Submitted to: Foodborne Pathogens and Disease
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/15/2008
Publication Date: 9/1/2008
Publication URL: www.liebertonline.com/doi/pdfplus/10.1089/fpd.2008.0117
Citation: Bhagwat, A.A., Bhagwat, M. 2008. Methods and tools for comparative genomics of food-borne pathogens. Foodborne Pathogens and Disease. 5(4):487-497. Interpretive Summary: Outbreaks of enteric human pathogens such as E. coli, Salmonella and Shigella spp. have been reported and the isolated outbreak stains have shown a wide range of genetic differences. Understanding the molecular basis of genetic diversity is important to analyze the risk associated with a particular pathogenic strain. We demonstrated the utility of several software programs to interpret the genetic information obtained from several genome sequence projects. Genetic analysis revealed new pathways in several Shigella spp. that could aid the pathogen to overcome the human gastric barrier. Whole genome sequence analysis tools will strengthen food-borne pathogen surveillance and subsequent risk assessment by various regulatory agencies to make the U.S. food supply safer.
Technical Abstract: A comparison of protein sequences encoded by a given genome with the database of existing proteins could be an informative approach since proteins with a high degree of similarity are likely to perform similar functions. 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 make the U.S. food supply safer.