{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T22:04:16Z","timestamp":1789596256962,"version":"build-2803163510"},"reference-count":49,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T00:00:00Z","timestamp":1637193600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000270","name":"Natural Environment Research Council","doi-asserted-by":"publisher","award":["NE\/P000940\/1"],"award-info":[{"award-number":["NE\/P000940\/1"]}],"id":[{"id":"10.13039\/501100000270","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CropLife International","award":["14209"],"award-info":[{"award-number":["14209"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Pan-azole resistant isolates are found in clinical and environmental Aspergillus fumigatus (Af) populations. Azole resistance can evolve in both settings, with Af directly targeted by antifungals in patients and, in the environment, Af unintendedly exposed to fungicides used for material preservation and plant disease control. Resistance to non-azole fungicides, including methyl benzimidazole carbamates (MBCs), quinone outside inhibitors (QoIs) and succinate dehydrogenase inhibitors (SDHIs), has recently been reported. These fungicide groups are not used in medicine but can play an important role in the further spread of pan-azole resistant genotypes. We investigated the multi-fungicide resistance status and the genetic diversity of Af populations sampled from tulip field soils, tulip peel waste and flower compost heaps using fungicide sensitivity testing and a range of genotyping tools, including STRAf typing and sequencing of fungicide resistant alleles. Two major clones were present in the tulip bulb population. Comparisons with clinical isolates and literature data revealed that several common clonal lineages of TR34\/L98H and TR46\/Y121F\/T289A strains that have expanded successfully in the environment have also acquired resistance to MBC, QoI and\/or SDHI fungicides. Strains carrying multiple fungicide resistant alleles have a competitive advantage in environments where residues of multiple fungicides belonging to different modes of action are present.<\/jats:p>","DOI":"10.3390\/microorganisms9112379","type":"journal-article","created":{"date-parts":[[2021,11,19]],"date-time":"2021-11-19T02:43:09Z","timestamp":1637289789000},"page":"2379","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Epidemiological Studies of Pan-Azole Resistant Aspergillus fumigatus Populations Sampled during Tulip Cultivation Show Clonal Expansion with Acquisition of Multi-Fungicide Resistance as Potential Driver"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8176-2258","authenticated-orcid":false,"given":"Bart A.","family":"Fraaije","sequence":"first","affiliation":[{"name":"NIAB, Cambridge CB3 0LE, UK"},{"name":"Rothamsted Research, Harpenden AL5 2Q, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah L.","family":"Atkins","sequence":"additional","affiliation":[{"name":"NIAB, Cambridge CB3 0LE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ricardo F.","family":"Santos","sequence":"additional","affiliation":[{"name":"Luiz de Queiroz College of Agriculture, University of S\u00e3o Paulo, Piracicaba 13418-900, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven J.","family":"Hanley","sequence":"additional","affiliation":[{"name":"Rothamsted Research, Harpenden AL5 2Q, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5211-2405","authenticated-orcid":false,"given":"Jonathan S.","family":"West","sequence":"additional","affiliation":[{"name":"Rothamsted Research, Harpenden AL5 2Q, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John A.","family":"Lucas","sequence":"additional","affiliation":[{"name":"Rothamsted Research, Harpenden AL5 2Q, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1128\/AAC.41.6.1364","article-title":"Itraconazole resistance in Aspergillus fumigatus","volume":"41","author":"Denning","year":"1997","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Snelders, E., van der Lee, H.A.L., Kuijpers, J., Rijs, A.J.M.M., Varga, J., Samson, R.A., Mellado, E., Donders, A.R.T., Melchers, W.J.G., and Verweij, P.E. (2008). Emergence of azole resistance in Aspergillus fumigatus and spread of a single resistance mechanism. PLoS Med., 5.","DOI":"10.4016\/8254.01"},{"key":"ref_3","doi-asserted-by":"crossref","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":"ref_4","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1093\/cid\/ciy859","article-title":"Voriconazole resistance and mortality in invasive aspergillosis: A multicentre retrospective cohort study","volume":"68","author":"Lestrade","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1486","DOI":"10.1093\/jac\/dkt075","article-title":"The crd1B efflux transporter is associated with non-cyp51a-mediated itraconazole resistance in Aspergillus fumigatus","volume":"68","author":"Fraczek","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.3201\/eid2410.180730","article-title":"Non-cyp51A azole-resistant Aspergillus fumigatus isolates with mutation in HMG-CoA reductase","volume":"24","author":"Hagiwara","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e02101-16","DOI":"10.1128\/AAC.02101-16","article-title":"Screening and characterization of a non-cyp51A mutation in an Aspergillus fumigatus cox10 strain conferring azole resistance","volume":"61","author":"Wei","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Rivero-Menendez, O., Alastruey-Izquierdo, A., Mellado, E., and Cuenca-Estrella, M. (2016). Triazole Resistance in Aspergillus spp.: A Worldwide Problem?. J. Fungi, 2.","DOI":"10.3390\/jof2030021"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.3389\/fmicb.2017.01024","article-title":"Azole resistance in Aspergillus fumigatus: A consequence of antifungal use in agriculture?","volume":"8","author":"Berger","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1128\/AAC.02234-15","article-title":"Azole resistance in Aspergillus fumigatus clinical isolates from an Italian culture collection","volume":"60","author":"Lazzarini","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"4465","DOI":"10.1128\/AAC.00185-11","article-title":"Azole resistance in Aspergillus fumigatus isolates from the ARTEMIS global surveillance study is primarily due to the TR\/L98H mutation in the cyp51A gene","volume":"55","author":"Lockhart","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e01549-17","DOI":"10.1128\/AAC.01549-17","article-title":"Elevated MIC Values of Imidazole Drugs against Aspergillus fumigatus Isolates with TR34\/L98H\/S297T\/F495I Mutation","volume":"62","author":"Chen","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1128\/JCM.02478-15","article-title":"First detection of TR34 L98H and TR46 Y121F T289A cyp51 mutations in Aspergillus fumigatus isolates in the United States","volume":"54","author":"Wiederhold","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e00791-17","DOI":"10.1128\/mBio.00791-17","article-title":"A novel environmental azole resistance mutation in Aspergillus fumigatus and a possible role of sexual reproduction in its emergence","volume":"8","author":"Zhang","year":"2017","journal-title":"MBio"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e02295-20","DOI":"10.1128\/AEM.02295-20","article-title":"2021. Dynamics of Aspergillus fumigatus in azole fungicide-containing plant waste in the Netherlands (2016\u20132017)","volume":"87","author":"Zhang","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1016\/j.jiac.2020.05.008","article-title":"Characteristics of azole-resistant Aspergillus fumigatus attached to agricultural products imported to Japan","volume":"26","author":"Nakano","year":"2020","journal-title":"J. Infect. Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"599233","DOI":"10.3389\/fmicb.2020.599233","article-title":"The Multi-Fungicide Resistance Status of Aspergillus fumigatus Populations in Arable Soils and the Wider European Environment","volume":"11","author":"Fraaije","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Kang, S.E., Sumabat, L.G., Melie, T., Mangum, B., Momany, M., and Brewer, M.T. (2020). Evidence for the agricultural origin of antimicrobial resistance in a fungal pathogen of humans. bioRxiv.","DOI":"10.1101\/2020.05.24.113787"},{"key":"ref_19","first-page":"e00642-21","article-title":"2021. Multiresistance to nonazole fungicides in Aspergillus fumigatus TR34\/L98H azole-resistant isolates","volume":"65","author":"Monzon","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1524","DOI":"10.3201\/eid2408.171865","article-title":"Hospitalized Patient as Source of Aspergillus fumigatus, 2015","volume":"24","author":"Lemaire","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"797","DOI":"10.3201\/eid2504.181110","article-title":"Aerosol Transmission of Aspergillus fumigatus in Cystic Fibrosis Patients in the Netherlands","volume":"25","author":"Engel","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.fbr.2020.10.003","article-title":"The one health problem of azole resistance in Aspergillus fumigatus: Current insights and future research agenda","volume":"34","author":"Verweij","year":"2020","journal-title":"Fungal Biol. Rev."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1093\/cid\/cix257","article-title":"Intercountry transfer of triazole-resistant Aspergillus fumigatus on plant bulbs","volume":"65","author":"Dunne","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1584\/jpestics.D20-017","article-title":"Isolation of azole-resistant Aspergillus fumigatus from imported plant bulbs in Japan and the effect of fungicide treatment","volume":"45","author":"Hagiwara","year":"2020","journal-title":"J. Pestic. Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.3201\/eid2507.181625","article-title":"Environmental hotspots for azole resistance selection of Aspergillus fumigatus, the Netherlands","volume":"25","author":"Schoustra","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.mimet.2009.03.004","article-title":"Utility of CSP typing to sub-type clinical Aspergillus fumigatus isolates and proposal for a new CSP type nomenclature","volume":"77","author":"Klaassen","year":"2009","journal-title":"J. Microbiol. Methods"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"4112","DOI":"10.1128\/JCM.43.8.4112-4120.2005","article-title":"Use of a novel panel of nine short tandem repeats for exact and high-resolution fingerprinting of Aspergillus fumigatus isolates","volume":"43","author":"Meis","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","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":"ref_29","doi-asserted-by":"crossref","first-page":"1392","DOI":"10.1128\/EC.00164-07","article-title":"Characterization of a novel gene for strain typing reveals substructuring of Aspergillus fumigatus across North America","volume":"6","author":"Balajee","year":"2007","journal-title":"Eukaryot. Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"82","DOI":"10.3389\/fcimb.2019.00082","article-title":"Microsatellite stability in STR analysis Aspergillus fumigatus depends on number of repeat units","volume":"9","author":"Meis","year":"2019","journal-title":"Front. Cell Infect. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/bioinformatics\/bts460","article-title":"GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research--an update","volume":"28","author":"Peakall","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e281","DOI":"10.7717\/peerj.281","article-title":"Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and\/or sexual reproduction","volume":"2","author":"Kamvar","year":"2014","journal-title":"PeerJ"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1111\/j.1365-294X.2004.02209.x","article-title":"A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level","volume":"13","author":"Bruvo","year":"2004","journal-title":"Mol. Ecol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.jiac.2016.12.004","article-title":"First clinical isolation report of azole-resistant Aspergillus fumigatus with TR34\/L98H-type mutation in Japan","volume":"23","author":"Toyotome","year":"2017","journal-title":"J. Infect. Chemother."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"4331","DOI":"10.1128\/AAC.00127-15","article-title":"First description of azole-resistant Aspergillus fumigatus due to TR46\/Y121F\/T289A mutation in France","volume":"59","author":"Lavergne","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2979","DOI":"10.1093\/jac\/dku259","article-title":"Multi-Azole-Resistant Aspergillus fumigatus in the Environment in Tanzania","volume":"69","author":"Chowdhary","year":"2014","journal-title":"J. Antimicrob. Chem."},{"key":"ref_37","first-page":"1","article-title":"Mechanisms of resistance to QoI fungicides in phytopathogenic fungi","volume":"11","year":"2008","journal-title":"Int. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Chowdhary, A., Kathuria, S., Xu, J., Sharma, C., Sundar, G., Singh, P.K., Gaur, S.N., Hagen, F., Klaassen, C.H., and Meis, J.F. (2012). Clonal expansion and emergence of environmental multiple-triazole-resistant Aspergillus fumigatus strains carrying the TR\u2083\u2084\/L98H mutations in the cyp51A gene in India. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0052871"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Ahangarkani, F., Badali, H., Abbasi, K., Nabili, M., Khodavaisy, S., de Groot, T., and Meis, J.F. (2020). Clonal Expansion of Environmental Triazole Resistant Aspergillus fumigatus in Iran. J. Fungi, 6.","DOI":"10.3390\/jof6040199"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e02023-18","DOI":"10.1128\/JCM.02023-18","article-title":"Epidemiology and antifungal susceptibility profile of Aspergillus species: Comparison between environmental and clinical isolates from patients with hematologic malignancies","volume":"57","author":"Cho","year":"2019","journal-title":"J. Clin. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Rhodes, J., Abdolrasouli, A., Dunne, K., Sewell, T.R., Zhang, Y., Ballard, E., Brackin, A.P., van Rhijn, N., Tsitsopoulou, A., and Posso, R.B. (2021). Tracing patterns of evolution and acquisition of drug resistant Aspergillus fumigatus infection from the environment using population genomics. bioRxiv.","DOI":"10.1101\/2021.04.07.438821"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Shelton, J.M.G., Collins, R., Uzzell, C.B., Alghamdi, A., Dyer, P.S., Singer, A.C., and Fisher, M.C. (2021). Citizen-science surveillance of triazole-resistant Aspergillus fumigatus in UK residential garden soils. bioRxiv.","DOI":"10.1101\/2021.07.08.451577"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1002\/ps.3348","article-title":"Update on mechanisms of azole resistance in Mycosphaerella graminicola and implications for future control","volume":"69","author":"Cools","year":"2013","journal-title":"Pest Manag. Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1094\/Phyto-82-1348","article-title":"Characterisation of mutations in the \u03b2-tubulin gene of benomyl-resistant field strains of Venturia inaequalis and other plant pathogenic fungi","volume":"82","author":"Koenraadt","year":"1992","journal-title":"Phytopathology"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"81","DOI":"10.3201\/eid2601.190885","article-title":"High Azole Resistance in Aspergillus fumigatus Isolates from Strawberry Fields, China, 2018","volume":"26","author":"Chen","year":"2020","journal-title":"Emerg. Infect. Dis."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1626","DOI":"10.3389\/fmicb.2018.01626","article-title":"Comparison of Two Highly Discriminatory Typing Methods to Analyze Aspergillus fumigatus Azole Resistance","volume":"9","author":"Escribano","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_47","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."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Fan, Y., Wang, Y., Korfanty, G.A., Archer, M., and Xu, J. (2021). Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus. Pathogens, 10.","DOI":"10.3390\/pathogens10060701"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Slavin, M.A., Chen, Y.C., Cordonnier, C., Cornely, O.A., Cuenca-Estrella, M., Donnelly, J.P., Groll, A.H., Lortholary, O., Marty, F.M., and Nucci, M. (2021). When to change treatment of acute invasive aspergillosis: An expert viewpoint. J. Antimicrob. Chemother., dkab317.","DOI":"10.1093\/jac\/dkab317"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/11\/2379\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:31:58Z","timestamp":1760167918000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/11\/2379"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,18]]},"references-count":49,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2021,11]]}},"alternative-id":["microorganisms9112379"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms9112379","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,11,18]]}}}