WGS of Campylobacter jejuni strains isolated in broiler slaughterhouse in France

Campylobacter spp. is the leading cause of bacterial enteritis in humans, with broiler chicken meat being the primary source of contamination. Despite the application of a European Regulation for Campylobacter spp in broiler slaughterhouses, the prevalence of this pathogen in the poultry sector remains high in France. The main objective of this study was to use whole-genome sequencing to (i) assess and compare genomic diversity of Campylobacter isolated from carcasses and slaughterhouse environment during broiler processing in two French abattoirs, (ii) identify potential genetic factors putatively associated with resistance to stress and antimicrobial compounds. The genomes of 74 isolates from caecal contents, scalding water, evisceration room air and neck skin samples taken before or after chilling were sequenced using Illumina Novaseq 6000 instrument. All samples were collected during the slaughter of six broiler batches.