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Molecular Taxonomy

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Diagnosis and Treatment of Fungal Infections

Abstract

The wide-scale use of molecular phylogenetic studies in mycology has significantly changed our understanding of the relationships between fungal taxa at all levels, including species, genera, families, and beyond. After extensive evaluation in a large international barcoding consortium, the internal transcribed spacer (ITS) region was selected as the universal fungal barcode, despite the general knowledge that this marker does not distinguish between all fungal species. Multiple genes were used to improve phylogenetic resolution among ascomycetous and basidiomycetous yeasts, dermatophytes, dimorphic fungi, Aspergillus, Penicillium, and Fusarium. The most recent development is the use of whole genome-based data in phylogenomic studies. With respect to clinically important fungi, these studies have yielded several important new insights that are highlighted in this chapter.

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References

  1. Bowman BH, White TJ, Taylor JW. Human pathogenic fungi and their close nonpathogenic relatives. Mol Phylogenet Evol. 1996;6(1):89–96. https://doi.org/10.1006/mpev.1996.0061.

    Article  CAS  PubMed  Google Scholar 

  2. Fell JW, Boekhout T, Fonseca A, Scorzetti G, Statzell-Tallman A. Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int J Syst Evol Microbiol. 2000;50(Pt 3):1351–71. https://doi.org/10.1099/00207713-50-3-1351.

    Article  CAS  PubMed  Google Scholar 

  3. Kurtzman CP, Robnett CJ. Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5′ end of the large-subunit (26S) ribosomal DNA gene. J Clin Microbiol. 1997;35(5):1216–23. https://doi.org/10.1128/jcm.35.5.1216-1223.1997.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Kurtzman CP, Robnett CJ. Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species. FEMS Yeast Res. 2013;13(1):23–33. https://doi.org/10.1111/1567-1364.12006.

    Article  CAS  PubMed  Google Scholar 

  5. Kurtzman CP, Robnett CJ, Basehoar E, Ward TJ. Four new species of Metschnikowia and the transfer of seven Candida species to Metschnikowia and Clavispora as new combinations. Antonie van Leeuwenhoek. 2018;111(11):2017–35. https://doi.org/10.1007/s10482-018-1095-8.

    Article  CAS  PubMed  Google Scholar 

  6. Scorzetti G, Fell JW, Fonseca A, Statzell-Tallman A. Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Res. 2002;2(4):495–517. https://doi.org/10.1111/j.1567-1364.2002.tb00117.x.

    Article  CAS  PubMed  Google Scholar 

  7. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A. 2012;109(16):6241–6. https://doi.org/10.1073/pnas.1117018109.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Al-Hatmi AM, Hagen F, Menken SB, Meis JF, de Hoog GS. Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015. Emerg Microbes Infect. 2016;5(12):e124. https://doi.org/10.1038/emi.2016.126.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Houbraken J, Kocsubé S, Visagie CM, Yilmaz N, Wang XC, Meijer M, Kraak B, Hubka V, Bensch K, Samson RA, Frisvad JC. Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): An overview of families, genera, subgenera, sections, series and species. Stud Mycol. 2020;95:5–169. https://doi.org/10.1016/j.simyco.2020.05.002.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Irinyi L, Serena C, Garcia-Hermoso D, Arabatzis M, Desnos-Ollivier M, Vu D, Cardinali G, Arthur I, Normand AC, Giraldo A, da Cunha KC, Sandoval-Denis M, Hendrickx M, Nishikaku AS, de Azevedo Melo AS, Merseguel KB, Khan A, Parente Rocha JA, Sampaio P, da Silva Briones MR, e Ferreira RC, de Medeiros Muniz M, Castañón-Olivares LR, Estrada-Barcenas D, Cassagne C, Mary C, Duan SY, Kong F, Sun AY, Zeng X, Zhao Z, Gantois N, Botterel F, Robbertse B, Schoch C, Gams W, Ellis D, Halliday C, Chen S, Sorrell TC, Piarroux R, Colombo AL, Pais C, de Hoog S, Zancopé-Oliveira RM, Taylor ML, Toriello C, de Almeida Soares CM, Delhaes L, Stubbe D, Dromer F, Ranque S, Guarro J, Cano-Lira JF, Robert V, Velegraki A, Meyer W. International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi. Med Mycol. 2015;53(4):313–37. https://doi.org/10.1093/mmy/myv008.

    Article  CAS  PubMed  Google Scholar 

  11. Stielow JB, Lévesque CA, Seifert KA, Meyer W, Iriny L, Smits D, Renfurm R, Verkley GJ, Groenewald M, Chaduli D, Lomascolo A, Welti S, Lesage-Meessen L, Favel A, Al-Hatmi AM, Damm U, Yilmaz N, Houbraken J, Lombard L, Quaedvlieg W, Binder M, Vaas LA, Vu D, Yurkov A, Begerow D, Roehl O, Guerreiro M, Fonseca A, Samerpitak K, van Diepeningen AD, Dolatabadi S, Moreno LF, Casaregola S, Mallet S, Jacques N, Roscini L, Egidi E, Bizet C, Garcia-Hermoso D, Martín MP, Deng S, Groenewald JZ, Boekhout T, de Beer ZW, Barnes I, Duong TA, Wingfield MJ, de Hoog GS, Crous PW, Lewis CT, Hambleton S, Moussa TA, Al-Zahrani HS, Almaghrabi OA, Louis-Seize G, Assabgui R, McCormick W, Omer G, Dukik K, Cardinali G, Eberhardt U, de Vries M, Robert V. One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia. 2015;35:242–63. https://doi.org/10.3767/003158515X689135.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Vu D, Groenewald M, Szöke S, Cardinali G, Eberhardt U, Stielow B, de Vries M, Verkleij GJ, Crous PW, Boekhout T, Robert V. DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation. Stud Mycol. 2016;85:91–105. https://doi.org/10.1016/j.simyco.2016.11.007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Vu D, Groenewald M, de Vries M, Gehrmann T, Stielow B, Eberhardt U, Al-Hatmi A, Groenewald JZ, Cardinali G, Houbraken J, Boekhout T, Crous PW, Robert V, Verkley GJM. Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation. Stud Mycol. 2019;92:135–54. https://doi.org/10.1016/j.simyco.2018.05.001.

    Article  CAS  PubMed  Google Scholar 

  14. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung GH, Johnson D, O’Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schüssler A, Longcore JE, O’Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lücking R, Büdel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature. 2006;443(7113):818–22. https://doi.org/10.1038/nature05110.

    Article  CAS  PubMed  Google Scholar 

  15. Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Thorsten Lumbsch H, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai YC, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Kõljalg U, Kurtzman CP, Larsson KH, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo JM, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schüssler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao YJ, Zhang N. A higher-level phylogenetic classification of the Fungi. Mycol Res. 2007;111(Pt 5):509–47. https://doi.org/10.1016/j.mycres.2007.03.004.

    Article  PubMed  Google Scholar 

  16. Kurtzman CP. Use of gene sequence analyses and genome comparisons for yeast systematics. Int J Syst Evol Microbiol. 2014;64(Pt 2):325–32. https://doi.org/10.1099/ijs.0.054197-0.

    Article  PubMed  Google Scholar 

  17. Liu XZ, Wang QM, Theelen B, Groenewald M, Bai FY, Boekhout T. Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses. Stud Mycol. 2015;81:1–26. https://doi.org/10.1016/j.simyco.2015.08.001.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Liu XZ, Wang QM, Göker M, Groenewald M, Kachalkin AV, Lumbsch HT, Millanes AM, Wedin M, Yurkov AM, Boekhout T, Bai FY. Towards an integrated phylogenetic classification of the Tremellomycetes. Stud Mycol. 2015;81:85–147. https://doi.org/10.1016/j.simyco.2015.12.001.

    Article  PubMed  Google Scholar 

  19. Wang QM, Begerow D, Groenewald M, Liu XZ, Theelen B, Bai FY, Boekhout T. Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina. Stud Mycol. 2015;81:55–83. https://doi.org/10.1016/j.simyco.2015.10.004.

    Article  PubMed  PubMed Central  Google Scholar 

  20. Wang QM, Groenewald M, Takashima M, Theelen B, Han PJ, Liu XZ, Boekhout T, Bai FY. Phylogeny of yeasts and related filamentous fungi within Pucciniomycotina determined from multigene sequence analyses. Stud Mycol. 2015;81:27–53. https://doi.org/10.1016/j.simyco.2015.08.002.

    Article  PubMed  PubMed Central  Google Scholar 

  21. de Hoog GS, Dukik K, Monod M, Packeu A, Stubbe D, Hendrickx M, Kupsch C, Stielow JB, Freeke J, Göker M, Rezaei-Matehkolaei A, Mirhendi H, Gräser Y. Toward a novel multilocus phylogenetic taxonomy for the dermatophytes. Mycopathologia. 2017;182(1-2):5–31. https://doi.org/10.1007/s11046-016-0073-9.

    Article  PubMed  Google Scholar 

  22. Fisher MC, Koenig G, White TJ, Taylor JW. A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus Coccidioides immitis. Mol Biol Evol. 2000;17(8):1164–74. https://doi.org/10.1093/oxfordjournals.molbev.a026399.

    Article  CAS  PubMed  Google Scholar 

  23. Kasuga T, White TJ, Koenig G, McEwen J, Restrepo A, Castañeda E, Da Silva Lacaz C, Heins-Vaccari EM, De Freitas RS, Zancopé-Oliveira RM, Qin Z, Negroni R, Carter DA, Mikami Y, Tamura M, Taylor ML, Miller GF, Poonwan N, Taylor JW. Phylogeography of the fungal pathogen Histoplasma capsulatum. Mol Ecol. 2003;12(12):3383–401. https://doi.org/10.1046/j.1365-294x.2003.01995.x.

    Article  CAS  PubMed  Google Scholar 

  24. O’Donnell K, Rooney AP, Proctor RH, Brown DW, McCormick SP, Ward TJ, Frandsen RJ, Lysøe E, Rehner SA, Aoki T, Robert VA, Crous PW, Groenewald JZ, Kang S, Geiser DM. Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal Genet Biol. 2013;52:20–31. https://doi.org/10.1016/j.fgb.2012.12.004.

    Article  CAS  PubMed  Google Scholar 

  25. Schroers HJ, O’Donnell K, Lamprecht SC, Kammeyer PL, Johnson S, Sutton DA, Rinaldi MG, Geiser DM, Summerbell RC. Taxonomy and phylogeny of the Fusarium dimerum species group. Mycologia. 2009;101(1):44–70. https://doi.org/10.3852/08-002.

    Article  CAS  PubMed  Google Scholar 

  26. Burmester A, Shelest E, Glöckner G, Heddergott C, Schindler S, Staib P, Heidel A, Felder M, Petzold A, Szafranski K, Feuermann M, Pedruzzi I, Priebe S, Groth M, Winkler R, Li W, Kniemeyer O, Schroeckh V, Hertweck C, Hube B, White TC, Platzer M, Guthke R, Heitman J, Wöstemeyer J, Zipfel PF, Monod M, Brakhage AA. Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. Genome Biol. 2011;12(1):R7. https://doi.org/10.1186/gb-2011-12-1-r7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Crous PW, Lombard L, Sandoval-Denis M, Seifert KA, Schroers H-J, Chaverri P, Gené J, Guarro J, Hirooka Y, Bensch K, Kema GHJ, Lamprecht SC, Cai L, Rossman AY, Stadler M, Summerbell RC, Taylor JW, Ploch S, Visagie CM, Yilmaz N, Frisvad JC, Abdel-Azeem AM, Abdollahzadeh J, Abdolrasouli A, Akulov A, Alberts JF, Araújo JPM, Ariyawansa HA, Bakhshi M, Bendiksby M, Ben Hadj Amor A, Bezerra JDP, Boekhout T, Câmara MPS, Carbia M, Cardinali G, Castañeda-Ruiz RF, Celis A, Chaturvedi V, Collemare J, Croll D, Damm U, Decock CA, de Vries RP, Ezekiel CN, Fan XL, Fernández NB, Gaya E, González CD, Gramaje D, Groenewald JZ, Grube M, Guevara-Suarez M, Gupta VK, Guarnaccia V, Haddaji A, Hagen F, Haelewaters D, Hansen K, Hashimoto A, Hernández-Restrepo M, Houbraken J, Hubka V, Hyde KD, Iturriaga T, Jeewon R, Johnston PR, Jurjević Ž, Karalti I, Korsten L, Kuramae EE, Kušan I, Labuda R, Lawrence DP, Lee HB, Lechat C, Li HY, Litovka YA, Maharachchikumbura SSN, Marin-Felix Y, Matio Kemkuignou B, Matočec N, McTaggart AR, Mlčoch P, Mugnai L, Nakashima C, Nilsson RH, Noumeur SR, Pavlov IN, Peralta MP, Phillips AJL, Pitt JI, Polizzi G, Quaedvlieg W, Rajeshkumar KC, Restrepo S, Rhaiem A, Robert J, Robert V, Rodrigues AM, Salgado-Salazar C, Samson RA, Santos ACS, Shivas RG, Souza-Motta CM, Sun GY, Swart WJ, Szoke S, Tan YP, Taylor JE, Taylor PWJ, Tiago PV, Váczy KZ, van de Wiele N, van de Merwe NA, Verkley GJM, WAS V, Vizzini A, Weir BS, Wijayawardene NN, Xia JW, Yáñez-Morales MJ, Yurkov A, Zamora JC, Zare R, Zhang CL, Thines M. Fusarium: more than a node or a foot-shaped basal cell. Stud Mycol. 2021;98:10016.

    Article  Google Scholar 

  28. Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW. Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A. 2016;113(35):9882–7. https://doi.org/10.1073/pnas.1603941113.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Sepúlveda VE, Márquez R, Turissini DA, Goldman WE, Matute DR. Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum. mBio. 2017;8(6):e01339–17. https://doi.org/10.1128/mBio.01339-17.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res. 2009;19(10):1722–31. https://doi.org/10.1101/gr.087551.108.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Shen XX, Steenwyk JL, LaBella AL, Opulente DA, Zhou X, Kominek J, Li Y, Groenewald M, Hittinger CT, Rokas A. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Sci Adv. 2020;6(45):eabd0079. https://doi.org/10.1126/sciadv.abd0079.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Teixeira MM, Cattana ME, Matute DR, Muñoz JF, Arechavala A, Isbell K, Schipper R, Santiso G, Tracogna F, Sosa MLÁ, Cech N, Alvarado P, Barreto L, Chacón Y, Ortellado J, Lima CM, Chang MR, Niño-Vega G, Yasuda MAS, Felipe MSS, Negroni R, Cuomo CA, Barker B, Giusiano G. Genomic diversity of the human pathogen Paracoccidioides across the South American continent. Fungal Genet Biol. 2020;140:103395. https://doi.org/10.1016/j.fgb.2020.103395.

    Article  CAS  PubMed  Google Scholar 

  33. Liu YJ, Hall BD. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc Natl Acad Sci U S A. 2004;101(13):4507–12. https://doi.org/10.1073/pnas.0400938101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Liu Y, Leigh JW, Brinkmann H, Cushion MT, Rodriguez-Ezpeleta N, Philippe H, Lang BF. Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts. Mol Biol Evol. 2009;26(1):27–34. https://doi.org/10.1093/molbev/msn221.

    Article  CAS  PubMed  Google Scholar 

  35. Sugiyama J, Hosaka K, Suh SO. Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas. Mycologia. 2006;98(6):996–1005. https://doi.org/10.3852/mycologia.98.6.996.

    Article  PubMed  Google Scholar 

  36. Guého-Kellermann E, Boekhout T, Begerow D. Biodiversity, phylogeny and ultrastructure. In: Boekhout T, Guého E, Mayser P, Velegraki A, editors. Malassezia and the skin: science and clinical practice. Heidelberg: Springer; 2010. p. 17–63.

    Chapter  Google Scholar 

  37. Wu G, Zhao H, Li C, Rajapakse MP, Wong WC, Xu J, Saunders CW, Reeder NL, Reilman RA, Scheynius A, Sun S, Billmyre BR, Li W, Averette AF, Mieczkowski P, Heitman J, Theelen B, Schröder MS, De Sessions PF, Butler G, Maurer-Stroh S, Boekhout T, Nagarajan N, Dawson TL Jr. Genus-wide comparative genomics of Malassezia delineates its phylogeny, physiology, and niche adaptation on human skin. PLoS Genet. 2015;11(11):e1005614. https://doi.org/10.1371/journal.pgen.1005614.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Xu J, Saunders CW, Hu P, Grant RA, Boekhout T, Kuramae EE, Kronstad JW, Deangelis YM, Reeder NL, Johnstone KR, Leland M, Fieno AM, Begley WM, Sun Y, Lacey MP, Chaudhary T, Keough T, Chu L, Sears R, Yuan B, Dawson TL Jr. Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proc Natl Acad Sci U S A. 2007;104(47):18730–5. https://doi.org/10.1073/pnas.0706756104.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Daniel HM, Lachance MA, Kurtzman CP. On the reclassification of species assigned to Candida and other anamorphic ascomycetous yeast genera based on phylogenetic circumscription. Antonie van Leeuwenhoek. 2014;106(1):67–84. https://doi.org/10.1007/s10482-014-0170-z.

    Article  PubMed  Google Scholar 

  40. Lachance MA, Boekhout T, Scorzetti G, Fell JW, Kurtzman CP. Candida berkhout (1923). In: Kurtzman CP, Fell JW, Boekhout T, editors. The yeasts, a taxonomic study, vol. 2. 5th ed. Amsterdam: Elsevier; 2011. p. 987–1278.

    Chapter  Google Scholar 

  41. Borman AM, Johnson EM. Name changes for Fungi of medical importance, 2018 to 2019. J Clin Microbiol. 2021;59(2):e01811–20. https://doi.org/10.1128/JCM.01811-20.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Warnock DW. Name changes for Fungi of medical importance, 2012 to 2015. J Clin Microbiol. 2016;55(1):53–9. https://doi.org/10.1128/JCM.00829-16.

    Article  PubMed  PubMed Central  Google Scholar 

  43. Warnock DW. Name changes for Fungi of medical importance, 2016-2017. J Clin Microbiol. 2019;57(2):e01183–18. https://doi.org/10.1128/JCM.01183-18.

    Article  PubMed  PubMed Central  Google Scholar 

  44. Schmalreck AF, Lackner M, Becker K, Fegeler W, Czaika V, Ulmer H, Lass-Flörl C. Phylogenetic relationships matter: antifungal susceptibility among clinically relevant yeasts. Antimicrob Agents Chemother. 2014;58(3):1575–85. https://doi.org/10.1128/AAC.01799-13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Stavrou AA, Lackner M, Lass-Flörl C, Boekhout T. The changing spectrum of Saccharomycotina yeasts causing candidemia: phylogeny mirrors antifungal susceptibility patterns for azole drugs and amphotericin B. FEMS Yeast Res. 2019;19(4):foz037. https://doi.org/10.1093/femsyr/foz037.

    Article  CAS  PubMed  Google Scholar 

  46. Kwon-Chung KJ, Bennett JE, Wickes BL, Meyer W, Cuomo CA, Wollenburg KR, Bicanic TA, Castañeda E, Chang YC, Chen J, Cogliati M, Dromer F, Ellis D, Filler SG, Fisher MC, Harrison TS, Holland SM, Kohno S, Kronstad JW, Lazera M, Levitz SM, Lionakis MS, May RC, Ngamskulrongroj P, Pappas PG, Perfect JR, Rickerts V, Sorrell TC, Walsh TJ, Williamson PR, Xu J, Zelazny AM, Casadevall A. The case for adopting the “species complex” nomenclature for the etiologic agents of cryptococcosis. mSphere. 2017;2(1):e00357–16. https://doi.org/10.1128/mSphere.00357-16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. O’Donnell K, Al-Hatmi AMS, Aoki T, Brankovics B, Cano-Lira JF, Coleman JJ, de Hoog GS, Di Pietro A, Frandsen RJN, Geiser DM, Gibas CFC, Guarro J, Kim HS, Kistler HC, Laraba I, Leslie JF, López-Berges MS, Lysøe E, Meis JF, Monod M, Proctor RH, Rep M, Ruiz-Roldán C, Šišić A, Stajich JE, Steenkamp ET, Summerell BA, van der Lee TAJ, van Diepeningen AD, Verweij PE, Waalwijk C, Ward TJ, Wickes BL, Wiederhold NP, Wingfield MJ, Zhang N, Zhang SX. No to Neocosmospora: phylogenomic and practical reasons for continued inclusion of the Fusarium solani species complex in the genus Fusarium. mSphere. 2020;5(5):e00810–20. https://doi.org/10.1128/mSphere.00810-20.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Koehler P, Stecher M, Cornely OA, Koehler D, Vehreschild MJGT, Bohlius J, Wisplinghoff H, Vehreschild JJ. Morbidity and mortality of candidaemia in Europe: an epidemiologic meta-analysis. Clin Microbiol Infect. 2019;25(10):1200–12. https://doi.org/10.1016/j.cmi.2019.04.024.

    Article  CAS  PubMed  Google Scholar 

  49. Boekhout T, Bai FY, Daniel HM, Groenewald M, Robert V, Tan S, Yurkov A. https://www.theyeasts.org.

  50. Khunnamwong P, Lertwattanasakul N, Jindamorakot S, Limtong S, Lachance MA. Description of Diutina gen. nov., Diutina siamensis, f.a. sp. nov., and reassignment of Candida catenulata, Candida mesorugosa, Candida neorugosa, Candida pseudorugosa, Candida ranongensis, Candida rugosa and Candida scorzettiae to the genus Diutina. Int J Syst Evol Microbiol. 2015;65(12):4701–9. https://doi.org/10.1099/ijsem.0.000634.

    Article  CAS  PubMed  Google Scholar 

  51. Kurtzman CP, Robnett CJ. Three new anascosporic genera of the Saccharomycotina: Danielozyma gen. nov., Deakozyma gen. nov. and Middelhovenomyces gen. nov. Antonie van Leeuwenhoek. 2014;105(5):933–42. https://doi.org/10.1007/s10482-014-0149-9.

    Article  PubMed  Google Scholar 

  52. Kurtzman CP. Description of Groenewaldozyma gen. nov. for placement of Candida auringiensis, Candida salmanticensis and Candida tartarivorans. Antonie van Leeuwenhoek. 2016;109(7):1041–5. https://doi.org/10.1007/s10482-016-0703-8.

    Article  PubMed  Google Scholar 

  53. Kurtzman CP, Robnett CJ, Blackwell M. Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov. FEMS Yeast Res. 2016;16(5):fow041. https://doi.org/10.1093/femsyr/fow041.

    Article  CAS  PubMed  Google Scholar 

  54. Aime MC, Miller AN, Aoki T, Bensch K, Cai L, Crous PW, Hawksworth DL, Hyde KD, Kirk PM, Lücking R, May TW, Malosso E, Redhead SA, Rossman AY, Stadler M, Thines M, Yurkov AM, Zhang N, Schoch CL. How to publish a new fungal species, or name, version 3.0. IMA Fungus. 2021;12(1):11. https://doi.org/10.1186/s43008-021-00063-1.

    Article  PubMed  PubMed Central  Google Scholar 

  55. Lücking R, Leavitt SD, Hawksworth DL. Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics. Fung Div. 2021;109:99. https://doi.org/10.1007/s13225-021-00477-7.

    Article  Google Scholar 

  56. Turland NJ, Wiersema JH, Barrie FR, Greuter W, Hawksworth DL, Herendeen PS, Knapp S, Kusber W-H, Li D-Z, Marhold K, May TW, McNeill J, Monro AM, Prado J, Price MJ, Smith GF. International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Glashütten: Koeltz Botanical Books; 2018. https://doi.org/10.12705/Code.2018.

    Book  Google Scholar 

  57. Turland N. Coded decoded: a user’s guide to the International Code of Nomenclature for Algae, Fungi, and Plants. 2nd ed. Sofia: Pensoft Publishers; 2019.

    Book  Google Scholar 

  58. Yurkov A, Alves A, Bai FY, Boundy-Mills K, Buzzini P, Čadež N, Cardinali G, Casaregola S, Chaturvedi V, Collin V, Fell JW, Girard V, Groenewald M, Hagen F, Hittinger CT, Kachalkin AV, Kostrzewa M, Kouvelis V, Libkind D, Liu X, Maier T, Meyer W, Péter G, Piątek M, Robert V, Rosa CA, Sampaio JP, Sipiczki M, Stadler M, Sugita T, Sugiyama J, Takagi H, Takashima M, Turchetti B, Wang QM, Boekhout T. Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes. IMA Fungus. 2021;12(1):18. https://doi.org/10.1186/s43008-021-00067-x.

    Article  PubMed  PubMed Central  Google Scholar 

  59. Alcoba-Flórez J, Méndez-Alvarez S, Cano J, Guarro J, Pérez-Roth E, del Pilar Arévalo M. Phenotypic and molecular characterization of Candida nivariensis sp. nov., a possible new opportunistic fungus. J Clin Microbiol. 2005;43(8):4107–11. https://doi.org/10.1128/JCM.43.8.4107-4111.2005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Cendejas-Bueno E, Kolecka A, Alastruey-Izquierdo A, Theelen B, Groenewald M, Kostrzewa M, Cuenca-Estrella M, Gómez-López A, Boekhout T. Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: three multiresistant human pathogenic yeasts. J Clin Microbiol. 2012;50(11):3641–51. https://doi.org/10.1128/JCM.02248-12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Correia A, Sampaio P, James S, Pais C. Candida bracarensis sp. nov., a novel anamorphic yeast species phenotypically similar to Candida glabrata. Int j syst evol microbiol. 2006;56(Pt 1):313–7. https://doi.org/10.1099/ijs.0.64076-0.

  62. Satoh K, Makimura K, Hasumi Y, Nishiyama Y, Uchida K, Yamaguchi H. Candida auris sp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital. Microbiol Immunol. 2009;53(1):41–4. https://doi.org/10.1111/j.1348-0421.2008.00083.x.

    Article  CAS  PubMed  Google Scholar 

  63. Sipiczki M, Tap RM. Candida vulturna pro tempore sp. nov., a dimorphic yeast species related to the Candida haemulonii species complex isolated from flowers and clinical sample. Int J Syst Evol Microbiol. 2016;66(10):4009–15. https://doi.org/10.1099/ijsem.0.001302.

    Article  CAS  PubMed  Google Scholar 

  64. Tavanti A, Davidson AD, Gow NA, Maiden MC, Odds FC. Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III. J Clin Microbiol. 2005;43(1):284–92. https://doi.org/10.1128/JCM.43.1.284-292.2005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Calvo B, Melo AS, Perozo-Mena A, Hernandez M, Francisco EC, Hagen F, Meis JF, Colombo AL. First report of Candida auris in America: clinical and microbiological aspects of 18 episodes of candidemia. J Infect. 2016;73(4):369–74. https://doi.org/10.1016/j.jinf.2016.07.008.

    Article  PubMed  Google Scholar 

  66. Chowdhary A, Anil Kumar V, Sharma C, Prakash A, Agarwal K, Babu R, Dinesh KR, Karim S, Singh SK, Hagen F, Meis JF. Multidrug-resistant endemic clonal strain of Candida auris in India. Eur J Clin Microbiol Infect Dis. 2014;33(6):919–26. https://doi.org/10.1007/s10096-013-2027-1.

    Article  CAS  PubMed  Google Scholar 

  67. Chowdhary A, Sharma C, Meis JF. Candida auris: a rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally. PLoS Pathog. 2017;13(5):e1006290. https://doi.org/10.1371/journal.ppat.1006290.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. de Jong AW, Hagen F. Attack, defend and persist: how the fungal pathogen Candida auris was able to emerge globally in healthcare environments. Mycopathologia. 2019;184(3):353–65. https://doi.org/10.1007/s11046-019-00351-w.

    Article  PubMed  Google Scholar 

  69. Lockhart SR, Etienne KA, Vallabhaneni S, Farooqi J, Chowdhary A, Govender NP, Colombo AL, Calvo B, Cuomo CA, Desjardins CA, Berkow EL, Castanheira M, Magobo RE, Jabeen K, Asghar RJ, Meis JF, Jackson B, Chiller T, Litvintseva AP. Simultaneous emergence of multidrug-resistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clin Infect Dis. 2017;64(2):134–40. https://doi.org/10.1093/cid/ciw691.

    Article  CAS  PubMed  Google Scholar 

  70. Ostrowsky B, Greenko J, Adams E, Quinn M, O’Brien B, Chaturvedi V, Berkow E, Vallabhaneni S, Forsberg K, Chaturvedi S, Lutterloh E, Blog D, C. auris Investigation Work Group. Candida auris isolates resistant to three classes of antifungal medications - New York, 2019. MMWR Morb Mortal Wkly Rep. 2020;69(1):6–9. https://doi.org/10.15585/mmwr.mm6901a2.

    Article  PubMed  PubMed Central  Google Scholar 

  71. Sullivan DJ, Moran GP, Pinjon E, Al-Mosaid A, Stokes C, Vaughan C, Coleman DC. Comparison of the epidemiology, drug resistance mechanisms, and virulence of Candida dubliniensis and Candida albicans. FEMS Yeast Res. 2004;4(4-5):369–76. https://doi.org/10.1016/S1567-1356(03)00240-X.

    Article  CAS  PubMed  Google Scholar 

  72. Wahab AA, Taj-Aldeen SJ, Kolecka A, ElGindi M, Finkel JS, Boekhout T. High prevalence of Candida dubliniensis in lower respiratory tract secretions from cystic fibrosis patients may be related to increased adherence properties. Int J Infect Dis. 2014;24:14–9. https://doi.org/10.1016/j.ijid.2014.03.1380.

    Article  PubMed  Google Scholar 

  73. Bishop JA, Chase N, Magill SS, Kurtzman CP, Fiandaca MJ, Merz WG. Candida bracarensis detected among isolates of Candida glabrata by peptide nucleic acid fluorescence in situ hybridization: susceptibility data and documentation of presumed infection. J Clin Microbiol. 2008;46(2):443–6. https://doi.org/10.1128/JCM.01986-07.

    Article  CAS  PubMed  Google Scholar 

  74. Borman AM, Petch R, Linton CJ, Palmer MD, Bridge PD, Johnson EM. Candida nivariensis, an emerging pathogenic fungus with multidrug resistance to antifungal agents. J Clin Microbiol. 2008;46(3):933–8. https://doi.org/10.1128/JCM.02116-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Lockhart SR, Messer SA, Gherna M, Bishop JA, Merz WG, Pfaller MA, Diekema DJ. Identification of Candida nivariensis and Candida bracarensis in a large global collection of Candida glabrata isolates: comparison to the literature. J Clin Microbiol. 2009;47(4):1216–7. https://doi.org/10.1128/JCM.02315-08.

  76. Lockhart SR, Messer SA, Pfaller MA, Diekema DJ. Geographic distribution and antifungal susceptibility of the newly described species Candida orthopsilosis and Candida metapsilosis in comparison to the closely related species Candida parapsilosis. J Clin Microbiol. 2008;46(8):2659–64. https://doi.org/10.1128/JCM.00803-08.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Odds FC, Jacobsen MD. Multilocus sequence typing of pathogenic Candida species. Eukaryot Cell. 2008;7(7):1075–84. https://doi.org/10.1128/EC.00062-08.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Pryszcz LP, Németh T, Gácser A, Gabaldón T. Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies. Genome Biol Evol. 2014;6(5):1069–78. https://doi.org/10.1093/gbe/evu082.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedűsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T. The genomic aftermath of hybridization in the opportunistic pathogen Candida metapsilosis. PLoS Genet. 2015;11(10):e1005626. https://doi.org/10.1371/journal.pgen.1005626.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Kocsubé S, Perrone G, Magistà D, Houbraken J, Varga J, Szigeti G, Hubka V, Hong SB, Frisvad JC, Samson RA. Aspergillus is monophyletic: evidence from multiple gene phylogenies and extrolites profiles. Stud Mycol. 2016;85:199–213. https://doi.org/10.1016/j.simyco.2016.11.006.

    Article  PubMed  PubMed Central  Google Scholar 

  81. Pitt JI, Taylor JW. Aspergillus, its sexual states and the new International Code of Nomenclature. Mycologia. 2014;106(5):1051–62. https://doi.org/10.3852/14-060.

    Article  PubMed  Google Scholar 

  82. Samson RA, Hubka V, Varga J, Houbraken J, Hong SB, Klaassen CHW, Perrone G, Seifert KA, Magistà D, Visagie CM, Kocsubé S, Szigeti G, Yaguchi T, Peterson SW, Frisvad JC. Response to Pitt & Taylor 2016: conservation of Aspergillus with A. niger as the conserved type is unnecessary and potentially disruptive. Taxon. 2017;66:1439–46.

    Article  Google Scholar 

  83. Arastehfar A, Carvalho A, Houbraken J, Lombardi L, Garcia-Rubio R, Jenks JD, Rivero-Menendez O, Aljohani R, Jacobsen ID, Berman J, Osherov N, Hedayati MT, Ilkit M, Armstrong-James D, Gabaldón T, Meletiadis J, Kostrzewa M, Pan W, Lass-Flörl C, Perlin DS, Hoenigl M. Aspergillus fumigatus and aspergillosis: From basics to clinics. Stud Mycol. 2021;100:100115. https://doi.org/10.1016/j.simyco.2021.100115.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Samson RA, Visagie CM, Houbraken J, Hong SB, Hubka V, Klaassen CH, Perrone G, Seifert KA, Susca A, Tanney JB, Varga J, Kocsubé S, Szigeti G, Yaguchi T, Frisvad JC. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud Mycol. 2014;78:141–73. https://doi.org/10.1016/j.simyco.2014.07.004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Verweij PE, Ananda-Rajah M, Andes D, Arendrup MC, Brüggemann RJ, Chowdhary A, Cornely OA, Denning DW, Groll AH, Izumikawa K, Kullberg BJ, Lagrou K, Maertens J, Meis JF, Newton P, Page I, Seyedmousavi S, Sheppard DC, Viscoli C, Warris A, Donnelly JP. International expert opinion on the management of infection caused by azole-resistant Aspergillus fumigatus. Drug Resist Updat. 2015;21–22:30–40. https://doi.org/10.1016/j.drup.2015.08.001.

    Article  PubMed  Google Scholar 

  86. Verweij PE, Chowdhary A, Melchers WJ, Meis JF. Azole resistance in Aspergillus fumigatus: can we retain the clinical use of mold-active antifungal azoles? Clin Infect Dis. 2016;62(3):362–8. https://doi.org/10.1093/cid/civ885.

    Article  CAS  PubMed  Google Scholar 

  87. Alcazar-Fuoli L, Mellado E, Alastruey-Izquierdo A, Cuenca-Estrella M, Rodriguez-Tudela JL. Aspergillus section Fumigati: antifungal susceptibility patterns and sequence-based identification. Antimicrob Agents Chemother. 2008;52(4):1244–51. https://doi.org/10.1128/AAC.00942-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Najafzadeh MJ, Dolatabadi S, Zarrinfar H, Houbraken J. Molecular diversity of Aspergilli in two Iranian hospitals. Mycopathologia. 2021;186(4):519–33. https://doi.org/10.1007/s11046-021-00563-z.

    Article  PubMed  Google Scholar 

  89. Takeda K, Suzuki J, Watanabe A, Matsuki M, Higa K, Inoue E, Akashi S, Shimada M, Kawashima M, Ohshima N, Fukami T, Masuda K, Yamane A, Tamura A, Nagai H, Matsui H, Tohma S, Kamei K. Species identification, antifungal susceptibility, and clinical feature association of Aspergillus section Nigri isolates from the lower respiratory tract. Med Mycol. 2020;58(3):310–4. https://doi.org/10.1093/mmy/myz072.

    Article  CAS  PubMed  Google Scholar 

  90. Glampedakis E, Cassaing S, Fekkar A, Dannaoui E, Bougnoux ME, Bretagne S, Neofytos D, Schreiber PW, Hennequin C, Morio F, Shadrivova O, Bongomin F, Fernández-Ruiz M, Bellanger AP, Arikan-Akdagli S, Erard V, Aigner M, Paolucci M, Khanna N, Charpentier E, Bonnal C, Brun S, Gabriel F, Riat A, Zbinden R, Le Pape P, Klimko N, Lewis RE, Richardson M, İnkaya AC, Coste AT, Bochud PY, Lamoth F. Invasive aspergillosis due to Aspergillus section Usti: a multicenter retrospective study. Clin Infect Dis. 2021;72(8):1379–85. https://doi.org/10.1093/cid/ciaa230.

    Article  PubMed  Google Scholar 

  91. Varga J, Houbraken J, Van Der Lee HA, Verweij PE, Samson RA. Aspergillus calidoustus sp. nov., causative agent of human infections previously assigned to Aspergillus ustus. Eukaryot Cell. 2008;7(4):630–8. https://doi.org/10.1128/EC.00425-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Steenwyk JL, Lind AL, Ries LNA, Dos Reis TF, Silva LP, Almeida F, Bastos RW, Fraga da Silva TFC, Bonato VLD, Pessoni AM, Rodrigues F, Raja HA, Knowles SL, Oberlies NH, Lagrou K, Goldman GH, Rokas A. Pathogenic allodiploid hybrids of Aspergillus fungi. Curr Biol. 2020;30(13):2495–2507.e7. https://doi.org/10.1016/j.cub.2020.04.071.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Geiser DM, Al-Hatmi A, Aoki T, Arie T, Balmas V, Barnes I, Bergstrom GC, Bhattacharyya MKK, Blomquist CL, Bowden R, Brankovics B, Brown DW, Burgess LW, Bushley K, Busman M, Cano-Lira JF, Carrillo JD, Chang HX, Chen CY, Chen W, Chilvers MI, Chulze SN, Coleman JJ, Cuomo CA, de Beer ZW, de Hoog GS, Del Castillo-Múnera J, Del Ponte E, Diéguez-Uribeondo J, Di Pietro A, Edel-Hermann V, Elmer WH, Epstein L, Eskalen A, Esposto MC, Everts KL, Fernández-Pavía SP, da Silva GF, Foroud NA, Fourie G, Frandsen RJN, Freeman S, Freitag M, Frenkel O, Fuller KK, Gagkaeva T, Gardiner DM, Glenn AE, Gold S, Gordon T, Gregory NF, Gryzenhout M, Guarro J, Gugino B, Gutiérrez S, Hammond-Kosack K, Harris LJ, Homa M, Hong CF, Hornok L, Huang JW, Ilkit M, Jacobs A, Jacobs K, Jiang C, Jimenez-Gasco MDM, Kang S, Kasson MT, Kazan K, Kennell JC, Kim H, Kistler HC, Kuldau GA, Kulik T, Kurzai O, Laraba I, Laurence MH, Lee TY, Lee YW, Lee YH, Leslie JF, Liew ECY, Lofton LW, Logrieco A, Sánchez López-Berges M, Luque AG, Lysøe E, Ma LJ, Marra RE, Martin FN, May SR, McCormick S, McGee CT, Meis JF, Migheli Q, Mohamed Nor NMI, Monod M, Moretti A, Mostert D, Mulé G, Munaut F, Munkvold GP, Nicholson P, Nucci M, O’Donnell K, Pasquali M, Pfenning LH, Prigitano A, Proctor R, Ranque S, Rehner S, Rep M, Rodríguez-Alvarado G, Rose LJ, Roth MG, Ruiz-Roldán C, Saleh AA, Salleh B, Sang H, Scandiani M, Scauflaire J, Schmale D III, Short DP, Šišić A, Smith J, Smyth CW, Son H, Spahr E, Stajich JE, Steenkamp E, Steinberg C, Subramaniam R, Suga H, Summerell BA, Susca A, Swett CL, Toomajian C, Torres-Cruz TJ, Tortorano AM, Urban M, Vaillancourt LJ, Vallad GE, van der Lee T, Vanderpool D, van Diepeningen AD, Vaughan M, Venter E, Vermeulen M, Verweij PE, Viljoen A, Waalwijk C, Wallace EC, Walther G, Wang J, Ward T, Wickes B, Wiederhold NP, Wingfield MJ, AKM W, Xu JR, Yang XB, Yli-Matilla T, Yun SH, Zakaria L, Zhang H, Zhang N, Zhang S, Zhang X. Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani species complex. Phytopathology. 2021;111:1064. https://doi.org/10.1094/PHYTO-08-20-0330-LE.

    Article  CAS  PubMed  Google Scholar 

  94. Geiser DM, Aoki T, Bacon CW, Baker SE, Bhattacharyya MK, Brandt ME, Brown DW, Burgess LW, Chulze S, Coleman JJ, Correll JC, Covert SF, Crous PW, Cuomo CA, De Hoog GS, Di Pietro A, Elmer WH, Epstein L, Frandsen RJ, Freeman S, Gagkaeva T, Glenn AE, Gordon TR, Gregory NF, Hammond-Kosack KE, Hanson LE, Jímenez-Gasco Mdel M, Kang S, Kistler HC, Kuldau GA, Leslie JF, Logrieco A, Lu G, Lysøe E, Ma LJ, McCormick SP, Migheli Q, Moretti A, Munaut F, O’Donnell K, Pfenning L, Ploetz RC, Proctor RH, Rehner SA, Robert VA, Rooney AP, Bin Salleh B, Scandiani MM, Scauflaire J, Short DP, Steenkamp E, Suga H, Summerell BA, Sutton DA, Thrane U, Trail F, Van Diepeningen A, Vanetten HD, Viljoen A, Waalwijk C, Ward TJ, Wingfield MJ, Xu JR, Yang XB, Yli-Mattila T, Zhang N. One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology. 2013;103(5):400–8. https://doi.org/10.1094/PHYTO-07-12-0150-LE.

    Article  PubMed  Google Scholar 

  95. Sandoval-Denis M, Crous PW. Removing chaos from confusion: assigning names to common human and animal pathogens in Neocosmospora. Persoonia. 2018;41:109–29. https://doi.org/10.3767/persoonia.2018.41.06.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Sandoval-Denis M, Guarnaccia V, Polizzi G, Crous PW. Symptomatic Citrus trees reveal a new pathogenic lineage in Fusarium and two new Neocosmospora species. Persoonia. 2018;40:1–25. https://doi.org/10.3767/persoonia.2018.40.01.

    Article  CAS  PubMed  Google Scholar 

  97. Sandoval-Denis M, Lombard L, Crous PW. Back to the roots: a reappraisal of Neocosmospora. Persoonia. 2019;43:90–185. https://doi.org/10.3767/persoonia.2019.43.04.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Anaissie EJ, Kuchar RT, Rex JH, Francesconi A, Kasai M, Müller FM, Lozano-Chiu M, Summerbell RC, Dignani MC, Chanock SJ, Walsh TJ. Fusariosis associated with pathogenic Fusarium species colonization of a hospital water system: a new paradigm for the epidemiology of opportunistic mold infections. Clin Infect Dis. 2001;33(11):1871–8. https://doi.org/10.1086/324501.

    Article  CAS  PubMed  Google Scholar 

  99. Chang DC, Grant GB, O’Donnell K, Wannemuehler KA, Noble-Wang J, Rao CY, Jacobson LM, Crowell CS, Sneed RS, Lewis FM, Schaffzin JK, Kainer MA, Genese CA, Alfonso EC, Jones DB, Srinivasan A, Fridkin SK, Park BJ, Fusarium Keratitis Investigation Team. Multistate outbreak of Fusarium keratitis associated with use of a contact lens solution. JAMA. 2006;296(8):953–63. https://doi.org/10.1001/jama.296.8.953.

    Article  CAS  PubMed  Google Scholar 

  100. O’Donnell K, Sarver BA, Brandt M, Chang DC, Noble-Wang J, Park BJ, Sutton DA, Benjamin L, Lindsley M, Padhye A, Geiser DM, Ward TJ. Phylogenetic diversity and microsphere array-based genotyping of human pathogenic Fusaria, including isolates from the multistate contact lens-associated U.S. keratitis outbreaks of 2005 and 2006. J Clin Microbiol. 2007;45(7):2235–48. https://doi.org/10.1128/JCM.00533-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. O’Donnell K, Sutton DA, Fothergill A, McCarthy D, Rinaldi MG, Brandt ME, Zhang N, Geiser DM. Molecular phylogenetic diversity, multilocus haplotype nomenclature, and in vitro antifungal resistance within the Fusarium solani species complex. J Clin Microbiol. 2008;46(8):2477–90. https://doi.org/10.1128/JCM.02371-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. O’Donnell K, Sutton DA, Rinaldi MG, Magnon KC, Cox PA, Revankar SG, Sanche S, Geiser DM, Juba JH, van Burik JA, Padhye A, Anaissie EJ, Francesconi A, Walsh TJ, Robinson JS. Genetic diversity of human pathogenic members of the Fusarium oxysporum complex inferred from multilocus DNA sequence data and amplified fragment length polymorphism analyses: evidence for the recent dispersion of a geographically widespread clonal lineage and nosocomial origin. J Clin Microbiol. 2004;42(11):5109–20. https://doi.org/10.1128/JCM.42.11.5109-5120.2004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Summerbell RC, Schroers HJ. Analysis of phylogenetic relationship of Cylindrocarpon lichenicola and Acremonium falciforme to the Fusarium solani species complex and a review of similarities in the spectrum of opportunistic infections caused by these fungi. J Clin Microbiol. 2002;40(8):2866–75. https://doi.org/10.1128/JCM.40.8.2866-2875.2002.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Summerbell RC, Scott JA. Conidiogenesis: its evolutionary aspects in the context of a philosophy of opportunity (lectics). In: Li DW, editor. Biology of microfungi. New York: Springer; 2016. p. 169–95.

    Chapter  Google Scholar 

  105. O’Donnell K, Gueidan C, Sink S, Johnston PR, Crous PW, Glenn A, Riley R, Zitomer NC, Colyer P, Waalwijk C, Lee TV, Moretti A, Kang S, Kim HS, Geiser DM, Juba JH, Baayen RP, Cromey MG, Bithell S, Sutton DA, Skovgaard K, Ploetz R, Corby Kistler H, Elliott M, Davis M, Sarver BA. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex. Fungal Genet Biol. 2009;46(12):936–48. https://doi.org/10.1016/j.fgb.2009.08.006.

    Article  CAS  PubMed  Google Scholar 

  106. Geiser DM, del Mar Jiménez-Gasco M, Kang S, Makalowska I, Veeraraghavan N, Ward TJ, Zhang N, Kuldau GA, O’Donnell K. FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium. Eur J Plant Pathol. 2004;110:473–9. https://doi.org/10.1023/B:EJPP.0000032386.75915.a0.

    Article  CAS  Google Scholar 

  107. Chowdhary A, Perfect J, de Hoog GS. Black molds and nelanized yeasts pathogenic to humans. Cold Spring Harb Perspect Med. 2014;5(8):a019570. https://doi.org/10.1101/cshperspect.a019570.

    Article  CAS  PubMed  Google Scholar 

  108. Guevara A, Siqueira NP, Nery AF, Cavalcante LRDS, Hagen F, Hahn RC. Chromoblastomycosis in Latin America and the Caribbean: epidemiology over the past 50 years. Med Mycol. 2021;60:myab062. https://doi.org/10.1093/mmy/myab062.

    Article  CAS  PubMed  Google Scholar 

  109. Santos DWCL, de Azevedo CMPES, Vicente VA, Queiroz-Telles F, Rodrigues AM, de Hoog GS, Denning DW, Colombo AL. The global burden of chromoblastomycosis. PLoS Negl Trop Dis. 2021;15(8):e0009611. https://doi.org/10.1371/journal.pntd.0009611.

    Article  PubMed  PubMed Central  Google Scholar 

  110. Badali H, Gueidan C, Najafzadeh MJ, Bonifaz A, van den Ende AH, de Hoog GS. Biodiversity of the genus Cladophialophora. Stud Mycol. 2008;61:175–91. https://doi.org/10.3114/sim.2008.61.18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. de Hoog GS, Nishikaku AS, Fernandez-Zeppenfeldt G, Padín-González C, Burger E, Badali H, Richard-Yegres N, van den Ende AH. Molecular analysis and pathogenicity of the Cladophialophora carrionii complex, with the description of a novel species. Stud Mycol. 2007;58:219–34. https://doi.org/10.3114/sim.2007.58.08.

    Article  PubMed  PubMed Central  Google Scholar 

  112. Das K, Lee SY, Jung HY. Cladophialophora lanosa sp. nov., a new species isolated from soil. Mycobiology. 2019;47(2):173–9. https://doi.org/10.1080/12298093.2019.1611242.

  113. Chakrabarti A, Kaur H, Rudramurthy SM, Appannanavar SB, Patel A, Mukherjee KK, Ghosh A, Ray U. Brain abscess due to Cladophialophora bantiana: a review of 124 cases. Med Mycol. 2016;54(2):111–9. https://doi.org/10.1093/mmy/myv091.

    Article  PubMed  Google Scholar 

  114. Gomes RR, Vicente VA, Azevedo CM, Salgado CG, da Silva MB, Queiroz-Telles F, Marques SG, Santos DW, de Andrade TS, Takagi EH, Cruz KS, Fornari G, Hahn RC, Scroferneker ML, Caligine RB, Ramirez-Castrillon M, de Araújo DP, Heidrich D, Colombo AL, de Hoog GS. Molecular epidemiology of agents of human chromoblastomycosis in Brazil with the description of two novel species. PLoS Negl Trop Dis. 2016;10(11):e0005102. https://doi.org/10.1371/journal.pntd.0005102.

    Article  PubMed  PubMed Central  Google Scholar 

  115. Najafzadeh MJ, Sun J, Vicente V, Xi L, van den Ende AH, de Hoog GS. Fonsecaea nubica sp. nov, a new agent of human chromoblastomycosis revealed using molecular data. Med Mycol. 2010;48(6):800–6. https://doi.org/10.3109/13693780903503081.

    Article  CAS  PubMed  Google Scholar 

  116. Najafzadeh MJ, Vicente VA, Sun J, Meis JF, de Hoog GS. Fonsecaea multimorphosa sp. nov, a new species of Chaetothyriales isolated from a feline cerebral abscess. Fungal Biol. 2011;115(10):1066–76. https://doi.org/10.1016/j.funbio.2011.06.007.

    Article  CAS  PubMed  Google Scholar 

  117. Schneider GX, Gomes RR, Bombassaro A, Zamarchi K, Voidaleski MF, Costa FF, Leão ACR, Lima BJFS, Soley BS, Colombo IR, Cândido GZ, Najafzadeh MJ, Sun J, de Azevedo CMPS, Marques SG, de Hoog GS, Vicente VA. New molecular markers distinguishing Fonsecaea agents of chromoblastomycosis. Mycopathologia. 2019;184(4):493–504. https://doi.org/10.1007/s11046-019-00359-2.

    Article  PubMed  Google Scholar 

  118. Li Y, Xiao J, de Hoog GS, Wang X, Wan Z, Yu J, Liu W, Li R. Biodiversity and human-pathogenicity of Phialophora verrucosa and relatives in Chaetothyriales. Persoonia. 2017;38:1–19. https://doi.org/10.3767/003158517X692779.

    Article  PubMed  Google Scholar 

  119. Feng P, Lu Q, Najafzadeh MJ, Gerrits van den Ende AHG, Sun J, Li R, Xi L, Vicente VA, Lai W, Lu C, de Hoog GS. Cyphellophora and its relatives in Phialophora: biodiversity and possible role in human infection. Fung Div. 2014;65:17–45. https://doi.org/10.1007/s13225-012-0194-5.

    Article  Google Scholar 

  120. Badali H, Bonifaz A, Barrón-Tapia T, Vázquez-González D, Estrada-Aguilar L, Oliveira NM, Sobral Filho JF, Guarro J, Meis JF, De Hoog GS. Rhinocladiella aquaspersa, proven agent of verrucous skin infection and a novel type of chromoblastomycosis. Med Mycol. 2010;48(5):696–703. https://doi.org/10.3109/13693780903471073.

    Article  CAS  PubMed  Google Scholar 

  121. Mohammadi R, Mohammadi A, Ashtari F, Khorvash F, Hakamifard A, Vaezi A, Javidnia J, Meis JF, Badali H. Cerebral phaeohyphomycosis due to Rhinocladiella mackenziei in Persian Gulf region: a case and review. Mycoses. 2018;61(4):261–5. https://doi.org/10.1111/myc.12734.

    Article  PubMed  Google Scholar 

  122. Borman AM, Fraser M, Szekely A, Larcombe DE, Johnson EM. Rapid identification of clinically relevant members of the genus Exophiala by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and description of two novel species, Exophiala campbellii and Exophiala lavatrina. J Clin Microbiol. 2017;55(4):1162–76. https://doi.org/10.1128/JCM.02459-16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Singh S, Rudramurthy SM, Padhye AA, Hemashetter BM, Iyer R, Hallur V, Sharma A, Agnihotri S, Gupta S, Ghosh A, Kaur H. Clinical spectrum, molecular characterization, antifungal susceptibility testing of Exophiala spp. from India and description of a novel Exophiala species, E. arunalokei sp. nov. Front Cell Infect Microbiol. 2021;11:686120. https://doi.org/10.3389/fcimb.2021.686120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Yong LK, Wiederhold NP, Sutton DA, Sandoval-Denis M, Lindner JR, Fan H, Sanders C, Guarro J. Morphological and molecular characterization of Exophiala polymorpha sp. nov. isolated from sporotrichoid lymphocutaneous lesions in a patient with myasthenia gravis. J Clin Microbiol. 2015;53:2816–22. https://doi.org/10.1128/JCM.00622-15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Chen SC, Halliday CL, Hoenigl M, Cornely OA, Meyer W. Scedosporium and Lomentospora infections: contemporary microbiological tools for the diagnosis of invasive disease. J Fungi (Basel). 2021;7(1):23. https://doi.org/10.3390/jof7010023.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Ramirez-Garcia A, Pellon A, Rementeria A, Buldain I, Barreto-Bergter E, Rollin-Pinheiro R, de Meirelles JV, Xisto MIDS, Ranque S, Havlicek V, Vandeputte P, Govic YL, Bouchara JP, Giraud S, Chen S, Rainer J, Alastruey-Izquierdo A, Martin-Gomez MT, López-Soria LM, Peman J, Schwarz C, Bernhardt A, Tintelnot K, Capilla J, Martin-Vicente A, Cano-Lira J, Nagl M, Lackner M, Irinyi L, Meyer W, de Hoog S, Hernando FL. Scedosporium and Lomentospora: an updated overview of underrated opportunists. Med Mycol. 2018;56(Suppl_1):102–25. https://doi.org/10.1093/mmy/myx113.

    Article  PubMed  Google Scholar 

  127. Abrantes RA, Refojo N, Hevia AI, Fernández J, Isla G, Córdoba S, Dávalos MF, Lubovich S, Maldonado I, Davel GO, Stchigel AM. Scedosporium spp. from clinical setting in Argentina, with the proposal of the new pathogenic species Scedosporium americanum. J Fungi (Basel). 2021;7(3):160. https://doi.org/10.3390/jof7030160.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O’Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016;108(5):1028–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Kwon-Chung KJ. Taxonomy of fungi causing mucormycosis and entomophthoramycosis (zygomycosis) and nomenclature of the disease: molecular mycologic perspectives. Clin Infect Dis. 2012;54 Suppl 1(Suppl 1):S8–S15. https://doi.org/10.1093/cid/cir864.

    Article  Google Scholar 

  130. Li Y, Steenwyk JL, Chang Y, Wang Y, James TY, Stajich JE, Spatafora JW, Groenewald M, Dunn CW, Hittinger CT, Shen XX, Rokas A. A genome-scale phylogeny of the kingdom Fungi. Curr Biol. 2021;31(8):1653–1665.e5. https://doi.org/10.1016/j.cub.2021.01.074.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Alvarez E, Garcia-Hermoso D, Sutton DA, Cano JF, Stchigel AM, Hoinard D, Fothergill AW, Rinaldi MG, Dromer F, Guarro J. Molecular phylogeny and proposal of two new species of the emerging pathogenic fungus Saksenaea. J Clin Microbiol. 2010;48(12):4410–6. https://doi.org/10.1128/JCM.01646-10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Alvarez E, Stchigel AM, Cano J, Sutton DA, Fothergill AW, Chander J, Salas V, Rinaldi MG, Guarro J. Molecular phylogenetic diversity of the emerging mucoralean fungus Apophysomyces: proposal of three new species. Rev Iberoam Micol. 2010;27(2):80–9. https://doi.org/10.1016/j.riam.2010.01.006.

    Article  PubMed  Google Scholar 

  133. Wagner L, Stielow JB, de Hoog GS, Bensch K, Schwartze VU, Voigt K, Alastruey-Izquierdo A, Kurzai O, Walther G. A new species concept for the clinically relevant Mucor circinelloides complex. Persoonia. 2020;44:67–97. https://doi.org/10.3767/persoonia.2020.44.03.

    Article  CAS  PubMed  Google Scholar 

  134. Walther G, Wagner L, Kurzai O. Updates on the taxonomy of Mucorales with an emphasis on clinically important taxa. J Fungi (Basel). 2019;5(4):106. https://doi.org/10.3390/jof5040106.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Jeong W, Keighley C, Wolfe R, Lee WL, Slavin MA, Kong DCM, Chen SC. The epidemiology and clinical manifestations of mucormycosis: a systematic review and meta-analysis of case reports. Clin Microbiol Infect. 2019;25(1):26–34. https://doi.org/10.1016/j.cmi.2018.07.011.

    Article  CAS  PubMed  Google Scholar 

  136. Prakash H, Chakrabarti A. Global epidemiology of mucormycosis. J Fungi (Basel). 2019;5(1):26. https://doi.org/10.3390/jof5010026.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Roden MM, Zaoutis TE, Buchanan WL, Knudsen TA, Sarkisova TA, Schaufele RL, Sein M, Sein T, Chiou CC, Chu JH, Kontoyiannis DP, Walsh TJ. Epidemiology and outcome of zygomycosis: a review of 929 reported cases. Clin Infect Dis. 2005;41(5):634–53. https://doi.org/10.1086/432579.

    Article  PubMed  Google Scholar 

  138. Bonifaz A, Stchigel AM, Guarro J, Guevara E, Pintos L, Sanchis M, Cano-Lira JF. Primary cutaneous mucormycosis produced by the new species Apophysomyces mexicanus. J Clin Microbiol. 2014;52(12):4428–31. https://doi.org/10.1128/JCM.02138-14.

    Article  PubMed  PubMed Central  Google Scholar 

  139. Hoffmann K, Discher S, Voigt K. Revision of the genus Absidia (Mucorales, Zygomycetes) based on physiological, phylogenetic, and morphological characters; thermotolerant Absidia spp. form a coherent group, Mycocladiaceae fam. nov. Mycol Res. 2007;111(Pt 10):1169–83. https://doi.org/10.1016/j.mycres.2007.07.002.

    Article  CAS  PubMed  Google Scholar 

  140. Hoffmann K, Voigt K. Absidia parricida plays a dominant role in biotrophic fusion parasitism among mucoralean fungi (Zygomycetes): Lentamyces, a new genus for A. parricida and A. zychae. Plant Biol (Stuttg). 2009;11(4):537–54. https://doi.org/10.1111/j.1438-8677.2008.00145.x.

    Article  CAS  PubMed  Google Scholar 

  141. Hoffmann K, Walther G, Kerstin V. Macocladus vs. Lichtheimia: a correction (Lichtheimiaceae fam. nov, Mucorales, Mucoromycotina). Mycol Res. 2009;113:277–8.

    Google Scholar 

  142. Garcia-Hermoso D, Hoinard D, Gantier JC, Grenouillet F, Dromer F, Dannaoui E. Molecular and phenotypic evaluation of Lichtheimia corymbifera (formerly Absidia corymbifera) complex isolates associated with human mucormycosis: rehabilitation of L. ramosa. J Clin Microbiol. 2009;47(12):3862–70. https://doi.org/10.1128/JCM.02094-08.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Alastruey-Izquierdo A, Hoffmann K, de Hoog GS, Rodriguez-Tudela JL, Voigt K, Bibashi E, Walther G. Species recognition and clinical relevance of the zygomycetous genus Lichtheimia (syn. Absidia pro parte, Mycocladus). J Clin Microbiol. 2010;48(6):2154–70. https://doi.org/10.1128/JCM.01744-09.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Walther G, Pawłowska J, Alastruey-Izquierdo A, Wrzosek M, Rodriguez-Tudela JL, Dolatabadi S, Chakrabarti A, de Hoog GS. DNA barcoding in Mucorales: an inventory of biodiversity. Persoonia. 2013;30:11–47. https://doi.org/10.3767/003158513X665070.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Alvarez E, Cano J, Stchigel AM, Sutton DA, Fothergill AW, Salas V, Rinaldi MG, Guarro J. Two new species of Mucor from clinical samples. Med Mycol. 2011;49(1):62–72. https://doi.org/10.3109/13693786.2010.499521.

    Article  PubMed  Google Scholar 

  146. Wagner L, de Hoog S, Alastruey-Izquierdo A, Voigt K, Kurzai O, Walther G. A revised species concept for opportunistic Mucor species reveals species-specific antifungal susceptibility profiles. Antimicrob Agents Chemother. 2019;63(8):e00653–19. https://doi.org/10.1128/AAC.00653-19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Vitale RG, de Hoog GS, Schwarz P, Dannaoui E, Deng S, Machouart M, Voigt K, van de Sande WW, Dolatabadi S, Meis JF, Walther G. Antifungal susceptibility and phylogeny of opportunistic members of the order Mucorales. J Clin Microbiol. 2012;50(1):66–75. https://doi.org/10.1128/JCM.06133-11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Dolatabadi S, de Hoog GS, Meis JF, Walther G. Species boundaries and nomenclature of Rhizopus arrhizus (syn. R. oryzae). Mycoses. 2014;57(Suppl 3):108–27. https://doi.org/10.1111/myc.12228.

    Article  CAS  PubMed  Google Scholar 

  149. Dolatabadi S, Walther G, Gerrits van den Ende AHG, de Hoog GS. Diversity and delimitation of Rhizopus microsporus. Fung Div. 2014;64:145–63. https://doi.org/10.1007/s13225-013-0229-6.

    Article  Google Scholar 

  150. Chakrabarti A, Marak RS, Shivaprakash MR, Gupta S, Garg R, Sakhuja V, Singhal S, Baghela A, Dixit A, Garg MK, Padhye AA. Cavitary pulmonary zygomycosis caused by Rhizopus homothallicus. J Clin Microbiol. 2010;48(5):1965–9. https://doi.org/10.1128/JCM.01272-09.

    Article  PubMed  PubMed Central  Google Scholar 

  151. Weitzman I, Whittier S, McKitrick JC, Della-Latta P. Zygospores: the last word in identification of rare or atypical zygomycetes isolated from clinical specimens. J Clin Microbiol. 1995;33(3):781–3. https://doi.org/10.1128/jcm.33.3.781-783.1995.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Abe A, Oda Y, Asano K, Sone T. Rhizopus delemar is the proper name for Rhizopus oryzae fumaric-malic acid producers. Mycologia. 2007;99:714–22. https://doi.org/10.1080/15572536.2007.11832535.

    Article  CAS  PubMed  Google Scholar 

  153. Gryganskyi AP, Lee SC, Litvintseva AP, Smith ME, Bonito G, Porter TM, Anishchenko IM, Heitman J, Vilgalys R. Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex. PLoS One. 2010;5(12):e15273. https://doi.org/10.1371/journal.pone.0015273.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Gryganskyi AP, Golan J, Dolatabadi S, Mondo S, Robb S, Idnurm A, Muszewska A, Steczkiewicz K, Masonjones S, Liao HL, Gajdeczka MT, Anike F, Vuek A, Anishchenko IM, Voigt K, de Hoog GS, Smith ME, Heitman J, Vilgalys R, Stajich JE. Phylogenetic and phylogenomic definition of Rhizopus species. G3 (Bethesda). 2018;8(6):2007–18. https://doi.org/10.1534/g3.118.200235.

    Article  CAS  PubMed  Google Scholar 

  155. Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O’Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM. An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. Nat Commun. 2016;7:12218. https://doi.org/10.1038/ncomms12218.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Liu X, Huang H, Zheng R. Molecular phylogenetic relationships within Rhizopus based on combined analyses of ITS rDNA and pyrG gene sequences. Sydowia. 2007;59:235–53.

    Google Scholar 

  157. Gryganskyi AP, Humber RA, Smith ME, Hodge K, Huang B, Voigt K, Vilgalys R. Phylogenetic lineages in Entomophthoromycota. Persoonia. 2013;30:94–105. https://doi.org/10.3767/003158513X666330.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Nie Y, Yu DS, Wang CF, Liu XY, Huang B. A taxonomic revision of the genus Conidiobolus (Ancylistaceae, Entomophthorales): four clades including three new genera. MycoKeys. 2020;66:55–81. https://doi.org/10.3897/mycokeys.66.46575.

    Article  PubMed  PubMed Central  Google Scholar 

  159. Bshabshe AA, Joseph MRP, Hakami AMA, Azraqi TA, Humayed SA, Hamid ME. Basidiobolus haptosporus-like fungus as a causal agent of gastrointestinal basidiobolomycosis. Med Mycol. 2020;58(2):264–7. https://doi.org/10.1093/mmy/myz046.

    Article  CAS  PubMed  Google Scholar 

  160. Sitterlé E, Rodriguez C, Mounier R, Calderaro J, Foulet F, Develoux M, Pawlotsky JM, Botterel F. Contribution of ultra deep sequencing in the clinical diagnosis of a new fungal pathogen species: Basidiobolus meristosporus. Front Microbiol. 2017;8:334. https://doi.org/10.3389/fmicb.2017.00334.

    Article  PubMed  PubMed Central  Google Scholar 

  161. Wang QM, Yurkov AM, Göker M, Lumbsch HT, Leavitt SD, Groenewald M, Theelen B, Liu XZ, Boekhout T, Bai FY. Phylogenetic classification of yeasts and related taxa within Pucciniomycotina. Stud Mycol. 2015;81:149–89. https://doi.org/10.1016/j.simyco.2015.12.002.

    Article  PubMed  Google Scholar 

  162. Francisco EC, de Jong AW, Hagen F. Cryptococcosis and Cryptococcus. Mycopathologia. 2021;186:729. https://doi.org/10.1007/s11046-021-00577-7.

    Article  PubMed  PubMed Central  Google Scholar 

  163. Fonseca A, Boekhout T, Fell JW. Cryptococcus Vuillemin (1901). In: Kurtzman CP, Fell JW, Boekhout T, editors. The yeasts, a taxonomic study, vol. 3. 5th ed. Amsterdam: Elsevier; 2011. p. 1661–737.

    Chapter  Google Scholar 

  164. Hagen F, Khayhan K, Theelen B, Kolecka A, Polacheck I, Sionov E, Falk R, Parnmen S, Lumbsch HT, Boekhout T. Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex. Fungal Genet Biol. 2015;78:16–48. https://doi.org/10.1016/j.fgb.2015.02.009.

    Article  CAS  PubMed  Google Scholar 

  165. Hagen F, Lumbsch HT, Arsic Arsenijevic V, Badali H, Bertout S, Billmyre RB, Bragulat MR, Cabañes FJ, Carbia M, Chakrabarti A, Chaturvedi S, Chaturvedi V, Chen M, Chowdhary A, Colom MF, Cornely OA, Crous PW, Cuétara MS, Diaz MR, Espinel-Ingroff A, Fakhim H, Falk R, Fang W, Herkert PF, Ferrer Rodríguez C, Fraser JA, Gené J, Guarro J, Idnurm A, Illnait-Zaragozi MT, Khan Z, Khayhan K, Kolecka A, Kurtzman CP, Lagrou K, Liao W, Linares C, Meis JF, Nielsen K, Nyazika TK, Pan W, Pekmezovic M, Polacheck I, Posteraro B, de Queiroz TF, Filho RO, Sánchez M, Sampaio A, Sanguinetti M, Sriburee P, Sugita T, Taj-Aldeen SJ, Takashima M, Taylor JW, Theelen B, Tomazin R, Verweij PE, Wahyuningsih R, Wang P, Boekhout T. Importance of resolving fungal nomenclature: the case of multiple pathogenic species in the Cryptococcus genus. mSphere. 2017;2(4):e00238–17. https://doi.org/10.1128/mSphere.00238-17.

  166. Farrer RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, Fisher MC, Cuomo CA. Genome evolution and innovation across the four major lineages of Cryptococcus gattii. mBio. 2015;6(5):e00868–15. https://doi.org/10.1128/mBio.00868-15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Passer AR, Coelho MA, Billmyre RB, Nowrousian M, Mittelbach M, Yurkov AM, Averette AF, Cuomo CA, Sun S, Heitman J. Genetic and genomic analyses reveal boundaries between species closely related to Cryptococcus pathogens. mBio. 2019;10(3):e00764–19. https://doi.org/10.1128/mBio.00764-19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Bovers M, Hagen F, Kuramae EE, Diaz MR, Spanjaard L, Dromer F, Hoogveld HL, Boekhout T. Unique hybrids between the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii. FEMS Yeast Res. 2006;6(4):599–607. https://doi.org/10.1111/j.1567-1364.2006.00082.x.

    Article  CAS  PubMed  Google Scholar 

  169. Bovers M, Hagen F, Kuramae EE, Hoogveld HL, Dromer F, St-Germain G, Boekhout T. AIDS patient death caused by novel Cryptococcus neoformans x C. gattii hybrid. Emerg Infect Dis. 2008;14(7):1105–8. https://doi.org/10.3201/eid1407.080122.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Litvintseva AP, Lin X, Templeton I, Heitman J, Mitchell TG. Many globally isolated AD hybrid strains of Cryptococcus neoformans originated in Africa. PLoS Pathog. 2007;3(8):e114. https://doi.org/10.1371/journal.ppat.0030114.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Samarasinghe H, Xu J. Hybrids and hybridization in the Cryptococcus neoformans and Cryptococcus gattii species complexes. Infect Genet Evol. 2018;66:245–55. https://doi.org/10.1016/j.meegid.2018.10.011.

    Article  CAS  PubMed  Google Scholar 

  172. Sugita T. Trichosporon Behrend (1890). In: Kurtzman CP, Fell JW, Boekhout T, editors. The yeasts, a taxonomic study, vol. 3. 5th ed. Amsterdam: Elsevier; 2011. p. 2015–61.

    Chapter  Google Scholar 

  173. Boekhout T, Fonseca A, Sampaio JP, Bandoni RJ, Fell JW, Kwon-Chung KJ. Discussion of teleomorphic and anamorphic basidiomycetous yeasts. In: Kurtzman CP, Fell JW, Boekhout T, editors. The yeasts, a taxonomic study, vol. 3. 5th ed. Amsterdam: Elsevier; 2011. p. 1339–72.

    Chapter  Google Scholar 

  174. Okoli I, Oyeka CA, Kwon-Chung KJ, Theelen B, Robert V, Groenewald JZ, McFadden DC, Casadevall A, Boekhout T. Cryptotrichosporon anacardii gen. nov., sp. nov., a new trichosporonoid capsulate basidiomycetous yeast from Nigeria that is able to form melanin on niger seed agar. FEMS Yeast Res. 2007;7(2):339–50. https://doi.org/10.1111/j.1567-1364.2006.00164.x.

    Article  CAS  PubMed  Google Scholar 

  175. Takashima M, Manabe RI, Nishimura Y, Endoh R, Ohkuma M, Sriswasdi S, Sugita T, Iwasaki W. Recognition and delineation of yeast genera based on genomic data: lessons from Trichosporonales. Fungal Genet Biol. 2019;130:31–42. https://doi.org/10.1016/j.fgb.2019.04.013.

    Article  CAS  PubMed  Google Scholar 

  176. Wang L, Wang QM. Molecular phylogenetic analysis of ballistoconidium-forming yeasts in Trichosporonales (Tremellomycetes): a proposal for Takashimella gen. nov. and Cryptotrichosporon tibetense sp. nov. PLoS One. 2015;10(7):e0132653. https://doi.org/10.1371/journal.pone.0132653.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Fungsin B, Takashima M, Sugita T, Artjariyasripong S, Potacharoen W, Tanticharoen M, Nakase T. Bullera koratensis sp. nov. and Bullera lagerstroemiae sp. nov., two new ballistoconidium-forming yeast species in the Trichosporonales clade isolated from plant leaves in Thailand. J Gen Appl Microbiol. 2006;52(2):73–81. https://doi.org/10.2323/jgam.52.73.

    Article  CAS  PubMed  Google Scholar 

  178. Middelhoven WJ, Scorzetti G, Fell JW. Trichosporon porosum comb. nov., an anamorphic basidiomycetous yeast inhabiting soil, related to the loubieri/laibachii group of species that assimilate hemicelluloses and phenolic compounds. FEMS Yeast Res. 2001;1(1):15–22. https://doi.org/10.1111/j.1567-1364.2001.tb00009.x.

    Article  CAS  PubMed  Google Scholar 

  179. Middelhoven WJ. Trichosporon wieringae sp. nov., an anamorphic basidiomycetous yeast from soil, and assimilation of some phenolic compounds, polysaccharides and other non-conventional carbon sources by saprophytic Trichosporon species. Antonie van Leeuwenhoek. 2004;86(4):329–37. https://doi.org/10.1007/s10482-004-0226-6.

    Article  CAS  PubMed  Google Scholar 

  180. Sugita T, Kikuchi K, Makimura K, Urata K, Someya T, Kamei K, Niimi M, Uehara Y. Trichosporon species isolated from guano samples obtained from bat-inhabited caves in Japan. Appl Environ Microbiol. 2005;71(11):7626–9. https://doi.org/10.1128/AEM.71.11.7626-7629.2005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Sugita T, Takashima M, Nakase T, Ichikawa T, Ikeda R, Shinoda T. Two new yeasts, Trichosporon debeurmannianum sp. nov. and Trichosporon dermatis sp. nov., transferred from the Cryptococcus humicola complex. Int J Syst Evol Microbiol. 2001;51(Pt 3):1221–8. https://doi.org/10.1099/00207713-51-3-1221.

    Article  CAS  PubMed  Google Scholar 

  182. Takashima M, Sugita T, Shinoda T, Nakase T. Reclassification of the Cryptococcus humicola complex. Int J Syst Evol Microbiol. 2001;51(Pt 6):2199–210. https://doi.org/10.1099/00207713-51-6-2199.

    Article  CAS  PubMed  Google Scholar 

  183. Middelhoven WJ, Scorzetti G, Fell JW. Trichosporon guehoae sp. nov., an anamorphic basidiomycetous yeast. Can J Microbiol. 1999;45(8):686–90. https://doi.org/10.1139/w99-055.

    Article  CAS  PubMed  Google Scholar 

  184. Fell JW, Scorzetti G. Reassignment of the basidiomycetous yeasts Trichosporon pullulans to Guehomyces pullulans gen. nov., comb. nov. and Hyalodendron lignicola to Trichosporon lignicola comb. nov. Int J Syst Evol Microbiol. 2004;54(Pt 3):995–8. https://doi.org/10.1099/ijs.0.03017-0.

    Article  CAS  PubMed  Google Scholar 

  185. Dukik K, Muñoz JF, Jiang Y, Feng P, Sigler L, Stielow JB, Freeke J, Jamalian A, Gerrits van den Ende B, McEwen JG, Clay OK, Schwartz IS, Govender NP, Maphanga TG, Cuomo CA, Moreno LF, Kenyon C, Borman AM, de Hoog S. Novel taxa of thermally dimorphic systemic pathogens in the Ajellomycetaceae (Onygenales). Mycoses. 2017;60(5):296–309. https://doi.org/10.1111/myc.12601.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Jiang Y, Dukik K, Muñoz JF, Sigler L, Schwartz IS, Govender NP, Kenyon C, Feng P, Gerrits van den Ende B, Stielow BJ, Stchigel AM, Lu H, de Hoog GS. Phylogeny, ecology and taxonomy of systemic pathogens and their relatives in Ajellomycetaceae (Onygenales): Blastomyces, Emergomyces, Emmonsia, Emmonsiellopsis. Fung Div. 2018;90:245–91. https://doi.org/10.1007/s13225-018-0403-y.

    Article  Google Scholar 

  187. Jiang Y, Tsui CKM, Ahmed SA, Hagen F, Shang Z, Gerrits van den Ende AHG, Verweij PE, Lu H, de Hoog GS. Intraspecific diversity and taxonomy of Emmonsia crescens. Mycopathologia. 2020;185(4):613–27. https://doi.org/10.1007/s11046-020-00475-4.

    Article  CAS  PubMed  Google Scholar 

  188. Wang P, Kenyon C, de Hoog S, Guo L, Fan H, Liu H, Li Z, Sheng R, Yang Y, Jiang Y, Zhang L, Xu Y. A novel dimorphic pathogen, Emergomyces orientalis (Onygenales), agent of disseminated infection. Mycoses. 2017;60(5):310–9. https://doi.org/10.1111/myc.12583.

    Article  PubMed  Google Scholar 

  189. Schwartz IS, Sanche S, Wiederhold NP, Patterson TF, Sigler L. Emergomyces canadensis, a dimorphic fungus causing fatal systemic human disease in North America. Emerg Infect Dis. 2018;24(4):758–61. https://doi.org/10.3201/eid2404.171765.

    Article  PubMed  PubMed Central  Google Scholar 

  190. Kenyon C, Bonorchis K, Corcoran C, Meintjes G, Locketz M, Lehloenya R, Vismer HF, Naicker P, Prozesky H, van Wyk M, Bamford C, du Plooy M, Imrie G, Dlamini S, Borman AM, Colebunders R, Yansouni CP, Mendelson M, Govender NP. A dimorphic fungus causing disseminated infection in South Africa. N Engl J Med. 2013;369(15):1416–24. https://doi.org/10.1056/NEJMoa1215460.

    Article  CAS  PubMed  Google Scholar 

  191. Schwartz IS, Lerm B, Hoving JC, Kenyon C, Horsnell WG, Basson WJ, Otieno-Odhiambo P, Govender NP, Colebunders R, Botha A. Emergomyces africanus in soil, South Africa. Emerg Infect Dis. 2018;24(2):377–80. https://doi.org/10.3201/eid2402.171351.

    Article  PubMed  PubMed Central  Google Scholar 

  192. Brown EM, McTaggart LR, Zhang SX, Low DE, Stevens DA, Richardson SE. Phylogenetic analysis reveals a cryptic species Blastomyces gilchristii, sp. nov. within the human pathogenic fungus Blastomyces dermatitidis. PLoS One. 2013;8(3):e59237. https://doi.org/10.1371/journal.pone.0059237.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Schwartz IS, Wiederhold NP, Hanson KE, Patterson TF, Sigler L. Blastomyces helicus, a new dimorphic fungus causing fatal pulmonary and systemic disease in humans and animals in Western Canada and the United States. Clin Infect Dis. 2019;68(2):188–95. https://doi.org/10.1093/cid/ciy483.

    Article  PubMed  Google Scholar 

  194. Maphanga TG, Birkhead M, Muñoz JF, Allam M, Zulu TG, Cuomo CA, Schwartz IS, Ismail A, Naicker SD, Mpembe RS, Corcoran C, de Hoog S, Kenyon C, Borman AM, Frean JA, Govender NP. Human blastomycosis in South Africa caused by Blastomyces percursus and Blastomyces emzantsi sp. nov., 1967 to 2014. J Clin Microbiol. 2020;58(3):e01661–19. https://doi.org/10.1128/JCM.01661-19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Schwartz IS, Muñoz JF, Kenyon CR, Govender NP, McTaggart L, Maphanga TG, Richardson S, Becker P, Cuomo CA, McEwen JG, Sigler L. Blastomycosis in Africa and the Middle East: a comprehensive review of reported cases and reanalysis of historical isolates based on molecular data. Clin Infect Dis. 2021;73:e1560. https://doi.org/10.1093/cid/ciaa1100.

    Article  CAS  PubMed  Google Scholar 

  196. Ashraf N, Kubat RC, Poplin V, Adenis AA, Denning DW, Wright L, McCotter O, Schwartz IS, Jackson BR, Chiller T, Bahr NC. Re-drawing the maps for endemic mycoses. Mycopathologia. 2020;185(5):843–65. https://doi.org/10.1007/s11046-020-00431-2.

    Article  PubMed  PubMed Central  Google Scholar 

  197. Rodrigues AM, Beale MA, Hagen F, Fisher MC, Terra PPD, de Hoog S, Brilhante RSN, de Aguiar Cordeiro R, de Souza Collares Maia Castelo-Branco D, Rocha MFG, Sidrim JJC, de Camargo ZP. The global epidemiology of emerging Histoplasma species in recent years. Stud Mycol. 2020;97:100095. https://doi.org/10.1016/j.simyco.2020.02.001.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Kasuga T, Taylor JW, White TJ. Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulatum Darling. J Clin Microbiol. 1999;37(3):653–63. https://doi.org/10.1128/JCM.37.3.653-663.1999.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Teixeira Mde M, Patané JS, Taylor ML, Gómez BL, Theodoro RC, de Hoog S, Engelthaler DM, Zancopé-Oliveira RM, Felipe MS, Barker BM. Worldwide phylogenetic distributions and population dynamics of the genus Histoplasma. PLoS Negl Trop Dis. 2016;10(6):e0004732. https://doi.org/10.1371/journal.pntd.0004732.

    Article  PubMed  Google Scholar 

  200. Turissini DA, Gomez OM, Teixeira MM, McEwen JG, Matute DR. Species boundaries in the human pathogen Paracoccidioides. Fungal Genet Biol. 2017;106:9–25. https://doi.org/10.1016/j.fgb.2017.05.007.

    Article  PubMed  PubMed Central  Google Scholar 

  201. Teixeira Mde M, Theodoro RC, Oliveira FF, Machado GC, Hahn RC, Bagagli E, San-Blas G, Soares Felipe MS. Paracoccidioides lutzii sp. nov.: biological and clinical implications. Med Mycol. 2014;52(1):19–28. https://doi.org/10.3109/13693786.2013.794311.

    Article  PubMed  Google Scholar 

  202. Muñoz JF, Farrer RA, Desjardins CA, Gallo JE, Sykes S, Sakthikumar S, Misas E, Whiston EA, Bagagli E, Soares CM, Teixeira MM, Taylor JW, Clay OK, McEwen JG, Cuomo CA. Genome diversity, recombination, and virulence across the major lineages of Paracoccidioides. mSphere. 2016;1(5):e00213–6. https://doi.org/10.1128/mSphere.00213-16.

  203. Hahn RC, Rodrigues AM, Della Terra PP, Nery AF, Hoffmann-Santos HD, Góis HM, Fontes CJF, de Camargo ZP. Clinical and epidemiological features of paracoccidioidomycosis due to Paracoccidioides lutzii. PLoS Negl Trop Dis. 2019;13(6):e0007437. https://doi.org/10.1371/journal.pntd.0007437.

    Article  PubMed  PubMed Central  Google Scholar 

  204. Fisher MC, Koenig GL, White TJ, Taylor JW. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis. Mycologia. 2002;94(1):73–84.

    Article  CAS  PubMed  Google Scholar 

  205. Teixeira MM, Barker BM. Use of population genetics to assess the ecology, evolution, and population structure of Coccidioides. Emerg Infect Dis. 2016;22(6):1022–30. https://doi.org/10.3201/eid2206.151565.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Teixeira MM, Alvarado P, Roe CC, Thompson GR 3rd, Patané JSL, Sahl JW, Keim P, Galgiani JN, Litvintseva AP, Matute DR, Barker BM. Population structure and genetic diversity among isolates of Coccidioides posadasii in Venezuela and surrounding regions. mBio. 2019;10(6):e01976–19. https://doi.org/10.1128/mBio.01976-19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Rodrigues AM, Della Terra PP, Gremião ID, Pereira SA, Orofino-Costa R, de Camargo ZP. The threat of emerging and re-emerging pathogenic Sporothrix species. Mycopathologia. 2020;185(5):813–42. https://doi.org/10.1007/s11046-020-00425-0.

    Article  PubMed  Google Scholar 

  208. Zhang Y, Hagen F, Stielow B, Rodrigues AM, Samerpitak K, Zhou X, Feng P, Yang L, Chen M, Deng S, Li S, Liao W, Li R, Li F, Meis JF, Guarro J, Teixeira M, Al-Zahrani HS, Pires de Camargo Z, Zhang L, de Hoog GS. Phylogeography and evolutionary patterns in Sporothrix spanning more than 14 000 human and animal case reports. Persoonia. 2015;35:1–20. https://doi.org/10.3767/003158515X687416.

  209. Marimon R, Cano J, Gené J, Sutton DA, Kawasaki M, Guarro J. Sporothrix brasiliensis, S. globosa, and S. mexicana, three new Sporothrix species of clinical interest. J Clin Microbiol. 2007;45(10):3198–206. https://doi.org/10.1128/JCM.00808-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Marimon R, Gené J, Cano J, Guarro J. Sporothrix luriei: a rare fungus from clinical origin. Med Mycol. 2008;46(6):621–5. https://doi.org/10.1080/13693780801992837.

    Article  PubMed  Google Scholar 

  211. Rodrigues AM, Cruz Choappa R, Fernandes GF, de Hoog GS, de Camargo ZP. Sporothrix chilensis sp. nov. (Ascomycota: Ophiostomatales), a soil-borne agent of human sporotrichosis with mild-pathogenic potential to mammals. Fungal Biol. 2016;120(2):246–64. https://doi.org/10.1016/j.funbio.2015.05.006.

    Article  PubMed  Google Scholar 

  212. Etchecopaz AN, Lanza N, Toscanini MA, Devoto TB, Pola SJ, Daneri GL, Iovannitti CA, Cuestas ML. Sporotrichosis caused by Sporothrix brasiliensis in Argentina: Case report, molecular identification and in vitro susceptibility pattern to antifungal drugs. J Mycol Med. 2020;30(1):100908. https://doi.org/10.1016/j.mycmed.2019.100908.

    Article  CAS  PubMed  Google Scholar 

  213. Čmoková A, Kolařík M, Dobiáš R, Hoyer LL, Janouskovcová H, Kano R, Kuklova I, Lyskova P, Machova L, Maier T, Mallátová N, Man M, Mencl K, Nenoff P, Peano A, Prausová SD, Uhrlab S, Vetrovsky T, Wiegand C, Hubka V. Resolving the taxonomy of emerging zoonotic pathogens in the Trichophyton benhamiae complex. Fung Div. 2020;104:333–87. https://doi.org/10.1007/s13225-020-00465-3.

    Article  CAS  Google Scholar 

  214. Summerbell RC. What is the evolutionary and taxonomic status of asexual lineages in the dermatophytes? Stud Mycol. 2002;47:97–101.

    Google Scholar 

  215. Kane J, Summerbell RC, Sigler L, Krajden S, Land G. Laboratory handbook of dermatophytes. A clinical guide and laboratory manual of dermatophytes and other filamentous fungi from skin, hair and nails. Belmont: Star Publishers; 1997.

    Google Scholar 

  216. Weitzman I, Summerbell RC. The dermatophytes. Clin Microbiol Rev. 1995;8(2):240–59. https://doi.org/10.1128/CMR.8.2.240.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Nishio K, Kawasaki M, Ishizaki H. Phylogeny of the genera Trichophyton using mitochondrial DNA analysis. Mycopathologia. 1992;117:127–32.

    Article  CAS  PubMed  Google Scholar 

  218. de Bièvre C, Dujon B. Organisation of the mitochondrial genome of Trichophyton rubrum III. DNA sequence analysis of the NADH dehydrogenase subunits 1, 2, 3, 4, 5 and the cytochrome b gene. Curr Genet. 1999;35(1):30–5. https://doi.org/10.1007/s002940050429.

    Article  PubMed  Google Scholar 

  219. Harmsen D, Schwinn A, Bröcker EB, Frosch M. Molecular differentiation of dermatophyte fungi. Mycoses. 1999;42(1-2):67–70. https://doi.org/10.1046/j.1439-0507.1999.00261.x.

    Article  CAS  PubMed  Google Scholar 

  220. Kano R, Nakamura Y, Watanabe S, Tsujimoto H, Hasegawa A. Phylogenetic relation of Epidermophyton floccosum to the species of Microsporum and Trichophyton in chitin synthase 1 (CHS1) gene sequences. Mycopathologia. 1999;146(3):111–3. https://doi.org/10.1023/a:1007091031124.

    Article  CAS  PubMed  Google Scholar 

  221. Kawasaki M, Aoki M, Ishizaki H, Nishimura K, Miyaji M. Phylogeny of Epidermophyton floccosum and other dermatophytes. Mycopathologia. 1996;134(3):121–8. https://doi.org/10.1007/BF00436718.

    Article  CAS  PubMed  Google Scholar 

  222. Makimura K, Tamura Y, Mochizuki T, Hasegawa A, Tajiri Y, Hanazawa R, Uchida K, Saito H, Yamaguchi H. Phylogenetic classification and species identification of dermatophyte strains based on DNA sequences of nuclear ribosomal internal transcribed spacer 1 regions. J Clin Microbiol. 1999;37(4):920–4. https://doi.org/10.1128/JCM.37.4.920-924.1999.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  223. Mochizuki T, Watanabe S, Uehara M. Genetic homogeneity of Trichophyton mentagrophytes var. interdigitale isolated from geographically distant regions. J Med Vet Mycol. 1996;34(2):139–43.

    Article  CAS  PubMed  Google Scholar 

  224. Summerbell RC, Haugland RA, Li A, Gupta AK. rRNA gene internal transcribed spacer 1 and 2 sequences of asexual, anthropophilic dermatophytes related to Trichophyton rubrum. J Clin Microbiol. 1999;37(12):4005–11. https://doi.org/10.1128/JCM.37.12.4005-4011.1999.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  225. Gräser Y, Kuijpers AF, Presber W, De Hoog GS. Molecular taxonomy of Trichophyton mentagrophytes and T. tonsurans. Med Mycol. 1999;37(5):315–30. https://doi.org/10.1046/j.1365-280x.1999.00234.x.

    Article  PubMed  Google Scholar 

  226. Stockdale PM. Sexual stimulation between Arthroderma simii and other dermatophytes. In: Vanbreuseghem R, De Vroey C, editors. Sexuality and pathogenicity of fungi. Paris: Masson; 1981. p. 57–68.

    Google Scholar 

  227. Summerbell RC, Moore MK, Starink-Willemse M, van Iperen A. ITS barcodes for Trichophyton tonsurans and T. equinum. Med Mycol. 2007;45:193–200.

    Article  CAS  PubMed  Google Scholar 

  228. Gräser Y, Kuijpers AF, Presber W, de Hoog GS. Molecular taxonomy of the Trichophyton rubrum complex. J Clin Microbiol. 2000;38:3329–36.

    Article  PubMed  PubMed Central  Google Scholar 

  229. Ohst T, de Hoog S, Presber W, Stavrakieva V, Gräser Y. Origins of microsatellite diversity in the Trichophyton rubrum-T. violaceum clade (Dermatophytes). J Clin Microbiol. 2004;42:4444–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  230. Woodgyer A. The curious adventures of Trichophyton equinum in the realm of molecular biology: a modern fairy tale. Med Mycol. 2004;42:397–403.

    Article  CAS  PubMed  Google Scholar 

  231. Packeu A, Stubbe D, Roesems S, Goens K, Van Rooij P, de Hoog S, Hendrickx M. Lineages within the Trichophyton rubrum complex. Mycopathologia. 2020;185(1):123–36. https://doi.org/10.1007/s11046-019-00386-z.

    Article  PubMed  Google Scholar 

  232. Symoens F, Jousson O, Packeu A, Fratti M, Staib P, Mignon B, Monod M. The dermatophyte species Arthroderma benhamiae: intraspecies variability and mating behaviour. J Med Microbiol. 2013;62(Pt 3):377–85. https://doi.org/10.1099/jmm.0.053223-0.

    Article  CAS  PubMed  Google Scholar 

  233. Zhan P, Dukik K, Li D, Sun J, Stielow JB, Gerrits van den Ende B, Brankovics B, Menken SBJ, Mei H, Bao W, Lv G, Liu W, de Hoog GS. Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. violaceum. Stud Mycol. 2018;89:153–75. https://doi.org/10.1016/j.simyco.2018.02.004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  234. Dukik K, de Hoog GS, Stielow JB, Freeke J, van den Ende BG, Vicente VA, Menken SBJ, Ahmed SA. Molecular and phenotypic characterization of Nannizzia (Arthrodermataceae). Mycopathologia. 2020;185(1):9–35. https://doi.org/10.1007/s11046-019-00336-9.

    Article  CAS  PubMed  Google Scholar 

  235. Nenoff P, Verma SB, Uhrlaß S, Burmester A, Gräser Y. A clarion call for preventing taxonomical errors of dermatophytes using the example of the novel Trichophyton mentagrophytes genotype VIII uniformly isolated in the Indian epidemic of superficial dermatophytosis. Mycoses. 2019;62:6–10.

    Article  CAS  PubMed  Google Scholar 

  236. Symoens F, Jousson O, Planard C, Fratti M, Staib P, Mignon B, Monod M. Molecular analysis and mating behaviour of the Trichophyton mentagrophytes species complex. Int J Med Microbiol. 2011;301(3):260–6. https://doi.org/10.1016/j.ijmm.2010.06.001.

    Article  CAS  PubMed  Google Scholar 

  237. Tang C, Kong X, Ahmed SA, Thakur R, Chowdhary A, Nenoff P, Uhrlass S, Verma SB, Meis JF, Kandemir H, Kang Y, de Hoog GS. Taxonomy of the Trichophyton mentagrophytes/T. interdigitale species complex harboring the highly virulent, multiresistant genotype T. indotineae. Mycopathologia. 2021;186(3):315–26. https://doi.org/10.1007/s11046-021-00544.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  238. Kaszubiak A, Klein S, de Hoog GS, Gräser Y. Population structure and evolutionary origins of Microsporum canis, M. ferrugineum and M. audouinii. Infect Genet Evol. 2004;4:179–86.

    Article  CAS  PubMed  Google Scholar 

  239. Hainsworth S, Kučerová I, Sharma R, Cañete-Gibas CF, Hubka V. Three-gene phylogeny of the genus Arthroderma: basis for future taxonomic studies. Med Mycol. 2021;59:355–65.

    Article  CAS  PubMed  Google Scholar 

  240. Kano R, Kimura U, Kakurai M, Hiruma J, Kamata H, Suga Y, Harada K. Trichophyton indotineae sp. nov.: a new highly terbinafine-resistant anthropophilic dermatophyte species. Mycopathologia. 2020;185:947–58.

    Article  CAS  PubMed  Google Scholar 

  241. Li W, Metin B, White TC, Heitman J. Organization and evolutionary trajectory of the mating type (MAT) locus in dermatophyte and dimorphic fungal pathogens. Eukaryot Cell. 2010;9:46–58.

    Article  CAS  PubMed  Google Scholar 

  242. Cornet L, D’hooge E, Magain N, Stubbe D, Packeu A, Baurain D, Becker P. The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach. Microb Genom. 2021;7(11):000707. https://doi.org/10.1099/mgen.0.000707.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  243. Kano R, Kawasaki M, Mochizuki T, Hiruma M, Hasegawa A. Mating genes of the Trichophyton mentagrophytes complex. Mycopathologia. 2012;173:103–12.

    Article  CAS  PubMed  Google Scholar 

  244. Kosanke S, Hamann L, Kupsch C, Moreno Garcia S, Chopra A, Gräser Y. Unequal distribution of the mating type (MAT) locus idiomorphs in dermatophyte species. Fungal Genet Biol. 2018;118:45–53. https://doi.org/10.1016/j.fgb.2018.07.003.

    Article  CAS  PubMed  Google Scholar 

  245. Liu J, Ge L, Mei H, Zheng H, Peng J, Liang G, Liu W. Comparative genomics and molecular analysis of Epidermophyton floccosum. Mycopathologia. 2021;186(4):487–97. https://doi.org/10.1007/s11046-021-00567-9.

    Article  CAS  PubMed  Google Scholar 

  246. Metin B, Heitman J. She loves me, she loves me not: on the dualistic asexual/sexual nature of dermatophyte fungi. Mycopathologia. 2020;185:87–101.

    CAS  PubMed  Google Scholar 

  247. Chang JC, Hsu MM, Barton RC, Jackson CJ. High-frequency intragenomic heterogeneity of the ribosomal DNA intergenic spacer region in Trichophyton violaceum. Eukaryot Cell. 2008;7(4):721–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  248. Martinez DA, Oliver BG, Gräser Y, Goldberg JM, Li W, Martinez-Rossi NM, Monod M, Shelest E, Barton RC, Birch E, Brakhage AA, Chen Z, Gurr SJ, Heiman D, Heitman J, Kosti I, Rossi A, Saif S, Samalova M, Saunders CW, Shea T, Summerbell RC, Xu J, Young S, Zeng Q, Birren BW, Cuomo CA, White TC. Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. mBio. 2012;3(5):e00259–12. https://doi.org/10.1128/mBio.00259-12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands

    Ferry Hagen & Jos Houbraken

  2. Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands

    Ferry Hagen

  3. Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands

    Ferry Hagen

  4. National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany

    Grit Walther

  5. Sporometrics, Toronto, ON, Canada

    James Scott & Richard Summerbell

  6. Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada

    James Scott & Richard Summerbell

  7. College of Science, King Saud University, Riyadh, Saudi Arabia

    Teun Boekhout

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  1. Ferry Hagen
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  3. Jos Houbraken
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  1. Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA

    Duane R. Hospenthal

  2. Departments of Pathology, Microbiology, and Clinical Laboratory Sciences, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA

    Michael G. Rinaldi

  3. Departments of Medicine and Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA

    Thomas J. Walsh

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Hagen, F., Walther, G., Houbraken, J., Scott, J., Summerbell, R., Boekhout, T. (2023). Molecular Taxonomy. In: Hospenthal, D.R., Rinaldi, M.G., Walsh, T.J. (eds) Diagnosis and Treatment of Fungal Infections. Springer, Cham. https://doi.org/10.1007/978-3-031-35803-6_3

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