ABSTRACT
Different microbes contaminate food in the field, transportation, and storage and from the processing plant to the consumer. Consumption of such food not only causes health-related problems, but they also have a major impact on the world economy. Next-generation sequencing (NGS) tools, together with powerful bioinformatics techniques, have played a key role in the evolution of modern-day food safety and quality. Today, whole-genome sequencing (WGS) allows detection and the most detailed comparison of individual strains of different food microbes via single nucleotide polymorphism and genomic multi-locus sequence typing in a single biological sample even if infected by multiple microbes. On the other hand, transcriptomic analysis gives detailed information about the number and types of genes activated in response to infection, the magnitude of up-regulation and/or down-regulation of genes in different tissues, at different points in time. Proteomics provides information about changes in the proteome as a result of microbial infection. These techniques, together with lipidomics and metabolomics, are now applied routinely in fields ranging from common diagnostics to investigations of disease outbreak, antimicrobial resistance, food authenticity, and tracking and tracing the source of pathogen in food supply chains. In this chapter, we discuss the role of NGS-based techniques, such as WGS, transcriptomics, proteomics, lipidomics, and metabolomics in microbial food safety and also discuss the benefits and drawbacks of NGS-based approaches in microbial food safety management.
