A recent fellowship project with the European Food Safety Authority (EFSA) served as an example for the standardization of whole genome sequencing (WGS) training and data reporting. While WGS provides rapid and useful results in foodborne illness outbreak investigations, there is a need to reach a certain level of standardization for the reproducibility and interoperability of results.
The report notes that WGS is a critical tool for strengthening global surveillance of foodborne pathogens and their important characteristics, such as antimicrobial resistance (AMR) and virulence. The fellowship project involved the exploration of AMR and virulence of foodborne pathogens, and the relationship of such characteristics to factors including geography, isolate source, and temporal distribution. To achieve the project’s objectives, the fellowship project participated in: