Whole-genome sequencing for national surveillance of Shiga toxin–producing Escherichia coli O157

Dallman, Timothy J., Byrne, Lisa, Ashton, Philip M., Cowley, Lauren A., Perry, Neil T., Adak, Goutam, Petrovska, Liljana, Ellis, Richard J., Elson, Richard, Underwood, Anthony, Green, Jonathan, Hanage, William P., Jenkins, Claire, Grant, Kathie and Wain, John (2015) Whole-genome sequencing for national surveillance of Shiga toxin–producing Escherichia coli O157. Clinical Infectious Diseases, 61 (3). pp. 305-312. ISSN 1058-4838

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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.

Item Type: Article
Uncontrolled Keywords: public health,whole-genome sequencing,shiga toxin–producing escherichia coli o157,national,sdg 3 - good health and well-being ,/dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups: Faculty of Medicine and Health Sciences > Research Groups > Medical Microbiology (former - to 2018)
Depositing User: Pure Connector
Date Deposited: 19 Nov 2015 08:11
Last Modified: 21 Oct 2022 01:06
URI: https://ueaeprints.uea.ac.uk/id/eprint/55391
DOI: 10.1093/cid/civ318


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