Microbial Genomics

The major opportunistic pathogen Escherichia coli is the largest cause of antimicrobial resistance (AMR) associated infections and deaths globally. Considerable antigenic diversity has been documented in Extra-intestinal pathogenic E. coli (ExPEC), however, phenotypic capsular (K) typing has fallen out of use. We assembled and curated an in silico capsular locus typing database for group 2 and group 3 K-loci from >20,000 genomes and applied it to carriage and disease cohorts to investigate capsu...

Whole genome sequencing of bacterial pathogens can positively impact infectious disease management in clinical contexts, both in individual settings and assisting infection prevention efforts. However, logistical issues have often prevented its translation into clinical settings. Oxford Nanopore Technologies (ONT) platforms are flexible, affordable, and now offer accuracy comparable to other sequencing platforms, making them uniquely well-suited for clinical bacterial isolate sequencing. We soug...

Defective OprD porins contribute to carbapenem resistance and may be important in Pseudomonas aeruginosa adaptation to cystic fibrosis airways. It is unclear whether oprD mutations are fixed in populations of shared strains that are transmitted between patients or whether novel variants arise during infection. We investigated oprD sequences and antimicrobial resistance of two common Australian shared strains, constructed P. aeruginosa mutants with the most common oprD allelic variants and compar...

Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and genomic determinants of disease outcomes. Across two wards over six months, we selectively cultured C. difficile from patients (n=384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from...

PurposeUrinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are a major public health concern due to their recurrent nature and antibiotic resistance. Biofilm formation plays a crucial role in UPEC persistence, yet the genetic mechanisms underlying this process remain poorly understood. This study employs next-generation sequencing (NGS) to investigate the genomic characteristics of biofilm-forming, multidrug-resistant (MDR) UPEC isolates, with a focus on antimicrobial...

BackgroundClostridioides difficile infections (CDIs) are among the most prevalent hospital-associated infections (HAIs), particularly for intensive care unit (ICU) patients. The risks for developing active CDI from asymptomatic carriage of C. difficile are not well understood. MethodsWe identified asymptomatic C. difficile carriage among 1897 ICU patients, using rectal swabs from an existing ICU vancomycin-resistant Enterococci (VRE) surveillance program. C. difficile isolates from VRE swabs, a...

BackgroundNeisseria gonorrhoeae genotyping by whole-genome sequencing (WGS) is expensive for a large sample set, a less expensive and more efficient genotyping method is required. We developed a high-throughput genotyping method for N. gonorrhoeae to improve molecular epidemiological typing and antimicrobial-resistant identification in N. gonorrhoeae antimicrobial susceptibility surveillance. MethodsWe used multiplex-tailed PCR to amplify and sequence 15 alleles from multilocus sequence typing ...

COVID19 genomic surveillance is instrumental to better understand transmission dynamics in a setting, detect emergence of new variants and monitor spread of variants at the national, regional and global levels. Complete viral genome sequences are powerful enough to approximate epidemiology and enable informed public health response policies and determine their success. Between 24th November to 9th December 2020, a workplace COVID-19 outbreak, assigned as the Hilir cluster, occurred among healthc...

Salmonella enterica serovar Enteritidis is a leading cause of bloodstream infections (BSIs), particularly in sub-Saharan Africa (sSA). While typhoidal salmonellosis is well documented in South Asia, the burden and genomic characteristics of non-typhoidal Salmonella (NTS)-associated BSIs remain understudied. This study investigates the clinical presentation, phylogenetic relationships, invasive potential, and transmission dynamics of S. Enteritidis causing BSIs in India. Clinical data were collec...

We summarize a genomic investigation of a 4-fold increase in disseminated gonococcal infections (DGI) in Minnesota, USA, in 2024. We detected the emergence of strain of Neisseria gonorrhoeae of a rarely observed sequence type, which carries a porB1a allele previously associated with disseminated disease and lacks a gonococcal genetic island. Article Summary LineA substantial increase in disseminated gonococcal infection cases in Minnesota, USA in 2024 was associated with the emergence of a rare...

We summarize an outbreak of N. gonorrhoeae ST16676 associated with disseminated gonococcal infections (DGIs) in Minnesota, USA in 2025. This novel strain replaced ST11184 as the predominant sequence type circulating among DGI cases in the state, encoded a porB1a allele, and carried a tetracycline resistance gene on a mobilizable plasmid.

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is recognized as an urgent public health threat due to its multidrug resistance and ability to spread rapidly in healthcare facilities. The frequent movement of colonized and infected patients between different facilities makes it challenging to discern where individual patients acquire CRKP, and in turn, identify facilities making the greatest contributions to regional spread. While high-intensity active surveillance combined with whole-genome s...

BackgroundPathogen 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. MethodsTo identify analytic strategies for conducting WGS-based HAI surveillance in high-burden settings, we modeled patient- and facility-level transmission risks of carbapenem-resistant Klebsiella pneumoniae (CRKP) in a long-term acute ca...

Doxycycline use for bacterial sexually transmitted infections (STIs) increased in recent years due to changes in treatment guidelines, the shortage of benzathine penicillin for treatment of syphilis, and adoption of doxycycline post-exposure prophylaxis. While this increased use is expected to select for doxycycline resistance, particularly in Neisseria gonorrhoeae, the impact has been unclear. Here, we analyzed over 14,000 publicly available N. gonorrhoeae genome sequences from 2018-2024 genera...

For the first time, Stenotrophomonas muris (S. muris) has been identified to be associated with human infections while studying the virulence of Stenotrophomonas maltophilia (S. maltophilia) clinical isolates. Previously, S. muris was only isolated from the intestines of mice but its pathogenic potential for humans has never been reported. In this work, the phenotype of S. muris virulence, the potential genes that encode higher virulence of S. muris, and host responses to S. muris infection were...

During March of 2017 a neonate patient suffered severe diarrhea and subsequently developed septicemia and died, with Klebsiella isolated as the causative microorganism. Coincident illness of an attending staff member and three other neonates with Klebsiella triggered a response, leading to a detailed microbiological and genomics investigation of isolates collected from the staff member and all 21 co-housed neonates. Multilocus sequence typing and genomic sequencing identified that the Klebsiella...

Salmonella Paratyphi A, one of the major etiologic agents of enteric fever, has been on the rise over the last decades in certain endemic regions compared to S. Typhi, the most prevalent cause of enteric fever. Despite this, data on the prevalence and molecular epidemiology of S. Paratyphi A remain scarce. Here, we analysed the whole genome sequences of a total of 216 S. Paratyphi A isolates originating in Nepal between 2005 and 2014, of which 200 were from acute patients and 16 from chronic car...

BackgroundA substantial and rapid increase, followed by a sharp decline in vanB-type vancomycin-resistant E. faecium (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. MethodsWe retrospectively analyzed 344 E. faecium bloodstream infection (BSI) isolates collected between 2017 and 2022. Isolates were classified as vanA-positive, vanB-positive, or van-negativ...

ObjectivesTo characterize carbapenem-resistant Acinetobacter baumannii isolates associated with healthcare-associated infections (HAIs) in Colombia using whole-genome sequencing (WGS). MethodsA total of 83 A. baumannii isolates collected between 2012 and 2015 were sequenced using the Illumina platform. Raw reads were assembled by SPAdes and classified via multilocus sequence typing (MLST), using the Pasteur, Oxford, and core genome MLST (cgMLST) schemes. Antimicrobial resistance determinants, c...

The World Health Organization ranks Klebsiella pneumoniae as a priority antimicrobial-resistant (AMR) pathogen requiring urgent study. New strategies for diagnosis and treatment, particularly for those Klebsiella that are classified as carbapenem-resistant Enterobacteriaceae (CRE) need to recognize the increased prevalence of non-carbapenemase producing CRE (non-CP CRE). By integrating diverse Klebsiella genomes with known CRE phenotypes, we successfully identified a synchronized presence of CRE...