Genome-guided detection of non-O157 STEC

Shigatoxigenic Escherichia coli (STEC) are a priority foodborne (FB) bacterial pathogen that cause serious clinical disease, transmitted by a range of foodstuffs. The most common STEC is serogroup O157. However, there are multiple serogroups that have been increasing in prevalence since 2000. Non-O157 STEC now accounts for ~ 30 % of all STEC in Scotland (FSS report, 2020), with similar numbers reported across the EU (Valilis, 2018). They have diverse genomes and variable virulence gene carriage compared to STEC O157, and some are non-pathogenic making associations with clinical disease outcome challenging. This also complicates regulatory control of food-business operators by food standards authorities. Therefore, there is a pressing need for accurate and informative identification. Here, we will define the requirements for computational approaches that distinguish clinical pathotypes of non-O157 STEC, and the steps required for applications to be used in detection and surveillance.