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Volume 6, Issue 11

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

Abstract

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 genomes are available and more complete genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22 . 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 genomes were analysed using bioinformatic tools. The enteric disease associations of plasmids were examined using 239 . strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete genomes in this study. Analysis of 16 complete 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 and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete 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 plasmids, genomospecies features, evolution, secretion systems and pathogenicity.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Campylobacter concisus , Campylobacters , inflammatory bowel disease , secretion system and ulcerative colitis
Funding
This study was supported by the:
  • University of New South Wales (Award PS46772)
    • Principle Award Recipient: Li Zhang
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2020-10-28
2024-04-23
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Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis
M Gen 6, e000457 (2020); https://doi.org/10.1099/mgen.0.000457
/content/journal/mgen/10.1099/mgen.0.000457
/content/journal/mgen/10.1099/mgen.0.000457
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