Japan, although several reports exist on the prevalence of extended-spectrum beta-lactamases and metallo-beta-lactamases, the prev...
Colonizing group B Streptococcus (GBS) capsular polysaccharide (CPS) type IV isolates were recovered from vaginal and rectal samples obtained from 97 (8.4%) nonpregnant women of 1,160 women enrolled in a U.S. multicenter GBS vaccine study from 2004 to 2008. Since this rate was much higher than the r...
In recent years, increased isolation of extended-spectrum beta-lactamase (ESBL)-producing Proteus mirabilis has been reported in Japan. We undertook an investigation to determine the prevalence of ESBL-producing P. mirabilis isolated in Japan and to characterise the genotype. Seventy-four P. mirabil...
Human echovirus types 6 (E-6) and 30 (E-30) cause seasonal epidemics of aseptic meningitis. These two enteroviruses are frequently observed in co-circulation, an epidemiological pattern that is prerequisite for the occurrence of dual infections, which can lead to recombination between co-infecting v...
Streptococcus pneumoniae is an important cause of community acquired pneumonia, sepsis, meningitis and otitis media globally and has been incriminated as a major cause of serious childhood bacterial infections in The Gambia. Better understanding of the dynamics of transmission and carriage will info...
Methicillin-resistant Staphylococcus aureus (MRSA) infections are increasingly being reported among cystic fibrosis (CF) populations worldwide. In this paper, we sought to examine at the epidemiology, the molecular characterisation and the antibiotic resistance of MRSA isolates in our cohort of CF p...
Bronchoscopes and the filters used for washing them were found to yield high numbers of Mycobacterium avium isolates sharing the same repetitive sequence-based PCR (rep-PCR) fingerprint pattern as M. avium isolates recovered from patient samples collected by bronchoscopy. Water and biofilm samples c...
Staphylocoagulase (SC) is a major phenotypic determinant of Staphylococcus aureus. Antigenic specificity of SC (SC serotype) has been classified into at least 10 types and employed as an epidemiological marker. In the present study, from the sequence information of SC genes, a novel multiplex PCR as...
Two outbreaks of Streptococcus suis ST7 occurred in humans in 1998 and 2005 in China. PFGE of chromosome restriction fragments found all ST7 isolates to be indistinguishable. Due to the genetic homogeneity of ST7 isolates, development of a rapid sub-typing method with high discriminatory power for S...
Taiwan initiated a multidrug-resistant tuberculosis (MDR-TB) programme in May 2007. Seventy-seven MDR-TB patients were enrolled from May 2007 to February 2009 in Eastern Taiwan. Isolates of 73 (94%) patients were available for genotyping using spoligotyping and MIRU-VNTR (mycobacterial interspersed...
To investigate antimicrobial resistance, 96 Salmonella enterica subspecies enterica serovar Enteritidis strains isolated from salmonellosis outbreaks and poultry-related products obtained in southern Brazil were analyzed. Macrorestriction patterns, obtained by pulsed-field gel electrophoresis and ph...
The objective of this study was to determine if the within-herd prevalence of fecal Salmonella shedding is higher in dairy herds with clinical outbreaks of disease, as compared to herds with subclinical infections only. Data were collected prospectively from dairy herds throughout New York that had...
Neisseria meningitidis meningitis represents approximately one-half of the meningococcal cases in French children. To explore the contribution of bacterial typing in improving the management of cases, we aimed to describe clinical characteristics and mortality of meningococcal meningitis in children...
Several methods are available for the molecular typing of Mycobacterium tuberculosis complex isolates. The results of the recent research demonstrated that Mycobacterial Interspersed Repetitive Unit (MIRU)-Variable Number Tandem Repeats (VNTR) method has high discriminatory power and reproducibility...
Continuous surveillance on resistance patterns and characterization of Staphylococcus aureus represent simple and low-cost techniques to understand and evaluate the effectiveness of infection control and antimicrobial prescribing measures. In this study we analyzed the antibiotic susceptibility and...
Burkholderia cepacia complex (Bcc) bacteria have gained notoriety as pathogens in cystic fibrosis (CF) because they are difficult to identify and treat, and also have the ability to spread between CF individuals. Of the 17 formally named species within the complex, Burkholderia multivorans and Burkh...
Staphylococcus aureus is an important cause of skin and soft-tissue infections (SSTIs), endovascular infections, pneumonia, septic arthritis, endocarditis, osteomyelitis, foreign-body infections, and sepsis. Methicillin-resistant S. aureus (MRSA) isolates were once confined largely to hospitals, oth...
We have noted that, during the last few years, there has been a redistribution of the most common Candida species with an increase in non-C. albicans Candida species, particularly Candida glabrata. In many countries, the high frequency of Candida glabrata shows the highest resistance rates. The main...
This study reports the dissemination of multidrug-resistant (MDR) OXA-23-producing Acinetobacter baumannii clones in hospitals in Antananarivo, Madagascar. A total of 53 carbapenem-resistant A. baumannii isolates were obtained from September 2006 to March 2009 in five hospitals. These resistant stra...
Between March and June 2008, 12 cases of hepatitis A were notified in Winchester. Cases were from a primary school and a nursery school with no direct linkage. Hepatitis A virus (HAV) RNA sequenced from nine cases confirmed the strain in both schools to be identical. The outbreak could have affected...
During a 15-month period in Scotland a small but important number of human Campylobacter cases (3·2%) arose from 91 putative household outbreaks. Of the 26 outbreaks with known strain composition, 89% were composed of the same MLST which supports the potential use of MLST in public health epidemiolo...
The genetic relatedness of Vibrio cholerae O1/O139 isolates obtained from 100 patients and 146 of their household contacts in Dhaka, Bangladesh, between 2002 and 2005 was assessed by multilocus variable-number tandem-repeat analysis. Isolate genotypes were analyzed at five loci containing tandem rep...
Nigeria has a high tuberculosis incidence, and genotyping studies of Mycobacterium tuberculosis Complex (MTC) in the country are necessary in order to improve our understanding of the epidemic. Isolates of MTC were isolated from cases of pulmonary tuberculosis in Jos, North Central region of Nigeria...
The prevalence of linezolid-resistant coagulase-negative Staphylococcus (CoNS) in the MD Anderson Cancer Center rose from 0.6% in 2007 to 5.5% in 2009. The aim of our study was to analyse the relationship between linezolid use and an outbreak of linezolid-resistant CoNS. We retrospectively identifie...
To understand the domestic population structure of Mycobacterium tuberculosis clinical isolates in the Republic of Korea, we genotypically analysed 80 isolates obtained from various geographical origins in the country. Of these, 64 (80.0 %) isolates were identified as Beijing family strains. It is p...
In 2006 and 2007, a large outbreak of Clostridium difficile infections (CDIs) with PCR-ribotype 027 was identified in northern France. Overall, 38 healthcare facilities notified 529 CDIs over a 22-month period, including 281 laboratory-confirmed CDI 027 and 248 non-confirmed CDI 027 cases (incidence...
Pseudomonas aeruginosa is an opportunistic pathogen that causes nosocomial infections in intensive care units. Determining a system of typing that is discriminatory is essential for epidemiological surveillance of P. aeruginosa. We developed a method for the typing of Pseudomonas aeruginosa, namely,...
To determine the phylogenetic group distribution and prevalence of three major globally disseminated clonal groups [clonal group A (CGA) and O15:K52:H1, associated with phylogenetic group D, and sequence type ST131, associated with phylogenetic group B2] among fluoroquinolone-resistant extra-intesti...
This study aimed to evaluate the incidence of Staphylococcus aureus infections in different departments of Belcolle Hospital in Viterbo and the surrounding area between January 2003 and June 2008. Isolates of methicillin-resistant S. aureus (MRSA) recovered in this time interval were characterized b...
(1) To identify newly diagnosed cases of methicillin-resistant Staphylococcus aureus ear infection in our local population; (2) to determine the risk factors involved in these patients' clinical courses, and (3) to type the bacterial strains isolated and thus identify whether they were hospital- or...
Multidrug-resistant Acinetobacter strain HK302 was isolated from an outbreak of nosocomial infections in Switzerland in 1977. The aim of the present study was to assess whether this archive strain belongs to one of the known international clonal lineages of Acinetobacter baumannii and whether it har...
In May 2010, a nationwide excess of infections with the specific monophasic variant Salmonella enterica serotype 4,12:i:- was investigated in France. Subtyping with multilocus variable number of tandem repeats analysis revealed a distinct epidemic strain within this excess. Epidemiological investiga...
Tuberculosis (TB) is one of the major public health problems in Zambia. However, information about lineages of M. tuberculosis complex (MTBC) isolates useful for epidemiology investigations is unknown. In this study, we investigated the diversity of MTBC isolates from Ndola, a typical Zambian urbani...
Clostridium difficile is an important healthcare-associated pathogen. Hypervirulent strains such as those belonging to ribotype 027 have been widely reported in recent years. A second strain associated with hypervirulence is ribotype 078 and the prevalence of Clostridium difficile infection (CDI) du...
The severe morbidity of human brucellosis is one of the main reasons for using molecular typing in the epidemiological surveillance of this worldwide zoonosis. Multiple-locus variable-number repeat analysis (MLVA-16), hypervariable octameric oligonucleotide fingerprinting (HOOF-print), and the diffe...
Vancomycin-resistant Enterococcus faecium (VRE) has become an important health care-associated pathogen because of its rapid spread, limited therapeutic options, and possible transfer of vancomycin resistance to more-virulent pathogens. In this study, we compared the ability to detect clonal relatio...
The spirochete Brachyspira hyodysenteriae is the causative agent of swine dysentery, a severe colonic infection of pigs that has a considerable economic impact in many swine-producing countries. In spite of its importance, knowledge about the global epidemiology and population structure of B. hyodys...
Recent evidence strongly suggests an association between the use of fluoroquinolones and Clostridium difficile infection (CDI). Resistance to fluoroquinolones has been described not only in the hypervirulent strain 027, but also in other important PCR ribotypes circulating in hospital settings. In a...
Molecular characterization of Escherichia coli with use of the random amplified polymorphic DNA (RAPD) assay allows the determination of clonal origin and geographic clustering. Presumed enterotoxigenic Escherichia coli (ETEC) from 213 adults with travelers' diarrhea acquired in Mexico during the su...
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Hepatitis E infections in humans are usually acquired in endemic countries in Asia or Africa. In Sweden 17 cases infected in Europe, between 1993 and 2009, were identified. All had clinical hepatitis E with unknown source of infection. Hepatitis E virus (HEV) was identified in faecal samples from 63...
Among 800 stool specimens from patients with diarrhea submitted by Primary Care Centers for routine analysis to the Hospital of León (NW Spain) Microbiology and Parasitology Service, 32 (4%) were tested positive for Aeromonas spp. Mixed infections with other enteric pathogens occurred in 12 patients...
We describe the long-term multilocus sequence typing (MLST) analysis of the population structure and dynamics of 454 Finnish human Campylobacter jejuni isolates, as well as 208 chicken isolates, collected during the mid-1990s to 2007. The sequence type clonal complexes (ST CC) ST-45 CC, ST-21 CC, an...
Recently, methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) have been increasingly isolated from veterinarians and companion animals. With a view to preventing the spread of MRSA and MRSP, we evaluated the occurrence and molecular cha...
From June 22 through June 25, 2009, four outbreaks of infection with the pandemic influenza A (H1N1) virus occurred in Singapore military camps. We report the efficacy of ring chemoprophylaxis (geographically targeted containment by means of prophylaxis) with oseltamivir to control outbreaks of 2009...
In New Caledonia, Wallis and Futuna, and French Polynesia, an active surveillance system was established to monitor pneumococcal serotype prevalence between 2000 and 2007. The most prevalent serotype was serotype 1, which belonged to the major clonal complex sequence type 306 (ST306) and was respons...
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Listeriosis occurs mainly in persons at extremes of age and with immunocompromising conditions. It is believed that most cases of listeriosis are acquired in the community. A cluster of listeriosis in hospitalized patients prompted the present investigation. We conducted a case series study of liste...
In this study, we identified critically ill patients with Acinetobacter baumannii bacteremia and examined perirectal surveillance cultures for the presence of genetically related A baumannii strains using pulsed-field gel electrophoresis to determine whether gut colonization preceded clinical infect...
To investigate the serotype distribution, antimicrobial resistance patterns and molecular epidemiology of Streptococcus pneumoniae (S. pneumoniae) isolated from invasive pneumococcal diseases in order to provide rationales for antibiotics application and immunity control of S. pneumoniae. A total of...
Previous studies regarding the prognosis of patients infected with MRSA isolates characterized by a high minimum inhibitory concentration (MIC) for vancomycin have generally used a commercial Etest. Little research has been conducted on determining the vancomycin susceptibility of MRSA using a refer...
Following the first ever case of bluetongue in Denmark during late 2007, further outbreaks were observed in Denmark during 2008, despite vaccination against bluetongue virus (BTV) serotype 8 (BTV-8) in the southern part of the country. In total, 15 separate outbreaks of infection were identified, mo...
Genetic attribution of bacterial genotypes has become a major tool in the investigation of the epidemiology of campylobacteriosis and has implicated retail chicken meat as the major source of human infection in several countries. To investigate the robustness of this approach to the provenance of th...
Ventilator-associated pneumonia (VAP) is an important nosocomial infection at neonatal intensive care units (NICU), frequently caused by Pseudomonas aeruginosa. A 6-month prospective study from January 2009 through June 2009 was performed to investigate the respective contribution of endogenous and...
On 5 August 2008, the National Centre of Microbiology in Madrid, Spain, notified an increase in Salmonella Kedougou isolations compared to 2007, with 21 cases including 19 children under one year of age. Active case finding and a matched case-control study were carried out to confirm this increase,...
We report on a successful eradication of methicillin-resistant S. aureus (MRSA) after an epidemic in 1992 in the geriatric ward of a tertiary-care hospital. After identification of MRSA in seven patients, all patients and staff members in the geriatric ward underwent screening. A multifaceted interv...
Among patients with cirrhosis, infections caused by Escherichia coli organisms that translocate from the gut are a frequent and severe complication. One hundred ten E. coli isolates from 110 cirrhotic patients with spontaneous bacterial peritonitis and/or spontaneous bacteremia were characterized fo...
The relatively high-level clonality of methicillin-resistant Staphylococcus aureus (MRSA) and its frequent high-level endemicity in nosocomial settings complicate the development of methods for rapid subtyping of MRSA strains that are capable of identifying person-to-person transmission in hospitals...
The prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBLEC) in Spain increased 8-fold from 2000 to 2006. ESBL type, clonal relationship, antimicrobial susceptibility, and clinical data about infections caused by ESBLEC are evaluated in a second nationwide study deve...
Following an outbreak of vanA-positive Enterococcus faecium in 2005 in Kyoto prefecture, regional surveillance of vancomycin-resistant enterococci (VRE) was initiated. This revealed vanA- or vanB-positive Enterococcus gallinarum in multiple facilities. Eighty-eight vanA-positive E. gallinarum faecal...
In 2007 there was an epidemic of cholera in Iraq with 4667 cases. The first case in Baghdad was diagnosed on 19 September 2007 and the last case on 13 December 2007. In all, 136 cases were reported (2.9% of the country total) in 6 of the 13 districts of Baghdad. The median age of the cases was 11 ye...
A commercial duck company that raises approximately two million Pekin ducks per year experienced an outbreak of Riemerella anatipestifer (RA) on nine farms over a 1-yr period. Owing to concerns that the bacteria was being spread from farm to farm, an investigation using serotyping and DNA fingerprin...
Our aim is to investigate if the clusters of postsurgical mycobacterial infections, reported between 2004 and 2008 in seven geographically distant states in Brazil, were caused by a single mycobacterial strain. Available information from 929 surgical patients was obtained from local health authoriti...
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Shigellosis is the third most common enteric bacterial infection in the United States. Although infection is typically self-limiting, empiric treatment is often prescribed. Because of increasing antimicrobial resistance to Shigella, empiric treatment options are decreasing. Identifying resistance pa...
BACKGROUND. The high transmissibility and widespread environmental contamination by Clostridium difficile suggests the possibility of airborne dissemination of spores. We measured airborne and environmental C. difficile adjacent to patients with symptomatic C. difficile infection (CDI). METHODS. We...
Neonatal infections may be caused by various microorganisms, but as far as we are aware, Acinetobacter ursingii has not yet been reported in connection with nosocomial infections of premature infants. During 2 months, 3 premature babies were treated with nosocomial infection caused by A. ursingii at...
Mobile genetic elements (MGEs) including plasmids and transposons are pivotal in the dissemination and persistence of antimicrobial resistance in Enterococcus faecalis and Enterococcus faecium. Enterococcal MGEs have also been shown to be able to transfer resistance determinants to more pathogenic b...
No abstract available
Highly virulent strains of Clostridium difficile have emerged since 2003, causing large outbreaks of severe, often fatal, colitis in North America and Europe. In 2008-10, virulent strains spread between continents, with the first reported cases of fluoroquinolone-resistant C difficile PCR ribotype 0...
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Resistance to carbapenems among Acinetobacter baumannii and Klebsiella pneumoniae presents a serious therapeutic and infection control challenge. We describe the epidemiology and genetic basis of carbapenem resistance in A. baumannii and K. pneumoniae in a six-hospital healthcare system in Northeast...
Genetic relationships among 81 strains of Y. enterocolitica biovar 1A isolated from clinical and non-clinical sources were discerned by multilocus enzyme electrophoresis (MLEE) and multilocus restriction typing (MLRT) using six loci each. Such studies may reveal associations between the genotypes of...
We investigated prevalence and risk factors for methicillin-resistant Staphylococcus aureus (MRSA) in a case-control study performed in a 900-bed tertiary governmental healthcare facility in Bangkok, Thailand. Multivariate unconditional logistic regression was used to identify risk profiles for MRSA...
Neisseria meningitidis is an invasive pathogen contributing significantly to childhood mortality worldwide. The organism is adapted to the human host and transmitted by close contact or droplet aerosols. In comparison to healthy carriage, invasive disease is a rare event. Nevertheless, due to a high...
Staphylococcus aureus, particularly methicillin-resistant S. aureus (MRSA), is an important cause of pyogenic skin and soft tissue infections (SSTIs). The aim of present study is to investigate the molecular characteristic of Staphylococcus aureus isolates isolated from the pus samples from the pati...
Two women in labor received intrapartum spinal anesthesia from the same anesthesiologist approximately 1 h apart. Within 15 h, both patients developed Streptococcus salivarius meningitis and one patient died. Blood and cerebrospinal fluid (CSF) samples from both patients and tongue swab specimens fr...
An outbreak due to a Klebsiella pneumoniae clone occurred in a neonatal intensive care unit of a Spanish Hospital in which three newborns were infected (all with gestational age ≤29 weeks; two of them died) and seven were colonized (gestational age >32 weeks; none died). One K. pneumoniae strain per...
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Recently, multiple-locus variable-number tandem-repeat analysis (MLVA) has been proposed as an alternative to pulsed-field gel electrophoresis (PFGE) for characterization of Escherichia coli O157:H7. In this study we characterized 118 E. coli O157:H7 isolates from cases of gastrointestinal disease i...
Venereal syphilis is a multi-stage, sexually transmitted disease caused by the spirochetal bacterium Treponema pallidum (Tp). Herein we describe a cohort of 57 patients (age 18-68 years) with secondary syphilis (SS) identified through a network of public sector primary health care providers in Cali,...
To develop an easy-to-use method for the rapid detection of antibiotic-resistant bacteria. Here, a new immunochromatographic assay specific for aminoglycoside 6'-N-acetyltransferase AAC(6')-Iae was designed. AAC(6')-Iae is a significant marker molecule for multidrug-resistant (MDR) Pseudomonas aerug...
Salmonella enterica subsp. enterica serovar 4,[5],12:i:- is a monophasic variant of S. enterica serovar Typhimurium (antigenic formula 4,[5],12:i:1,2). Worldwide, especially in several European countries and the United States, it has been reported among the 10 most frequently isolated serovars in pi...
To investigate the high prevalence of extended-spectrum beta-lactamase (ESBL)-producing strains of Escherichia coli (4%, 10/250 consecutive isolates) recovered during a 5 month period in the maternity ward of the University Hospital of Bordeaux, France. beta-Lactam resistance transfer was analysed b...
This article describes a community-based intervention to manage an outbreak of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) skin infections in a midwestern county jail. A systematic investigation conducted by a family medicine residency program identified 64 total cases...
Bats are hosts to a variety of viruses capable of zoonotic transmissions. Because of increased contact between bats, humans, and other animal species, the possibility exists for further cross-species transmissions and ensuing disease outbreaks. We describe here full and partial viral genomes identif...
Cephalosporins resistance is increasing in Escherichia coli in Spain. We characterize infections by E. coli with reduced susceptibility to third-generation cephalosporins (3GCs) with the AmpC phenotype. Between January 2004 and March 2007, 121 E. coli isolates with the AmpC phenotype were collected...
Clostridium difficile is a major cause of antibiotic-associated diarrhea and frequently results in healthcare-associated infections. The epidemiology of C. difficile infection (CDI), including the prevalent polymerase chain reaction (PCR) ribotypes and the clinical characteristics of the patients, i...
Multi-resistant Pseudomonas aeruginosa (MRPa) has been isolated from patients in a Western Australian teaching hospital with increasing frequency since first encountered in 2006. Between 2006 and 2008 the number of patients with MRPa increased from three to nine per annum, and their location shifted...
This study was conducted to determine the types of M. pneumoniae prevalent in adults presenting with community-acquired pneumonia during an epidemic period, and to scrutinize a variable region of the RepMP4 element for the detection of P1 variants. All 23 clinical specimens PCR-positive for M. pneum...
The transition between infection of the mammalian host and colonization of an arthropod vector is required for the ongoing transmission of a broad array of pathogens, from viruses to protozoa. Understanding how this transition is mediated provides opportunities to disrupt transmission through either...
To investigate the contribution of recent transmission in the epidemic of drug-resistant Mycobacterium tuberculosis (M.TB) and related factors from biomedical and social-demographic perspectives in the Eastern rural areas of China. Identified by proportion method of drug susceptibility test, 223 dru...
To identify the Beijing family strain of Mycobacterium tuberculosis (M. tuberculosis) in order to find out the distribution of the Beijing family strain in the south region of Xinjiang, and therefore to provide scientific basis for the prevention and treatment of tuberculosis and the study of molecu...
Staphylococcus aureus (SA) is an important cause of catheter-related bacteremia (CRB). The USA300 clone increasingly causes healthcare associated infections. We compared children with SA-CRB due to USA300 versus non-USA300 isolates and identified risk factors for complications. Children at Texas Chi...
In Singapore, after a major outbreak of dengue in 2005, another outbreak occurred in 2007. Laboratory-based surveillance detected a switch from dengue virus serotype 1 (DENV-1) to DENV-2. Phylogenetic analysis showed a clade replacement within DENV-2 cosmopolitan genotype, which accompanied the pred...
The aim of this study was to characterize invasive penicillin non-susceptible pneumococci (PNSP) isolated in Denmark from 2001 to 2005, describe the genetic changes in the penicillin-binding proteins (PBPs) and compare the isolates to the international recognized PNSP clones. All isolates were chara...
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A total of 66 Shigella sonnei isolates from 1999 to 2008 in Seoul was analyzed for their antimicrobial resistance, carriage of integron, and the patterns of Pulsed-field gel electrophoresis (PFGE). A high level of antimicrobial resistance to streptomycin (100%), trimethoprim/sulfamethoxazole (95%),...
Extended-spectrum beta-lactamases (ESBLs) are bacterial enzymes that confer resistance to advanced generation cephalosporins and can lead to therapeutic failures. There has been no analysis of factors associated with the risk of acquisition of ESBLs in neonates in an intensive care unit from norther...
In a survey of staphylococcal colonization, Staphylococcus aureus was detected in 7 of 67 infants (10%). Two of the infants (3%) carried methicillin-resistant S aureus (MRSA), revealing an unsuspected transmission of MRSA within the neonatal intensive care unit. Molecular surveillance of S aureus pr...
We previously reported an outbreak of listeriosis in Austria and Germany due to consumption of Quargel cheese. It comprised 14 cases (including five fatalities) infected by a serotype 1/2a Listeria monocytogenes (clone 1), with onset of illness from June 2009 to January 2010. A second strain of L. m...
During the 2000s, a new clonal group with resistances to ampicillin, streptomycin, sulfonamides, and tetracycline (ASSuT) emerged in Italy among strains of Salmonella enterica serovar Typhimurium and its monophasic variant, Salmonella enterica subspecies enterica serovar 4,[5],12:i:-. The PulseNet E...
The Liverpool epidemic strain (LES) of Pseudomonas aeruginosa is widespread among cystic fibrosis (CF) patients in the United Kingdom and has emerged recently in North America. In this study, we report the analysis of 24 "anomalous" CF isolates of P. aeruginosa that produced inconsistent results wit...
The aim of this study was to characterise invasive methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) strains from Italy and to investigate the presence of heteroresistant vancomycin-intermediate S. aureus (h-VISA). Eighty-two MSSA and 66 MRSA strains obt...
An outbreak of Legionnaires' disease affected 12 customers of a supermarket in a town in Catalonia, Spain, between August and November 2006. An epidemiological and environmental investigation was undertaken. Preliminary investigation showed that all patients had visited the same supermarket in this...
In 2005, pandemic Vibrio parahaemolyticus was reported to have been introduced in Europe: O3:K6 strains were isolated from clinical cases in France and Spain, and were found to be associated with consumption of contaminated seafood. On the contrary, pandemic strains were not isolated from seafood or...
In genetic analysis of bovine Staphylococcus aureus isolates that are recognized as an important pathogenic bacterium in bovine mastitis, multilocus sequence typing (MLST) showed strong correlation to the results of pulsed-field gel electrophoresis, coa PCR-restriction fragment length polymorphism (...
Knowledge of circulating Chlamydia trachomatis serovars can be beneficial for sexual network surveillance, monitoring treatment success, and associating specific clinical manifestations. Typically, C. trachomatis serovars are predicted by nucleotide sequencing of four variable domains within the omp...
Staphylococcus epidermidis is a significant pathogen in neonatal sepsis and other nosocomial infections. For further investigations of the colonisation patterns and invasive pathways, typing methods that are applicable on large populations of bacterial isolates are warranted. In the present study, a...
The aim of this study was to investigate both the genetic features of MRSA strains and the occurrence of virulence factors produced by Staphylococcus aureus strains isolated from Peking University People's Hospital in Beijing, China, between 2005 and 2009. A total of 179 S. aureus strains were isola...
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Dengue has been reportable in Cambodia since 1980. Virological surveillance began in 2000 and sentinel surveillance was established at six hospitals in 2001. Currently, national surveillance comprises passive and active data collection and reporting on hospitalized children aged 0-15 years. This rep...
To determine if members of the European clonal lineages are present amongst multiply antibiotic-resistant Acinetobacter baumannii isolates from Australia. To search for AbaR-type genomic antibiotic resistance islands and determine the genetic organization of any AbaR detected. Two groups of multiply...
No abstract available
The presence of Panton-Valentine leukocidin expressing Staphylococcus aureus colonization was investigated with a qualitative nucleic acid hybridization assay among 122 children and 19 staff in a child care center. Genotyping of 5 Panton-Valentine leukocidin-positive isolates by pulsed-field gel ele...
In 2000 to 2001, 2003 to 2004, and 2005 to 2006, three outbreaks of Salmonella enterica serovar Enteritidis were linked with the consumption of raw almonds. The S. Enteritidis strains from these outbreaks had rare phage types (PT), PT30 and PT9c. Clinical and environmental S. Enteritidis strains wer...
We conducted a cross-sectional study involving culture of cell phones of 288 health care providers (HCP) during a 6-month period. One hundred nine (43.6%) HCP carried infective organisms on their cell phones. It is recommended that cell phones be cleaned regularly.
An evaluation of the utility of rep PCR typing compared to the 15 loci discriminatory set of MIRU-VNTR was undertaken. Twenty-nine isolates of Mycobacterium tuberculosis from patients were examined. Genomic DNA was extracted from the isolates by standard method. The number of copies of tandem repeat...
To perform a molecular epidemiological investigation on the types of Leptospira interrogans isolates from leptospirosis patients and animal hosts in Jiangxi province, using a pulsed-field gel electrophoresis (PFGE). The extracted chromosomal DNA from leptospiral isolates were digested with restricti...
We estimated the prevalence of Campylobacter spp. in retail meat (n = 352 samples; 104 chicken, 106 pork, and 142 beef) collected in Campobasso, Italy, comparing two microbiological methods. All the isolates were characterized by biomolecular techniques for epidemiological purposes. Campylobacter is...
In Argentina, Escherichia coli O157:H7/NM (STEC O157) is the prevalent serotype associated with hemolytic uremic syndrome (HUS), which is endemic in the country with more than 400 cases per year. In order to estimate the prevalence and characteristics of STEC O157 in beef cattle at slaughter, a surv...
We report 2 cases of O3:K6 and O1:KUT Vibrio parahaemolyticus gastroenteritis associated with consumption of local mussels in Italy in 2008. Serotypic, antibiogram, toxigenic, and pulsed-field gel electrophoresis patterns of these strains were compared to those of other isolates collected from local...
Among the 53 serotypes of human adenoviruses (HAdVs), identified to date, only a limited number have been associated with human respiratory infections. The epidemiology of each of the serotypes differs depending on the location and/or time of surveillance. This study was performed to elucidate the e...
Cattle are recognized as an important source of foodborne Salmonella causing human illness, particularly for antimicrobial-resistant strains. The transmission dynamics of multidrug-resistant (MDR) Salmonella after the onset of a clinical outbreak in a dairy farm has been rarely monitored. The early...
In spring 2008, 15 Salmonella Panama laboratory-confirmed cases were reported within 2 weeks, twice the average annual number of reported cases of this infrequent serotype in The Netherlands. To identify the source responsible for this national outbreak, we carried out an epidemiological, microbiolo...
Tularemia is primarily caused by two subspecies of Francisella tularensis worldwide, ssp. tularensis (type A) and ssp. holarctica (type B), which were originally delineated by phenotypic differences. Application of molecular typing methods to investigate population structure of F. tularensis has con...
To determine the incidence rate of infections with North American pulsed-field types 7 and 8 (NAP7/NAP8) strains of Clostrodium difficile, ribotype 078, and toxinotype V strains, we examined data collected for the Canadian Nosocomial Infections Surveillance Program (CNISP) CDI surveillance project d...
Bacteria harboring CTX-M extended-spectrum beta-lactamases (ESBLs) have been identified worldwide, with most reports coming from regions outside North America. We have identified CTX-M enzymes in 31% of ESBL-positive Escherichia coli isolates from our hospital and more than half (53%) of the isolate...
Multidrug-resistant tuberculosis (MDR-TB) is a serious health problem in Eastern European countries, including Latvia. To investigate the proportion of tuberculosis, including MDR-TB cases, attributable to recent transmission and risk factors associated with clustering. Retrospective nested case-con...
One hundred forty-six fecal specimens collected between 2007 and 2008 from infants with acute gastroenteritis were screened for rotavirus by ELISA with VP6-specific antibody. One hundred twenty-three of the samples (84.2%) were confirmed to be positive for group A rotavirus (community-acquired, n =...
This study was designed to characterise 30 non-duplicate extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli clinical isolates from the community in the Chicago metropolitan area collected during 2008. The majority of isolates (n=28) were recovered from urine and 2 isolates were from...
While Mycobacterium africanum is an important cause of TB in several sites in West Africa, its distribution in other African countries is not well documented. In this study, conducted in Cape Town, 1175 isolates yielded 110 unique RFLP patterns; one of each of these 110 strains was tested for genomi...
A total of 412 methicillin-resistant Staphylococcus aureus (MRSA) strains isolated between October 2006 and June 2009, representing a mixed hospital- and community-associated patient population from Mumbai, India, were evaluated. MRSA was characterized by multiplex PCR amplification of the Panton-Va...
It has proven challenging to investigate the molecular epidemiology of Mycobacterium leprae, the causative agent of leprosy, due to difficulties with culturing of the organism and a lack of genetic heterogeneity between strains. Recently, a cost-effective panel of variable-number tandem-repeat (VNTR...
We describe 66 ciprofloxacin-nonsusceptible Streptococcus pyogenes isolates recovered from colonized and infected children. The ParC S79A substitution was frequent and associated with the emm6/sequence type 382 (emm6/ST382) lineage. The ParC D83G substitution was detected in two isolates (emm5/ST99...
Most viruses are maintained by complex processes of evolution that enable them to survive but also complicate efforts to achieve their control. In this paper, we study patterns of evolution in foot-and-mouth disease (FMD) serotype C virus isolates from Kenya, one of the few places in the world where...
One of the largest reported campylobacteriosis outbreaks in Canada occurred in June 2007 in British Columbia, associated with a mountain bike race that took place in muddy conditions. A retrospective cohort study was conducted and environmental samples were collected and tested. There were 537 racer...
The applicability of the repetitive-sequence-based PCR (rep-PCR)-based DiversiLab system was tested compared with the pulsed field gel electrophoresis (PFGE) to type a phenotypically similar subset of a large collection of multiresistant Pseudomonas aeruginosa strains isolated during a 17-month peri...
A(-)B(+)Clostridium difficile strains are prevalent in Korea. We performed pulsed-field gel electrophoresis (PFGE), polymerase chain reaction ribotyping, and toxinotyping in 82 A(-)B(+) clinical isolates in Korea. PFGE showed highest discriminatory capability among the 3 methods. By PFGE, persistenc...
Migratory waterfowls are the natural reservoir of influenza A viruses. However, interspecies transmission had occasionally caused outbreaks in various hosts including humans. To characterize the genetic origins of H5 avian influenza viruses isolated from migratory birds in South Korea, phylogenetic...
In 2006, monophasic, multidrug-resistant Salmonella enterica spp. enterica serovar 4,[5],12:i:- strains appeared as a novel serotype in Germany, associated with large diffuse outbreaks and increased need for hospitalisation. The emerging 4,[5],12:i:- strains isolated from patients in Germany belong...
A semiautomated, repetitive-sequence-based PCR (rep-PCR) instrument (DiversiLab system) was evaluated in comparison with pulsed-field gel electrophoresis (PFGE) to investigate an outbreak of Serratia marcescens infections in a neonatal intensive care unit (NICU). A selection of 36 epidemiologically...
International adoption from developing countries has become an increasing phenomenon in recent years. Given the high prevalence of multidrug-resistant (MDR) bacteria in these countries, the adopted children represent a group at risk for both carriage and infection with MDR bacteria. The dynamics of...
From April through June 2008, we identified 12 patients in the intensive care unit and 3 patients on other wards infected with methicillin-resistant Staphylococcus aureus that was also resistant to linezolid. We investigated the mechanism of resistance--point mutations in domain V of 23S ribosomal R...
To evaluate the epidemiology and molecular features of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) and methicillin-sensitive S. aureus (MSSA) from children with skin and soft tissue infections (SSTIs) in Beijing, China, prospective community-acquired S. aureus SSTIs su...
In recent years the rates of Clostridium difficile infection (CDI) have increased worldwide with several large outbreaks occurring within the UK. New guidance from the UK Department of Health describes measures to investigate periods of increased incidence (PII) of CDI which include informing staff,...
Despite the launch of the national plan for measles elimination, in Italy, immunization coverage remains suboptimal and outbreaks continue to occur. Two measles outbreaks, occurred in Lazio region during 2006-2007, were investigated to identify sources of infection, transmission routes, and assess o...
Vibrio cholerae O1 are classified into two biotypes, classical and El Tor, each encoding a biotype-specific cholera toxin. However, El Tor strains have recently emerged with a classical cholera-toxin genotype (El Tor variant). We characterized El Tor strains of V. cholerae O1 from travel-associated...
Enterococcus faecium has emerged as an important nosocomial pathogen worldwide, and this trend has been associated with the dissemination of a genetic lineage designated clonal cluster 17 (CC17). Enterococcal isolates were collected prospectively (2006 to 2008) from 32 hospitals in Colombia, Ecuador...
Helicobacter pullorum is a bacterial pathogen in humans. By using microaerobic culture techniques, H. pullorum was isolated from the feces of barrier-maintained mice and identified, on the basis of biochemical, restriction fragment length polymorphism, and 16S rRNA gene sequence analyses. This findi...
A total of 969 isolates of Campylobacter jejuni originating in the Preston, Lancashire postcode district over a 3-year period were characterized using multi-locus sequence typing. Recently developed statistical methods and a genetic model were used to investigate temporal, spatial, spatio-temporal a...
Staphylococcus aureus is an important human pathogen and is a growing public health concern. In this study, 130 S. aureus, 93 methicillin-resistant S. aureus (MRSA) and 37 methicillin-sensitive S. aureus (MSSA), clinical isolates recovered from Lebanon were typed by protein A gene (spa) sequencing a...
No abstract available
Methicillin-resistant S. aureus (MRSA) has been endemic in Hospital Universitari de Bellvitge, Barcelona, since 1990. During the 1990-95 period the Iberian clone (ST-247; SCCmec-I) was dominant. Isolates of clonal complex 5 (ST-125; SCCmec-IV) gradually replaced the Iberian clone from 1996 to 2003....
The local specificity of bacterial clones may be explained by long-term presence or recent importation/fast dissemination in an area. Mycobacterium tuberculosis spoligotype ST125, noticeably prevalent among Bulgaria-specific spoligotypes, has a characteristically 'abridged' profile and an uncertain...
Leptospira is the causative agent of leptospirosis. The O-antigen is the distal part of the lipopolysaccharide, which is a key component of outer membrane of Gram-negative bacteria and confers serological specificity. The epidemiology and clinical characteristics of leptospirosis are relative to the...
No abstract available
To establish the existence of concurrent infections by different dengue virus (DENV) serotypes in an outbreak in the Northwestern in Peru during 2008. 73 serum samples from patients with dengue were analyzed during an outbreak that occurred in Northwestern in Peru between May and June 2008. Molecula...
Forty isolates of V. cholorae O1, O139 and non-O1/non-O139 collected from outbreaks in Songkhla and Phuket Provinces of southern Thailand during 1999-2001 and sporadic cases from different regions of Thailand during 1993-2002 were characterized using pulsed field gel electrophoresis (PFGE). Digestio...
To establish the molecular characteristics of Mycobacterium tuberculosis and on factors influencing the recent transmission of drug resistant isolates in Shandong. Mycobacterium tuberculosis isolated from active pulmonary tuberculosis patients of 13 counties were genotyped by mycobacterial intersper...
To investigate the molecular epidemiological characteristics of Staphylococcus aureus associated with bloodstream infection in hospital. 47 Staphylococcus aureus strains isolated from bloodstream in PLA General Hospital were collected from January 2006 to December 2008. Susceptibility of the strains...
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We subtyped 117 Vibrio vulnificus isolates from 85 V. vulnificus sepsis patients and 32 environmental samples by performing automated ribotyping for the purpose of molecular epidemiological study. Although there was one indistinguishable ribotype among the four human isolates and one environmental i...
A total of 312 uropathogenic Escherichia coli strains were isolated from clinical specimens in 7 hospitals in Aichi Prefecture, Japan. Among them, 113 strains were resistant to quinolone, and 49 strains were resistant to fluoroquinolone. Phylogenetic group B2 was most prevalent in both susceptible s...
DNA fingerprinting data for 4,207 Mycobacterium tuberculosis isolates were combined with data from a computer program (Origins). Largest population groups were from England (n = 1,031) and India (n = 912), and most prevalent strains were the Euro-American (45%) and East African-Indian (34%) lineages...
The water-borne pathogen Legionella pneumophila serogroup 1 (Lp1) is the most commonly reported etiologic agent of legionellosis. To examine the genetic diversity, the long-term epidemiology, and the molecular evolution of Lp1 clinical isolates, we conducted sequence-based typing on a collection of...
The study aimed at determining the prevalence, risk factors, perinatal transmission, and serotypes of Group B Streptococcus (GBS) among pregnant women and their newborns in Beirut, Lebanon. This was a cross-sectional study of all pregnant women admitted from February to September 2006 to three major...
We compared antibiotic consumption between hospitals affected by a strain of Clostridium difficile designated as polymerase chain reaction-ribotype 027 (CD-027) and those unaffected during an outbreak in northern France. The mean consumption of several beta-lactams, amikacin, and fluoroquinolones wa...
Pseudomonas aeruginosa commonly colonizes the hospital environment. Between April 2006 and September 2008, we investigated an outbreak of P. aeruginosa infection occurring in a pediatric intensive care unit. We conducted epidemiologic and molecular investigations to identify the source of the outbre...
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The aim of this study was to investigate the molecular characteristics of isoniazid resistant Mycobacterium tuberculosis (MTB), as well as its contribution to the dissemination of multi-drug resistant TB (MDR-TB) in rural areas of eastern China. A population-based epidemiological study was conducted...
The objective of the study was to determine if a clonal complex (CC) of Staphylococcus aureus or certain virulence and adhesion factors were associated with infections of bones and prosthetic implants. One hundred and nineteen isolates were characterised using microarrays. There was no evidence for...
The human commensal yeast Candida glabrata is becoming increasingly important as an agent of nosocomial bloodstream infection. However, relatively little is known concerning the genetics and population structure of this species. We have analyzed 230 incident bloodstream isolates from previous and cu...
The spread of antibiotic-resistant bacteria has become a large problem in most countries including Kuwait. This antibiotic resistance is usually due to the production of extended-spectrum beta-lactamase (ESBL) enzymes such as SHV, TEM and CTX-M. This study reports the emergence and spread of an ESBL...
We collected 86 unrelated clinical Legionella pneumophila strains that were isolated in Japan during the period 1980-2008. Most (80.2%) belonged to serogroup 1, followed by serogroups 5, 3 and 2. Interestingly, the patients with L. pneumophila serogroup 1 had a significantly higher male-to-female ra...
We investigated the molecular epidemiology and carbapenem resistance mechanisms of 258 non-duplicate carbapenem-resistant clinical isolates of Pseudomonas aeruginosa collected from 2006 to 2007 at 28 hospitals in China. Up to 88% of the carbapenem-resistant isolates were multidrug-resistant. Pulsed-...
We isolated 326 Yersinia enterocolitica strains from 5,919 specimens from patients with diarrhea at outpatient clinics, livestock, poultry, wild animals, insect vectors, food, and the environment in the cities of Nantong and Xuzhou in Jiangsu Province, China, from 2004 to 2008. The results showed th...
In northern Europe, bluetongue (BT) caused by the BT virus (BTV), serotype 8, was first notified in August 2006 and numerous ruminant herds were affected in 2007 and 2008. However, the origin and the time and place of the original introduction have not yet been determined. Four retrospective epidemi...
The molecular epidemiology of multidrug-resistant Acinetobacter baumannii was investigated in two intensive care units of the V. Monaldi university hospital in Naples, Italy, from May 2006 to December 2007. Genotype analysis by pulsed-field gel electrophoresis (PFGE), trilocus sequence-based typing...
The strain diversity and the population structure of nosocomial Acinetobacter isolated from patients admitted to different hospitals in Florence, Italy, during a 3-year surveillance program, were investigated by amplified fragment length polymorphism (AFLP). The majority of isolates (84.5%) were ide...
The incidence of methicillin-resistant Staphylococcus aureus (MRSA) has been increasing yearly at Peking Union Medical College Hospital (PUMCH). In order to understand the molecular evolution of MRSA at PUMCH, a total of 466 nonduplicate S. aureus isolates, including 302 MRSA and 164 methicillin-sus...
Bluetongue (BT) is a viral disease of ruminants transmitted by Culicoides biting midges and has the ability to spread rapidly over large distances. In the summer of 2006, BTV serotype 8 (BTV-8) emerged for the first time in northern Europe, resulting in over 2000 infected farms by the end of the yea...
The objective of this study was to investigate the clinical characteristics of patients with dengue viral infection during the 2008 outbreak in Lahore in order to better understand the clinical pattern and severity of disease in Lahore. We analyzed the clinical characteristics of 110 patients infect...
Infection control personnel performing surveillance activities noticed a cluster of patients with isolates of carbapenem-resistant Pseudomonas aeruginosa (CRPA) in the surgical intensive care unit (SICU) of a German University Hospital. An outbreak investigation including a descriptive analysis, a c...
Consumption of inadequately pasteurized dairy products is the most common means of transmission of brucellosis. This report describes two foodborne outbreaks that occurred in families infected after consumption of fresh home-made cheese bought in different Argentine provinces. High resolution variab...
Due to non-existing or limited surveillance in Africa, little is known about the epidemiology of dengue illness in the continent. Serological and virological data obtained from returning European travellers is a key complement to this often flawed information. In the past years, dengue 3 virus has e...
Vancomycin-resistant enterococci (VRE) were isolated from 41 patients at a medical centre in southern Taiwan from 1999 to 2005. This accounted for 0.55% of 7449 patients with clinical colonisation or infection due to Enterococcus species. Nine (22%) patients had clinical infections caused by VRE. Tw...
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In winter 2007-2008, an outbreak of pediatric pneumonia caused by serotype 5 pneumococci was identified in a northeast London suburb. Variable number of tandem repeat analyses clustered these pneumococci from the other serotype 5 pneumococci in the United Kingdom, highlighting the importance of this...
Twenty-five MRSA ST398 isolates from cases of bovine clinical mastitis and two isolates from farm personnel collected from 17 dairy farms in Germany were investigated for genetic relatedness, antimicrobial resistance and virulence properties. Genomic relationships were determined by ApaI PFGE, spa t...
To determine whether the high proportion of antimicrobial resistance among hospital isolates of Pseudomonas aeruginosa in the Czech Republic is associated with the spread of multidrug-resistant clones, we investigated 108 bloodstream isolates collected prospectively in 2007. The isolates originated...
In New Zealand the number of campylobacteriosis notifications increased markedly between 2000 and 2007. Notably, this country's poultry supply is different than that of many developed countries as the fresh and frozen poultry available at retail are exclusively of domestic origin. To examine the pos...
We assessed the risk factors and molecular epidemiology of multidrug-resistant Acinetobacter baumannii (MDR-AB) in Hong Kong. The patients were treated in five hospitals in a healthcare region during 2005-2006. We performed genomic identification by amplified rRNA gene restriction analysis (ARDRA) a...
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This study was conducted to detect the genes encoding extended-spectrum beta-lactamases (ESBLs) and determine the epidemiological relatedness of 69 Escherichia coli and 33 Klebsiella pneumoniae isolates collected from a regional hospital in central Taiwan, mostly from inpatients (E. coli 87.0%; K. p...
The epidemiology of Staphylococcus aureus has changed radically since 1999, in particular, methicillin-resistant S. aureus (MRSA), originally restricted to hospital, has emerged as a significant pathogen in the community, and true community-acquired MRSA (CA-MRSA) infections have been reported in pa...
The aim of this study was to analyze trends in adult invasive pneumococcal disease (IPD) due to macrolide-resistant strains and to study the evolution of serotypes, genotypes, and macrolide-resistant determinants of strains collected in a prospective study between 1999 and 2007 in Barcelona, Spain....
A survey for the prevalence if Burkholderia pseudomallei in soil in Taiwan found that its incidence is comparable to that in other regions of the world where melioidosis is endemic. The presence of identical genetic patterns among the clinical and environmental isolates evaluated suggested a link be...
The epidemiology of human campylobacteriosis is complex but in recent years understanding of this disease has advanced considerably. Despite being a major public health concern in many countries, the presence of multiple hosts, genotypes and transmission pathways has made it difficult to identify an...
Outbreak cases of acute respiratory disease (ARD) associated with subspecies B2 human adenovirus 11a (HAdV-11a) infection were detected during 2005 in a military basic training camp in Singapore. The Singapore HAdV-11a strain is highly similar to other Asian strains of HAdV-11, including strain QS-D...
A five-year (2004-2008) study was conducted on patients with acute gastroenteritis from different cities of Maharashtra, western India to detect and characterize astrovirus infections. A total of 1340 fecal specimens were collected from sporadic cases that included 1240 children (<or=8 years) and 10...
This meeting focused on infections in humans and animals due to methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing bacteria and Clostridium difficile, and their corresponding treatments. MRSA is predominantly a human pathogen, and molecular typing h...
In Japan, infection with Yersinia enterocolitica of the pathogenic serobiogroup serotype O9 biotype 2 (O9/2) has rarely occurred, and familial outbreaks of Y. enterocolitica are also infrequently reported. We found a familial outbreak of Y. enterocolitica O9/2. Y. enterocolitica O9/2 was detected fr...
We describe the emergence and spread of Klebsiella pneumoniae carbapenemase 2 (KPC-2)-producing K. pneumoniae at a Greek University hospital. Isolates with a carbapenem minimum inhibitory concentration >1 microg/mL and a negative EDTA-imipenem disk synergy test result were submitted to boronic acid...
The major aim of this study was to establish the molecular epidemiology dynamics of Streptococcus pneumoniae serotype 6A in acute otitis media, before the introduction of the 7-valent pneumococcal conjugate vaccine. Acute otitis media in Jewish and Bedouin children <5 years old undergoing tympanocen...
We investigated the molecular epidemiology and OXA-type carbapenemase genes of 83 imipenem-resistant Acinetobacter spp. collected from 2 university hospitals (hospitals A and B) and a regional hospital (hospital C) during 2007 in Taiwan. Genotyping by pulsed-field gel electrophoresis identified 51 p...
C. difficile is a spore-forming anaerobic enteropathogen. This bacillus is responsible for virtually all cases of pseudomembranous colitis and for 15 to 25% of cases of antibiotic-associated diarrhoea. Clostridium difficile associated-infections (CDI) have a wide range of clinical features which var...
The wide geographic distribution of one clade of Mycobacterium tuberculosis, the Beijing genotype family, and its genetic homogeneity, suggests that strains belonging to this grouping might have a selective advantage over other M tuberculosis strains. This hypothesis was addressed by reviewing molec...
King George V (KGV) Hospital has the largest tuberculosis (TB) facility in KwaZulu-Natal (KZN), the province with the highest prevalence of TB-HIV (human immunodeficiency virus) co-infection in South Africa. During the study, KGV was the only provincial referral hospital for patients with drug-resis...
In the last few years, carbapenem-resistant Acinetobacter baumannii isolates (CR-AB) have been identified worldwide. The first description of OXA-23-producing A baumannii in Brazil was from the city of Curitiba in 2003. The aim of the present study was to evaluate the persistence and dissemination o...
To better understand the epidemiology of colonization of vancomycin-resistant enterococci (VRE), we performed an 8-year retrospective study of all hospitalized patients with recurrent VRE colonization after they were documented as being clear of VRE and compared the primary colonization isolates and...
Escherichia coli isolates from diseased pigs were examined for antimicrobial susceptibility to 12 antimicrobials and possession of virulence genes (VGs), and then grouped according to the phylogenetic background and genetic relatedness. Associations between antimicrobial resistance (AMR) and VGs and...
In view of the intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15 extended-spectrum beta-lactamase (ESBL) in human clinical settings it would be of great interest to explore its existence in animals to unravel a possible reservoir function and the origin and transmi...
A multiplex PCR is described which detects capsular types K1, K2, K5, K54 and K57, which are those most associated with invasive disease or pathogenicity, a further capsular type (K20), two putative virulence factors (rmpA and wcaG) and the 16S-23S internal transcribed spacer unit of Klebsiella pneu...
Phage typing has for decades been useful as a phenotypical, definitive method for epidemiological characterisation of Salmonella Typhimurium. The system recommended by the World Health Organization (WHO) Collaborative Centre for phage typing of Salmonella has, however, become rather complex, and the...
The accurate identification of a pathogen beyond the species level is critical in epidemiological studies and investigations of nosocomial outbreaks of infection. The clonal relatedness of 66 multidrug resistant (MDR) strains of extended spectrum beta-lactamase (ESBL) producing K. pneumoniae isolate...
In order to gain a deeper insight into the phylogenetic background and diversity of methicillin-resistant S. pseudintermedius (MRSP) of animal origin, genetic relationships and clonal distribution among 146 European MRSP were examined using different molecular and phenotypical typing approaches. MRS...
The endogenous or exogenous origin of Staphylococcus aureus, responsible for orthopaedic surgical-site infections (SSI), remains debated. We conducted a multicentre prospective cohort study to analyse the respective part of exogenous contamination and endogenous self-inoculation by S. aureus during...
Tuberculosis cases infected by the same Mycobacterium tuberculosis (MTB) strain are considered to be clustered and involved in a transmission chain. Large clusters are assumed to represent active transmission chains in a population. In the present study, we focused on the analysis of large clusters...
Achromobacter xylosoxidans is an emerging pathogen increasingly being isolated from respiratory samples of cystic fibrosis (CF) patients. Its role and clinical significance in lung pathogenesis have not yet been clarified. The aim of the present study was to genetically characterize A. xylosoxidans...
Members of the Mycobacterium avium complex (MAC) are ubiquitous bacteria that can be found in water, food, and other environmental samples and are considered opportunistic pathogens for numerous animal species, mainly birds and pigs, as well as for humans. We have recently demonstrated the usefulnes...
Escherichia coli is a major cause of bloodstream infections and death due to sepsis. It is the most frequent Gram-negative bacterial pathogen recovered from cultures of blood from both community-acquired and nosocomial cases. We set out to determine the relationships between E. coli virulence factor...
Multidrug-resistant (MDR) Escherichia coli causes extraintestinal infections in both humans and animals. This study aimed to determine whether MDR E. coli isolates cultured from extraintestinal infections in several animal species were clonal and crossed host-species boundaries, as suggested by init...
We define the epidemiology of predominant and sporadic methicillin-resistant Staphylococcus aureus (MRSA) strains in a central teaching and referral hospital in Kuala Lumpur, Malaysia. This is done on the basis of spa sequencing, multilocus sequence typing (MLST), staphylococcal cassette chromosome...
No abstract available
The Gram-negative anaerobe Dichelobacter nodosus is the primary etiologic agent of ovine footrot. Few studies of the genetic diversity and epidemiology of D. nodosus have been done, despite the economic cost and welfare implications of the disease. This study examined a large collection of Australia...
We investigated whether multilocus variable-number tandem-repeat analysis (MLVA) typing could identify different subtypes of Clostridium difficile ribotype 027 within the same feces specimen. Five of 39 specimens yielded at least one isolate with an MLVA profile different (more than five summed tand...
Since 2000, Escherichia coli producing CTX-M enzymes have emerged worldwide as important causes of community-onset urinary tract and bloodstream infections owing to extended-spectrum beta-lactamase (ESBL)-producing bacteria. Molecular epidemiological studies suggested that the sudden worldwide incre...
Infection with bluetongue virus serotype (BTV)-8 occurred in ruminants in 2006 in Central-Western Europe. The trans-placental passage of this virus has been demonstrated in naturally- and experimentally-infected cattle and in experimentally-infected sheep. Trans-placental transmission is potentially...
To study the prevalence, nature, involved genetic elements and epidemiology of metallo-beta-lactamase (MBL)-producing Pseudomonas aeruginosa and Pseudomonas putida isolated in a Spanish hospital between 2005 and 2008. Etests were used for susceptibility testing and screening for MBLs, confirmed thro...
Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe. In each country,...
Neisseria meningitidis serogroup W135 has been associated with global outbreaks since the 2000 Hajj. Considering that N. meningitidis serogroup W135 is the third most prevalent serogroup isolated in Brazil in the last 10 years, and the possibility that the Hajj-related N. meningitidis serogroup W135...
No detailed reports regarding extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are currently available from Indonesia, the fourth most populous country in the world. A survey was carried out to investigate the molecular epidemiology and genetic characteristics of clinical ESBL-pr...
The current gold standard for Mycobacterium tuberculosis complex (MTBC) genotyping is insertion sequence (IS) 6110 restriction fragment length polymorphism (RFLP) as it provides the highest discriminatory power of all available MTBC genotyping methods. However, RFLP is labour intensive and the inter...
Since the spread of H5N1 highly pathogenic avian influenza virus in 2005, many surveillance programmes have been initiated in poultry and wild birds worldwide. This study describes for the first time the detection of different subtypes of avian influenza viruses (AIV) in wild birds in the West Medit...
The prevalence of MRSA in patients with CF has risen in recent years. We adhere to a policy of segregation and barrier nursing to manage patients with MRSA, and we actively pursue eradication of MRSA. We have evaluated our experiences of MRSA infection in our large adult CF centre. A retrospective r...
Foodborne disease due to Staphylococcus aureus is a common and important disease worldwide. Molecular typing of S. aureus strains plays a crucial role in epidemiological studies examining the origin and performing surveillance of major infections. In this survey, we collected 913 food samples and de...
Analysis of 3555 HIV-seropositive specimens, collected in Cameroon from 2002 to 2006, led to the identification of four HIV-1 group N infections based on differential seroreactivity to HIV env-derived peptides and proteins and confirmation by nucleic acid amplification. Group N prevalence continues...
To establish a PFGE protocol using Cfr9I, neoschizomer of SmaI, for typing of Staphylococcus aureus isolates belonging to the emerging MRSA ST398 clone. Staphylococcus aureus ST398 and non-ST398 isolates were analysed using the PFGE conditions recommended by the HARMONY consensus protocol. Genomic D...
Community-associated methicillin-resistant Staphylococcus aureus (MRSA) including those encoding Panton-Valentine leucocidin (PVL) are often described as more susceptible to a range of antibiotics than their hospital-associated counterparts. Recent scattered reports of the emergence of multiresistan...
In Romania, Salmonella enterica serovar Typhimurium isolates are currently typed by antimicrobial resistance profiles and phage typing, as part of the national laboratory-based surveillance system of human enteric infections. The aim of the present study was to assess the added value of complementin...
Enter-net surveillance system has detected the re-emergence of Salmonella enterica subsp enterica serotype Napoli (S. Napoli) since 2002. Preliminary data show that food vehicle could not be the only one implicated in the transmission of this serotype. A nested case-control study has been conducted...
Comparative molecular-genetic typing of Brucella strains isolated in Mongolia from different animal species as well as from humans. Twenty-one strains of Brucella isolated from different hosts in 7 provinces of Mongolia were typed. Conventional phenotypic methods, genotyping by PCR with primers for...
To describe the epidemiological characteristics of Clostridium difficile infection (CDI) in the Netherlands. Descriptive. After the first outbreaks in 2005 of Clostridium difficile infection (CDI) due to the hypervirulent PCR ribotype 027, a national reference laboratory was started in the Leiden Un...
To investigate whether or not Neisseria meningitidis was present in the throat of Kuwaiti pilgrims after returning from the Hajj. Throat swabs were taken from 177 participants 1 week after returning from the Hajj. The participants were asked about: associated medical conditions, meningococcal vaccin...
To compare the molecular relationships and antibiograms of nosocomial isolates of Pseudomonas aeruginosa obtained from three different genres of hospitals located in Southern India, two located at Hyderabad (one private hospital and an ophthalmic hospital) and one in Puducherry (tertiary care teachi...
A point prevalence study was carried out in a teaching hospital in Assam to characterise S. aureus strains, establish the rate of colonisation of methicillin resistant S. aureus (MRSA) and associated risk factors for its acquisition. Antibiogram-Resistogram profile was done by BSAC standardized disc...
Genotyping of Hib strains isolated in regions of Russia as well as characterization of genetic relations of typed strains with strains isolated in other areas. Genetic characterization of 31 strains of Hib isolated in Russian regions during 2005-2008 was performed by multilocus sequence typing. Stud...
Over a 6-month period in 2008, approximately 15% of all Staphylococcus aureus isolates from our neonatal intensive care unit were resistant to penicillin, gentamicin, erythromycin and clindamycin. Extended antibiotic susceptibility testing and molecular profiling revealed an outbreak of an S. aureus...
C. difficile is recognised as the main cause for colitis in hospitalised patients which are treated with antibiotics, chemotherapics or other drugs that disturb intestinal microbiota. Thus, a rapid and correct diagnostic of Clostridium difficile infections is essential for preventing nosocomial infe...
Effective diagnosis of infectious pathogens is essential for disease identification and subsequent adequate treatment, to prevent drug resistance and to adopt suitable public health interventions for the prevention and control of epidemic outbreaks. Particular situations under which medical diagnost...
Methicillin-Resistant Staphylococcus aureus (MRSA) is one of the most common and important causes of nosocomial infections. Rapid detection of this pathogen is important for conducting good and swift infection control. This prospective study evaluates two chromogenic media for the detection of MRSA....
Staphylococcus aureus is one of the most devastating human pathogen. The organism has a differential ability to spread and cause outbreak of infections. Characterization of these strains is important to control the spread of infection in the hospitals as well as in the community. To identify the cur...
To assess the epidemiologic characteristics of invasive pneumococcal diseases (IPD) among a population in a pediatric hospital in Mexico City and analyze mortality-related risk factors, serotype distribution and antibiotic susceptibility related to S.pneumoniae. We performed a retrospective review o...
No abstract available
Transient bacteremia occurs in healthy populations from toothbrushing. With the high incidence of bacteremia in the intensive care unit and toothbrushing as an oral care method, this study examined the incidence and clinical significance of transient bacteremia from toothbrushing in mechanically ven...
No abstract available
No abstract available
Community-associated methicillin-resistant Staphylococcus aureus strains (CA-MRSA) have emerged as the causative agent of health care-associated infections. An observational and prospective study was carried out in 5 hospitals in Bogotá, Colombia; severe MRSA infections were identified, and their or...
Nonserotypeable pneumococci (NSP) are commonly carried by Australian Indigenous children in remote communities. The purpose of this study was to characterize carriage isolates of NSP from Indigenous children vaccinated with the seven-valent pneumococcal conjugate vaccine (PCV7) and to use these data...
The hospital epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) has changed in the past few years due to the encroachment of community-associated MRSA (CA-MRSA) strains into health care settings. MRSA strains that were isolated during a 2-year period from patients of the Luzerner Kan...
In response to epidemic levels of serogroup B meningococcal disease in Cuba during the 1980s, the VA-MENGOC-BC vaccine was developed and introduced into the National Infant Immunization Program in 1991. Since then the incidence of meningococcal disease in Cuba has returned to the low levels recorded...
To date, little has been reported on the susceptibility patterns and molecular characterisation of multidrug-resistant Acinetobacter baumannii (MDRAB) clinical isolates from different Chinese military hospitals. In this study, 49 MDRAB strains were collected from three military hospitals during 2007...
Between 1998 and 2000, 95.6% of methicillin-resistant Staphylococcus aureus (MRSA) bacteraemias in the UK were due to two epidemic strains, namely EMRSA-15 or EMRSA-16 (60.2% and 35.4%, respectively). We sought to determine the proportions of these strains before and after the general decline in MRS...
The objective of this study was to characterize extended-spectrum cephalosporinase (ESC)-producing isolates of Salmonella enterica serovar Choleraesuis recovered from patients in Thailand and Denmark. Twenty-four blood culture isolates from 22 patients were included in the study, of which 23 isolate...
Two tributyrin hydrolysis-negative Moraxella isolates obtained in cases of keratoconjunctivitis in Camelus dromedarius in the Canary Islands showed highest degrees of 16S rRNA gene sequence similarity to Moraxella canis. A level of DNA relatedness to the M. canis type strain of 79% confirmed the ide...
The use of IS6110 as a marker for molecular epidemiological studies is limited when a Mycobacterium tuberculosis isolate has five or fewer copies of IS6110. Restriction fragment length polymorphism analysis with a highly polymorphic GC-rich repetitive sequence located in the plasmid pTBN12 (PGRS RFL...
In September 2007, the Tennessee Department of Health was notified of a cluster of late-onset group B streptococcal (GBS) infections in a neonatal intensive care unit (NICU). Outbreaks of late-onset GBS are rare. A case was defined as culture-confirmed invasive GBS infection in a neonate aged > or =...
To overcome some of the deficiencies with current molecular typing schema for Campylobacter spp., we developed a prototype PCR binary typing (P-BIT) approach. We investigated the distribution of 68 gene targets in 58 Campylobacter jejuni strains, one Campylobacter lari strain, and two Campylobacter...
Tuberculosis (TB) remains an immense public health problem in the Republic of Korea despite a more than fivefold decrease in the prevalence of the disease over the last 3 decades. The rise in drug-resistant TB has compounded the situation. We analyzed 208 clinical isolates of M. tuberculosis from th...
Utah had a high rate of pediatric pneumococcal empyema (PPE) prior to licensure of the pneumococcal conjugate vaccine (PCV-7) in 2000. The majority (62%) of PPE cases was due to nonvaccine serotypes, primarily Streptococcus pneumoniae serotype 1, multilocus sequence type (MLST) 227. PPE in Utah chil...
Circulation of methicillin-resistant Staphylococcus aureus (MRSA) outside hospitals could alter the impact of hospital-based control strategies. We investigated two groups of cases (each matched to controls with MRSA): 61 'community cases' not in acute hospital in the year before MRSA isolation; and...
This paper describes the clonal diversity of vancomycin-resistant Enterococcus faecium isolated from patients with haematological malignancies in Russia. Pulsed-field gel electrophoresis (PFGE) typing of 129 vanA-positive E. faecium strains revealed 23 independent restriction profiles with two predo...
A 4-year bacteriological survey (2003-2007) of four molluscs cultivated in France and faced with mortality episodes was performed by the French shellfish pathology network. The more abundant bacteria isolated during 92 mortality episodes, occurring mainly in Pacific oyster Crassostrea gigas, were id...
Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for molecular epidemiological study. Repetitive extragenic palindromic PCR (rep-PCR) is less time-consuming and more suitable for analyzing large numbers of bacterial strains in human populations. PFGE and rep-PCR provide comp...
We report a skin and soft-tissue infection outbreak among football team members due to a USA300 methicillin-susceptible Staphylococcus aureus (MRSA) strain with genes coding for Panton-Valentine leukocidin and the arginine catabolic mobile element. We postulate that the strain is a community-associa...
There are few data about the epidemiology of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) among children in Israel. This study was intended to identify risk factors for CA-MRSA colonization in healthy infants, to characterize the molecular features of colonizing organis...
We have investigated the molecular epidemiology and distribution of carbapenemase genes in 492 imipenem-non-susceptible Acinetobacter baumannii worldwide isolates (North and Latin America, Europe, Asia, South Africa and Australia). MICs were determined by broth microdilution and Etest. The presence...
Coagulase-negative staphylococci (CNS) are increasingly recognized to cause clinically significant infections, with S. epidermidis often cited as the third most common cause of nosocomial sepsis. Among CNS, there is a high prevalence of methicillin resistance associated with staphylococcal cassette...
The presence of broad-spectrum-cephalosporin-resistant Escherichia coli isolates and the implicated mechanisms of resistance were investigated in 79 food samples of animal origin obtained in different supermarkets and local butcheries in Tunisia. Ten of these samples (12.6%) harbored extended-spectr...
The objective of this study was to investigate the occurrence of vancomycin-resistant Enterococcus (VRE) cross-transmission between two patient groups (long-term dialysis and kidney transplant patients). Molecular typing, by automated ribotyping with the RiboPrinter Microbial Characterization System...
Legionella pneumophila (Lp) is a significant cause of nosocomial, community-acquired, and travel-associated pneumonia in industrialized regions. Legionellosis has been a nationally notifiable disease in Canada since 1986, with an average of 75 cases reported annually; however, only the most severe,...
This study calculates the financial consequences of the bluetongue serotype 8 (BTV8) epidemics of 2006 and 2007 in the Netherlands. We constructed a deterministic economic model that is compatible with the Dutch livestock production systems for cattle, sheep and goats. Two hundred cattle farms and 2...
In this study, the biodiversity of Coagulase-Negative Staphylococci (CNS) strains isolated in France from cheese related samples (227 isolates) and dry sausage related samples (204 isolates) was compared to the biodiversity of 297 clinical isolates. Species identification was performed using differe...
Shigella spp. are the causative agent of shigellosis with Shigella flexneri serotype 2a being the most prevalent in developing countries. Epidemiological surveillance in China found that a new serotype of S. flexneri appeared in 2001 and replaced serotype 2a in 2003 as the most prevalent serotype in...
Numbers of Clostridium difficile infections have increased worldwide in the past decade. While infection with C. difficile remains predominantly a health care-associated infection, there may also be an increased incidence of community-associated infections. C. difficile strains of public health sign...
Six patients with Acinetobacter genomic species 10 bacteremia were identified. The clinical features of the patients, phenotypic and genotypic identifications, antimicrobial susceptibilities, and genes flanking ISAba1 of the bacteria were described. The results revealed that this bacterium is a pote...
An increase in the incidence of clinical cases of Clostridium difficile infection has been reported in recent years, but few studies have examined changes in molecular epidemiology and antibiotic resistance over a long period of time. A collection of 179 isolates of C. difficile obtained from sympto...
Determinants of bacterial colonization in children have been described. In the Generation R Study, a population-based cohort study, we determined whether the colonization statuses of mothers and children are correlated. Such a correlation was observed for Staphylococcus aureus and Haemophilus influe...
A total of 565 methicillin-resistant Staphylococcus aureus (MRSA) isolates were collected mostly from Europe and the Americas (2004 to 2007) during a phase IV clinical trial comparing linezolid with vancomycin for the treatment of complicated skin and skin structure infections proven to be due to MR...
Although tuberculosis is still a public health problem in Mexico, there is little information about the genetic characteristics of the isolates. In the present study, we analyzed by spoligotyping 180 Mycobacterium tuberculosis clinical isolates from the urban area of Monterrey, Mexico, including dru...
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An exploratory study of methicillin-resistant Staphylococcus aureus (MRSA) and SCCmec elements in bacteria along the Mexican border of south Texas was performed. Between September and December of 2008, 375 swabs of anterior nares were self-collected by students attending the University of Texas-Pan...
A policy of weekly faecal cultures for vancomycin-resistant enterococci (VRE) was instituted following the investigation of an outbreak of VRE in our neonatal intensive care unit in 2005. We found that 11 of 18 patients were infected or colonised during the outbreak, including three cases of bloodst...
Ciprofloxacin-resistant Escherichia coli is growing concern in clinical settings. In this study, we investigated the distribution of virulence determinants and phylogenetic groups among community-onset, ciprofloxacin-resistant E. coli isolates causing urinary tract infections (UTIs) in Korea. In add...
A 29-year-old pregnant woman was admitted to hospital with signs of sepsis and threatened pre-term labour. The premature neonate also showed signs of sepsis. Haemophilus influenzae biotype III was cultured from a midstream urine sample taken from the mother, maternal placental swabs and neonatal blo...
The levels of meticillin-resistant Staphylococcus aureus (MRSA) in Pakistan and India are known to be high, but few studies have described the epidemiology of the different MRSA clones present. In order to gain an understanding of the epidemiology of MRSA within this region, 60 MRSA isolates from Pa...
In September 2006, the seven-valent pneumococcal conjugate vaccine (PCV7; Prevenar) was introduced into the childhood vaccination schedule in the United Kingdom. We monitored the population of invasive pneumococci in Scotland in the 5 years preceding the introduction of PCV7 by using serogrouping, m...
A PCR-based typing scheme was applied to identify plasmids in an epidemiologically and geographically diverse strain collection of Enterococcus faecium (n=93). Replicon types of pRE25 (n=56), pRUM (n=41), pIP501 (n=17) and pHTbeta (n=14) were observed in 83% of the strains, while pS86, pCF10, pAM373...
The aim of this study was to identify methicillin-resistant Staphylococcus aureus (MRSA) strains gathered from 2002 to 2006 from milk samples in Aydin region in Turkey. Among 93 S. aureus strains isolated from bovine milk with mastitis, 16 were resistant to methicillin. Methicillin-resistant S. aure...
Malta has one of the highest prevalence rates of methicillin-resistant Staphylococcus aureus (MRSA) in Europe. However, only limited typing data are currently available. In order to address this situation, 45 MRSA isolates from the Mater Dei Hospital in Msida, Malta, were characterised using DNA mic...
Spoligotyping and variable-number tandem repeats (VNTR) typing have been increasingly used for differentiating Mycobacterium tuberculosis strains with low copy numbers of IS6110. However, there are few studies comparing their potential to type the strains originating from South and Southeast Asia wh...
Seven Proteus mirabilis strains from five Polish patients (five isolates from urea and two from feces) appeared to be a bacterial clone widespread in hospitals, most probably due to nosocomial infection and autoinfection. Enzyme-linked immunosorbent assay and Western blot showed that lipopolysacchar...
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an increasing problem, predominantly in previously healthy individuals including notable risk groups such as the homeless, those who play close-contact sports, military personnel, men who have sex with men (MSM) and inject...
Between June 1, 2004, and March 14, 2005, 16 patients in the surgical/medical intensive care unit (ICU) were infected and another 2 were colonized with multidrug-resistant (MDR) Acinetobacter baumannii. We describe the systematic investigation initiated to discover an environmental reservoir and a n...
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Classical swine fever (CSF), a highly contagious viral disease of pigs, is endemic in India. As there is no information concerning the accurate genetic typing of classical swine fever virus (CSFV) isolates in India, 16 CSF viruses isolated during 2005-2007 from domestic pigs in different districts o...
Pseudomonas (P.) aeruginosa strains isolated from the sputum of cystic fibrosis patients (CFP) are frequently difficult to type by conventional typing methods. The purpose of this study was to develop a random amplified polymorphic DNA (RAPD) analysis for the routine typing of these strains. Sixty P...
Burkholderia cenocepacia can cause serious infections and epidemics in patients with cystic fibrosis (CF). A CF population in the Czech Republic experienced an epidemic outbreak caused by a B. cenocepacia ST-32 strain. The clonality of the isolates was evident by multilocus sequence typing; however,...
We reviewed pneumococcal serotype 3 cases reported from 2000 through 2005 to a laboratory-based surveillance system for invasive pneumococcal disease in South Africa. The prevalence of serotype 3 invasive isolates was compared to their prevalence in carriage isolates to determine the odds of invasiv...
Phenotypic and genotypic characterization of 96 clinical isolates of Pseudomonas aeruginosa recovered in a Tunisian teaching hospital during a 16-month period. All the isolates were characterized by serotyping, antimicrobial susceptibility typing and genotyping with randomly amplified polymorphic DN...
Between 1st January and 31st December 2007, 331 Streptococcus pneumoniae strains were collected from 20 participating laboratories in the Pneumococcus Network Pays de la Loire county to assess their susceptibility to antibiotics and to evaluate serogroups of strains. The coordinating centre performe...
Scandinavia is considered a region with a low prevalence of antimicrobial resistance. However, the number of multidrug-resistant (MDR) Gram-negative bacteria is increasing, including metallo-beta-lactamase (MBL)-producing Pseudomonas aeruginosa. In this study MBL-producing P. aeruginosa isolates ide...
Staphylococcus aureus, especially when it is methicillin resistant, has been recognised as a major cause of nosocomial and community-acquired infections. It has also been shown that certain strains were able to cause clonal epidemics whereas others showed a more incidental occurrence. On the basis o...
The objective of this study was to determine the association between mycoplasma mastitis and colonization of mycoplasma organisms at body sites of asymptomatic carriers. The investigation was done in a dairy herd with a first outbreak of mycoplasma mastitis. Milk and swab solution specimens from acc...
Glycopeptides and linezolid are the most widely used antibiotics to treat infections by methicillin-resistant Staphylococcus spp. We report the presence of various isolates of methicillin-resistant S. hominis subsp. hominis with resistance to linezolid and reduced susceptibility to glycopeptides. We...
Pneumococci of serotype 19A are increasingly found to be the cause of infection in various geographic regions. We have characterized the serotype 19A isolates (n = 288) found among pneumococci responsible for infections (n = 1,925) and pneumococci recovered from asymptomatic carriers (n = 1,973) in...
TARGET OF THE STUDY: Strain typing of pathogens is essential to pinpoint the sources and routes of transmission and to forecast future trends. In a general hospital, we studied possible changes in the MRSA population. MRSA isolates received from a Belgian general hospital, during 2002 (n=150) and th...
This study uses multilocus sequence typing (MLST) to investigate the epidemiology of Campylobacter coli in a continuous study of a population in Northwest England. All cases of Campylobacter identified in four Local Authorities (government administrative boundaries) between 2003 and 2006 were identi...
Geographically related Staphylococcus epidermidis isolates from human patients (n=30), dairy farms (farmers and individual raw milk from cattle, n=36) and a dairy plant (n=55) were examined for epidemiological relatedness by pulsed-field gel electrophoresis and, using in vitro methods, for the abili...
In addition to its known status as a disseminated disease in HIV-positive patients, Mycobacterium avium complex (MAC) is increasingly recognized as a causative pathogen of respiratory disease in HIV-negative patients. MAC is divided into Mycobacterium avium, and the less-epidemiologically studied My...
Although serotype O157:H7 has been implicated in most cases of haemolytic-uraemic syndrome (HUS), there is growing concern about non-O157 serotypes of verocytotoxigenic Escherichia coli (VTEC). Multiple-locus variable-number tandem repeat analysis (MLVA) has been focused on the specific typing of O1...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infections worldwide. To differentiate reliably among S. aureus isolates, we recently developed double locus sequence typing (DLST) based on the analysis of partial sequences of clfB and spa genes. In the present study...
We used DNA fingerprinting to analyse tuberculosis (TB) epidemiology in immigrant patients living in two major northern Italian urban areas. The study population included 1999 TB patients (1500 Italian-born and 499 immigrants). Univariate and multivariate logistic regression models were used to iden...
In this retrospective study, the occurrence and genetic relatedness of methicillin-resistant Staphylococcus aureus (MRSA) ST398 in Austrian MRSA patients was investigated. From 2002 to 2008, 14 MRSA ST398 were detected. First occurrence of MRSA ST398 was already found in 2004. Spa ribotyping assigne...
To screen for the globally spread cluster of Enterococcus faecium, clonal complex 17 (CC17) and characterize the genetic profile of Swedish clinical Ent. faecium isolates. A total of 203 consecutive isolates collected from 2004 to 2007 from patients with bacteraemia in Sweden. All isolates were geno...
Canadian cases and outbreaks of illness caused by Listeria monocytogenes between 1995 and 2004 were assessed. Isolates (722 total) were characterized by serotyping, and pulsed-field gel electrophoresis (PFGE) was performed to provide a means of detecting case clusters. Rates of listeriosis remained...
The microbiologic investigations of an outbreak implicating 17 inmates demonstrated the spread of a pneumococcal serotype 1 clone not only in this jail but also in the area of Tunis. This clone, which is fully susceptible to antibiotics but not included in the heptavalent conjugate vaccine, should b...
Previous outbreaks of Pontiac fever have invariably been associated with water droplet spread of Legionella spp. In January 2007 three workers from a horticultural nursery were admitted to hospital with non-pneumonic legionellosis. Investigations showed that a working party of ten people had been ex...
During a national outbreak of carbapenem-resistant Klebsiella pneumoniae (CRKP) in Israel, we conducted a point prevalence survey to determine the extent of asymptomatic carriage. Subsequently, a retrospective case-control study was done, comparing carriers of CRKP with non-carriers, in order to det...
Methicillin-resistant Staphylococcus aureus (MRSA) from Malaysia were shown to possess staphylococcal cassette chromosome mec (SCCmec)-III and IIIA. Spa sequencing and multi-locus sequence typing (MLST) documented t037 and ST 239 (CC8) for 83.3% of the isolates. This confirms observations in several...
Levofloxacin susceptibility testing was carried out for a total of 2539 Streptococcus pneumoniae isolates obtained from January 2001 to February 2008 at the National Taiwan University Hospital (NTUH) and a further 228 pneumococcal isolates obtained from January 2004 to December 2006 at three other h...
During a period of 6 years and 5 months (January 1999 to May 2005), 103 extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae isolates, each from an individual patient or site, were collected at Mongi Slim University Hospital Centre, Tunis, Tunisia. The objectives of our work were...
From May 2007 to January 2008, 30 isolates of vancomycin-resistant enterococci (VRE), including 29 Enterococcus faecium (96.7%) and 1 E. faecalis (3.3%) were obtained from various clinical specimens of 30 patients treated at a university hospital in Taiwan. Among these patients, 27 had VRE infection...
This study investigated the MICs of 17 antimicrobials, for 606 toxigenic clinical isolates of Clostridium difficile collected between 1993 and 2007 in Sweden. Low MIC(90) values were found for metronidazole (0.5 mg/L), vancomycin (1.0 mg/L), teicoplanin (0.125 mg/L), fusidic acid (1.0 mg/L), linezol...
The aim of the present study was to investigate the antibiotic susceptibility patterns and molecular epidemiology of clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered in 24 hospitals in 20 cities in Croatia from October to December 2004. A total of 1815 consecutive S. au...
An increasing number of neonates require intensive care, and this population has a high risk of developing infections. The Enterobacteriaceae most commonly related to healthcare-associated infection in neonatal intensive care units (NICU) are Escherichia coli, Klebsiella spp and Enterobacter cloacae...
Fifty-seven nosocomial Klebsiella pneumoniae isolates producing extended-spectrum beta-lactamases (ESBLs) were collected between February 2007 and November 2007 in different wards of the Sarajevo (Bosnia-Herzegovina) reference hospital. These isolates comprise two major epidemic pulsed-field electro...
Campylobacter jejuni isolates from a national Swedish Campylobacter monitoring in broilers were characterized by multilocus sequencing typing (MLST) in order to study the genetic diversity of this bacterial population. Isolates were initially characterized by pulsed-field gel electrophoresis (PFGE)....
During a 2-year period (2003-2004), tuberculosis (TB) transmission in Barcelona and the factors related to transmission among the Spanish- and foreign-born populations were studied by molecular epidemiology. Data were obtained from TB cases and Conventional Contact Tracing registries and genotyping...
A prospective study was conducted during an 8-month period, from August 2006 to April 2007, to describe the epidemiology of Staphylococcus aureus-associated infections. In addition, the molecular characteristics, antimicrobial susceptibilities and antibiotic resistance determinants were identified i...
Forty infection-associated VanA-type vancomycin-resistant Enterococcus faecium (VRE) strains obtained from five collaborating hospitals in Asunción, Paraguay were investigated. Genotyping using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing revealed the presence of 17 cluster...
Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) expressing Panton-Valentine leukocidin (PVL) have been characterized worldwide, but it has not been done in Egypt. In this study, we analyzed the molecular characteristics of PVL+CA-MRSA in Egypt, compared their genetic pattern...
An epidemiological investigation with Legionella and molecular subtyping was conducted to determine the source of a case of nosocomial Legionnaires' disease (LD) who was hospitalized in three hospitals within a month. Legionella pneumophila serogroup 3, an uncommon serogroup for infection, was isola...
Cholera diarrhea is still a major health challenge for a large part of globe. Global replacement of Vibrio cholerae classical biotype by El Tor biotype, emergence of O139 serogroup and rapid spread of antibiotic resistant strains indicate the continuous evolution in V. cholerae. In this study, 114 V...
Clinical isolates of Escherichia coli with reduced susceptibility to oxyimino-cephalosporins and not susceptible to clavulanic acid synergy (n = 402), collected from Norwegian diagnostic laboratories in 2003-2007, were examined for the presence of plasmid-mediated AmpC beta-lactamases (PABLs). Antim...
Four cases of Streptococcus pyogenes infection due to an emm-type 11 strain, including one with a fatal outcome, occurred within a seven-member family. All strains shared biotype 5, pyrogenic exotoxin genes speB and speC, and resistance to kanamycin, tetracycline, macrolides and lincosamides. The id...
Necrotizing fasciitis due to methicillin-resistant Staphylococcus aureus (MRSA) is an uncommon but life-threatening infection, and has mainly been reported as occurring in adults and the elderly. Recently, infant cases involving Panton-Valentine leukocidin (PVL)-positive community-acquired MRSA have...
Recent genetic studies have revealed that several epidemiological factors affect Mycobacterium avium complex (MAC) infection in pig populations. However, mechanisms underlying the spread of MAC infection among hog farms have not been clarified. In consideration of this situation, we cross-sectionall...
Malaria, a vector-borne disease, is caused by Plasmodium species and transmitted by Anopheles species. Among these vectors, Anopheles subpictus has emerged as a potent malarial vector in coastal areas of India. Numerous studies have highlighted that bacterial communities within mosquito influence ve...
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The genomic surveillance of foodborne pathogens in the United States has grown exponentially in the past decade, grounded in a powerful combination of novel sequencing technologies, bioinformatic approaches, data-sharing networks, and metadata harmonization efforts. This practice report examines rec...
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