Director, Division of Microbiology
Office of Regulatory Science
Center for Food Safety and Applied Nutrition
US Food & Drug Administration
5100 Paint Branch Pkwy
College Park, MD 20740 USA
Whole-genome sequencing for regulatory science: A new way forward in the forensics of food safety investigations
High-resolution genomic typing tools are greatly enhancing the tracing foodborne contamination events back to their source, and in this regard, whole genome sequencing (WGS) is now transforming pathogen subtyping in the food safety laboratory. When coupled with powerful bioinformatic pipelines, accurate and stable genetic changes can be identified across pathogen genomes that can distinguish strains to their source level including individual farms or facilities as well as specific geographic locales. This is true even among highly homogeneous strain populations such as Salmonella Enteritidis and other salmonellae that have remained largely recalcitrant to differentiation by conventional typing approaches. Numerous published examples illustrate the ability of WGS to discern genetic relatedness of otherwise indistinguishable isolates and point to WGS as an important tool in the traceability of contamination events with heretorfore unprecedented levels of certainty. Moreover, recent successes have demonstrated its utility in surveillance, providing potential links between environmental isolates of Salmonella and Listeria and known illnesses even in the absence of a food vehicle. WGS impacts regulatory science in FDA’s Foods Program in several ways including: (i) supporting traceability efforts during foodborne contamination events; (ii) enhancing regulatory casework for high-risk commodities and compliance standards; and (iii) providing quality assurance of FDA’s food microbiological sampling programs. Taken together, these early applications of WGS deployments underscore its extraordinary utility in food safety as well as the potential for complete characterization of bacterial pathogens as they emerge in the food supply.