5. Next-generation sequencing methods

5.1 Next-generation sequencing

In recent years, next-generation sequencing (NGS) methods combined with powerful bioinformatics approaches have revolutionized food microbiology. These technologies are developing rapidly, with ongoing improvements and ever-decreasing costs. In food microbiology, NGS methods are used in two main ways.

The first involves determining the complete genome sequence of a single bacterial colony in culture. Determining the complete genome sequence is highly resolvable compared with PCR-based detection systems. It also enables the precise typing of bacterial strains, and greatly facilitates the detection of food-borne disease outbreaks. Recent studies have demonstrated its application for Salmonella enterica serovar Enteritidis...