{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T13:29:10Z","timestamp":1783517350796,"version":"3.55.0"},"reference-count":53,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"State Key Program of National Natural Science Foundation of China","award":["12031016"],"award-info":[{"award-number":["12031016"]}]},{"name":"Scientific Research Project of National Natural Science Foundation of China","award":["82372273"],"award-info":[{"award-number":["82372273"]}]},{"name":"Scientific Research Project of National Natural Science Foundation of China","award":["82172293"],"award-info":[{"award-number":["82172293"]}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Azole resistance in\n                    <jats:italic>Aspergillus fumigatus<\/jats:italic>\n                    , a major cause of invasive aspergillosis, threatens public health. Known drivers include\n                    <jats:italic>cyp51A\/B<\/jats:italic>\n                    mutations (e.g., TR34\/L98H and TR46\/Y121F\/T289A), yet existing studies have largely focused on clinical isolates and known genetic determinants, leaving gaps in understanding broader genomic contributions. This study aimed to develop a machine learning\u2013based framework to overcome limitations of traditional GWAS and identify novel resistance loci beyond\n                    <jats:italic>cyp51A<\/jats:italic>\n                    . A global collection of 590\n                    <jats:italic>A. fumigatus<\/jats:italic>\n                    strains was analyzed, including whole-genome sequencing (WGS) data from 15 countries and resistance phenotypes using CLSI\/EUCAST guidelines. Phylogenetic analysis revealed four clades without geographic clustering. Clade III harbored the highest proportion of resistant strains (ITR: 51.89%, POS: 50.48%, VOR: 38.68%), predominantly linked to\n                    <jats:italic>cyp51A<\/jats:italic>\n                    tandem repeats. In contrast, Clade IV strains frequently carried point mutations but showed lower resistance rates. GWAS was performed using PLINK and GAPIT frameworks, and 7,098 high confidence SNPs were selected for ML modeling. Ten classifiers were evaluated using repeated random 80:20 train-test splits, with five-fold cross-validation used for RFECV-based feature selection and model tuning where applicable. RF and XGBoost achieved superior performance, with mean AUCs &amp;gt; 95% and accuracy &amp;gt; 88% across all azoles. Penalized logistic regression outperformed SVM and AdaBoost. Decision trees exhibited the lowest accuracy. The SNP SCM000172.1_1781459 was identified as a key predictor for all three azoles. Cross-resistance analysis revealed significant overlap between ITR and POS resistance loci, whereas VOR-associated loci were distinct, suggesting divergent mechanisms. The findings provide actionable insights for resistance surveillance, antifungal development, and tailored treatment strategies.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1891518","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T05:46:01Z","timestamp":1783403161000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic variant-driven prediction of azole resistance in Aspergillus fumigatus using GWAS and machine learning"],"prefix":"10.3389","volume":"17","author":[{"given":"Dingchen","family":"Li","sequence":"first","affiliation":[{"name":"Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]},{"name":"Department of Information, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinkai","family":"Yue","sequence":"additional","affiliation":[{"name":"Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]},{"name":"School of Mathematics and Statistics, Xi\u2019an Jiaotong University","place":["Xi\u2019an, Shaanxi, China"]},{"name":"School of Mathematics and Statistics, Shaanxi Normal University","place":["Xi\u2019an, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjuan","family":"Hu","sequence":"additional","affiliation":[{"name":"Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]},{"name":"School of Mathematics and Statistics, Shaanxi Normal University","place":["Xi\u2019an, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanying","family":"Zhong","sequence":"additional","affiliation":[{"name":"Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangyan","family":"Chen","sequence":"additional","affiliation":[{"name":"Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingya","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luyao","family":"Cao","sequence":"additional","affiliation":[{"name":"Department of Information, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xia","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Shaanxi Normal University","place":["Xi\u2019an, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Han","sequence":"additional","affiliation":[{"name":"Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,7]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e00536","DOI":"10.1128\/mbio.00536-15","article-title":"Genomic context of azole resistance mutations in Aspergillus fumigatus determined using whole-genome sequencing","volume":"6","author":"Abdolrasouli","year":"2015","journal-title":"MBio"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"3380","DOI":"10.1128\/AAC.00383-13","article-title":"Population-based survey of filamentous fungi and antifungal resistance in Spain (FILPOP study)","volume":"57","author":"Alastruey-Izquierdo","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"e1002374","DOI":"10.1371\/journal.pgen.1002374","article-title":"SREBP coordinates iron and ergosterol homeostasis to mediate triazole drug and hypoxia responses in the human fungal pathogen Aspergillus fumigatus","volume":"7","author":"Blatzer","year":"2011","journal-title":"PLoS Genet."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"e02136-20","DOI":"10.1128\/jcm.02136-20","article-title":"COVID-19-associated invasive aspergillosis: data from the UK national mycology reference laboratory","volume":"59","author":"Borman","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"2633","DOI":"10.1093\/bioinformatics\/btm308","article-title":"TASSEL: software for association mapping of complex traits in diverse samples","volume":"23","author":"Bradbury","year":"2007","journal-title":"Bioinformatics"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"165rv13","DOI":"10.1126\/scitranslmed.3004404","article-title":"Hidden killers: human fungal infections","volume":"4","author":"Brown","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1086\/521987","article-title":"Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering","volume":"81","author":"Browning","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"2116","DOI":"10.1093\/jac\/dkq279","article-title":"Azole antifungal resistance in Aspergillus fumigatus: 2008 and 2009","volume":"65","author":"Bueid","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"e50034","DOI":"10.1371\/journal.pone.0050034","article-title":"Discovery of a HapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing","volume":"7","author":"Camps","year":"2012","journal-title":"PLoS One"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e1003633","DOI":"10.1371\/journal.ppat.1003633","article-title":"Emergence of azole-resistant Aspergillus fumigatus strains due to agricultural azole use creates an increasing threat to human health","volume":"9","author":"Chowdhary","year":"2013","journal-title":"PLoS Pathog."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"ref13","first-page":"1","volume-title":"Reference Method for Broth Dilution Antifungal Susceptibility Testing of Filamentous Fungi; Approved Standard-Second Edition","year":"2008"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"361","DOI":"10.3109\/13693786.2012.738312","article-title":"Global burden of allergic bronchopulmonary aspergillosis with asthma and its complication chronic pulmonary aspergillosis in adults","volume":"51","author":"Denning","year":"2013","journal-title":"Med. Mycol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1920","DOI":"10.1161\/CIRCULATIONAHA.115.001593","article-title":"Machine learning in medicine","volume":"132","author":"Deo","year":"2015","journal-title":"Circulation"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"17203","DOI":"10.1038\/s41598-023-44005-w","article-title":"Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits","volume":"13","author":"Dort","year":"2023","journal-title":"Sci. Rep."},{"key":"ref18","doi-asserted-by":"publisher","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":"ref19","doi-asserted-by":"publisher","first-page":"701","DOI":"10.3390\/pathogens10060701","article-title":"Genome-wide association analysis for triazole resistance in Aspergillus fumigatus","volume":"10","author":"Fan","year":"2021","journal-title":"Pathogens"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1673","DOI":"10.3390\/microorganisms8111673","article-title":"Comparative genome sequence analyses of geographic samples of Aspergillus fumigatus\u2014relevance for amphotericin B resistance","volume":"8","author":"Fan","year":"2020","journal-title":"Microorganisms"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1944","DOI":"10.1128\/AAC.01902-12","article-title":"In vitro antifungal susceptibility of clinically relevant species belonging to aspergillus section Flavi","volume":"57","author":"Gon\u00e7alves","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e1006096","DOI":"10.1371\/journal.ppat.1006096","article-title":"A novel Zn2-Cys6 transcription factor AtrR plays a key role in an azole resistance mechanism of Aspergillus fumigatus by co-regulating cyp51A and cdr1B expressions","volume":"13","author":"Hagiwara","year":"2017","journal-title":"PLoS Pathog."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e1012091","DOI":"10.1371\/journal.pgen.1012091","article-title":"Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts","volume":"22","author":"Harrison","year":"2026","journal-title":"PLoS Genet."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"e01519-22","DOI":"10.1128\/mbio.01519-22","article-title":"Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus","volume":"13","author":"Horta","year":"2022","journal-title":"MBio"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.3201\/eid1507.090043","article-title":"Frequency and evolution of azole resistance in Aspergillus fumigatus associated with treatment failure","volume":"15","author":"Howard","year":"2009","journal-title":"Emerg. Infect. Dis."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"e24","DOI":"10.1371\/journal.ppat.0030024","article-title":"Essential gene identification and drug target prioritization in Aspergillus fumigatus","volume":"3","author":"Hu","year":"2007","journal-title":"PLoS Pathog."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1101\/gr.165415.113","article-title":"Predicting the virulence of MRSA from its genome sequence","volume":"24","author":"Laabei","year":"2014","journal-title":"Genome Res."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.jmii.2020.09.004","article-title":"COVID-19 associated with pulmonary aspergillosis: a literature review","volume":"54","author":"Lai","year":"2021","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1016\/j.cmi.2018.11.027","article-title":"Triazole resistance in Aspergillus fumigatus: recent insights and challenges for patient management","volume":"25","author":"Lestrade","year":"2019","journal-title":"Clin. Microbiol. Infect."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with burrows\u2013wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"2397","DOI":"10.1093\/bioinformatics\/bts444","article-title":"GAPIT: genome association and prediction integrated tool","volume":"28","author":"Lipka","year":"2012","journal-title":"Bioinformatics"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e1004834","DOI":"10.1371\/journal.ppat.1004834","article-title":"Genetic analysis using an isogenic mating pair of Aspergillus fumigatus identifies azole resistance genes and lack of MAT locus\u2019s role in virulence","volume":"11","author":"Losada","year":"2015","journal-title":"PLoS Pathog."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"2536","DOI":"10.1128\/AAC.49.6.2536-2538.2005","article-title":"Targeted gene disruption of the 14-\u03b1 sterol demethylase (cyp51A) in Aspergillus fumigatus and its role in azole drug susceptibility","volume":"49","author":"Mellado","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1039\/C7MT00110J","article-title":"The cytochrome b 5 CybE is regulated by iron availability and is crucial for azole resistance in A. fumigatus","volume":"9","author":"Misslinger","year":"2017","journal-title":"Metallomics"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"6124","DOI":"10.1111\/mec.13916","article-title":"Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations","volume":"25","author":"Mohd-Assaad","year":"2016","journal-title":"Mol. Ecol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"e02563-18","DOI":"10.1128\/mbio.02563-18","article-title":"AtrR is an essential determinant of azole resistance in Aspergillus fumigatus","volume":"10","author":"Paul","year":"2019","journal-title":"MBio"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"2825","DOI":"10.48550\/arXiv.1201.0490","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J. Mach. Learn. Res."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1824","DOI":"10.1086\/323900","article-title":"The impact of culture isolation of aspergillus species: a hospital-based survey of aspergillosis","volume":"33","author":"Perfect","year":"2001","journal-title":"Clin. Infect. Dis."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e00392-19","DOI":"10.1128\/mBio.00392-19","article-title":"Nonrandom distribution of azole resistance across the global population of Aspergillus fumigatus","volume":"10","author":"Sewell","year":"2019","journal-title":"mBio"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"832","DOI":"10.3201\/eid1905.130075","article-title":"Azole-resistant Aspergillus fumigatus, Iran","volume":"19","author":"Seyedmousavi","year":"2013","journal-title":"Emerg. Infect. Dis."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e219","DOI":"10.1371\/journal.pmed.0050219","article-title":"Emergence of azole resistance in Aspergillus fumigatus and spread of a single resistance mechanism","volume":"5","author":"Snelders","year":"2008","journal-title":"PLoS Med."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1094\/MPMI-09-15-0218-R","article-title":"Genome-wide association study identifies novel candidate genes for aggressiveness, deoxynivalenol production, and azole sensitivity in natural field populations of Fusarium graminearum","volume":"29","author":"Talas","year":"2016","journal-title":"Mol. Plant-Microbe Interact."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"e251","DOI":"10.1016\/S1473-3099(16)30138-4","article-title":"In-host adaptation and acquired triazole resistance in Aspergillus fumigatus: a dilemma for clinical management","volume":"16","author":"Verweij","year":"2016","journal-title":"Lancet Infect. Dis."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"e107684","DOI":"10.1371\/journal.pone.0107684","article-title":"A SUPER powerful method for genome wide association study","volume":"9","author":"Wang","year":"2014","journal-title":"PLoS One"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"1666","DOI":"10.1093\/bioinformatics\/btx801","article-title":"Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data","volume":"34","author":"Yang","year":"2018","journal-title":"Bioinformatics"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"uhac225","DOI":"10.1093\/hr\/uhac225","article-title":"Application of machine learning to explore the genomic prediction accuracy of fall dormancy in autotetraploid alfalfa","volume":"10","author":"Zhang","year":"2023","journal-title":"Hortic. Res."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1255","DOI":"10.1038\/ng.2735","article-title":"Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance","volume":"45","author":"Zhang","year":"2013","journal-title":"Nat. Genet."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"617338","DOI":"10.3389\/ffunb.2020.617338","article-title":"Genome-wide association for itraconazole sensitivity in non-resistant clinical isolates of Aspergillus fumigatus","volume":"1","author":"Zhao","year":"2021","journal-title":"Front. Fungal Biol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1891518\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T13:08:45Z","timestamp":1783516125000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1891518\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,7]]},"references-count":53,"alternative-id":["10.3389\/fmicb.2026.1891518"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1891518","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,7]]},"article-number":"1891518"}}