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The zoonotic pathogen and causative agent of human Q fever,\n              <jats:italic>Coxiella burnetii<\/jats:italic>\n              , represents the best-characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here, we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the species previously referred to as Candidatus\n              <jats:italic>Coxiella cheraxi<\/jats:italic>\n              represents a novel genus within this family, herein denoted Candidatus\n              <jats:italic>Paracoxiella cheracis<\/jats:italic>\n              . Interestingly, we demonstrate that Candidatus\n              <jats:italic>P. cheracis<\/jats:italic>\n              encodes a complete, putatively functional Dot\/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen.\n              <jats:italic>In silico<\/jats:italic>\n              analysis defined a unique repertoire of Dot\/Icm effector proteins and highlighted homologs of several important\n              <jats:italic>C. burnetii<\/jats:italic>\n              effectors, including a homolog of CpeB that was demonstrated to be a Dot\/Icm substrate in\n              <jats:italic>C. burnetii<\/jats:italic>\n              .\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>\n                Using long-read sequencing technology, we have uncovered the full genome sequence of Candidatus\n                <jats:italic>Paracoxiella cheracis<\/jats:italic>\n                , a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insights into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. Candidatus\n                <jats:italic>P. cheracis<\/jats:italic>\n                also represents a new member of Dot\/Icm pathogens that rely on this system to establish an intracellular niche. Candidatus\n                <jats:italic>P. cheracis<\/jats:italic>\n                possesses a unique cohort of putative Dot\/Icm substrates that constitute a collection of new eukaryotic cell biology-manipulating effector proteins.\n              <\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/msphere.01002-24","type":"journal-article","created":{"date-parts":[[2025,3,10]],"date-time":"2025-03-10T14:00:24Z","timestamp":1741615224000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["The complete genome sequence of the crayfish pathogen Candidatus\n            <i>Paracoxiella cheracis<\/i>\n            n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family"],"prefix":"10.1128","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0707-6537","authenticated-orcid":true,"given":"Danielle 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University","place":["Clayton, Australia"]},{"name":"Department of Microbiology, Monash University","place":["Clayton, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8349-0778","authenticated-orcid":false,"given":"Ryan R.","family":"Wick","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity","place":["Melbourne, Australia"]},{"name":"Centre for Pathogen Genomics, University of Melbourne","place":["Parkville, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4467-6083","authenticated-orcid":true,"given":"Nadav","family":"Davidovich","sequence":"additional","affiliation":[{"name":"Israeli Veterinary Services","place":["Bet Dagan, Israel"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4601-9543","authenticated-orcid":false,"given":"Eleonora","family":"Fiocchi","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale delle Venezie","place":["Legnaro, Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3613-4839","authenticated-orcid":false,"given":"Louise M.","family":"Judd","sequence":"additional","affiliation":[{"name":"Centre for Pathogen Genomics, University of Melbourne","place":["Parkville, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6460-1604","authenticated-orcid":false,"given":"Jennifer","family":"Elliman","sequence":"additional","affiliation":[{"name":"College of Public Health, Medical and Veterinary Sciences, James Cook University","place":["Townsville, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leigh","family":"Owens","sequence":"additional","affiliation":[{"name":"College of Public Health, Medical and Veterinary Sciences, James Cook University","place":["Townsville, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0150-123X","authenticated-orcid":true,"given":"Timothy P.","family":"Stinear","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity","place":["Melbourne, Australia"]},{"name":"Centre for Pathogen Genomics, University of Melbourne","place":["Parkville, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6784-7271","authenticated-orcid":false,"given":"Andrea","family":"Basso","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale delle Venezie","place":["Legnaro, Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7699-9728","authenticated-orcid":false,"given":"Tobia","family":"Pretto","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale delle Venezie","place":["Legnaro, Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9240-2001","authenticated-orcid":true,"given":"Hayley J.","family":"Newton","sequence":"additional","affiliation":[{"name":"Infection Program, Monash Biomedicine Discovery Institute, Monash University","place":["Clayton, Australia"]},{"name":"Department of Microbiology, Monash University","place":["Clayton, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1111\/jfd.13314"},{"key":"e_1_3_4_3_2","first-page":"173","volume-title":"Diseases in Asian 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Systemic rickettsia-like infection in farmed freshwater crayfish, Cherax quadricarinatus, p 173\u2013179. In Shariff M, Subasinghe RP (ed), Diseases in Asian aquaculture. Asian Fisheries Society."},{"key":"e_1_3_4_4_2","first-page":"165","volume-title":"Diseases in Asian aquaculture","author":"Owens L","year":"1992","unstructured":"Owens L, Muir P, Sutton D, Wingfield M. 1992. The pathology of microbial diseases in tropical Australian Crustacea, p 165\u2013172. In Shariff M, Subasinghe RP (ed), Diseases in Asian aquaculture. 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