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:

  • Training on risk assessment methodologies and common software
  • Training on various integrated platforms for the use of genomics in foodborne pathogen surveillance and outbreak investigation
  • In silico analysis of genomes from foodborne pathogens
  • Assessment of the potential of WGS in outbreak investigations
  • Collaboration in dissemination and outreach activities.

Findings from the fellowship project will be published in peer-reviewed journals and will cover topics such as a literature review on the use of WGS for food safety; a review on the use of WGS for outbreak investigation; and two research papers on the AMR of several pathogen strains.