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: 10,603 papers.
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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)...
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...
: 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
, 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
(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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
() 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
(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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
, 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...
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...
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...
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....
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...
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...
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...
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...
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...
: 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...
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....
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...
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...
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...
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...
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...
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...
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
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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-...
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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-...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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),...
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...
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...
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...
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...
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...
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.
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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-...
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-...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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-...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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),...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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,...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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,...
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 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...
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...
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...
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...
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...
, 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...
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...
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...
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...
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,...
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...
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,...
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...
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 (...
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...
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,...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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,...
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...
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...
No abstract available
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
: 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)...
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...
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...
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...
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...
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...
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...
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...
(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...
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...
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...
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...
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,...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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,...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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....
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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,...
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...
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...
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...
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...
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...
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...
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...
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...
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-...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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....
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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
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...
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...
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...
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...
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,...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
-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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 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....
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
: , 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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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...
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....
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
(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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 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...
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...
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...
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...
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...
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...
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...
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...
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,...
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 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...
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...
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...
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...
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...
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...
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...
No abstract available
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 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...
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...
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 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 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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,...
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...
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...
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...
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...
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)...
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...
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...
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...
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 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...
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...
: () 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
(), 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...
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...
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...
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...
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...
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...
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...
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...
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...
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...