Sequencing and Validation of the Genome of a Campylobacter concisus Reveals Intra-Species Diversity

Nandan P Deshpande,Hazel Mitchell,Simone S Li,Karolina Janitz,Nadeem O Kaakoush,Mark J Raftery,Marc R Wilkins,Indra Neil Sarkar

doi:10.1371/journal.pone.0022170

Abstract

Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. Here, we sequence and analyze the genome of a C. concisus from a biopsy of a child with Crohn's disease (UNSWCD); the second such genome for this species. A 1.8 Mb genome was assembled with paired-end reads from a next-generation sequencer. This genome is smaller than the 2.1 Mb C. concisus reference BAA-1457. While 1593 genes were conserved across UNSWCD and BAA-1457, 138 genes from UNSWCD and 281 from BAA-1457 were unique when compared against the other. To further validate the genome assembly and annotation, comprehensive shotgun proteomics was performed. This confirmed 78% of open reading frames in UNSWCD and, importantly, provided evidence of expression for 217 proteins previously defined as ‘hypothetical’ in Campylobacter. Substantial functional differences were observed between the UNSWCD and the reference strain. Enrichment analysis revealed differences in membrane proteins, response to stimulus, molecular transport and electron carriers. Synteny maps for the 281 genes not present in UNSWCD identified seven functionally associated gene clusters. These included one associated with the CRISPR family and another which encoded multiple restriction endonucleases; these genes are all involved in resistance to phage attack. Many of the observed differences are consistent with UNSWCD having adapted to greater surface interaction with host cells, as opposed to BAA-1457 which may prefer a free-living environment.

Highlights

There is mounting evidence that members of the Campylobacter genus other than the well-established Campylobacter jejuni and Campylobacter coli play a role in intestinal disease
Genome assembly of Campylobacter concisus UNSWCD The isolation of C. concisus from an intestinal biopsy of a child with Crohn’s disease (CD) allows for the investigation of heterogeneity within this bacterial species [14,15]
A study by Matsheka et al has suggested that the species of C. concisus as it is currently defined could represent a taxonomic continuum comprised of several genomospecies [18], based on the high genetic diversity observed between strains of this species

Summary

Introduction

There is mounting evidence that members of the Campylobacter genus other than the well-established Campylobacter jejuni and Campylobacter coli play a role in intestinal disease They have been reported to account for a proportion of cases of acute gastroenteritis where no etiological agent is identified [1,2]. A number of recent studies have reported both the detection and isolation of C. concisus from biopsy specimens and fecal samples of children with newly diagnosed Crohn’s disease (CD) [14,15] While such studies would support the role of C. concisus as an intestinal pathogen, the isolation of C. concisus from healthy individuals, and the failure of some studies to show a significant difference in the prevalence of C. concisus in subjects with diarrhea and healthy controls [12,13,16,17], has raised contention as to the role of C. concisus in intestinal disease. While these latter findings would argue, to some degree, against the role of C. concisus in gastroenteritis, the fact that great sequence diversity exists within C. concisus strains [12,17] raises the possibility that differences may exist in the pathogenic potential of C. concisus strains [3]

Methods

Results

Conclusion