Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease

Abstract

Campylobacter concisus is an emerging pathogen associated with inflammatory bowel disease (IBD), yet little is known about the genetic diversity of C. concisus in relation to host niches and disease. We isolated 104 C. concisus isolates from saliva, mucosal biopsies and faecal samples from 41 individuals (26 IBD, 3 Gastroenteritis (GE), 12 Healthy controls (HC)). Whole genomes were sequenced and the dataset pan-genome examined, and genomic information was used for typing using multi-locus-sequence typing (MLST). C. concisus isolates clustered into two main groups/genomospecies (GS) with 71 distinct sequence types (STs) represented. Sampling site (p < 0.001), rather than disease phenotype (p = 1.00) was associated with particular GS. We identified 97 candidate genes associated with increase or decrease in prevalence during the anatomical descent from the oral cavity to mucosal biopsies to faeces. Genes related to cell wall/membrane biogenesis were more common in oral isolates, whereas genes involved in cell transport, metabolism and secretory pathways were more prevalent in enteric isolates. Furthermore, there was no correlation between individual genetic diversity and clinical phenotype. This study confirms the genetic heterogeneity of C. concisus and provides evidence that genomic variation is related to the source of isolation, but not clinical phenotype.

Figure 1

Genetic relatedness of C. concisus isolates. Each dot represents a single isolate, coloured according to: (A) disease phenotype (red = IBD, blue = gastroenteritis (GE), green = healthy controls (HC)) and (B) sample collection site (red = gut mucosal biopsies, blue = faeces, green = saliva). Left and right clusters represent genomospecies (GS) I and II, respectively. The proportion of isolates from IBD patients and healthy controls in the two genomospecies was not statistically different (p = 1.0), whereas isolates from saliva were more frequent in GS I compared to gut mucosal biopsy isolates, more frequent in GS II (p < 0.001). Phylogenetic trees were created from concatenated sequences of seven housekeeping genes.

Figure 2

Panel A: Overview of the pangenome and prevalence of detected genes per genome. A total of 864 core genes were present in all isolates and 1,095 genes were present in > 95% isolates. Panel B: Isolates belonging to GS II had a higher number of detected genes per genome compared to isolates from GS I. In average there were 313 ± 13 more genes per genomes in GS II isolates (1,914 ± 7, n = 78) compared to GS I isolates (1602 ± 9, n = 34) (p < 0.0001). Panel C: Seventy-three genes were found to increase in prevalence from oral isolates to gut mucosal isolates and to faecal isolates, with a minimum increase of 30% from saliva to gut mucosal biopsies. Panel D: Twenty-four genes decreased in prevalence from saliva to gut mucosal biopsies and to faeces, with a minimum 30% decrease from saliva to gut mucosal biopsies.

Figure 3

A phylogenetic tree based on the concatenated sequences of the zot gene, in 14 C. concisus isolates. Colours indicate clinical presentation (red = IBD, green = HC), shapes indicate sampling site: (dots = gut mucosal biopsies, triangles = saliva samples, diamonds = faecal samples).