Genomically Informed Custom Selective Enrichment of Shiga-toxigenic E. coli (STEC) outbreak strains in foods

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  • Foodborne bacterial outbreaks caused by Shiga-toxigenic E. coli (STEC) continue to place a burden on public health systems in developed countries. The STEC family of pathogens is biochemically diverse and current microbiological methods for detecting STEC may be encumbered by lack of a universal selective enrichment method. Here we build upon a previously described method where genomic antimicrobial resistance (AMR) prediction tools are used to inform a selection of custom enrichment techniques for recovery of a target STEC strain from ground beef, and demonstrate the broader applicability of custom selective enrichment using recovery of five unique STEC strains from additional food commodities. Drastically improved recovery of STEC strains was shown for all 9 antibiotics examined in this study. The ability to accurately leverage AMR traits in specific pathogens for their recovery from high levels of background microbiota suggests this approach can be universally applicable in support of foodborne illness investigations.

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  • Copyright © 2022 the author(s). Theses may be used for non-commercial research, educational, or related academic purposes only. Such uses include personal study, research, scholarship, and teaching. Theses may only be shared by linking to Carleton University Institutional Repository and no part may be used without proper attribution to the author. No part may be used for commercial purposes directly or indirectly via a for-profit platform; no adaptation or derivative works are permitted without consent from the copyright owner.
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  • 2022


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