CAMPYSTRAIN : Feasibility of shotgun metagenomics to study the variability of Campylobacter strains on broiler skin without prior isolation [MICA INRAE Project ].

Campylobacter, a commensal bacterial pathogen of the poultry digestive tract, remains the leading cause of zoonosis reported in the European Union (EU), ahead of salmonella infections. Studying and controlling the persistence of Campylobacter in the food production chain, as well as its increasing resistance to antibiotics, represents a real scientific and economic challenge. Current methods for identifying this pathogen require a long and tedious isolation phase. They also require selection of the isolates to be identified, with the risk that genotypic variability may not be completely covered. The aim of this project is to test the applicability of a shotgun metagenomic approach for the identification and typing of several Campylobacter strains present on broiler neck skins, without prior isolation. This method will make it possible to assess the effect of selection pressure on Campylobacter diversity throughout the slaughter-dressing process, and to identify the genetic determinants associated with the persistence of this pathogen in an industrial environment (slaughterhouse).