{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T01:11:04Z","timestamp":1775783464905,"version":"3.50.1"},"reference-count":58,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2020,3,10]],"date-time":"2020-03-10T00:00:00Z","timestamp":1583798400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/doi.org\/10.1128\/AuthorWarrantyLicense.v1"},{"start":{"date-parts":[[2020,4,28]],"date-time":"2020-04-28T00:00:00Z","timestamp":1588032000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U54DK102556"],"award-info":[{"award-number":["U54DK102556"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000098","name":"HHS | NIH | NIH Clinical Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000098","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2020,4,28]]},"abstract":"<jats:p>\n            Environmental exposure has a significant impact on human health. While some airborne fungi can cause life-threatening infections, the impact of environment on fungal spore dispersal and transmission is poorly understood. The democratization of shotgun metagenomics allows us to explore important questions about fungal propagation. We focus on\n            <jats:italic>Pneumocystis<\/jats:italic>\n            , a genus of host-specific fungi that infect mammals via airborne particles. In humans,\n            <jats:named-content content-type=\"genus-species\">Pneumocystis jirovecii<\/jats:named-content>\n            causes lethal infections in immunocompromised patients if untreated, although its environmental reservoir and transmission route remain unclear.\n          <\/jats:p>","DOI":"10.1128\/mbio.03138-19","type":"journal-article","created":{"date-parts":[[2020,3,9]],"date-time":"2020-03-09T09:55:17Z","timestamp":1583747717000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":17,"title":["Humans Are Selectively Exposed to Pneumocystis jirovecii"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2990-2185","authenticated-orcid":false,"given":"Ousmane H.","family":"Ciss\u00e9","sequence":"first","affiliation":[{"name":"Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6078-5730","authenticated-orcid":false,"given":"Liang","family":"Ma","sequence":"additional","affiliation":[{"name":"Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0784-7987","authenticated-orcid":false,"given":"Michael","family":"Snyder","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep39606"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00009-18"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3004404"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1590\/s0074-02762009000300004"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1007409"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2018.08.015"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0008524"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jir018"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cir996"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2017.06.027"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02531-13"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00733"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.71.7.3852-3856.2003"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.08.060"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2015.01.001"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0160124"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms10740"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00428-12"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01470-17"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1096\/fj.12-224444"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.213959.116"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229202"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-62"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0015152"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0168-9525(00)02024-2"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh340"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu531"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz305"},{"key":"e_1_3_2_32_2","unstructured":"Li H. 2013. Aligning sequence reads clone sequences and assembly contigs with BWA-MEM. arXiv 1303.3997."},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"e_1_3_2_35_2","unstructured":"Garrison E. 2012. Haplotype-based variant detection from short-read sequencing. arXiv 1207.3907."},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.361602"},{"key":"e_1_3_2_37_2","unstructured":"R Core Team. 2018. R: a language and environment for statistical computing Vienna Austria. https:\/\/www.R-project.org\/."},{"key":"e_1_3_2_38_2","unstructured":"Kolde R. 2012. pheatmap: pretty heatmaps. R. package. https:\/\/cran.r-project.org\/web\/packages\/pheatmap\/index.html."},{"key":"e_1_3_2_39_2","volume-title":"FigTree, a graphical viewer of phylogenetic trees","author":"Rambaut A","year":"2009","unstructured":"Rambaut A. 2009. FigTree, a graphical viewer of phylogenetic trees. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom. https:\/\/github.com\/rambaut\/figtree\/releases."},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts480"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2019.103934"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.66.11.4954-4961.2000"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1177\/104063879600800124"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1136\/vr.140.14.372"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1177\/1040638717710237"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1550-7408.2001.tb00471.x"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/mmy\/myy139"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.3390\/v10040206"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.2307\/3282686"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1086\/324208"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1086\/653933"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/145.6.842"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/147.3.595"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1567-1364.2010.00698.x"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1086\/644643"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1097\/TP.0b013e3182a1618c"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00133-16"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1086\/319340"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1542\/peds.61.1.35"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mBio.03138-19","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mBio.03138-19","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,8]],"date-time":"2022-03-08T02:50:53Z","timestamp":1646707853000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mBio.03138-19"}},"subtitle":[],"editor":[{"given":"Louis M.","family":"Weiss","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2020,4,28]]},"references-count":58,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2020,4,28]]}},"alternative-id":["10.1128\/mBio.03138-19"],"URL":"https:\/\/doi.org\/10.1128\/mbio.03138-19","relation":{},"ISSN":["2161-2129","2150-7511"],"issn-type":[{"value":"2161-2129","type":"print"},{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,28]]},"assertion":[{"value":"2020-03-10","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e03138-19"}}