Abstract
A standardised method for determining Escherichia coli O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or k-mer clustering to discriminate between outbreak-associated and sporadic E. coli O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and k-mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. k-mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.
Highlights
Shiga toxin-producing Escherichia coli (STEC) consisting of O157 and non-O157 serogroups are a major public health concern
From 14 July to 17 September 2014, 149 clinical isolates of E. coli O157:H7 were received by the Alberta ProvLab for molecular typing (Figure 1)
None of the haemolytic uraemic syndrome (HUS) cases were negative for any virulence genes other than sfpA. Technologies such as high throughput screening of virulence genes [32,33] and whole genome sequencing (WGS) have the potential to be used for early outbreak detection and characterisation
Summary
Shiga toxin-producing Escherichia coli (STEC) consisting of O157 and non-O157 serogroups are a major public health concern. Cattle and other ruminants are natural reservoirs for STEC organisms, shedding the organisms in their faeces, which can cause food and/ or water contamination [1]. Consumption of contaminated meat, dairy products, vegetables/fruit, water, contact with animals [1] and person-to-person transmission [2] have all been associated with STEC infections. Infection may be asymptomatic or can cause gastrointestinal symptoms, including mild diarrhoea to haemorrhagic colitis [3]. Paediatric and elderly patients are at greatest risk for developing systemic STEC complications, which are not limited to HUS and can include cardiac, central nervous system, pancreatic, and pulmonary complications [3,4,5]. Shiga toxins (Stx and Stx2) are the major virulence determinants responsible for symptoms associated with both haemorrhagic colitis and systemic infections [5]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
