Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis

Campylobacter concisus is an oral bacterium that has been shown to be associated with inflammatory bowel disease (IBD). C. concisus has been consistently shown to be a bacterium of two genomospecies by a number of studies using a number of techniques including amplified fragment length polymorphism (AFLP), analysis of housekeeping genes and 23S rRNA gene. A number of studies have reported C. concisus strains of GS2 to invade human epithelial cell line Caco2, and suggested that C. concisus strains of the two genomospecies may have different virulence potential. However, no studies to date have examined the genomes of C. concisus strains from different genomospecies. The comparative genome analysis of C. concisus strains may provide insights into genomospecies and their virulence. The aims of this thesis was therefore 1) To examine the genomic features of C. concisus strains of different genomospecies, and 2) To identify new potential virulence genes in C. concisus strains. In Chapter 2, genomes of 27 C. concisus strains were sequenced and an additional 9 publically available were analysed. It was found that the C. concisus core-genome, sequences of housekeeping genes and 23S rRNA gene consistently defined the two C. concisus genomospecies. Furthermore, genomospecies-specific genes were identified, including 9 GS1-specfic genes and 14 GS2-specific genes. CRISPR-Cas system-associated proteins were only found in some GS2 strains but completely absent from GS1 strains. These results suggest that the two C. concisus genomospecies may differ in their virulence potential and the ability to adapt to different environments. In Chapter 3, two novel C. concisus genomic islands were identified. The two genomic islands CON_PiiA and CON_PiiB were found in 37.5% (3/8) of enteric strains and 18.5% (5/27) of oral strains, respectively. These two genomic islands were found in both genomospecies and hence are not associated to a specific genomospecies. Both islands were found to carry T4SS homologous proteins and a number of putative effector proteins similar to known pathogen effector proteins were identified. These results suggest that the two novel C. concisus genomic islands are likely to be involved in C. concisus virulence. In conclusion, this thesis reports novel C. concisus genomic features that may provide insights into understanding the pathogenicity of this opportunistic pathogen.

Grantor dc:publisher

UNSW, Sydney

Year dc:date

2016

Author dc:creator

• Chung, Heung Kit Leslie

• Genome analysis
• IBD
• Campylobacter concisus

Statement dc:rights

• open access
• CC BY-NC-ND 3.0
• free_to_read

Licence

• https://purl.org/coar/access_right/c_abf2
• https://creativecommons.org/licenses/by-nc-nd/3.0/au/

Language dc:language

EN

Identifier

https://doi.org/10.26190/unsworks/19704

OAI identifier oai:identifier

oai:unsworks.library.unsw.edu.au:1959.4/57963