Foodborne illness remains an ongoing public health challenge in both the developing and industrialized worlds. In the United States, almost 50 million reported cases of infectious disease occur every year from a food product, resulting in substantial morbidity and mortality with economic burdens to health care and productivity. Despite recognition as a leader in food safety, the U.S. experiences longstanding and novel issues in food safety. Advances in whole genome sequencing (WGS) promise to bolster food safety regulators’ capabilities to identify pathogens and determine their source. However, inefficiencies in tracing food products through the supply chain remain