Identification of genetic determinants that drive population differentiation and host adaptation in Campylobacter jejuni in California

<i>Campylobacter jejuni</i> is a commensal bacterium that colonizes livestock and wild animals and is responsible for more than 80% of campylobacteriosis cases in humans, which all ultimately have an animal source. Its high genome plasticity and recombination rate allow it to adapt to multiple hosts and lead to the rapid emergence of lineages, some of which can be antibiotic resistant. Our aim in this study was to examine the population structure of <i>Campylobacter</i> in California and assess its differentiation between animal hosts and humans. We sequenced 69 human clinical isolates of <i>C. jejuni</i> from California and collected a dataset of human and animal Californian genomes to contextualize them. By comparing groups of isolates, we detected significant levels of differentiation between the human and animal Californian isolates. Through phylogenetic reconstruction, we demonstrated that, as expected, the human <i>C. jejuni</i> clinical isolates were derived from both avian and ruminant sources but represented a distinct subset of those populations. By identifying the genomic regions that were contributing to population differentiation amongst the host groups, we were able to identify protein variants potentially responsible for host adaptation and propensity to cause infection in humans.