Single nucleotide polymorphism analysis of whole genome sequencing data for pathogen traceback detection

One of the significant challenges associated with foodborne disease outbreak investigation has been a lack of ability to rapidly identify the source of a contamination event and eliminate it from the food supply. Whole genome sequencing (WGS) is quickly emerging as a powerful tool for strain-level identification of foodborne pathogens. Here, we demonstrate retrospective outbreak investigations where WGS combined with single nucleotide polymorphism (SNP) analyses were able to precise traceback the foodborne contamination event. For example, we show, on a global scale the value of WGS using a representative set of S. Bareilly isolates, including those obtained from the 2012 outbreak. Phylogenetic analysis of WGS data revealed a common origin for the outbreak strains, indicating that patients in the USA were infected from sources originating at the India facility. WGS can distinguish relationships among bacterial pathogens with such certainty that it is a powerful tool for tracing bacterial foodborne outbreaks back to their source. The larger the WGS reference database, the stronger the “leads” are when new clinical data are added. With this in mind, in 2013 the United States Food and Drug Administration (FDA) started the GenomeTrakr network with the goal of creating a public, high-resolution, diverse, pathogen database of isolates collected from food and environmental sources. As more WGS data are gathered and analytical tools developed, we anticipate significant improvements in timeliness of outbreak investigations.