{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T21:51:57Z","timestamp":1791755517203,"version":"4.3.4"},"reference-count":59,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2022,10,31]],"date-time":"2022-10-31T00:00:00Z","timestamp":1667174400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"crossref","award":["DE190100238"],"award-info":[{"award-number":["DE190100238"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100009207","name":"Agrifutures Australia","doi-asserted-by":"crossref","award":["PRJ-011402"],"award-info":[{"award-number":["PRJ-011402"]}],"id":[{"id":"10.13039\/501100009207","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,31]]},"abstract":"\n \n \n Chlamydia psittaci<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> is an avian pathogen with zoonotic potential. In Australia, \n \n C. psittaci<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> has been well reported as a cause of reproductive loss in mares which subsequently have been the source of infection and illness in some in-contact humans. To date, molecular typing studies describe the predominant and clonal \n \n C. psittaci<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> sequence type (ST)24 strains in horse, psittacine, and human infections. We sought to assess the clonality between ST24 strains and the emergence of equine ST24 with a comprehensive genomics approach. We used culture-independent probe-based and metagenomic whole-genome sequencing to investigate 13 \n \n C<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>. \n \n psittaci<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> genomes from horses, psittacines, and a pigeon from Australia. Published genomes of 36 \n \n C<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>. \n \n psittaci<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> strains were also used to contextualise our Australian dataset and investigate lineage diversity. We utilised a single-nucleotide polymorphism (SNP) based clustering and multi-locus sequence typing (MLST) approach. \n \n C. psittaci<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> has four major phylogenetic groups (PG1-4) based on core-genome SNP-based phylogeny. PG1 contained clonal global and Australian equine, psittacine, and human ST24 genomes, with a median pairwise SNP distance of 68 SNPs. PG2, PG3, and PG4 had greater genomic diversity, including diverse STs collected from birds, livestock, human, and horse hosts from Europe and North America and a racing pigeon from Australia. We show that the clustering of \n \n C. psittaci<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> by MLST was congruent with SNP-based phylogeny. The monophyletic ST24 clade has four major sub-lineages. The genomes of 17 Australian human, equine, and psittacine strains collected between 2008 and 2021 formed the predominant ST24 sub-lineage 1 (emerged circa 1979). Despite a temporal distribution of 13\u2009years, the genomes within sub-lineage 1 had a median pairwise SNP distance of 32 SNPs, suggesting a recent population expansion or potential cross-host transmission. However, two \n \n C. psittaci<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> genomes collected in 2015 from Victorian parrots clustered into distinct ST24 sub-lineage 4 (emerged circa 1965) with ovine strain C19\/98 from Germany. This work describes a comprehensive phylogenomic characterisation of ST24 and identifies a timeline of potential bird-to-equine spillover events.<\/jats:p>","DOI":"10.1099\/mgen.0.000888","type":"journal-article","created":{"date-parts":[[2022,10,21]],"date-time":"2022-10-21T14:18:36Z","timestamp":1666361916000},"source":"Crossref","is-referenced-by-count":16,"title":["One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia"],"prefix":"10.1099","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6620-758X","authenticated-orcid":false,"given":"Rhys T.","family":"White","sequence":"first","affiliation":[{"name":"University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia"},{"name":"The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia"},{"name":"The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan I.","family":"Anstey","sequence":"additional","affiliation":[{"name":"University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3284-2168","authenticated-orcid":false,"given":"Vasilli","family":"Kasimov","sequence":"additional","affiliation":[{"name":"University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5966-072X","authenticated-orcid":false,"given":"Cheryl","family":"Jenkins","sequence":"additional","affiliation":[{"name":"NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0400-9670","authenticated-orcid":false,"given":"Joanne","family":"Devlin","sequence":"additional","affiliation":[{"name":"The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6999-2664","authenticated-orcid":false,"given":"Charles","family":"El-Hage","sequence":"additional","affiliation":[{"name":"The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1154-652X","authenticated-orcid":false,"given":"Yvonne","family":"Pannekoek","sequence":"additional","affiliation":[{"name":"University of Amsterdam, Amsterdam UMC, Department of Medical Microbiology and Infection Prevention, Amsterdam 1105, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2407-4496","authenticated-orcid":false,"given":"Alistair R.","family":"Legione","sequence":"additional","affiliation":[{"name":"The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1340-2562","authenticated-orcid":false,"given":"Martina","family":"Jelocnik","sequence":"additional","affiliation":[{"name":"University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.20348031"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1093\/femspd\/ftu007"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1038\/emi.2016.135"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1111\/tbed.12817"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1016\/j.tvjl.2021.105683"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1111\/avj.13010"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1038\/s41426-018-0089-y"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.001284"},{"key":"R9","volume-title":"Safety in Laboratories. Part 3: Microbiological Safety and Containment","year":"2010"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000145"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens9110899"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0035097"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00604-12"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1038\/srep30019"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10081015"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0014179"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9030625"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1186\/s12917-021-02986-8"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-3-r46"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn741"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10121543"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0524-x"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx610"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2109"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1080\/10635150390235520"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14694.1"},{"key":"R33","article-title":"R: a language and environment for statistical computing","year":"2021"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst028"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vew007"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003537"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9694-0_7"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msw080"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-021-08010-5"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1101\/gr.212647.116"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.01302-20"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.03534-14"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1111\/tbed.14457"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10080968"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2021.104990"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-3657-y"},{"key":"R48","first-page":"149","article-title":"Veterinary management of horse transport","volume":"44","author":"Leadon","year":"2008","journal-title":"Vet Ital"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000528"},{"key":"R50","volume-title":"Walers: Australian horses abroad","author":"Yarwood","year":"2015"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msn160"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1017\/s0022172400032435"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.5694\/j.1326-5377.1939.tb98795.x"},{"key":"R54","article-title":"Avian psittacosis","volume":"29","author":"Meyer","year":"1935","journal-title":"J Bacteriol"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.656209"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1080\/23744235.2018.1495840"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.E14-11-1530"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1111\/imj.14726"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1017\/S1466252311000041"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000888?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T18:32:43Z","timestamp":1702578763000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000888"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,31]]},"references-count":59,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2022,10,31]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000888","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,10,31]]}}}