Safety assessment of biological agents for regulatory applications
Whole Genome Sequence Analysis (WGS) of microorganisms used in the food chain or for plant protection
EFSA is requested to analyse the complete genome sequence of bacteria and yeasts when these microorganisms are used in the food chain or for plant protection (regulated products).
Whole genome sequencing (or WGS) and WGS data analysis allow to identify, characterise and in-depth assess the safety of microorganisms for the European consumer.
To support applicants, we have developed a tailor-made workflow that meets EFSA’s requirements point by point. This workflow includes high-quality sequencing of the microorganism using the latest generation sequencing technologies to ensure unambiguous interpretation of the results.
The output report includes :
- The taxonomic identification at the species level
- A search for antimicrobial resistance (AMR) genes
- A search for genes coding for known virulence factors or known pathways involved in toxigenicity
Similar analyses could be provided under request for the QPS ( qualified presumption of safety ) assesment.
Sequencing applications
- Illumina MiSeq sequencing
- Illumina NovaSeq sequencing
- PacBio Sequel II
- Oxford Nanopore GridION
- Oxford Nanopore PrometION