Whole-genome sequencing for food safety

Next-generation sequencing (NGS) technologies are increasingly being embraced and adopted by public health agencies and the food industry for the control of foodborne pathogens. This chapter describes the application of these technologies for whole-genome sequencing (WGS) of bacterial pathogens in the food chain. Examples are provided showing how WGS has been used for different applications, from global to local and factory-scale. Applications include outbreak investigation, source attribution and genomic epidemiology, processing plant investigations of contamination, and understanding pathogen evolution. Despite the promise and potential of WGS and NGS technology, there remain concerns regarding access to the technology, particularly in low- and middle-income settings, and issues relating to speed and cost, data governance, and the implications of sharing data. Advances in bioinformatics and visualization, and a strong focus on collaboration, standardization, and harmonization, will help to ensure the tools and technologies are adopted and used effectively for food safety decision-making.