Campylobacter jejuni and Campylobacter coli autotransporter genes exhibit lineage-associated distribution and decay

Abstract

Background: Campylobacter jejuni and Campylobacter coli are major global causes of bacterial gastroenteritis. Whilst several individual colonisation and virulence factors have been identified, our understanding of their role in the transmission, pathogenesis and ecology of Campylobacter has been hampered by the genotypic and phenotypic diversity within C. jejuni and C. coli. Autotransporter proteins are a family of outer membrane or secreted proteins in Gram-negative bacteria such as Campylobacter, which are associated with virulence functions. In this study we have examined the distribution and predicted functionality of the previously described capC and the newly identified, related capD autotransporter gene families in Campylobacter. Results: Two capC-like autotransporter families, designated capC and capD, were identified by homology searches of genomes of the genus Campylobacter. Each family contained four distinct orthologs of CapC and CapD. The distribution of these autotransporter genes was determined in 5829 C. jejuni and 1347 C. coli genomes. Autotransporter genes were found as intact, complete copies and inactive formats due to premature stop codons and frameshift mutations. Presence of inactive and intact autotransporter genes was associated with C. jejuni and C. coli multi-locus sequence types, but for capC, inactivation was independent from the length of homopolymeric tracts in the region upstream of the capC gene. Inactivation of capC or capD genes appears to represent lineagespecific gene decay of autotransporter genes. Intact capC genes were predominantly associated with the C. jejuni ST-45 and C. coli ST-828 generalist lineages. The capD3 gene was only found in the environmental C. coli Clade 3 lineage. These combined data support a scenario of inter-lineage and interspecies exchange of capC and subsets of capD autotransporters. Conclusions: In this study we have identified two novel, related autotransporter gene families in the genus Campylobacter, which are not uniformly present and exhibit lineage-specific associations and gene decay. The distribution and decay of the capC and capD genes exemplifies the erosion of species barriers between certain lineages of C. jejuni and C. coli, probably arising through co-habitation. This may have implications for the phenotypic variability of these two pathogens and provide opportunity for new, hybrid genotypes to emerge.

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

“…coli ( N =1347) (Table S1) were obtained from the NCBI Genomes database (http://www.ncbi.nlm.nih.gov/genome/browse/) and the Campylobacter pubMLST website (http://pubmlst.org/campylobacter/) [35]. Genome assemblies were quality checked based on N 50 , L 50 , genome size and number of contigs, and have been used previously for studying gene distribution in Campylobacter [36, 37]. Genome sequences for non-jejuni/coli Campylobacter species such as C.…”

“…org/ campylobacter/) [35]. Genome assemblies were quality checked based on N 50 , L 50 , genome size and number of contigs, and have been used previously for studying gene distribution in Campylobacter [36,37]. Genome sequences for non-jejuni/coli Campylobacter species such as C. hepaticus, the C. lari group and C. upsaliensis were obtained from the NCBI genome database using ncbigenome-download version 0.2.11 (https:// github.…”

The Distribution of Campylobacter jejuni Virulence Genes in Genomes Worldwide Derived from the NCBI Pathogen Detection Database

“…Collective components such as the helical shape, amphitrichous flagella, capsular polysaccharide (CPS), Lipooligosaccharide (LOS), O-linked glycosylation of flagellins, and genotypic and phenotypic variation owing to an augmented number of phase-variable loci are some particularities that promote the successful enteric lifestyle of C. jejuni [9]. Some mechanisms of pathogenesis over C. jejuni, such as the discovery of the novel autotransporter CapC and other virulence factors, have constantly been elucidated [12,13].…”

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

“…To assess whether the distribution of CampyICE1 and other MGEs was linked to specific MLST-types or isolation source, we screened a collection of 5,829 C. jejuni and 1,347 C. coli genomes [36] using BLAST+ for the presence of CampyICE1, CJIE1, CJIE2, CJIE3, CJIE4, the plasmids pVir, pTet, pCC42, and the CJIE3-associated T6SS (Table 1). The CJIE1 element was the most common in C. jejuni, while CJIE4 was the least common of the MGEs from C. jejuni RM1221, although still more common than CampyICE1.…”

“…A collection of complete and draft genome sequences of C. jejuni (N=5,829) and C. coli (N=1,347) (Table S1) were obtained from the NCBI Genomes database (http://www.ncbi.nlm.nih.gov/genome/browse/) and the Campylobacter pubMLST website (http://pubmlst.org/campylobacter/) [35]. Genome assemblies were quality checked based on N50, L50, genome size and number of contigs, and have been used previously for studying gene distribution in Campylobacter [36,37]. Genome sequences for non-jejuni/coli Campylobacter species such as C. hepaticus, C. lari group and C. upsaliensis were obtained from the NCBI genome database using ncbi-genome-download version 0.2.11 (https://github.com/kblin/ncbi-genomedownload/).…”