title: Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria.
abstract: Several Chlamydiales families are associated with epitheliocystis, a common condition of the fish gill epithelium. These families share common ancestors with the Chlamydiaceae and environmental Chlamydiae. Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange-spotted grouper (Epinephelus coioides) from North Queensland, Australia. Basophilic inclusions were present in the gills of 22/31 fish and the presence of the chlamydial pathogen in the cysts was confirmed by in situ hybridization. Giant grouper (Epinephelus lanceolatus) cultured in the same systems were epitheliocystis free. 16S rRNA gene sequencing revealed a novel member of the Candidatus Parilichlamydiaceae: Ca. Similichlamydia epinephelii. Using metagenomic approaches, we obtained an estimated 68% of the chlamydial genome, revealing that this novel chlamydial pathogen shares a number of key pathogenic hallmarks with the Chlamydiaceae, including an intact Type III Secretion system and several chlamydial virulence factors. This provides additional evidence that these pathogenic mechanisms were acquired early in the evolution of this unique bacterial phylum. The identification and genomic characterization of Ca. S. epinephelii provides new opportunities to study the biology of distantly-related chlamydial pathogens while shining a new light on the evolution of pathogenicity of the Chlamydiaceae.
authors.affiliation: Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia.
authors.forename: Alyce
authors.initials: A
authors.lastname: Taylor-Brown
authors.affiliation: Institute of Microbiology, University of Lausanne, Lausanne, CH-1011, Switzerland.
authors.forename: Trestan
authors.initials: T
authors.lastname: Pillonel
authors.affiliation: Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, 7248, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Bridle
authors.affiliation: Functional Genomics Centre, University of Zurich, Zurich, CH-8057, Switzerland.
authors.forename: Weihong
authors.initials: W
authors.lastname: Qi
authors.affiliation: Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia.
authors.forename: Nathan L
authors.initials: NL
authors.lastname: Bachmann
authors.affiliation: Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Cairns, Queensland, 4878, Australia.
authors.forename: Terrence L
authors.initials: TL
authors.lastname: Miller
authors.affiliation: Institute of Microbiology, University of Lausanne, Lausanne, CH-1011, Switzerland.
authors.forename: Gilbert
authors.initials: G
authors.lastname: Greub
authors.affiliation: Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, 7248, Australia.
authors.forename: Barbara
authors.initials: B
authors.lastname: Nowak
authors.affiliation: Functional Genomics Centre, University of Zurich, Zurich, CH-8057, Switzerland.|Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland.
authors.forename: Helena M B
authors.initials: HMB
authors.lastname: Seth-Smith
authors.affiliation: Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland.
authors.forename: Lloyd
authors.initials: L
authors.lastname: Vaughan
authors.affiliation: Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia.
authors.forename: Adam
authors.initials: A
authors.lastname: Polkinghorne
mesh_terms: D000818:Animals; D001315:Australia; D001482:Base Composition / Q000235:genetics; D001492:Bass / Q000382:microbiology*; D002689:Chlamydia / Q000145:classification* / Q000235:genetics* / Q000472:pathogenicity; D002690:Chlamydia Infections / Q000382:microbiology* / Q000473:pathology; D004269:DNA, Bacterial / Q000235:genetics; D005393:Fish Diseases / Q000382:microbiology*; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D005880:Gills / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D000069296:Type III Secretion Systems / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D000069296:Type III Secretion Systems; D037521:Virulence Factors