Chapter 5: Omics for the Identification and Characterization of Foodborne Pathogens

Foodborne disease is caused in great part by the ingestion of food contaminated with bacterial pathogens, representing a serious but also largely preventable global burden. The detection of the most important foodborne pathogens forms a main part of risk assessment systems to guarantee food safety. No less important is the investigation of foodborne outbreaks, including effective source-tracking and obtaining information about epidemiology, virulence and antibiotic resistance. This chapter reviews the application of omics as powerful tools for screening and subtyping of the most relevant foodborne pathogenic bacteria in foodstuffs and carrying out robust risk assessment in the field of food safety. The approaches discussed include genomics, proteomics and metabolomics, giving special attention to high-throughput techniques, such as next-generation sequencing and mass spectrometry.