Ability of Whole-Genome Sequencing to Refine a Salmonella I 4,[5],12:i:- Cluster in New York State and Detect a Multistate Outbreak Linked to Raw Poultry

Whole-genome sequencing (WGS) has proven to be a more powerful tool than pulsed-field gel electrophoresis for foodborne illness cluster definition because of improved resolution. Between November 2017 and May 2018, the New York State (NYS) Dept. of Health investigated 10 cases of Salmonella I 4,[5],12:i:- with pulsed-field gel electrophoresis pattern JPXX01.0621; comparison of case exposures did not identify a common source of infection. In June 2018, the NYS Dept. of Health’s Wadsworth Center analyzed the isolates using WGS and defined a subcluster of five isolates related within zero to six single-nucleotide polymorphisms. The National Center for Biotechnology Information Pathogen Detection browser advanced this investigation by identifying additional clinical and food (chicken) isolates related within zero to eight single-nucleotide polymorphisms to the original subcluster. Comparison of WGS-related isolates would support the hypothesis that illness was associated with exposure to a kosher poultry product. This outbreak ultimately consisted of 25 cases from six states. Of 20 cases interviewed, all reported chicken consumption, and of those able to recall brand information, 83% cited a brand produced at a facility linked to the WGS-related chicken isolates. This paper demonstrates how WGS was able to refine a Salmonella I 4,[5],12:i:- cluster in NYS to uncover a multistate outbreak linked to raw poultry.