Purpose: I attempted to use whole genome sequencing (WGS) methodologies to differentiate between the closely related SE strains that come from different food commodities to explore genomic regions that are indicative of their sources.
Methods: I used WGS data (e.g., complete genomic sequences and single nucleotide polymorphisms (SNPs)) from SE isolates collected from various food commodities and maintained in GenomeTrakr, which was developed by FDA CFSAN in collaboration with other state and federal labs and houses the genomic sequences of thousands of clinical and environment/food isolates at NCBI. I performed phylogenetic analysis to identify the variability of SE strains among the different food commodities and genomic profiles were then explored to identify genetic loci that differentiated SE sources.
Results: WGS data was collected from over 600 SE isolates in GenomeTrakr according to two parameters: if it (1) came from the United States; (2) had associated metadata indicating geographic location, clinical/environmental status, isolation source (e.g., chicken/egg), and/or other relevant attributes. Preliminary phylogenetic analysis based on SNPs derived from sequence data revealed distinct separation between SE collected from egg and chicken.
Significance: I am currently in the process of determining the exact genetic loci that lead to this separation as well as continuing to develop genomic profile data (e.g., presence or absence of gene/plasmid) to inform sources of clinical cases of salmonellosis. Furthermore, the genomic profiles could be improved as more data becomes available to elucidate the nature of the genetic differences that allow for source specificity.