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It came to prominence as an opportunistic pathogen that not only can cause life-threatening pneumonia in patients with HIV infection and other immunodeficiencies but also can colonize the lungs of healthy individuals from a very early age. The genus<jats:named-content content-type=\"genus-species\">Pneumocystis<\/jats:named-content>includes a group of closely related but heterogeneous organisms that have a worldwide distribution, have been detected in multiple mammalian species, are highly host species specific, inhabit the lungs almost exclusively, and have never convincingly been cultured<jats:italic>in vitro<\/jats:italic>, making<jats:named-content content-type=\"genus-species\">Pneumocystis<\/jats:named-content>a fascinating but difficult-to-study organism. Improved molecular biologic methodologies have opened a new window into the biology and epidemiology of<jats:named-content content-type=\"genus-species\">Pneumocystis<\/jats:named-content>. Advances include an improved taxonomic classification, identification of an extremely reduced genome and concomitant inability to metabolize and grow independent of the host lungs, insights into its transmission mode, recognition of its widespread colonization in both immunocompetent and immunodeficient hosts, and utilization of strain variation to study drug resistance, epidemiology, and outbreaks of infection among transplant patients. This review summarizes these advances and also identifies some major questions and challenges that need to be addressed to better understand<jats:named-content content-type=\"genus-species\">Pneumocystis<\/jats:named-content>biology and its relevance to clinical care.<\/jats:p>","DOI":"10.1128\/cmr.00009-18","type":"journal-article","created":{"date-parts":[[2018,8,3]],"date-time":"2018-08-03T10:24:50Z","timestamp":1533291890000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":81,"title":["A Molecular Window into the Biology and Epidemiology of Pneumocystis spp"],"prefix":"10.1128","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6078-5730","authenticated-orcid":false,"given":"Liang","family":"Ma","sequence":"first","affiliation":[{"name":"Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2990-2185","authenticated-orcid":false,"given":"Ousmane H.","family":"Ciss\u00e9","sequence":"additional","affiliation":[{"name":"Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5191-9880","authenticated-orcid":false,"given":"Joseph A.","family":"Kovacs","sequence":"additional","affiliation":[{"name":"Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1086\/497381"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1086\/319340"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1542\/peds.19.4.543"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1542\/peds.2004-2157"},{"key":"e_1_3_3_6_2","first-page":"305","article-title":"A cluster of Kaposi's sarcoma and Pneumocystis carinii pneumonia among homosexual male residents of Los Angeles and Orange Counties, California","volume":"31","author":"Centers for Disease Control and Prevention","year":"1982","unstructured":"Centers for Disease Control and Prevention. 1982. 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