Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes.

Summary Although the major food-borne pathogen Campylo- bacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more com- monly associated with particular sources. Using com- parative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal com- plexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with mul- tilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequenc- ing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified dele- tions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken coloni- zation or in virulence. Novel genomic insertions con- tributingtotheaccessorygenomesofstrains1336and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of iso- lates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novelaccessoryregions.Whilestrain1336wasableto colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414mayplayanimportantroleinthiscommonrouteof Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evi- dence of adaptation leading to niche specialization.