Head of E. coli, Shigella,Yersinia & Vibrio Reference Services
Deputy Head Gastrointestinal Bacteria Reference Unit
Public Health England
61 Colindale Ave, NW9 5HT
Whole genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157
The role of the national reference laboratory is to provide gold standard microbial typing, support national surveillance activities, and facilitate the national and international outbreak detection and investigation. In preparation for the implementation of whole genome sequencing (WGS) service delivery at Public Health England, we retrospectively analysed 334 isolates randomly sampled from 1002 strains of Shiga Toxin Producing Escherichia coli (STEC) O157 received by the Gastrointestinal Bacteria Reference Unit in 2012. Given the link between Shiga Toxin (Stx) 2a subtype and disease severity, we also sought to identify the stx subtypes present in WGS of 444 isolates of STEC O157. All strains of STEC O157 in this study had stx1a, stx2a or stx2c or a combination of these three genes. There was over 99% (442/444) concordance between PCR and WGS. Estimates of linked clusters representing STEC O157 outbreaks in England increased by two 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 the identification of temporally distinct cases that shared common exposures as well as delineating those that shared epidemiological and temporal links. WGS data enabled us to identify outbreaks with unprecedented specificity and sensitivity and, in the future, will facilitate targeted and appropriate public health investigations.