Genomically-informed custom selective enrichment of Shiga-Toxigenic Escherichia coli (STEC) outbreak strains in foods using antibiotics

Abstract

Shiga toxigenic Escherichia coli (STEC) have been implicated in major foodborne outbreaks worldwide. The STEC family of pathogens is biochemically diverse, and current microbiological methods for detecting STEC are limited by the lack of a universal selective enrichment approach and prone to interference by high levels of background microbiota associated with certain types of foods. A novel approach has been developed for the recovery of foodborne illness outbreak strains during outbreak investigations based on the analysis of whole genome sequence data of implicated clinical isolates to determine antimicrobial resistance (AMR) genes. The presence of certain AMR genes in STEC has been correlated with the ability to grow in the presence of a specific antibiotic, which can be used to supplement enrichment broths to improve the recovery of a target strain. The enhanced recovery of STEC strains with different AMR profiles from various food types (beef, sprouts, leafy greens, and raw milk cheese) containing high levels of background microbiota was demonstrated using AMR predictions for nine different antibiotics. This genomically informed custom selective enrichment approach increases the availability of analytical options and improves the reliability of food microbiological analyses in confirming food vehicles implicated in outbreak events and defining the scope of product contamination to support risk assessment and risk management actions.