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These families share common ancestors with the\n                    <jats:italic>Chlamydiaceae<\/jats:italic>\n                    and environmental\n                    <jats:italic>Chlamydiae<\/jats:italic>\n                    . Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange\u2010spotted grouper (\n                    <jats:italic>Epinephelus coioides<\/jats:italic>\n                    ) 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\n                    <jats:italic>in situ<\/jats:italic>\n                    hybridization. Giant grouper (\n                    <jats:italic>Epinephelus lanceolatus<\/jats:italic>\n                    ) cultured in the same systems were epitheliocystis free. 16S rRNA gene sequencing revealed a novel member of the\n                    <jats:italic>Candidatus<\/jats:italic>\n                    Parilichlamydiaceae:\n                    <jats:italic>Ca<\/jats:italic>\n                    . 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\n                    <jats:italic>Chlamydiaceae<\/jats:italic>\n                    , 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\n                    <jats:italic>Ca<\/jats:italic>\n                    . S. epinephelii provides new opportunities to study the biology of distantly\u2010related chlamydial pathogens while shining a new light on the evolution of pathogenicity of the\n                    <jats:italic>Chlamydiaceae<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1111\/1462-2920.13694","type":"journal-article","created":{"date-parts":[[2017,2,15]],"date-time":"2017-02-15T23:06:46Z","timestamp":1487200006000},"page":"1899-1913","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":31,"title":["Culture\u2010independent genomics of a novel chlamydial pathogen of fish provides new insight into host\u2010specific adaptations utilized by these intracellular bacteria"],"prefix":"10.1111","volume":"19","author":[{"given":"Alyce","family":"Taylor\u2010Brown","sequence":"first","affiliation":[{"name":"Centre for Animal Health Innovation, Faculty of Science, Engineering and Education University of the 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