{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T14:47:39Z","timestamp":1791557259526,"version":"4.3.4"},"reference-count":46,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2014,12,1]],"date-time":"2014-12-01T00:00:00Z","timestamp":1417392000000},"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":["J Clin Microbiol"],"published-print":{"date-parts":[[2014,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    The emergence of azole-resistant strains of\n                    <jats:named-content content-type=\"genus-species\">Aspergillus fumigatus<\/jats:named-content>\n                    during treatment for aspergillosis occurs by a mutation selection process. Understanding how antifungal resistance mechanisms evolve in the host environment during infection is of great clinical importance and biological interest. Here, we used next-generation sequencing (NGS) to identify mutations that arose during infection by\n                    <jats:named-content content-type=\"genus-species\">A. fumigatus<\/jats:named-content>\n                    strains sequentially isolated from two patients, one with invasive pulmonary aspergillosis (IPA) (five isolations) and the other with aspergilloma (three isolations). The serial isolates had identical microsatellite types, but their growth rates and conidia production levels were dissimilar. A whole-genome comparison showed that three of the five isolates from the IPA patient carried a mutation, while 22 mutations, including six nonsynonymous ones, were found among three isolates from the aspergilloma patient. One aspergilloma isolate carried the\n                    <jats:italic>cyp51A<\/jats:italic>\n                    mutation P216L, which is reported to confer azole resistance, and it displayed an MIC indicating resistance to itraconazole. This isolate harbored five other nonsynonymous mutations, some of which were found in the\n                    <jats:italic>afyap1<\/jats:italic>\n                    and\n                    <jats:italic>aldA<\/jats:italic>\n                    genes. We further identified a large deletion in the aspergilloma isolate in a region containing 11 genes. This finding suggested the possibility that genomic deletions can occur during chronic infection with\n                    <jats:named-content content-type=\"genus-species\">A. fumigatus<\/jats:named-content>\n                    . Overall, our results revealed dynamic alterations that occur in the\n                    <jats:named-content content-type=\"genus-species\">A. fumigatus<\/jats:named-content>\n                    genome within its host during infection and treatment.\n                  <\/jats:p>","DOI":"10.1128\/jcm.01105-14","type":"journal-article","created":{"date-parts":[[2014,9,17]],"date-time":"2014-09-17T23:38:14Z","timestamp":1410997094000},"page":"4202-4209","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":111,"title":["Whole-Genome Comparison of Aspergillus fumigatus Strains Serially Isolated from Patients with Aspergillosis"],"prefix":"10.1128","volume":"52","author":[{"given":"Daisuke","family":"Hagiwara","sequence":"first","affiliation":[{"name":"Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroki","family":"Takahashi","sequence":"additional","affiliation":[{"name":"Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akira","family":"Watanabe","sequence":"additional","affiliation":[{"name":"Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan"},{"name":"Division of Control and Treatment of Infectious Diseases, Chiba University Hospital, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Azusa","family":"Takahashi-Nakaguchi","sequence":"additional","affiliation":[{"name":"Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susumu","family":"Kawamoto","sequence":"additional","affiliation":[{"name":"Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katsuhiko","family":"Kamei","sequence":"additional","affiliation":[{"name":"Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan"},{"name":"Division of Control and Treatment of Infectious Diseases, Chiba University Hospital, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tohru","family":"Gonoi","sequence":"additional","affiliation":[{"name":"Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1086\/513943"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.12.2.310"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1507.090043"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.medmal.2013.02.010"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.05088-11"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00514-12"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1086\/525258"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.41.6.1364"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.3109\/13693786.2010.508469"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1097\/QCO.0000000000000005"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2012.06.030"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.47.2.577-581.2003"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkh507"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.8.4112-4120.2005"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1080\/13693780802382244"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1080\/02681219180000521"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.31.5.1117-1121.1993"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1111\/myc.12047"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0050034"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1086\/588660"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2001.tb00006.x"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/157.2.591"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0080881"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.2174\/1875036201307010001"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr875"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature04332"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0028550"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp344"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbs017"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg1080"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1029"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiac.2014.01.003"},{"key":"e_1_3_3_38_2","volume-title":"CLSI document M38-A2","author":"Clinical and Laboratory Standards Institute","year":"2008","unstructured":"Clinical and Laboratory Standards Institute. 2008. Reference method for broth dilution antifungal susceptibility testing of filamentous fungi; approved standard, 2nd ed. CLSI document M38-A2. Clinical and Laboratory Standards Institute, Wayne, PA.","edition":"2"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000046"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2011.02483.x"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkr168"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00388-13"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1534\/g3.113.005660"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.12032"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1271\/bbb.70133"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2004.03.119"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1080\/13693780802054215"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01105-14","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01105-14","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T06:52:41Z","timestamp":1646463161000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.01105-14"}},"subtitle":[],"editor":[{"given":"G. A.","family":"Land","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,12]]},"references-count":46,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["10.1128\/JCM.01105-14"],"URL":"https:\/\/doi.org\/10.1128\/jcm.01105-14","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.718880846.793528022","asserted-by":"object"}]},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12]]},"assertion":[{"value":"2014-04-15","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2014-09-12","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2014-11-14","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}