ABSTRACT
Whole-genome sequencing (WGS) is a technology which has the potential to become a standard methodology in food safety for the identification and characterization of foodborne pathogens. It can be used for the retrospective comparison of microorganisms associated with epidemiologically suspected outbreaks and for prospective laboratory surveillance of high-burden diseases. Resolution efficiency offered by the WGS for subtyping bacterial, viral, fungal, and parasitic pathogens is also very high. The recent advances in the field of WGS technology enable the fast identification and characterization of pathogens and provide extremely superior precision. Rapidly declining cost and the compatible data provided by WGS indicate its potential in food safety management. In this chapter, the basic principles of WGS subtyping, sequencing technologies, and data analysis are discussed; and applications for the use of WGS for food safety and management, as well as quality analysis are detailed.
