ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2015
Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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114 citing papers in PubMed.
- Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.Antibiotics (Basel, Switzerland) · 2026Review
- Mind the gap! TypingMicrobial genomics · 2026Article
- Clonal and plasmid-mediated dissemination of CTX-M-14-producingFrontiers in microbiology · 2026Article
- Lessons from 5 Years of Routine Whole-Genome Sequencing for Epidemiologic Surveillance of Shiga Toxin-Producing Escherichia coli, France, 2018-2022.Emerging infectious diseases · 2025Article
- One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings.The Journal of antimicrobial chemotherapy · 2025Article
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- An outbreak of Shiga toxin-producingEpidemiology and infection · 2025Article
- Hybrid strains of enterotoxigenic/Shiga toxin-producingJournal of medical microbiology · 2025Article
- Whole-Genome Sequencing Reveals Temporal Trends in Antibiotic Resistance Genes inAntibiotics (Basel, Switzerland) · 2024Article
- Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world.Nature reviews. Microbiology · 2024Review
- Re-analysis of an outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with raw drinking milk using Nanopore sequencing.Scientific reports · 2024Article
- Uncovering the spread of drug-resistant bacteria through next-generation sequencing based surveillance: transmission of extended-spectrum β-lactamase-producing Enterobacterales by a contaminated duodenoscope.Antimicrobial resistance and infection control · 2024Article
- Use of whole genome sequencing for surveillance and control of foodborne diseases:Frontiers in microbiology · 2024Review
- The phylogenomic landscape of extended-spectrum β-lactamase producing Citrobacter species isolated from surface water.BMC genomics · 2023Article
- Using SNP addresses forEpidemiology and infection · 2023Article
- Sporadic Shiga Toxin-Producing Escherichia coli-Associated Pediatric Hemolytic Uremic Syndrome, France, 2012-2021.Emerging infectious diseases · 2023Article
- Evaluation of core genome and whole genome multilocus sequence typing schemes forMicrobial genomics · 2023Article
- Optimizing hierarchical tree dissection parameters using historic epidemiologic data as 'ground truth'.PloS one · 2023Article
- Phylogenetic relationship and virulence composition ofFrontiers in microbiology · 2023Article
- Whole-genome sequencing of multidrug resistanceFrontiers in public health · 2023Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
Abstract
backgroundNational surveillance of gastrointestinal pathogens, such as Shiga toxin-producing Escherichia coli O157 (STEC O157), is key to rapidly identifying linked cases in the distributed food network to facilitate public health interventions. In this study, we used whole-genome sequencing (WGS) as a tool to inform national surveillance of STEC O157 in terms of identifying linked cases and clusters and guiding epidemiological investigation.
methodsWe retrospectively analyzed 334 isolates randomly sampled from 1002 strains of STEC O157 received by the Gastrointestinal Bacteria Reference Unit at Public Health England, Colindale, in 2012. The genetic distance between each isolate, as estimated by WGS, was calculated and phylogenetic methods were used to place strains in an evolutionary context.
resultsEstimates of linked clusters representing STEC O157 outbreaks in England and Wales increased by 2-fold when WGS was used instead of traditional typing techniques. The previously unidentified clusters were often widely geographically distributed and small in size. Phylogenetic analysis facilitated identification of temporally distinct cases sharing common exposures and delineating those that shared epidemiological and temporal links. Comparison with multi locus variable number tandem repeat analysis (MLVA) showed that although MLVA is as sensitive as WGS, WGS provides a more timely resolution to outbreak clustering.
conclusionsWGS has come of age as a molecular typing tool to inform national surveillance of STEC O157; it can be used in real time to provide the highest strain-level resolution for outbreak investigation. WGS allows linked cases to be identified with unprecedented specificity and sensitivity that will facilitate targeted and appropriate public health investigations.
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