Pangenome analysis reveals genetic isolation inCampylobacter hyointestinalissubspecies adapted to different mammalian hosts

Abstract

Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. 40 hyointestinalis subsp. lawsonii which is restricted to pigs, and C. hyointestinalis subsp. hyointestinalis which can 41 be found in a much wider range of mammalian hosts. Despite C. hyointestinalis has been reported as an 42 emerging pathogen, its evolutionary and host-associated diversification patterns are still vastly unexplored. For 43 this reason, we whole-genome sequenced 13 C. hyointestinalis subsp. hyointestinalis strains and performed a 44 comprehensive comparative analysis including publicly available genomes of C. hyointestinalis subsp.45 hyointestinalis and C. hyointestinalis subsp. lawsonii to gain insight into the genomic variation of these 46 differentially-adapted subspecies. Both subspecies are distinct phylogenetic lineages which present a barrier to 47 homologous recombination, suggesting genetic isolation. This is further supported by accessory gene patterns 48 that recapitulate the core genome phylogeny. Additionally, C. hyointestinalis subsp. hyointestinalis presents a 49 bigger and more diverse accessory genome, which probably reflects its capacity to colonize different mammalian 50 hosts unlike C. hyointestinalis subsp. lawsonii that is host-restricted. This greater plasticity in the accessory 51 genome of C. hyointestinalis subsp. hyointestinalis correlates to a higher incidence of genome-wide 52 recombination events, that may be the underlying mechanism driving its diversification. Concordantly, both 53 subspecies present distinct patterns of gene families involved in genome plasticity and DNA repair like CRISPR-54 associated proteins and restriction-modification systems. Together, our results provide an overview of the 55 genetic mechanisms shaping the genomes of C. hyointestinalis subspecies, contributing to understand the 56 biology of Campylobacter species that are increasingly found as emerging pathogens.

Pathogenomics of EmergingCampylobacterSpecies

“…hyointestinalis (a generalist colonizing several mammalian species) and C. hyointestinalis subsp. lawsonii (a specialist adapted to pigs), which represent clearly divergent phylogenetic lineages (82). The genomes of these host-adapted subspecies are characterized by distinct accessory gene patterns which reflect dissimilarities in their functional repertories.…”

“…However, different types of barriers to homologous recombination can be implicated in a maintaining population structure, particularly in host-associated lineages, where strains colonizing a certain host are typically not in contact with those colonizing a different host. For example, the C. hyointestinalis subspecies found in different mammalian species are separated by a strong recombination barrier (82). Interestingly, these subspecies present a borderline average nucleotide identity indicating an underlying speciation process driven by genetic and ecological isolation.…”