Methods and Tools for Comparative Genomics of Foodborne Pathogens

Abstract

A comparison of genome sequences and of encoded proteins with the database of existing annotated sequences is a useful approach to understand the information at the genome level. Here we demonstrate the utility of several DNA and protein sequence comparison tools to interpret the information obtained from several genome projects. Comparisons are presented between closely related strains of Escherichia coli commensal isolates, different isolates of O157:H7 and Shigella spp. It is expected that comparative genome analysis will generate a wealth of data to compare pathogenic isolates with varying levels of pathogenicity, which in turn may reveal mechanisms by which the pathogen may adapt to a particular nutrient supply in certain foods. These genome sequence analysis tools will strengthen food-borne pathogen surveillance and subsequent risk assessment to enhance the safety of the food supply.

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“…Similar to pangenomics, but ORFs are chosen by screening of genomes from multiple strains of pathogenic and commensal strains of a species [18,21].…”

Latest developments in foodborne pathogen risk assessment

“…Omic methods could help to progress in this direction. For instance, identification of pathways involved in pathogen stress adaptation patterns has been determined by comparative genome analysis in food [30]. More recently, differential gene expression analysis and genome-wide transcriptome analysis have been used to identify food-related stress resistance biomarkers [31][32][33][34].…”

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