{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T23:58:58Z","timestamp":1790812738814,"version":"4.1.0"},"reference-count":67,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2013,3,26]],"date-time":"2013-03-26T00:00:00Z","timestamp":1364256000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"},{"start":{"date-parts":[[2013,5,1]],"date-time":"2013-05-01T00:00:00Z","timestamp":1367366400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2013,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            <jats:named-content content-type=\"genus-species\">Chlamydia psittaci<\/jats:named-content>\n            is an obligate intracellular bacterium. Interest in\n            <jats:italic>Chlamydia<\/jats:italic>\n            stems from its high degree of virulence as an intestinal and pulmonary pathogen across a broad range of animals, including humans.\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            human pulmonary infections, referred to as psittacosis, can be life-threatening, which is why the organism was developed as a bioweapon in the 20th century and is listed as a CDC biothreat agent. One remarkable recent result from comparative genomics is the finding of frequent homologous recombination across the genome of the sexually transmitted and trachoma pathogen\n            <jats:named-content content-type=\"genus-species\">Chlamydia trachomatis<\/jats:named-content>\n            . We sought to determine if similar evolutionary dynamics occurred in\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            . We analyzed 20\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            genomes from diverse strains representing the nine known serotypes of the organism as well as infections in a range of birds and mammals, including humans. Genome annotation revealed a core genome in all strains of 911 genes. Our analyses showed that\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            has a history of frequently switching hosts and undergoing recombination more often than\n            <jats:named-content content-type=\"genus-species\">C. trachomatis<\/jats:named-content>\n            . Evolutionary history reconstructions showed genome-wide homologous recombination and evidence of whole-plasmid exchange. Tracking the origins of recombinant segments revealed that some strains have imported DNA from as-yet-unsampled or -unsequenced\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            lineages or other\n            <jats:named-content content-type=\"genus-species\">Chlamydiaceae<\/jats:named-content>\n            species. Three ancestral populations of\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            were predicted, explaining the current population structure. Molecular clock analysis found that certain strains are part of a clonal epidemic expansion likely introduced into North America by South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots.\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            <jats:named-content content-type=\"genus-species\">Chlamydia psittaci<\/jats:named-content>\n            is classified as a CDC biothreat agent based on its association with life-threatening lung disease, termed psittacosis, in humans. Because of the recent remarkable findings of frequent recombination across the genome of the human sexually transmitted and ocular trachoma pathogen\n            <jats:named-content content-type=\"genus-species\">Chlamydia trachomatis<\/jats:named-content>\n            , we sought to determine if similar evolutionary dynamics occur in\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            . Twenty\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            genomes were analyzed from diverse strains that may play a pathogenic role in human disease. Evolution of the strains revealed genome-wide recombination occurring at a higher rate than for\n            <jats:named-content content-type=\"genus-species\">C. trachomatis<\/jats:named-content>\n            . Certain strains were discovered to be part of a recent epidemic clonal expansion originating in South America. These strains may have been introduced into the United States from South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. Our analyses indicate that\n            <jats:named-content content-type=\"genus-species\">C. psittaci<\/jats:named-content>\n            strains have a history of frequently switching hosts and undergoing recombination.\n          <\/jats:p>","DOI":"10.1128\/mbio.00604-12","type":"journal-article","created":{"date-parts":[[2013,3,27]],"date-time":"2013-03-27T03:22:10Z","timestamp":1364354530000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":88,"title":["Comparative Analysis of Chlamydia psittaci Genomes Reveals the Recent Emergence of a Pathogenic Lineage with a Broad Host Range"],"prefix":"10.1128","volume":"4","author":[{"given":"Timothy D.","family":"Read","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA"},{"name":"Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, 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