ena-STUDY-Univeristy of Aberdeen-02-09-2017-12:42:22:540-148
Comparative genomics of Campylobacter concisus: Analysis of  clinical strains reveals genome diversity and pathogenic potential
In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. One such Campylobacter species is Campylobacter concisus, an oral commensal, which has historically been linked to gingivitis and periodontitis. This has offered the tantalising question of whether virulence potential of these strains changes through the gastrointestinal tract. Our aim was to generate robust genome sequence data for a number of clinical C. concisus strains and undertake a comprehensive pangenome assessment to identify properties that could explain C. concisus pathogenic potential. Results: Genomes of 53 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). The new genomes contained an average of 2006 unique genes (range 1811 - 2115 genes). The majority of the genomes were shown to have high contiguity, high completeness and a low amount of errors. 92% of the genomes had 50 or less contigs. When compared to 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 indicated that there are few genetic differences between oral and gut isolates which may show that oral to gut transmission is possible. Conclusions: Our findings indicate that C. concisus strains are phenotypically and genetically diverse, and suggest that the variability in bacterial secretion system content may play an important role in their virulence potential.
In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. One such Campylobacter species is Campylobacter concisus, an oral commensal, which has historically been linked to gingivitis and periodontitis. This has offered the tantalising question of whether virulence potential of these strains changes through the gastrointestinal tract. Our aim was to generate robust genome sequence data for a number of clinical C. concisus strains and undertake a comprehensive pangenome assessment to identify properties that could explain C. concisus pathogenic potential. Results: Genomes of 53 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). The new genomes contained an average of 2006 unique genes (range 1811 - 2115 genes). The majority of the genomes were shown to have high contiguity, high completeness and a low amount of errors. 92% of the genomes had 50 or less contigs. When compared to 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 indicated that there are few genetic differences between oral and gut isolates which may show that oral to gut transmission is possible. Conclusions: Our findings indicate that C. concisus strains are phenotypically and genetically diverse, and suggest that the variability in bacterial secretion system content may play an important role in their virulence potential.