Comparative genomics of Campylobacter concisus

Analysis of clinical strains reveals genome diversity and pathogenic potential

Matthew R. Gemmell, Susan Berry, Indrani Mukhopadhya, Richard Hansen, Hans L. Nielsen, Mona Bajaj-Elliott, Henrik Nielsen, Georgina L. Hold*

*Corresponding author for this work

Research output: Contribution to journalArticle

6 Citations (Scopus)
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Abstract

In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. Campylobacter concisus, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from C. concisus strains and undertook a comprehensive pangenome assessment to identify C. concisus virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new C. concisus strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn's disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the Campylobacter genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that C. concisus strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.

Original languageEnglish
Article number116
JournalEmerging Microbes and Infections
Volume7
Early online date26 Jun 2018
DOIs
Publication statusPublished - 2018

Fingerprint

Campylobacter
Genomics
Genome
Virulence
Gastroenteritis
Bacterial Secretion Systems
Lymphocytic Colitis
Collagenous Colitis
Lower Gastrointestinal Tract
Genes
Gingivitis
Gastrointestinal Diseases
Periodontitis
Colitis
Inflammatory Bowel Diseases
Crohn Disease
Cluster Analysis
Gastrointestinal Tract
Colorectal Neoplasms
Phenotype

ASJC Scopus subject areas

  • Epidemiology
  • Parasitology
  • Microbiology
  • Immunology
  • Drug Discovery
  • Infectious Diseases
  • Virology

Cite this

Comparative genomics of Campylobacter concisus : Analysis of clinical strains reveals genome diversity and pathogenic potential. / Gemmell, Matthew R.; Berry, Susan; Mukhopadhya, Indrani; Hansen, Richard; Nielsen, Hans L.; Bajaj-Elliott, Mona; Nielsen, Henrik; Hold, Georgina L.

In: Emerging Microbes and Infections, Vol. 7, 116, 2018.

Research output: Contribution to journalArticle

Gemmell, Matthew R. ; Berry, Susan ; Mukhopadhya, Indrani ; Hansen, Richard ; Nielsen, Hans L. ; Bajaj-Elliott, Mona ; Nielsen, Henrik ; Hold, Georgina L. / Comparative genomics of Campylobacter concisus : Analysis of clinical strains reveals genome diversity and pathogenic potential. In: Emerging Microbes and Infections. 2018 ; Vol. 7.
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abstract = "In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. Campylobacter concisus, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from C. concisus strains and undertook a comprehensive pangenome assessment to identify C. concisus virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new C. concisus strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn's disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the Campylobacter genus, were present in the genomes assemblies, with 82{\%} containing Type VI secretion system genes. Our findings indicate that C. concisus strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.",
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note = "We thank members of the GI Research Team for discussions and advice. The authors thank Brennan Martin and the Centre for Genome Enabled Biology and Medicine for Illumina sequencing and useful discussions. This work was supported by a Fulbright Scholarship to G.L.H., an NHS Grampian Endowment grant fund to I.M. and G.L.H., a CSO clinical academic fellowship to R.H. (CAF/08/01). R.H. is supported by an NHS Research Scotland Career Researcher Fellowship. This work was generously supported by the Catherine McEwan Foundation. Sequence deposition The C. concisus raw sequencing reads and genome assemblies are freely available from the EMBL-EBI ENA under the study Accession PRJEB22351.",
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AU - Hold, Georgina L.

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