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

• Published in: Scientific reports Vol. 8; no. 1; pp. 1902 - 8
• Main Authors: Kirk, Karina Frahm, Méric, Guillaume, Nielsen, Hans Linde, Pascoe, Ben, Sheppard, Samuel K, Thorlacius-Ussing, Ole, Nielsen, Henrik
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 30.01.2018; Nature Publishing Group UK
• Subjects: Adult; Aged; Biopsy; Biopsy - methods; Campylobacter; Campylobacter - genetics; Campylobacter Infections - microbiology; Cell walls; Epidemiology; Feces; Feces - microbiology; Female; Gastroenteritis; Gastroenteritis - microbiology; Gastrointestinal Microbiome - genetics; Genetic diversity; Genetic Variation - genetics; Genomics; Genomics - methods; Humans; Inflammatory bowel disease; Inflammatory bowel diseases; Inflammatory Bowel Diseases - microbiology; Intestine; Male; Middle Aged; Molecular Epidemiology - methods; Mouth - microbiology; Mucosa; Multilocus sequence typing; Multilocus Sequence Typing - methods; Nucleotide sequence; Oral cavity; Phenotype; Phylogeny; Saliva; Saliva - microbiology; Young Adult
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-20135-4

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.