title: Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.
abstract: BACKGROUND
  National 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.
  
  
  METHODS
  We 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.
  
  
  RESULTS
  Estimates 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.
  
  
  CONCLUSIONS
  WGS 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.
authors.affiliation: Public Health England, London.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Dallman
authors.affiliation: Public Health England, London.
authors.forename: Lisa
authors.initials: L
authors.lastname: Byrne
authors.affiliation: Public Health England, London.
authors.forename: Philip M
authors.initials: PM
authors.lastname: Ashton
authors.affiliation: Public Health England, London.
authors.forename: Lauren A
authors.initials: LA
authors.lastname: Cowley
authors.affiliation: Public Health England, London.
authors.forename: Neil T
authors.initials: NT
authors.lastname: Perry
authors.affiliation: Public Health England, London.
authors.forename: Goutam
authors.initials: G
authors.lastname: Adak
authors.affiliation: Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom.
authors.forename: Liljana
authors.initials: L
authors.lastname: Petrovska
authors.affiliation: Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Ellis
authors.affiliation: Public Health England, London.
authors.forename: Richard
authors.initials: R
authors.lastname: Elson
authors.affiliation: Public Health England, London.
authors.forename: Anthony
authors.initials: A
authors.lastname: Underwood
authors.affiliation: Public Health England, London.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Green
authors.affiliation: Harvard School of Public Health, Boston, Massachusetts.
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
authors.affiliation: Public Health England, London.
authors.forename: Claire
authors.initials: C
authors.lastname: Jenkins
authors.affiliation: Public Health England, London.
authors.forename: Kathie
authors.initials: K
authors.lastname: Grant
authors.affiliation: University of East Anglia, Norwich, United Kingdom.
authors.forename: John
authors.initials: J
authors.lastname: Wain
mesh_terms: D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004196:Disease Outbreaks; D004927:Escherichia coli Infections / Q000382:microbiology*; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D062486:Public Health Surveillance; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D054323:Shiga-Toxigenic Escherichia coli / Q000145:classification / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial
keywords: Shiga toxin–producing Escherichia coli O157; national surveillance; public health; whole-genome sequencing