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Illuminating the role of whole genome sequencing in produce safety

Kerry Cooper
University of Arizona
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Due to its higher resolution, whole genome sequencing (WGS) is rapidly becoming the new gold standard for foodborne outbreak investigations. But, there is still a continued effort to refine the implementation of WGS thus improving accuracy while reducing investigation time. Foodborne pathogens often cycle around defined regions, which was a major factor behind the creation of the FDA's GenomeTrakr network, because if you can match clinical cases to a defined region then the investigation can quickly narrow the search to that region. GenomeTrakr involves state, federal, commercial and international laboratories genome sequencing regional foodborne pathogens to create a public database of regional genomic pathogen profiles for investigations. However, as the pathogens continue to cycle through the environment in those regions the genomes may accrue mutations that could alter the regional genomic pathogen profile, which could limit the positive impact of GenomeTrakr on investigations. The goal of this project is to determine the mutation rates of Salmonella, Listeria, and Escherichia coli O157:H7 during long-term persistence in agricultural soil and irrigation water maintained under different geographical conditions. Understanding these mutational rates will help improve the development of GenomeTrakr for regional identification during an outbreak investigation. Furthermore, data from this project will assist the produce industry in developing WGS for internal source tracking to identify "resident" versus "transient" pathogens, sources of contamination for either, and better understand the breakdowns or gaps in prevention methods, thus improving produce safety by closing these gaps.

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Bacterial Pathogens