Scott Jackson, Principal Investigator - Molecular Epidemiologist, United States Food and Drug Administration
E. coli, Salmonellae, and Vibrio cholerae are recognized as 3 of the major food-borne bacterial pathogens in the United States, causing a combined total of over 3 million cases of illness annually. Recent outbreaks of such illnesses suggest a rapid capacity for these pathogens to adapt to novel environmental niches specifically involving new food sources. From a genomic perspective, horizontal gene transfer among and between these pathotypes may account for a majority of such adaptation potential and has resulted in a mosaic genomic milieu. To investigate the genomic diversity and evolution of these pathogens, we utilized a comprehensive DNA microarray to characterize a broad and diverse collection of food borne isolates. Our Affymetrix array contains over 2.5 million features and represents over 85 whole genome sequences (WGSs), 90 plasmids, and all known antimicrobial resistance and virulence genes from various public and private DNA sequence repositories. This array additionally includes a tiling design that represents 3k conserved genes from the three genera; thereby giving the ability to accurately predict SNPs de novo. The novelty of this array design necessitated non-traditional data analysis methods that were developed and validated in-house and provide for statistically accurate genotype determinations. Genomes from over 450 isolates of Salmonella, E. coli, and Vibrio spp were interrogated. Strains were chosen based on their importance to human and animal health, inclusion in historical collections, and other molecular subtyping discrimination. Our findings demonstrate strain-level discrimination and a rich diversity that exists among each of the pathogen types.