{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T07:04:20Z","timestamp":1791097460258,"version":"4.1.0"},"reference-count":16,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2012,12,26]],"date-time":"2012-12-26T00:00:00Z","timestamp":1356480000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"},{"start":{"date-parts":[[2013,3,1]],"date-time":"2013-03-01T00:00:00Z","timestamp":1362096000000},"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":[[2013,3]]},"abstract":"ABSTRACT<\/jats:title>\n \n Pneumocystis jirovecii<\/jats:named-content>\n is a fungus that causes severe pneumonia in immunocompromised patients. However, its study is hindered by the lack of an\n in vitro<\/jats:italic>\n culture method. We report here the genome of\n P.\u00a0jirovecii<\/jats:italic>\n that was obtained from a single bronchoalveolar lavage fluid specimen from a patient. The major challenge was the\n in silico<\/jats:italic>\n sorting of the reads from a mixture representing the different organisms of the lung microbiome. This genome lacks virulence factors and most amino acid biosynthesis enzymes and presents reduced GC content and size. Together with epidemiological observations, these features suggest that\n P.\u00a0jirovecii<\/jats:italic>\n is an obligate parasite specialized in the colonization of human lungs, which causes disease only in immune-deficient individuals. This genome sequence will boost research on this deadly pathogen.\n <\/jats:p>\n \n IMPORTANCE<\/jats:bold>\n Pneumocystis<\/jats:italic>\n pneumonia is a major cause of mortality in patients with impaired immune systems. The availability of the\n P.\u00a0jirovecii<\/jats:italic>\n genome sequence allows new analyses to be performed which open avenues to solve critical issues for this deadly human disease. The most important ones are (i) identification of nutritional supplements for development of culture\n in vitro<\/jats:italic>\n , which is still lacking 100\u00a0years after discovery of the pathogen; (ii) identification of new targets for development of new drugs, given the paucity of present treatments and emerging resistance; and (iii) identification of targets for development of\u00a0vaccines.\n <\/jats:p>","DOI":"10.1128\/mbio.00428-12","type":"journal-article","created":{"date-parts":[[2012,12,26]],"date-time":"2012-12-26T20:25:22Z","timestamp":1356553522000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":93,"title":["De Novo<\/i>\n Assembly of the Pneumocystis jirovecii Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient"],"prefix":"10.1128","volume":"4","author":[{"given":"Ousmane H.","family":"Ciss\u00e9","sequence":"first","affiliation":[{"name":"Institute of Microbiology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland,"},{"name":"Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Pagni","sequence":"additional","affiliation":[{"name":"Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe M.","family":"Hauser","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland,"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1621"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.32.12.2904-2912.1994"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000423"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0015152"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/EC.5.2.272-276.2006"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.112408.134335"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1186\/1745-6150-4-13"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/35083594"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.39.6.2126-2133.2001"},{"key":"e_1_3_2_11_2","first-page":"183","article-title":"Genetics, metabolism and host specificity of Pneumocystis carinii","volume":"36","author":"Wakefield AE","year":"1998","unstructured":"WakefieldAE StringerJR TamburriniE Dei-CasE . 1998. Genetics, metabolism and host specificity of Pneumocystis carinii. Med. Mycol. 36(Suppl 1):183\u2013193.","journal-title":"Med. Mycol."},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1086\/319340"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1086\/649869"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid0905.020660"},{"key":"e_1_3_2_15_2","doi-asserted-by":"crossref","unstructured":"MillerRF\nAmbroseHE\nWakefieldAE\n. 2001. Pneumocystis carinii f. sp. hominis DNA in immunocompetent health care workers in contact with patients with P. carinii pneumonia. J. Clin. Microbiol. 39:S89\u2013S91.","DOI":"10.1128\/JCM.39.11.3877-3882.2001"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1550-7408.2006.00184.x"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00438-009-0498-7"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mBio.00428-12","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mBio.00428-12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T20:46:14Z","timestamp":1646685974000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mBio.00428-12"}},"subtitle":[],"editor":[{"given":"Louis M.","family":"Weiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,3]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,3]]}},"alternative-id":["10.1128\/mBio.00428-12"],"URL":"https:\/\/doi.org\/10.1128\/mbio.00428-12","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.717999953.793482136","asserted-by":"object"},{"id-type":"doi","id":"10.3410\/f.717999953.793474783","asserted-by":"object"},{"id-type":"doi","id":"10.3410\/f.717999953.793478013","asserted-by":"object"}]},"ISSN":["2161-2129","2150-7511"],"issn-type":[{"value":"2161-2129","type":"print"},{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,3]]},"assertion":[{"value":"2012-10-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-11-26","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-12-26","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00428-12"}}