Taking account of genomics in quantitative microbial risk assessment: what methods? what issues?

Laurent Guillier (1) , Federica Palma (2) , Lena Fritsch (3)

1 DER - Direction de l'Evaluation des Risques
2 CRBIP - Centre de Ressources biologiques de l'Institut Pasteur - Biological Resource Center of the Institut Pasteur
3 Agroscope

The application of whole-genome sequencing (WGS) to the risk assessment of foodborne pathogens is a key challenge. WGS offers the highest level of strain discrimination for more precise hazard identification, hazard characterization, and exposure assessment, leading to deeper risk characterization. Genome-wide association studies represent today powerful tools for the identification of associations between genomic elements and microbial phenotypic properties. Other cutting-edge tools include machine learning or statistical methods to characterize phenotype distribution on a phylogenetic tree. A panorama of the available methods is presented as well as the specific issues associated with the application of these methods to phenotypes of interest for risk assessment.

Domaines: Sciences du Vivant [q-bio]

Laurent Guillier, Federica Palma, Lena Fritsch. Taking account of genomics in quantitative microbial risk assessment: what methods? what issues?. Current Opinion in Food Science, 2022, 48, pp.100922. ⟨10.1016/j.cofs.2022.100922⟩. ⟨anses-03920741⟩