Use of Whole-Genome Sequencing at the Food Safety and Inspection Service to Detectand Investigate Foodborne Illness Outbreaks

Whole-genome sequencing (WGS) is a powerful tool used for surveillance and monitoring for foodborne illnesses. WGS can be used to generate hypotheses about food products that might be making people sick and to determine and prioritize actions taken by the U.S. Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) during outbreaks. The use of WGS, in conjunction with epidemiologic evidence and food purchase histories, improves the likelihood of identifying associations between a food source and illness. Foodborne illness outbreaks due to Listeria monocytogenes and Salmonella are examples of the USDA-FSIS’s use of WGS in solving foodborne illness outbreaks. Based on evidence from WGS, epidemiologic investigation, and food purchase histories, the USDA-FSIS was able to identify and facilitate removal of adulterated product from commerce and prevent further illnesses.