Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis

Abstract

<i>Campylobacter concisus</i> is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC). Currently, only three complete <i>C. concisus</i> genomes are available and more complete <i>C. concisus</i> genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22 <i>C</i>. <i>concisus</i> strains were subjected to Oxford Nanopore genome sequencing. Complete genome assembly was performed using Nanopore genome data in combination with previously reported short-read Illumina data. Genome features of complete <i>C. concisus</i> genomes were analysed using bioinformatic tools. The enteric disease associations of <i>C. concisus</i> plasmids were examined using 239 <i>C</i>. <i>concisus</i> strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete <i>C. concisus</i> genomes in this study. Analysis of 16 complete <i>C. concisus</i> genomes (3 from public databases) identified multiple novel plasmids. pSma1 plasmid was found to be associated with severe UC. Sec-SRP, Tat and T6SS were found to be the main secretion systems in <i>C. concisus</i> and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete <i>C. concisus</i> genomes. This study also found that GS2 strains had larger genomes and higher GC content than GS1 strains and more often had plasmids. In conclusion, this study provides fundamental genomic data for understanding <i>C. concisus</i> plasmids, genomospecies features, evolution, secretion systems and pathogenicity.