Genome and Methylome analysis of a phylogenetic novel Campylobacter coli cluster with C. jejuni introgression
Authors: Dieckmann Anastasia-Lisa , Riedel Thomas , Bunk Boyke , Spröer Cathrin , Overmann Jörg , Groß Uwe , Bader Oliver , Bohne Wolfgang , Morgenstern Burkhard , Hosseini Morteza , Zautner Andreas E. 
Published: October 2021

The intriguing recent discovery of

Campylobacter coli

strains, especially of clade 1, that (i) possess mosaic

C. coli

/

C. jejuni

alleles, (ii) demonstrate mixed multilocus sequence types (MLSTs) and (iii) have undergone genome-wide introgression has led to the speculation that these two species may be involved in an accelerated rate of horizontal gene transfer that is progressively leading to the merging of both species in a process coined ‘despeciation’. In an MLST-based neighbour-joining tree of a number of

C. coli

and

C. jejuni

isolates of different clades, three prominent

Campylobacter

isolates formed a seemingly separate cluster besides the previously described

C. coli

and

C. jejuni

clades. In the light of the suspected, ongoing genetic introgression between the

C. coli

and

C. jejuni

species, this cluster of

Campylobacter

isolates is proposed to present one of the hybrid clonal complexes in the despeciation process of the genus. Specific DNA methylation as well as restriction modification systems are known to be involved in selective uptake of external DNA and their role in such genetic introgression remains to be further investigated. In this study, the phylogeny and DNA methylation of these putative

C. coli

/

C. jejuni

hybrid strains were explored, their genomic mosaic structure caused by

C. jejuni

introgression was demonstrated and basic phenotypic assays were used to characterize these isolates. The genomes of the three hybrid

Campylobacter

strains were sequenced using PacBio SMRT sequencing, followed by methylome analysis by Restriction-Modification Finder and genome analysis by Parsnp, Smash++ and blast. Additionally, the strains were phenotypically characterized with respect to growth behaviour, motility, eukaryotic cell invasion and adhesion, autoagglutination, biofilm formation, and water survival ability. Our analyses show that the three hybrid

Campylobacter

strains are clade 1

C

.

coli

strains, which have acquired between 8.1 and 9.1 % of their genome from

C. jejuni

. The

C. jejuni

genomic segments acquired are distributed over the entire genome and do not form a coherent cluster. Most of the genes originating from

C. jejuni

are involved in chemotaxis and motility, membrane transport, cell signalling, or the resistance to toxic compounds such as bile acids. Interspecies gene transfer from

C. jejuni

has contributed 8.1–9.1% to the genome of three

C. coli

isolates and initiated the despeciation between

C. jejuni

and

C. coli

. Based on their functional annotation, the genes originating from

C. jejuni

enable the adaptation of the three strains to an intra-intestinal habitat. The transfer of a fused type II restriction-modification system that recognizes the CAYNNNNNCTC/GAGNNNNNRTG motif seems to be the key for the recombination of the

C. jejuni

genetic material with

C. coli

genomes.