Whole Genome Sequencing in food outbreak investigation and microbial risk analysis

Abstract

Next Generation Sequencing (NGS) is a huge technological advance in the molecular typing of micro-organisms. This chapter describes the use of NGS in food-borne outbreak investigation, source attribution and also describes the first steps in using Whole Genome Sequencing (WGS) data in molecular risk assessment. The rapidly decreasing costs and operational time make that WGS will likely replace currently used molecular typing methods, such as MLST, MLVA and PFGE, in outbreak investigation and source attribution in the near future. Because of the superior level of resolution and because all genetic information (including virulence and antimicrobial resistance genes) of the organisms can be revealed, WGS can be considered as the ultimate "all-in-one" typing method.