Ph.D thesis of Morgane Nennig (2018-2022)

Campylobacter is the leading cause of bacterial gastroenteritis worldwide. The most common species, C. jejuni, is a microaerophilic, capnophilic, and thermotolerant pathogen. Given its growth requirements, C. jejuni’s ability to persist within food production chains has long intrigued scientists. This study aimed to compare different genetic profiles of C. jejuni isolates from Luxembourg based on the core genome (cg) and whole genome (wg) to clarify the genetic structure of its population. Using phenotypic tests under controlled conditions and functional genomics analyses based on wgMLST data, the link between phenotypic traits and genotype persistence was explored. The grouping of strains into genomic lineages is consistent with epidemic and endemic profiles, regardless of the cgMLST typing schemes used. The high genomic stability within these lineages supports the hypothesis of monomorphic clonal expansion over time and from different sources. Phenotypes are correlated with generalist or host-specific clonal complexes for responses to oxidative stress, adhesion to abiotic surfaces, biofilm formation, and adaptation to aerobic conditions. These data enabled the establishment of metaphenotypes specific to these genomic lineages. Functional genomics analysis has identified factors that may contribute to the spatiotemporal survival of recurrent strains. These findings suggest that C. jejuni strains better adapted to environmental stresses are being selected along the transmission routes to humans.