The Design and Implementation of Genomics Tools for Enhanced Detection and Characterization of Verotoxigenic Escherichia coli Implicated in Foodborne Illness

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Title: The Design and Implementation of Genomics Tools for Enhanced Detection and Characterization of Verotoxigenic Escherichia coli Implicated in Foodborne Illness
Authors: Knowles, Michael
Date: 2017
Abstract: Motivation Control strains of bacterial pathogens are commonly processed in parallel with test samples in food microbiology laboratories assuring the satisfactory performance of materials used in the analytical procedure. Before positive findings can be reported for risk management purposes, analysts must have a means of verifying that pathogenic bacteria recovered from test samples are not due to inadvertent contamination with the control strain. In addition to detection of laboratory control strains, genomic antimicro- bial resistance (AMR) prediction tools may be very useful in supporting food-borne ill- ness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile from an outbreak strain of interest could be compared with related bacteria to determine the presence of unique resistance mark- ers enabling customization of selective enrichment media facilitating their recovery from samples during food safety investigations. Food safety investigations focusing on both control strain and priority bacterial pathogen detection, characterization and selective recovery would benefit from a practical means of differentiating between phylogenetically similar isolates. Results We describe the implementation of a novel algorithm for the identification of DNA signature sequences enabling differentiation of phenotypically related bacterial strains within the same species. This tool, which we have named SigSeekr, was applied in the analysis of whole genome sequence data from select Escherchia coli and Salmonella enterica strains, enabled the development of primers for their specific detection and differ- entiation from closely related bacteria using polymerase chain reaction (PCR) techniques. We applied this tool enabling the identification of a common positive control strain using a simple PCR procedure. We combined SigSeekr with selective recovery (using AMR) and identification tools for the efficient detection of verotoxin-producing Escherichia coli (VTEC) outbreak strains within the timeframe of an active investigation. Conclusion We used SigSeekr in a simple PCR procedure to differentiate three E. coli and one Salmonella enterica between phylogenetically strains including control strains. We also discuss the relative merits of different AMR marker prediction tools employing bioinformatics alignment algorithms along with comprehensive AMR gene databases such as CARD (e.g., Antimicrobial Resistance Marker Identifier [ARMI]), or publicly avail- able tools which use more limited acquired AMR gene databases (e.g., ResFinder), and describe how such tools can be utilized to good effect in a typical outbreak investigation.
URL: http://hdl.handle.net/10393/35645
http://dx.doi.org/10.20381/ruor-602
CollectionThèses, 2011 - // Theses, 2011 -
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