{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T14:34:20Z","timestamp":1784039660677,"version":"3.55.0"},"reference-count":51,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2021,1,26]],"date-time":"2021-01-26T00:00:00Z","timestamp":1611619200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31670145"],"award-info":[{"award-number":["31670145"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81902043"],"award-info":[{"award-number":["81902043"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Mycoses"],"published-print":{"date-parts":[[2021,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Black opportunists <jats:italic>Phialophora verrucosa<\/jats:italic> complex species can cause different disease types in competent and in immunocompromised individuals, but are remarkably overrepresented in CARD9\u2010related infections.<\/jats:p><\/jats:sec><jats:sec><jats:title>Objectives<\/jats:title><jats:p>To better understand the ecology and potential pathogenicity of opportunistic <jats:italic>Phialophora<\/jats:italic> species and reveal eventual genetic parameters associated with the behaviour in vivo and genetic profiles in patients with CARD9 immunodeficiency.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Genomes of 26 strains belonging to six species of the <jats:italic>Phialophora verrucosa<\/jats:italic> complex were sequenced. Using multilocus analysis, all environmental and clinical strains were identified correctly. We compared the genomes of agents from different disease types among each other including CARD9 immunodeficiency.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We obtained genome sizes of the 26 <jats:italic>Phialophora<\/jats:italic> strains ranged between 32 and 37\u00a0MB. Some species showed considerable intraspecific genomic variation. <jats:italic>P americana<\/jats:italic> showed the highest degree of variability. <jats:italic>P verrucosa<\/jats:italic> was variable in CAZy enzymes, whereas <jats:italic>P americana<\/jats:italic> varied in PKS\u2010related genes. <jats:italic>Phialophora<\/jats:italic> species, particularly <jats:italic>P verrucosa<\/jats:italic>, are relatively frequent in patients with CARD9\u2010related immunodeficiency. Different mutations in the CARD9 gene seem to increase susceptibility for infection by different groups of species, that is either <jats:italic>Candida,<\/jats:italic> dermatophytes or black fungi. A number of patients with chromoblastomycosis revealed an as yet unknown CARD9 mutation. TNF\u03b1 impairment was prevalent in patients with CARD9 infections, while CBM patients were invariably IFN\u03b3.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>From genomic investigations, the known virulence factors between clinical and environmental strains did not reveal any significant difference. <jats:italic>Phialophora<\/jats:italic> complex has an equal chance to cause infection in humans, either healthy or CARD9\u2010impaired.<\/jats:p><\/jats:sec>","DOI":"10.1111\/myc.13244","type":"journal-article","created":{"date-parts":[[2021,1,17]],"date-time":"2021-01-17T11:17:35Z","timestamp":1610882255000},"page":"555-568","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Comparative genomics of opportunistic <i>Ph<\/i><i>ialophora<\/i> species involved in divergent disease types"],"prefix":"10.1111","volume":"64","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1644-6942","authenticated-orcid":false,"given":"Yinggai","family":"Song","sequence":"first","affiliation":[{"name":"Department of Dermatology and Venereology Peking University First Hospital Beijing China"},{"name":"Research Center for Medical Mycology Peking University Beijing China"},{"name":"National Clinical Research Center for Skin and Immune Diseases Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nickolas","family":"Menezes da Silva","sequence":"additional","affiliation":[{"name":"Graduate Program in Bioprocess Engineering and Biotechnology Federal University of Paran\u00e1 Curitiba Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vania A.","family":"Vicente","sequence":"additional","affiliation":[{"name":"Graduate Program in Bioprocess Engineering and Biotechnology Federal University of Paran\u00e1 Curitiba Brazil"},{"name":"Microbiology, Parasitology and Pathology Post\u2010Graduation Program Department of Pathology Federal University of Paran\u00e1 Curitiba Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Quan","sequence":"additional","affiliation":[{"name":"Center of Expertise in Mycology of Radboud University Medical Center Canisius Wilhelmina Hospital Nijmegen The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus","family":"Teixeira","sequence":"additional","affiliation":[{"name":"N\u00facleo de Medicina Tropical University of Bras\u00edlia Bras\u00edlia Brazil"},{"name":"Applied Research &amp; Development Building Northern Arizona University Flagstaff AZ USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Gong","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Infectious Disease Prevention and Control Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases National Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and Prevention Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5344-257X","authenticated-orcid":false,"given":"Sybren","family":"de Hoog","sequence":"additional","affiliation":[{"name":"Microbiology, Parasitology and Pathology Post\u2010Graduation Program Department of Pathology Federal University of Paran\u00e1 Curitiba Brazil"},{"name":"Center of Expertise in Mycology of Radboud University Medical Center Canisius Wilhelmina Hospital Nijmegen The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruoyu","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Dermatology and Venereology Peking University First Hospital Beijing China"},{"name":"Research Center for Medical Mycology Peking University Beijing China"},{"name":"National Clinical Research Center for Skin and Immune Diseases Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,1,26]]},"reference":[{"key":"e_1_2_8_2_1","volume-title":"Atlas of clinical fungi","author":"De Hoog GS","year":"2020"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00032-16"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02434"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.01880"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/jof7020095"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.5858\/2003-127-91-MSPCBP"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1439-0507.2002.00701.x"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.3767\/003158517X692779"},{"key":"e_1_2_8_10_1","first-page":"230","article-title":"First report of chromoblastomycosis caused by Phialophora expanda in a Chinese CARD9\u2010deficient patient","volume":"15","author":"Huang C","year":"2020","journal-title":"Chin J Mycol"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1111\/myc.12962"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1439-0507.2005.01150.x"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2474"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215087.116"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv280"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9173-0_14"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki937"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki442"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky418"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0721-2"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1007\/s13225-020-00452-8"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts507"},{"key":"e_1_2_8_24_1","first-page":"95","article-title":"BioEdit: a user\u2010friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT","volume":"41","author":"Hall TA","year":"1999","journal-title":"Nucleic Acids Symp"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2005.04.001"},{"key":"e_1_2_8_26_1","first-page":"307","article-title":"Missing data and the accuracy of Bayesian phylogenetics","volume":"46","author":"Wiens JJ","year":"2008","journal-title":"J Syst Evol"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.3897\/rio.5.e36178"},{"key":"e_1_2_8_28_1","first-page":"14","article-title":"CARD9 mutations and related immunological research of one case with disseminated phaeohyphomycosis","volume":"12","author":"Zhang R","year":"2017","journal-title":"J Microbes Infect"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2013.09.033"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu412"},{"key":"e_1_2_8_31_1","first-page":"3","article-title":"Impaired specific antifungal immunity in CARD9\u2010deficient patients with phaeohyphomycosis","volume":"138","author":"Wang X","year":"2017","journal-title":"J Invest Dermatol"},{"key":"e_1_2_8_32_1","unstructured":"Sobianski HermanT GomesRR Queiroz TellesF PedrosoCA VicenteVA.Identification of CARD9 mutation in patients with chromoblastomycosis and evaluation of the immunological response. 2021 (submitted)."},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1111\/bjd.14082"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10875-018-0549-0"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.2307\/3753363"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1007\/s13225-013-0275-0"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.00586"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.565439"},{"key":"e_1_2_8_39_1","first-page":"103","article-title":"Whole\u2010genome resequencing of Trichophyton rubrum provides insights into population differentiation and drug resistance","volume":"185","author":"Zheng H","year":"2020","journal-title":"Mycopathologia"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1439-0507.2010.01859.x"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1439-0507.2002.00779.x"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2016.00039"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.1177\/0883073808323524"},{"key":"e_1_2_8_44_1","first-page":"118","article-title":"A case of disseminated phaeohyphomycosis caused by Cladosporium devriesii","volume":"39","author":"Mitchell DM","year":"1990","journal-title":"West Ind Med J"},{"key":"e_1_2_8_45_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11046-013-9632-5"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2016.12.024"},{"key":"e_1_2_8_47_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2012-08-450551"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.02366"},{"key":"e_1_2_8_49_1","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jir458"},{"key":"e_1_2_8_50_1","doi-asserted-by":"publisher","DOI":"10.1080\/13693780500220373"},{"key":"e_1_2_8_51_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10875-019-00740-2"},{"key":"e_1_2_8_52_1","doi-asserted-by":"publisher","DOI":"10.3389\/fneur.2019.00938"}],"container-title":["Mycoses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/myc.13244","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/myc.13244","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/myc.13244","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,2]],"date-time":"2023-09-02T05:12:36Z","timestamp":1693631556000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/myc.13244"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,1,26]]},"references-count":51,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,5]]}},"alternative-id":["10.1111\/myc.13244"],"URL":"https:\/\/doi.org\/10.1111\/myc.13244","archive":["Portico"],"relation":{},"ISSN":["0933-7407","1439-0507"],"issn-type":[{"value":"0933-7407","type":"print"},{"value":"1439-0507","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,1,26]]},"assertion":[{"value":"2020-12-26","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-01-11","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-01-26","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}