title: Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes.
abstract: Although the major food-borne pathogen Campylobacter 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 commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing 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 deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization.
authors.affiliation: Institute of Infection and Global Health Institute of Integrative Biology National Centre for Zoonosis Research, University of Liverpool, Liverpool L69 3GA, UK.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Hepworth
authors.forename: Kevin E
authors.initials: KE
authors.lastname: Ashelford
authors.forename: Jason
authors.initials: J
authors.lastname: Hinds
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Gould
authors.forename: Adam A
authors.initials: AA
authors.lastname: Witney
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Williams
authors.forename: Howard
authors.initials: H
authors.lastname: Leatherbarrow
authors.forename: Nigel P
authors.initials: NP
authors.lastname: French
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Birtles
authors.forename: Chriselle
authors.initials: C
authors.lastname: Mendonca
authors.forename: Nick
authors.initials: N
authors.lastname: Dorrell
authors.forename: Brendan W
authors.initials: BW
authors.lastname: Wren
authors.forename: Paul
authors.initials: P
authors.lastname: Wigley
authors.forename: Neil
authors.initials: N
authors.lastname: Hall
authors.forename: Craig
authors.initials: C
authors.lastname: Winstanley
mesh_terms: D000818:Animals; D000835:Animals, Wild / Q000382:microbiology*; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D016123:Campylobacter jejuni / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D002874:Chromosome Mapping; D055028:Comparative Genomic Hybridization; D014644:Genetic Variation; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D014871:Water Microbiology