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

Karina Frahm Kirk, Guillaume Méric, Hans Linde Nielsen, Ben Pascoe, Samuel K Sheppard, Ole Thorlacius-Ussing, Henrik Nielsen

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish
Article number1902
JournalScientific Reports
Volume8
Issue number1
DOIs
Publication statusPublished - 30 Jan 2018

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Campylobacter
Molecular Epidemiology
Genomics
Inflammatory Bowel Diseases
Saliva
Feces
Phenotype
Biopsy
Genome
Genes
Genetic Heterogeneity
Secretory Pathway
Gastroenteritis
Cell Wall
Mouth
Cell Membrane

ASJC Scopus subject areas

  • General

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Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease. / Kirk, Karina Frahm; Méric, Guillaume; Nielsen, Hans Linde; Pascoe, Ben; Sheppard, Samuel K; Thorlacius-Ussing, Ole; Nielsen, Henrik.

In: Scientific Reports, Vol. 8, No. 1, 1902, 30.01.2018.

Research output: Contribution to journalArticle

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