Analysis of complete genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis.
Fang Liu, Siying Chen, Laurence Don Wai Luu, Seul A Lee, Alfred Chin Yen Tay, Ruochen Wu, Stephen M Riordan, Ruiting Lan, Lu Liu, Li Zhang
Author Information
Fang Liu: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
Siying Chen: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
Laurence Don Wai Luu: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
Seul A Lee: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
Alfred Chin Yen Tay: Helicobacter Research Laboratory, Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia.
Ruochen Wu: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
Stephen M Riordan: Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, Australia.
Ruiting Lan: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
Lu Liu: School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.
Li Zhang: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
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.
