{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T21:01:12Z","timestamp":1765486872755,"version":"3.41.2"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T00:00:00Z","timestamp":1674864000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006229","name":"Oak Ridge Institute for Science and Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006229","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Aspergillus fumigatus, an environmental mold, causes life-threatening infections. Studies on the phylogenetic structure of human clinical A. fumigatus isolates are limited. Here, we performed whole genome sequencing of 24 A. fumigatus isolates collected from 18 patients in U.S. healthcare facilities in California. Single-nucleotide polymorphism (SNP) differences between patient isolates ranged from 187 to 70\u2009829 SNPs. For five patients with multiple isolates, we calculated the within-host diversities. Three patients had a within-host diversity that ranged from 4 to 10 SNPs and two patients ranged from 2 to 16\u2009977 SNPs. Findings revealed highly diverse A. fumigatus strains among patients and two patterns of diversity for isolates that come from the same patient, low and extremely high diversity.<\/jats:p>","DOI":"10.1093\/mmy\/myad012","type":"journal-article","created":{"date-parts":[[2023,1,30]],"date-time":"2023-01-30T11:21:14Z","timestamp":1675077674000},"source":"Crossref","is-referenced-by-count":2,"title":["Genomic description of human clinical<i>Aspergillus fumigatus<\/i>isolates, California, 2020"],"prefix":"10.1093","volume":"61","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6243-7716","authenticated-orcid":false,"given":"Elizabeth","family":"Misas","sequence":"first","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John Z","family":"Deng","sequence":"additional","affiliation":[{"name":"David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeremy A W","family":"Gold","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lalitha","family":"Gade","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalie S","family":"Nunnally","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ourania","family":"Georgacopoulos","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meghan","family":"Bentz","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth L","family":"Berkow","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anastasia P","family":"Litvintseva","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom M","family":"Chiller","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey D","family":"Klausner","sequence":"additional","affiliation":[{"name":"Departments of Population and Public Health Sciences and Medicine, Keck School of Medicine, University of Southern California , Los Angeles, California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nancy A","family":"Chow","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention , Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,1,28]]},"reference":[{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.jhin.2006.02.014","article-title":"Nosocomial aspergillosis in outbreak settings","volume":"63","author":"Vonberg","year":"2006","journal-title":"J Hosp Infect"},{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1086\/318483","article-title":"Aspergillosis case-fatality rate: systematic review of the literature","volume":"32","author":"Lin","year":"2001","journal-title":"Clin Infect Dis"},{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1093\/cid\/civ885","article-title":"Azole resistance in Aspergillus fumigatus: can we retain the clinical use of mold-active antifungal azoles?","volume":"62","author":"Verweij","year":"2016","journal-title":"Clin Infect Dis"},{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"69","DOI":"10.3390\/jof5030069","article-title":"A guide to investigating suspected outbreaks of mucormycosis in healthcare","volume":"5","author":"Hartnett","year":"2019","journal-title":"J Fungi"},{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"3216","DOI":"10.1128\/JCM.00936-14","article-title":"Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections","volume":"52","author":"Litvintseva","year":"2014","journal-title":"J Clin Microbiol"},{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"476","DOI":"10.3201\/eid2203.151193","article-title":"Whole-genome sequencing to determine origin of multinational outbreak of Sarocladium kiliense bloodstream infections","volume":"22","author":"Etienne","year":"2016","journal-title":"Emerg Infect Dis"},{"key":"2023022214293038600_","first-page":"1886","article-title":"Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus","volume":"59","author":"Pringle","year":"2005","journal-title":"Evolution"},{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"e0180321","DOI":"10.1128\/mBio.01803-21","article-title":"Genomic diversity of azole-resistant Aspergillus fumigatus in the United States","volume":"12","author":"Etienne","year":"2021","journal-title":"mBio"},{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1111\/myc.12800","article-title":"Evaluation of three MALDI-TOF mass spectrometry libraries for the identification of filamentous fungi in three clinical microbiology laboratories in Manitoba, Canada","volume":"61","author":"Stein","year":"2018","journal-title":"Mycoses"},{"key":"2023022214293038600_","doi-asserted-by":"crossref","first-page":"729476","DOI":"10.3389\/fcimb.2021.729476","article-title":"Molecular epidemiology of azole-resistant Aspergillus fumigatus in France shows patient and healthcare links to environmentally occurring genotypes","volume":"11","author":"Rocchi","year":"2021","journal-title":"Front Cell Infect Microbiol"}],"container-title":["Medical Mycology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mmy\/advance-article-pdf\/doi\/10.1093\/mmy\/myad012\/48946970\/myad012.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mmy\/article-pdf\/61\/2\/myad012\/49296555\/myad012.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mmy\/article-pdf\/61\/2\/myad012\/49296555\/myad012.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,22]],"date-time":"2023-03-22T22:59:12Z","timestamp":1679525952000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mmy\/article\/doi\/10.1093\/mmy\/myad012\/7008854"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,28]]},"references-count":10,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2023,2,3]]}},"URL":"https:\/\/doi.org\/10.1093\/mmy\/myad012","relation":{},"ISSN":["1369-3786","1460-2709"],"issn-type":[{"type":"print","value":"1369-3786"},{"type":"electronic","value":"1460-2709"}],"subject":[],"published-other":{"date-parts":[[2023,2]]},"published":{"date-parts":[[2023,1,28]]},"article-number":"myad012"}}