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Advances in Genomics of Human Fungal Pathogens

  • Daniel Raymond Kollath
  • Marcus de Melo Teixeira
  • Bridget Marie BarkerEmail author
Chapter
Part of the Population Genomics book series (POGE)

Abstract

Fungi are responsible for 1.5 million deaths every year, and one-third of the human population has experienced a fungal infection. The increasing numbers of immunocompromised people are associated with the increased incidence of human mycosis, either from medical interventions such as cancer therapy or transplantation or due to other underlying diseases such as HIV/AIDS or diabetes. Additionally, climate change has been implicated in widening distributions of endemic fungi, potentially expanding beyond previously restricted ranges. In this chapter, we will address two main classes of fungal pathogens: first, the globally distributed fungi such as Candida, Aspergillus, and Cryptococcus, followed by a discussion of endemic fungal pathogens and their relatives Paracoccidioides, Histoplasma, Coccidioides, and Emmonsia. In the past, virulence and pathogenesis studies were limited to few infection models and biomarkers, but these studies have progressed significantly with the advances of DNA sequencing and genetic tools. Newly sequenced structural (DNA) and functional (RNA and protein) genomes provide a scaffold to understand gene gain and loss that might be associated with mammalian infection and disease progression. During infection, these pathogens express a wide range of genes that are associated with either establishment of infection or escaping recognition by host immune cells. Moreover, population genomic studies reveal that pathogen complexes exhibit different strategies to generate genetic diversity either via sexual or parasexual recombination, and this phenomenon may be implicated in altered virulence, disease presentation, and antifungal resistance. The literature of genomic studies of the abovementioned pathogenic fungal genera are summarized, and molecular taxonomy and population structure are explored, as well as a survey of the main genomic characteristics, chromosomal variation, gene content, and expression. Comparative genomics between pathogenic and nonpathogenic close-related species provides evidence of both convergent and unique adaptation of those fungal lineages to mammalian hosts. A better understanding of patterns of gene flow among species (hybridization), adaptation and evolutionary potential, fully closed reference genomes, and general improvement of gene annotation and function is needed.

Keywords

Comparative genomics Fungal infection Fungal pathogen genomics Population genetics of fungi 

References

  1. Almeida F. Estudos comparativos do granuloma coccidioidico nos Estados Unidos e no Brasil. Novo gênero para o parasito brasileiro. An Fac Med S Paulo. 1930;5:18.Google Scholar
  2. Almeida RS, Brunke S, Albrecht A, Thewes S, Laue M, Edwards JE, Filler SG, Hube B. the hyphal-associated adhesin and invasin Als3 of Candida albicans mediates iron acquisition from host ferritin. PLoS Pathog. 2008;4:e1000217.PubMedPubMedCentralGoogle Scholar
  3. Alspaugh JA. Virulence mechanisms and Cryptococcus neoformans pathogenesis. Fungal Genet Biol. 2015;78:55–8.PubMedGoogle Scholar
  4. Alves CT, Wei XQ, Silva S, Azeredo J, Henriques M, Williams DW. Candida albicans promotes invasion and colonisation of Candida glabrata in a reconstituted human vaginal epithelium. J Infect. 2014;69:396–407.PubMedGoogle Scholar
  5. Amaike S, Keller NP. Aspergillus flavus. Annu Rev Phytopathol. 2011;49:107–33.PubMedGoogle Scholar
  6. Anstead GM, Sutton DA, Graybill JR. Adiaspiromycosis causing respiratory failure and a review of human infections due to Emmonsia and Chrysosporium spp. J Clin Microbiol. 2012;50:1346–54.PubMedPubMedCentralGoogle Scholar
  7. Arendrup MC, Patterson TF. Multidrug-resistant Candida: epidemiology, molecular mechanisms, and treatment. J Infect Dis. 2017;216:S445–51.Google Scholar
  8. Ariyachet C, Solis NV, Liu Y, Prasadarao NV, Filler SG, McBride AE. SR-like RNA-binding protein Slr1 affects Candida albicans filamentation and virulence. Infect Immun. 2013;81:1267–76.PubMedPubMedCentralGoogle Scholar
  9. Bagagli E, Bosco SM, Theodoro RC, Franco M. Phylogenetic and evolutionary aspects of Paracoccidioides brasiliensis reveal a long coexistence with animal hosts that explain several biological features of the pathogen. Infect Genet Evol. 2006;6:344–51.PubMedGoogle Scholar
  10. Bahr NC, Antinori S, Wheat LJ, Sarosi GA. Histoplasmosis infections worldwide: thinking outside of the Ohio River valley. Curr Trop Med Rep. 2015;2:70–80.PubMedPubMedCentralGoogle Scholar
  11. Barberan A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci U S A. 2015;112:5756–61.PubMedPubMedCentralGoogle Scholar
  12. Basenko E, Pulman J, Shanmugasundram A, Harb O, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert C, Kissinger J, Roos D, Hertz-Fowler C. FungiDB: an integrated bioinformatic resource for fungi and oomycetes. J Fungi. 2018;4:39.Google Scholar
  13. Bennett RJ. Coming of age – sexual reproduction in Candida species. PLoS Pathog. 2010;6:e1001155.PubMedPubMedCentralGoogle Scholar
  14. Bennett RJ. The parasexual lifestyle of Candida albicans. Curr Opin Microbiol. 2015;28:10–7.PubMedPubMedCentralGoogle Scholar
  15. Billmyre RB, Calo S, Feretzaki M, Wang X, Heitman J. RNAi function, diversity, and loss in the fungal kingdom. Chromosom Res. 2013;21:561–72.Google Scholar
  16. Bocca AL, Amaral AC, Teixeira MM, Sato PK, Shikanai-Yasuda MA, Soares Felipe MS. Paracoccidioidomycosis: eco-epidemiology, taxonomy and clinical and therapeutic issues. Future Microbiol. 2013;8:1177–91.PubMedGoogle Scholar
  17. Boekhout T, Gueidan C, Hoog GS, Samson RA, Varga J, Walther G. Fungal taxonomy: new developments in medically important fungi. Curr Fungal Infect Rep. 2009;3:9.Google Scholar
  18. Bongomin F, Gago S, Oladele RO, Denning DW. Global and multi-national prevalence of fungal diseases-estimate precision. J Fungi (Basel). 2017;3:57.Google Scholar
  19. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980;32:314–31.PubMedPubMedCentralGoogle Scholar
  20. Bowman BH, Taylor JW, Brownlee AG, Lee J, Lu SD, White TJ. Molecular evolution of the fungi: relationship of the Basidiomycetes, Ascomycetes, and Chytridiomycetes. Mol Biol Evol. 1992a;9:285–96.PubMedGoogle Scholar
  21. Bowman BH, Taylor JW, White TJ. Molecular evolution of the fungi: human pathogens. Mol Biol Evol. 1992b;9:893–904.PubMedGoogle Scholar
  22. Boyce KJ, Andrianopoulos A. Fungal dimorphism: the switch from hyphae to yeast is a specialized morphogenetic adaptation allowing colonization of a host. FEMS Microbiol Rev. 2015;39:797–811.PubMedGoogle Scholar
  23. Brenier-Pinchart MP, Lebeau B, Devouassoux G, Mondon P, Pison C, Ambroise-Thomas P, Grillot R. Aspergillus and lung transplant recipients: a mycologic and molecular epidemiologic study. J Heart Lung Transplant. 1998;17:972–9.PubMedGoogle Scholar
  24. Brown SM, Campbell LT, Lodge JK. Cryptococcus neoformans, a fungus under stress. Curr Opin Microbiol. 2007;10:320–5.PubMedPubMedCentralGoogle Scholar
  25. Brown GD, Denning DW, Gow NA, Levitz SM, Netea MG, White TC. Hidden killers: human fungal infections. Sci Transl Med. 2012;4:165rv13.PubMedGoogle Scholar
  26. 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. 2013a;8:e59237.PubMedPubMedCentralGoogle Scholar
  27. Brown J, Benedict K, Park BJ, Thompson GR 3rd. Coccidioidomycosis: epidemiology. Clin Epidemiol. 2013b;5:185–97.PubMedPubMedCentralGoogle Scholar
  28. Brown GD, Meintjes G, Kolls JK, Gray C, Horsnell W, Working Group from The, E.-A. R. M. W, Achan B, Alber G, Aloisi M, Armstrong-James D, Beale M, Bicanic T, Black J, Bohjanen P, Botes A, Boulware DR, Brown G, Bunjun R, Carr W, Casadevall A, Chang C, Chivero E, Corcoran C, Cross A, Dawood H, Day J, De Bernardis F, de Jager V, De Repentigny L, Denning D, Eschke M, Finkelman M, Govender N, Gow N, Graham L, Gryschek R, Hammond-Aryee K, Harrison T, Heard N, Hill M, Hoving JC, Janoff E, Jarvis J, Kayuni S, King K, Kolls J, Kullberg BJ, Lalloo DG, Letang E, Levitz S, Limper A, Longley N, Machiridza TR, Mahabeer Y, Martinsons N, Meiring S, Meya D, Miller R, Molloy S, Morris L, Mukaremera L, Musubire AK, Muzoora C, Nair A, Nakiwala Kimbowa J, Netea M, Nielsen K, O’Hern J, Okurut S, Parker A, Patterson T, Pennap G, Perfect J, Prinsloo C, Rhein J, Rolfes MA, Samuel C, Schutz C, Scriven J, Sebolai OM, Sojane K, Sriruttan C, Stead D, Steyn A, Thawer NK, Thienemann F, von Hohenberg M, Vreulink JM, Wessels J, Wood K, Yang YL. AIDS-related mycoses: the way forward. Trends Microbiol. 2014;22:107–9.PubMedPubMedCentralGoogle Scholar
  29. Butler G. Fungal sex and pathogenesis. Clin Microbiol Rev. 2010;23:140–59.PubMedPubMedCentralGoogle Scholar
  30. Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, HUBE B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 2009;459:657–62.PubMedPubMedCentralGoogle Scholar
  31. Cain CW, Lohse MB, Homann OR, Sil A, Johnson AD. A conserved transcriptional regulator governs fungal morphology in widely diverged species. Genetics. 2012;190:511–21.PubMedPubMedCentralGoogle Scholar
  32. Calcagno AM, Bignell E, Warn P, Jones MD, Denning DW, Muhlschlegel FA, Rogers TR, Haynes K. Candida glabrata STE12 is required for wild-type levels of virulence and nitrogen starvation induced filamentation. Mol Microbiol. 2003;50:1309–18.PubMedGoogle Scholar
  33. Camacho E, Nino-Vega GA. Paracoccidioides spp.: virulence factors and immune-evasion strategies. Mediat Inflamm. 2017;2017:5313691.  https://doi.org/10.1155/2017/5313691.CrossRefGoogle Scholar
  34. Campins H. Coccidioidomycosis in South America. A review of its epidemiology and geographic distribution. Mycopathol Mycol Appl. 1970;41:25–34.PubMedGoogle Scholar
  35. Carreté L, Ksiezopolska E, Pegueroles C, Gómez-Molero E, Saus E, Iraola-Guzmán S, Loska D, Bader O, Fairhead C, Gabaldón T. Patterns of genomic variation in the opportunistic pathogen candida glabrata suggest the existence of mating and a secondary association with humans. Curr Biol. 2018;28:15–27.PubMedPubMedCentralGoogle Scholar
  36. Castillo CG, Kauffman CA, Miceli MH. Blastomycosis. Infect Dis Clin N Am. 2016;30:247–64.Google Scholar
  37. Chang YC, Ingavale SS, Bien C, Espenshade P, Kwon-Chung KJ. Conservation of the sterol regulatory element-binding protein pathway and its pathobiological importance in Cryptococcus neoformans. Eukaryot Cell. 2009;8:1770–9.PubMedPubMedCentralGoogle Scholar
  38. Charalambous LT, Premji A, Tybout C, Hunt A, Cutshaw D, Elsamadicy AA, Yang S, Xie J, Giamberardino C, Pagadala P, Perfect JR, Lad SP. Prevalence, healthcare resource utilization and overall burden of fungal meningitis in the United States. J Med Microbiol. 2018;67:215–27.PubMedGoogle Scholar
  39. Chastain DB, Henao-Martinez AF, Franco-Paredes C. Opportunistic invasive mycoses in AIDS: cryptococcosis, histoplasmosis, coccidiodomycosis, and talaromycosis. Curr Infect Dis Rep. 2017;19:36.PubMedGoogle Scholar
  40. Chun CD, Liu OW, Madhani HD. A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans. PLoS Pathog. 2007;3:e22.PubMedPubMedCentralGoogle Scholar
  41. Chung D, Barker BM, Carey CC, Merriman B, Werner ER, Lechner BE, Dhingra S, Cheng C, Xu W, Blosser SJ, Morohashi K, Mazurie A, Mitchell TK, Haas H, Mitchell AP, Cramer RA. ChIP-seq and in vivo transcriptome analyses of the Aspergillus fumigatus SREBP SrbA reveals a new regulator of the fungal hypoxia response and virulence. PLoS Pathog. 2014;10:e1004487.PubMedPubMedCentralGoogle Scholar
  42. Cisse OH, Pagni M, Hauser PM. Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss. Genome Biol Evol. 2014;6:1938–48.PubMedPubMedCentralGoogle Scholar
  43. Cisse OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA. Comparative population genomics analysis of the mammalian fungal pathogen pneumocystis. MBio. 2018;9:e00381–18.PubMedPubMedCentralGoogle Scholar
  44. Cormack BP, Ghori N, Falkow S. An adhesin of the yeast pathogen Candida glabrata mediating adherence to human epithelial cells. Science. 1999;285:578–82.PubMedGoogle Scholar
  45. Coste A, Selmecki A, Forche A, Diogo D, Bougnoux ME, D'Enfert C, Berman J, Sanglard D. Genotypic evolution of azole resistance mechanisms in sequential Candida albicans isolates. Eukaryot Cell. 2007;6:1889–904.PubMedPubMedCentralGoogle Scholar
  46. Cramer RA. Secretion stress and fungal pathogenesis: a new, exploitable chink in fungal armor? Virulence. 2011;2:1–3.PubMedPubMedCentralGoogle Scholar
  47. Cramer RA. In vivo veritas: Aspergillus fumigatus proliferation and pathogenesis – conditionally speaking. Virulence. 2016;7:7–10.PubMedGoogle Scholar
  48. Crombie K, Spengane Z, Locketz M, Dlamini S, Lehloenya R, Wasserman S, Maphanga TG, Govender NP, Kenyon C, Schwartz IS. Paradoxical worsening of Emergomyces africanus infection in an HIV-infected male on itraconazole and antiretroviral therapy. PLoS Negl Trop Dis. 2018;12:e0006173.PubMedPubMedCentralGoogle Scholar
  49. Cuomo CA. Harnessing whole genome sequencing in medical mycology. Curr Fungal Infect Rep. 2017;11:52–9.PubMedPubMedCentralGoogle Scholar
  50. Cuomo CA, Shea T, Yang B, Rao R, Forche A. Whole genome sequence of the heterozygous clinical isolate Candida krusei 81-B-5. G3 (Bethesda). 2017;7:2883–9.Google Scholar
  51. Cushion MT, Smulian AG, Slaven BE, Sesterhenn T, Arnold J, Staben C, Porollo A, Adamczak R, Meller J. Transcriptome of Pneumocystis carinii during fulminate infection: carbohydrate metabolism and the concept of a compatible parasite. PLoS One. 2007;2:e423.PubMedPubMedCentralGoogle Scholar
  52. Cushion MT, Ashbaugh A, Hendrix K, Linke MJ, Tisdale N, Sayson SG, Porollo A. Gene expression of Pneumocystis murina after treatment with anidulafungin results in strong signals for sexual reproduction, cell wall integrity, and cell cycle arrest, indicating a requirement for ascus formation for proliferation. Antimicrob Agents Chemother. 2018;62:e02513–7.PubMedPubMedCentralGoogle Scholar
  53. D’Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio. 2011;2:e00342–10.PubMedPubMedCentralGoogle Scholar
  54. De Farias MR, Condas LA, Ribeiro MG, Bosco SDM, Muro MD, Werner J, Theodoro RC, Bagagli E, Marques SA, Franco M. Paracoccidioidomycosis in a dog: case report of generalized lymphadenomegaly. Mycopathologia. 2011;172:147–52.PubMedGoogle Scholar
  55. De Jesus-Berrios M, Liu L, Nussbaum JC, Cox GM, Stamler JS, Heitman J. Enzymes that counteract nitrosative stress promote fungal virulence. Curr Biol. 2003;13:1963–8.PubMedGoogle Scholar
  56. De Jonge R, Van Esse HP, Kombrink A, Shinya T, Desaki Y, Bours R, Van Der Krol S, Shibuya N, Joosten MH, Thomma BP. Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants. Science. 2010;329:953–5.PubMedGoogle Scholar
  57. De Macedo PM, Almeida-Paes R, De Medeiros Muniz M, Oliveira MM, Zancope-Oliveira RM, Costa RL, Do Valle AC. Paracoccidioides brasiliensis PS2: first autochthonous paracoccidioidomycosis case report in Rio de Janeiro, Brazil, and literature review. Mycopathologia. 2016;181:701–8.PubMedGoogle Scholar
  58. Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailao AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, Leon-Narvaez H, Longo LV, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodriguez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter ME, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CM, Birren BW, Cuomo CA. Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. PLoS Genet. 2011;7:e1002345.PubMedPubMedCentralGoogle Scholar
  59. Dodgson AR, Pujol C, Denning DW, Soll DR, Fox AJ. Multilocus sequence typing of Candida glabrata reveals geographically enriched clades. J Clin Microbiol. 2003;41:5709–17.PubMedPubMedCentralGoogle Scholar
  60. Dukik K, Munoz 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;60:296–309.PubMedPubMedCentralGoogle Scholar
  61. Edwards JA, Chen C, Kemski MM, Hu J, Mitchell TK, Rappleye CA. Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles. BMC Genomics. 2013;14:695.PubMedPubMedCentralGoogle Scholar
  62. Eggimann P, Garbino J, Pittet D. Epidemiology of Candida species infections in critically ill non-immunosuppressed patients. Lancet Infect Dis. 2003;3:685–702.PubMedGoogle Scholar
  63. Emmons CW, Ashburn LL. The isolation of Haplosporangium parvum n. sp and Coccidioides immitis from wild rodents. Their relationship to coccidioidomycosis. Public Health Rep. 1942;57:1715–27.Google Scholar
  64. Engelthaler DM, Hicks ND, Gillece JD, Roe CC, Schupp JM, Driebe EM, Gilgado F, Carriconde F, Trilles L, Firacative C, Ngamskulrungroj P, Castaneda E, Lazera Mdos S, Melhem MS, Perez-Bercoff A, Huttley G, Sorrell TC, Voelz K, May RC, Fisher MC, Thompson GR 3rd, Lockhart SR, Keim P, Meyer W. Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal. MBio. 2014;5:e01464–14.PubMedPubMedCentralGoogle Scholar
  65. Engelthaler DM, Roe CC, Hepp CM, Teixeira M, Driebe EM, Schupp JM, Gade L, Waddell V, Komatsu K, Arathoon E, Logemann H, Thompson GR 3rd, Chiller T, Barker B, Keim P, Litvintseva AP. Local population structure and patterns of western hemisphere dispersal for Coccidioides spp., the fungal cause of valley fever. MBio. 2016;7:e00550–16.PubMedPubMedCentralGoogle Scholar
  66. 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:e00868–15.PubMedPubMedCentralGoogle Scholar
  67. Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 2008;4:e1000046.PubMedPubMedCentralGoogle Scholar
  68. Feretzaki M, Billmyre RB, Clancey SA, Wang X, Heitman J. Gene network polymorphism illuminates loss and retention of novel RNAi silencing components in the Cryptococcus pathogenic species complex. PLoS Genet. 2016;12:e1005868.PubMedPubMedCentralGoogle Scholar
  69. Fianchi L, Picardi M, Cudillo L, Corvatta L, Mele L, Trape G, Girmenia C, Pagano L. Aspergillus niger infection in patients with haematological diseases: a report of eight cases. Mycoses. 2004;47:163–7.PubMedGoogle Scholar
  70. Filler SG. Candida-host cell receptor-ligand interactions. Curr Opin Microbiol. 2006;9:333–9.PubMedGoogle Scholar
  71. Fisher MC, Koenig GL, White TJ, San-Blas G, Negroni R, Alvarez IG, Wanke B, Taylor JW. Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration. Proc Natl Acad Sci U S A. 2001;98:4558–62.PubMedPubMedCentralGoogle Scholar
  72. 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;94:73–84.PubMedGoogle Scholar
  73. Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ. Emerging fungal threats to animal, plant and ecosystem health. Nature. 2012;484:186–94.PubMedGoogle Scholar
  74. Flowers SA, Colon B, Whaley SG, Schuler MA, Rogers PD. Contribution of clinically derived mutations in ERG11 to azole resistance in Candida albicans. Antimicrob Agents Chemother. 2015;59:450–60.PubMedGoogle Scholar
  75. Fraser JA, Heitman J. Fungal mating-type loci. Curr Biol. 2003;13:R792–5.PubMedGoogle Scholar
  76. Fraser JA, Giles SS, Wenink EC, Geunes-Boyer SG, Wright JR, Diezmann S, Allen A, Stajich JE, Dietrich FS, Perfect JR, Heitman J. Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak. Nature. 2005;437:1360–4.PubMedGoogle Scholar
  77. Fu C, Sun S, Billmyre RB, Roach KC, Heitman J. Unisexual versus bisexual mating in Cryptococcus neoformans: consequences and biological impacts. Fungal Genet Biol. 2015;78:65–75.PubMedGoogle Scholar
  78. Gabaldon T, Martin T, Marcet-Houben M, Durrens P, Bolotin-Fukuhara M, Lespinet O, Arnaise S, Boisnard S, Aguileta G, Atanasova R, Bouchier C, Couloux A, Creno S, Almeida Cruz J, Devillers H, Enache-Angoulvant A, Guitard J, Jaouen L, Ma L, Marck C, Neuveglise C, Pelletier E, Pinard A, Poulain J, Recoquillay J, Westhof E, Wincker P, Dujon B, Hennequin C, Fairhead C. Comparative genomics of emerging pathogens in the Candida glabrata clade. BMC Genomics. 2013;14:623.PubMedPubMedCentralGoogle Scholar
  79. Gabaldon T, Naranjo-Ortiz MA, Marcet-Houben M. Evolutionary genomics of yeast pathogens in the Saccharomycotina. FEMS Yeast Res. 2016;16  https://doi.org/10.1093/femsyr/fow064.PubMedPubMedCentralGoogle Scholar
  80. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Basturkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D’Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Penalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature. 2005;438:1105–15.PubMedGoogle Scholar
  81. Gaona-Flores VA, Campos-Navarro LA, Cervantes-Tovar RM, Alcala-Martinez E. The epidemiology of fungemia in an infectious diseases hospital in Mexico city: a 10-year retrospective review. Med Mycol. 2016;54:600–4.PubMedGoogle Scholar
  82. Gauthier GM. Dimorphism in fungal pathogens of mammals, plants, and insects. PLoS Pathog. 2015;11:e1004608.PubMedPubMedCentralGoogle Scholar
  83. Gegembauer G, Araujo LM, Pereira EF, Rodrigues AM, Paniago AM, Hahn RC, De Camargo ZP. Serology of paracoccidioidomycosis due to Paracoccidioides lutzii. PLoS Negl Trop Dis. 2014;8:e2986.PubMedPubMedCentralGoogle Scholar
  84. Geiser DM, Dorner JW, Horn BW, Taylor JW. The phylogenetics of mycotoxin and sclerotium production in Aspergillus flavus and Aspergillus oryzae. Fungal Genet Biol. 2000;31:169–79.PubMedGoogle Scholar
  85. Gillece JD, Schupp JM, Balajee SA, Harris J, Pearson T, Yan Y, Keim P, Debess E, Marsden-Haug N, Wohrle R, Engelthaler DM, Lockhart SR. Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest reveals unexpected diversity. PLoS One. 2011;6:e28550.PubMedPubMedCentralGoogle Scholar
  86. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. Life with 6,000 genes. Science. 1996;274(546):563–7.Google Scholar
  87. Gomez-Raja J, Andaluz E, Magee B, Calderone R, Larriba G. A single SNP, G929T (Gly310Val), determines the presence of a functional and a non-functional allele of HIS4 in Candida albicans SC5314: detection of the non-functional allele in laboratory strains. Fungal Genet Biol. 2008;45:527–41.PubMedGoogle Scholar
  88. Grahl N, Shepardson KM, Chung D, Cramer RA. Hypoxia and fungal pathogenesis: to air or not to air? Eukaryot Cell. 2012;11:560–70.PubMedPubMedCentralGoogle Scholar
  89. Grigg ME, Bonnefoy S, Hehl AB, Suzuki Y, Boothroyd JC. Success and virulence in Toxoplasma as the result of sexual recombination between two distinct ancestries. Science. 2001;294:161–5.PubMedGoogle Scholar
  90. Hage CA, Knox KS, Wheat LJ. Endemic mycoses: overlooked causes of community acquired pneumonia. Respir Med. 2012;106:769–76.PubMedGoogle Scholar
  91. 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.PubMedGoogle Scholar
  92. Hardie WD, Glasser SW, Hagood JS. Emerging concepts in the pathogenesis of lung fibrosis. Am J Pathol. 2009;175:3–16.PubMedPubMedCentralGoogle Scholar
  93. Hawksworth DL. Pandora’s mycological box: molecular sequences vs. morphology in understanding fungal relationships and biodiversity. Rev Iberoam Micol. 2006;23:127–33.PubMedGoogle Scholar
  94. Hawksworth DL. Responsibility in naming pathogens: the case of Pneumocystis jirovecii, the causal agent of pneumocystis pneumonia. Lancet Infect Dis. 2007;7:3–5; discussion 5.PubMedGoogle Scholar
  95. Hawksworth DL, Lucking R. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol Spectr. 2017;5  https://doi.org/10.1128/microbiolspec.FUNK-0052-2016.
  96. Hawksworth DL, Rossman AY. Where are all the undescribed fungi? Phytopathology. 1997;87:888–91.PubMedGoogle Scholar
  97. Hedayati MT, Pasqualotto AC, Warn PA, Bowyer P, Denning DW. Aspergillus flavus: human pathogen, allergen and mycotoxin producer. Microbiology. 2007;153:1677–92.Google Scholar
  98. Heitman J. Evolution of eukaryotic microbial pathogens via covert sexual reproduction. Cell Host Microbe. 2010;8:86–99.PubMedPubMedCentralGoogle Scholar
  99. Hirakawa MP, Chyou DE, Huang D, Slan AR, Bennett RJ. Parasex generates phenotypic diversity de novo and impacts drug resistance and virulence in Candida albicans. Genetics. 2017;207:1195–211.PubMedPubMedCentralGoogle Scholar
  100. Holland LM, Schroder MS, Turner SA, Taff H, Andes D, Grozer Z, Gacser A, Ames L, Haynes K, Higgins DG, Butler G. Comparative phenotypic analysis of the major fungal pathogens Candida parapsilosis and Candida albicans. PLoS Pathog. 2014;10:e1004365.PubMedPubMedCentralGoogle Scholar
  101. Hrycyk MF, Garcia Garces H, Bosco SMG, De Oliveira SL, Marques SA, Bagagli E. Ecology of Paracoccidioides brasiliensis, P. Lutzii and related species: infection in armadillos, soil occurrence and mycological aspects. Med Mycol. 2018;  https://doi.org/10.1093/mmy/myx142.
  102. Huang SH, Wu CH, Chang YC, Kwon-Chung KJ, Brown RJ, Jong A. Cryptococcus neoformans-derived microvesicles enhance the pathogenesis of fungal brain infection. PLoS One. 2012;7:e48570.PubMedPubMedCentralGoogle Scholar
  103. Jackson AP, Gamble JA, Yeomans T, Moran GP, Saunders D, Harris D, Aslett M, Barrell JF, Butler G, Citiulo F, Coleman DC, De Groot PW, Goodwin TJ, Quail MA, McQuillan J, Munro CA, Pain A, Poulter RT, Rajandream MA, Renauld H, Spiering MJ, Tivey A, Gow NA, Barrell B, Sullivan DJ, Berriman M. Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans. Genome Res. 2009;19:2231–44.PubMedPubMedCentralGoogle Scholar
  104. Jacobsen MD, Gow NAR, Maiden MCJ, Shaw DJ, Odds FC. Strain typing and determination of population structure of Candida krusei by multilocus sequence typing. J Clin Microbiol. 2007;45:317–23.PubMedGoogle Scholar
  105. Janbon G, Ormerod KL, Paulet D, Byrnes EJ 3rd, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppee JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuveglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet. 2014;10:e1004261.PubMedPubMedCentralGoogle Scholar
  106. Jiménez-Ortigosa C, Perez WB, Angulo D, Borroto-Esoda K, Perlin DS. De novo acquisition of resistance to SCY-078 in Candida glabrata involves FKS mutations that both overlap and are distinct from those conferring echinocandin resistance. Antimicrob Agents Chemother. 2017;61:e00833–17.  https://doi.org/10.1128/AAC.00833-17.CrossRefPubMedPubMedCentralGoogle Scholar
  107. Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, Davis RW, Scherer S. The diploid genome sequence of Candida albicans. Proc Natl Acad Sci U S A. 2004;101:7329–34.PubMedPubMedCentralGoogle Scholar
  108. Jong A, Wu CH, Prasadarao NV, Kwon-Chung KJ, Chang YC, Ouyang Y, Shackleford GM, Huang SH. Invasion of Cryptococcus neoformans into human brain microvascular endothelial cells requires protein kinase C-alpha activation. Cell Microbiol. 2008;10:1854–65.PubMedPubMedCentralGoogle Scholar
  109. Kane J, Summerbell R, 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; 1997.Google Scholar
  110. Kasuga T, White TJ, Koenig G, McEwen J, Restrepo A, Castaneda E, Da Silva Lacaz C, Heins-Vaccari EM, De Freitas RS, Zancope-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;12:3383–401.PubMedGoogle Scholar
  111. Kauffman CA. Histoplasmosis: a clinical and laboratory update. Clin Microbiol Rev. 2007;20:115–32.PubMedPubMedCentralGoogle Scholar
  112. Kaur R, Domergue R, Zupancic ML, Cormack BP. A yeast by any other name: Candida glabrata and its interaction with the host. Curr Opin Microbiol. 2005;8:378–84.PubMedGoogle Scholar
  113. Kemen E, Jones JD. Obligate biotroph parasitism: can we link genomes to lifestyles? Trends Plant Sci. 2012;17:448–57.PubMedGoogle Scholar
  114. Kent LB, Juneann WM. What makes Cryptococcus neoformans a pathogen? Emerg Infect Dis J. 1998;4:71.Google Scholar
  115. 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;369:1416–24.PubMedGoogle Scholar
  116. Kidd SE, Hagen F, Tscharke RL, Huynh M, Bartlett KH, Fyfe M, MacDougall L, Boekhout T, Kwon-Chung KJ, Meyer W. A rare genotype of Cryptococcus gattii caused the cryptococcosis outbreak on Vancouver Island (British Columbia, Canada). Proc Natl Acad Sci U S A. 2004;101:17258–63.PubMedPubMedCentralGoogle Scholar
  117. Kohler JR, Hube B, Puccia R, Casadevall A, Perfect JR. Fungi that infect humans. Microbiol Spectr. 2017;5  https://doi.org/10.1128/microbiolspec.FUNK-0014-2016.
  118. Kronstad J, Saikia S, Nielson ED, Kretschmer M, Jung W, Hu G, Geddes JM, Griffiths EJ, Choi J, Cadieux B, Caza M, Attarian R. Adaptation of Cryptococcus neoformans to mammalian hosts: integrated regulation of metabolism and virulence. Eukaryot Cell. 2012;11:109–18.PubMedPubMedCentralGoogle Scholar
  119. Kwon-Chung KJ. Sexual stage of Histoplasma capsulatum. Science. 1972;175:326.PubMedGoogle Scholar
  120. Kwon-Chung KJ, Sugui JA. Aspergillus fumigatus – what makes the species a ubiquitous human fungal pathogen? PLoS Pathog. 2013;9:e1003743.PubMedPubMedCentralGoogle Scholar
  121. Kwon-Chung KJ, Fraser JA, Doering TL, Wang Z, Janbon G, Idnurm A, Bahn YS. Cryptococcus neoformans and Cryptococcus gattii, the etiologic agents of cryptococcosis. Cold Spring Harb Perspect Med. 2014;4:a019760.PubMedPubMedCentralGoogle Scholar
  122. Lengeler KB, Cox GM, Heitman J. Serotype Ad strains of Cryptococcus neoformans are diploid or aneuploid and are heterozygous at the mating-type locus. Infect Immun. 2001;69:115–22.PubMedPubMedCentralGoogle Scholar
  123. Lewis ER, Bowers JR, Barker BM. Dust devil: the life and times of the fungus that causes valley fever. PLoS Pathog. 2015;11:e1004762.PubMedPubMedCentralGoogle Scholar
  124. 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.PubMedGoogle Scholar
  125. Li J, Chang YC, Wu CH, Liu J, Kwon-Chung KJ, Huang SH, Shimada H, Fante R, Fu X, Jong A. The 14-3-3 gene function of Cryptococcus neoformans is required for its growth and virulence. J Microbiol Biotechnol. 2016;26:918–27.PubMedGoogle Scholar
  126. Lin SJ, Schranz J, Teutsch SM. Aspergillosis case-fatality rate: systematic review of the literature. Clin Infect Dis. 2001;32:358–66.PubMedGoogle Scholar
  127. Litvintseva AP, Marsden-Haug N, Hurst S, Hill H, Gade L, Driebe EM, Ralston C, Roe C, Barker BM, Goldoft M, Keim P, Wohrle R, Thompson GR 3rd, Engelthaler DM, Brandt ME, Chiller T. Valley fever: finding new places for an old disease: Coccidioides immitis found in Washington state soil associated with recent human infection. Clin Infect Dis. 2015;60:e1–3.PubMedGoogle Scholar
  128. Liu Y, Filler SG. Candida albicans Als3, a multifunctional adhesin and invasin. Eukaryot Cell. 2011;10:168–73.PubMedPubMedCentralGoogle Scholar
  129. Liu OW, Chun CD, Chow ED, Chen C, Madhani HD, Noble SM. Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell. 2008;135:174–88.PubMedPubMedCentralGoogle Scholar
  130. 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;64:134–40.PubMedGoogle Scholar
  131. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D’Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science. 2005;307:1321–4.PubMedPubMedCentralGoogle Scholar
  132. Losada L, Barker BM, Pakala S, Pakala S, Joardar V, Zafar N, Mounaud S, Fedorova N, Nierman WC, Cramer RA. Large-scale transcriptional response to hypoxia in Aspergillus fumigatus observed using RNAseq identifies a novel hypoxia regulated ncRNA. Mycopathologia. 2014;178:331–9.PubMedPubMedCentralGoogle Scholar
  133. Loza L, Fu Y, Ibrahim AS, Sheppard DC, Filler SG, Edwards JE Jr. Functional analysis of the Candida albicans ALS1 gene product. Yeast. 2004;21:473–82.PubMedGoogle Scholar
  134. Lutz A. A pseudococcidic mycosis localized in the mouth and observed in Brazil. Bras Med. 1908;22:20.Google Scholar
  135. Macpherson S, Akache B, Weber S, De Deken X, Raymond M, Turcotte B. Candida albicans zinc cluster protein Upc2p confers resistance to antifungal drugs and is an activator of ergosterol biosynthetic genes. Antimicrob Agents Chemother. 2005;49:1745–52.PubMedPubMedCentralGoogle Scholar
  136. Magee BB, Magee PT. Induction of mating in Candida albicans by construction of MTLa and MTLalpha strains. Science. 2000;289:310–3.PubMedGoogle Scholar
  137. Maguire SL, Oheigeartaigh SS, Byrne KP, Schroder MS, O’Gaora P, Wolfe KH, Butler G. Comparative genome analysis and gene finding in Candida species using CGOB. Mol Biol Evol. 2013;30:1281–91.PubMedPubMedCentralGoogle Scholar
  138. Maphanga TG, Britz E, Zulu TG, Mpembe RS, Naicker SD, Schwartz IS, Govender NP. In vitro antifungal susceptibility of yeast and mold phases of isolates of dimorphic fungal pathogen emergomyces africanus (formerly Emmonsia sp.) from HIV-infected South African patients. J Clin Microbiol. 2017;55:1812–20.PubMedPubMedCentralGoogle Scholar
  139. Martel CM, Parker JE, Bader O, Weig M, Gross U, Warrilow AG, Rolley N, Kelly DE, Kelly SL. Identification and characterization of four azole-resistant erg3 mutants of Candida albicans. Antimicrob Agents Chemother. 2010;54:4527–33.PubMedPubMedCentralGoogle Scholar
  140. Martinez R. New trends in paracoccidioidomycosis epidemiology. J Fungi. 2017;3:1.Google Scholar
  141. Martinez DA, Oliver BG, Graser 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:e00259–12.PubMedPubMedCentralGoogle Scholar
  142. Matute DR, McEwen JG, Puccia R, Montes BA, San-Blas G, Bagagli E, Rauscher JT, Restrepo A, Morais F, Nino-Vega G, Taylor JW. Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies. Mol Biol Evol. 2006;23:65–73.PubMedGoogle Scholar
  143. May RC, Stone NR, Wiesner DL, Bicanic T, Nielsen K. Cryptococcus: from environmental saprophyte to global pathogen. Nat Rev Microbiol. 2016;14:106–17.PubMedGoogle Scholar
  144. McDonough ES, Lewis AL. Blastomyces dermatitidis: production of the sexual stage. Science. 1967;156:528–9.PubMedGoogle Scholar
  145. McManus BA, Coleman DC. Molecular epidemiology, phylogeny and evolution of Candida albicans. Infect Genet Evol. 2014;21:166–78.PubMedGoogle Scholar
  146. McManus BA, Coleman DC, Moran G, Pinjon E, Diogo D, Bougnoux M-E, Borecká-Melkusova S, et al. Multilocus sequence typing reveals that the population structure of Candida dubliniensis is significantly less divergent than that of Candida albicans. J Clin Microbiol. 2018;46:652–64.Google Scholar
  147. McTaggart LR, Brown EM, Richardson SE. Phylogeographic analysis of Blastomyces dermatitidis and Blastomyces gilchristii reveals an association with North American freshwater drainage basins. PLoS One. 2016;11:e0159396.PubMedPubMedCentralGoogle Scholar
  148. Miranda I, Silva-Dias A, Rocha R, Teixeira-Santos R, Coelho C, Goncalves T, Santos MA, Pina-Vaz C, Solis NV, Filler SG, Rodrigues AG. Candida albicans CUG mistranslation is a mechanism to create cell surface variation. MBio. 2013;4:e00285–13.PubMedPubMedCentralGoogle Scholar
  149. Munoz JF, Gallo JE, Misas E, Priest M, Imamovic A, Young S, Zeng Q, Clay OK, McEwen JG, Cuomo CA. Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis. PLoS Negl Trop Dis. 2014;8:e3348.PubMedPubMedCentralGoogle Scholar
  150. Munoz JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J, Sullivan TD, Marty AJ, Carmen JC, Chen Z, Ding L, Gujja S, Magrini V, Misas E, Mitreva M, Priest M, Saif S, Whiston EA, Young S, Zeng Q, Goldman WE, Mardis ER, Taylor JW, McEwen JG, Clay OK, Klein BS, Cuomo CA. The dynamic genome and transcriptome of the human fungal pathogen Blastomyces and close relative Emmonsia. PLoS Genet. 2015;11:e1005493.PubMedPubMedCentralGoogle Scholar
  151. Munoz 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  https://doi.org/10.1128/mSphere.00213-16.
  152. Munoz JF, McEwen JG, Clay OK, Cuomo CA. Genome analysis reveals evolutionary mechanisms of adaptation in systemic dimorphic fungi. Sci Rep. 2018;8:4473.PubMedPubMedCentralGoogle Scholar
  153. Naglik JR, Challacombe SJ, Hube B. Candida albicans secreted aspartyl proteinases in virulence and pathogenesis. Microbiol Mol Biol Rev. 2003a;67:400–28. table of contents.PubMedPubMedCentralGoogle Scholar
  154. Naglik JR, Rodgers CA, Shirlaw PJ, Dobbie JL, Fernandes-Naglik LL, Greenspan D, Agabian N, Challacombe SJ. Differential expression of Candida albicans secreted aspartyl proteinase and phospholipase B genes in humans correlates with active oral and vaginal infections. J Infect Dis. 2003b;188:469–79.PubMedGoogle Scholar
  155. Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, Fitzgerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Res. 2010;20:938–46.PubMedPubMedCentralGoogle Scholar
  156. Nemecek JC, Wuthrich M, Klein BS. Global control of dimorphism and virulence in fungi. Science. 2006;312:583–8.PubMedGoogle Scholar
  157. Nguyen VQ, Sil A. Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator. Proc Natl Acad Sci U S A. 2008;105:4880–5.PubMedPubMedCentralGoogle Scholar
  158. Ni M, Feretzaki M, Sun S, Wang X, Heitman J. Sex in fungi. Annu Rev Genet. 2011;45:405–30.PubMedPubMedCentralGoogle Scholar
  159. Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, Garcia JL, Garcia MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jimenez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafon A, Latge JP, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O’Neil S, Paulsen I, Penalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, Rodriguez De Cordoba S, Rodriguez-Pena JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sanchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez De Aldana CR, Weidman J, White O, Woodward J, Yu JH, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 2005;438:1151–6.PubMedGoogle Scholar
  160. O’Gorman CM, Fuller HT, Dyer PS. Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus. Nature. 2009;457:471–4.PubMedGoogle Scholar
  161. Odio CD, Marciano BE, Galgiani JN, Holland SM. Risk factors for disseminated Coccidioidomycosis, United States. Emerg Infect Dis. 2017;23:308.PubMedCentralGoogle Scholar
  162. Oladele RO, Ayanlowo OO, Richardson MD, Denning DW. Histoplasmosis in Africa: an emerging or a neglected disease? PLoS Negl Trop Dis. 2018;12:e0006046.PubMedPubMedCentralGoogle Scholar
  163. Paoletti M, Rydholm C, Schwier EU, Anderson MJ, Szakacs G, Lutzoni F, Debeaupuis JP, Latge JP, Denning DW, Dyer PS. Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus. Curr Biol. 2005;15:1242–8.PubMedGoogle Scholar
  164. Park BJ, Sigel K, Vaz V, Komatsu K, McRill C, Phelan M, Colman T, Comrie AC, Warnock DW, Galgiani JN, Hajjeh RA. An epidemic of coccidioidomycosis in Arizona associated with climatic changes, 1998-2001. J Infect Dis. 2005;191:1981–7.PubMedGoogle Scholar
  165. Pel HJ, De Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, De Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, Van Den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, Van Dijck PW, Van Dijk A, Dijkhuizen L, Driessen AJ, D’Enfert C, Geysens S, Goosen C, Groot GS, De Groot PW, Guillemette T, Henrissat B, Herweijer M, Van Den Hombergh JP, Van Den Hondel CA, Van Der Heijden RT, Van Der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, Van Kuyk PA, Lauber J, Lu X, Van Der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, Van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, Van De Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, Van Ooyen AJ, Visser J, Stam H. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol. 2007;25:221–31.PubMedGoogle Scholar
  166. Persinoti GF, Martinez DA, Li W, Dogen A, Billmyre RB, Averette A, Goldberg JM, Shea T, Young S, Zeng Q, Oliver BG, Barton R, Metin B, Hilmioglu-Polat S, Ilkit M, Graser Y, Martinez-Rossi NM, White TC, Heitman J, Cuomo CA. Whole-genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogen trichophyton rubrum. Genetics. 2018;208:1657–69.PubMedPubMedCentralGoogle Scholar
  167. Porman AM, Alby K, Hirakawa MP, Bennett RJ. Discovery of a phenotypic switch regulating sexual mating in the opportunistic fungal pathogen Candida tropicalis. Proc Natl Acad Sci U S A. 2011;108:21158–63.PubMedPubMedCentralGoogle Scholar
  168. Queiroz-Telles F, Fahal AH, Falci DR, Caceres DH, Chiller T, Pasqualotto AC. Neglected endemic mycoses. Lancet Infect Dis. 2017;17:e367–77.PubMedGoogle Scholar
  169. Rhodes J, Beale MA, Vanhove M, Jarvis JN, Kannambath S, Simpson JA, Ryan A, Meintjes G, Harrison TS, Fisher MC, Bicanic T. A population genomics approach to assessing the genetic basis of within-host microevolution underlying recurrent cryptococcal meningitis infection. G3 (Bethesda). 2017;7:1165–76.Google Scholar
  170. Rodrigues ML, Alvarez M, Fonseca FL, Casadevall A. Binding of the wheat germ lectin to Cryptococcus neoformans suggests an association of chitinlike structures with yeast budding and capsular glucuronoxylomannan. Eukaryot Cell. 2008;7:602–9.PubMedGoogle Scholar
  171. Rodrigues CF, Silva S, Henriques M. Candida glabrata: a review of its features and resistance. Eur J Clin Microbiol Infect Dis. 2014;33:673–88.PubMedGoogle Scholar
  172. Ronning CM, Fedorova ND, Bowyer P, Coulson R, Goldman G, Kim HS, Turner G, Wortman JR, Yu J, Anderson MJ, Denning DW, Nierman WC. Genomics of Aspergillus fumigatus. Rev Iberoam Micol. 2005;22:223–8.PubMedGoogle Scholar
  173. Ropars J, Maufrais C, Diogo D, Marcet-Houben M, Perin A, Sertour N, Mosca K, et al. Gene flow contributes to diversification of the major fungal pathogen Candida albicans. Nat Commun. 2018;9:2253.PubMedPubMedCentralGoogle Scholar
  174. Saccente M, Woods GL. Clinical and laboratory update on blastomycosis. Clin Microbiol Rev. 2010;23:367–81.PubMedPubMedCentralGoogle Scholar
  175. Salazar SB, Wang C, Munsterkotter M, Okamoto M, Takahashi-Nakaguchi A, Chibana H, Lopes MM, Guldener U, Butler G, Mira NP. Comparative genomic and transcriptomic analyses unveil novel features of azole resistance and adaptation to the human host in Candida glabrata. FEMS Yeast Res. 2018;18:fox079.Google Scholar
  176. Santos MA, Cheesman C, Costa V, Moradas-Ferreira P, Tuite MF. Selective advantages created by codon ambiguity allowed for the evolution of an alternative genetic code in Candida spp. Mol Microbiol. 1999;31:937–47.PubMedGoogle Scholar
  177. Schuster E, Dunn-Coleman N, Frisvad JC, Van Dijck PW. On the safety of Aspergillus niger – a review. Appl Microbiol Biotechnol. 2002;59:426–35.PubMedGoogle Scholar
  178. Schwartz IS, Kenyon C, Feng P, Govender NP, Dukik K, Sigler L, Jiang Y, Stielow JB, Munoz JF, Cuomo CA, Botha A, Stchigel AM, De Hoog GS. 50 years of Emmonsia disease in humans: the dramatic emergence of a cluster of novel fungal pathogens. PLoS Pathog. 2015;11:e1005198.PubMedPubMedCentralGoogle Scholar
  179. Schwartz IS, Wiederhold NP, Patterson TF, Sigler L. Blastomyces helicus, an emerging dimorphic fungal pathogen causing fatal pulmonary and disseminated disease in humans and animals in western Canada and United States. Open Forum Infect Dis. 2017;4:2.Google Scholar
  180. Schwartz IS, Sanche S, Wiederhold NP, Patterson T, Sigler L. Emergomyces canadensis, a dimorphic fungus causing fatal systemic human disease in North America. Emerg Infect Dis. 2018;24:758–61.PubMedPubMedCentralGoogle Scholar
  181. Scordino F, Giuffrè L, Barberi G, Merlo FM, Orlando MG, Giosa D, Romeo O. Multilocus sequence typing reveals a new cluster of closely related Candida tropicalis genotypes in Italian patients with neurological disorders. Front Microbiol. 2018;9:679.PubMedPubMedCentralGoogle Scholar
  182. Sepulveda VE, Williams CL, Goldman WE. Comparison of phylogenetically distinct Histoplasma strains reveals evolutionarily divergent virulence strategies. MBio. 2014;5:e01376–14.PubMedPubMedCentralGoogle Scholar
  183. Sepulveda VE, Marquez R, Turissini DA, Goldman WE, Matute DR. Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum. MBio. 2017;8:e01339–17.PubMedPubMedCentralGoogle Scholar
  184. Sharma KK. Fungal genome sequencing: basic biology to biotechnology. Crit Rev Biotechnol. 2016;36:743–59.PubMedGoogle Scholar
  185. 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;19:1722–31.PubMedPubMedCentralGoogle Scholar
  186. Sheppard DC, Yeaman MR, Welch WH, Phan QT, Fu Y, Ibrahim AS, Filler SG, Zhang M, Waring AJ, Edwards JE Jr. Functional and structural diversity in the Als protein family of Candida albicans. J Biol Chem. 2004;279:30480–9.PubMedGoogle Scholar
  187. Shikanai-Yasuda MA, Mendes RP, Colombo AL, Queiroz-Telles F, Kono ASG, Paniago AM, Nathan A, Valle A, Bagagli E, Benard G, Ferreira MS, Teixeira MM, Silva-Vergara ML, Pereira RM, Cavalcante RS, Hahn R, Durlacher RR, Khoury Z, Camargo ZP, Moretti ML, Martinez R. Brazilian guidelines for the clinical management of paracoccidioidomycosis. Rev Soc Bras Med Trop. 2017;50:715–40.PubMedGoogle Scholar
  188. Sigler L. Ajellomyces crescens sp. nov., taxonomy of Emmonsia spp., and relatedness with Blastomyces dermatitidis (teleomorph Ajellomyces dermatitidis). J Med Vet Mycol. 1996;34:303–14.PubMedGoogle Scholar
  189. Sil A, Andrianopoulos A. Thermally dimorphic human fungal pathogens – polyphyletic pathogens with a convergent pathogenicity trait. Cold Spring Harb Perspect Med. 2014;5:a019794.PubMedGoogle Scholar
  190. Silva AP, Miranda IM, Guida A, Synnott J, Rocha R, Silva R, Amorim A, Pina-Vaz C, Butler G, Rodrigues AG. Transcriptional profiling of azole-resistant Candida parapsilosis strains. Antimicrob Agents Chemother. 2011;55:3546–56.PubMedPubMedCentralGoogle Scholar
  191. Smith JA, Kauffman CA. Blastomycosis. Proc Am Thorac Soc. 2010;7:173–80.PubMedGoogle Scholar
  192. Stephen C, Lester S, Black W, Fyfe M, Raverty S. Multispecies outbreak of cryptococcosis on southern Vancouver Island, British Columbia. Can Vet J. 2002;43:792–4.PubMedPubMedCentralGoogle Scholar
  193. Takahashi H, Kusuya Y, Hagiwara D, Takahashi-Nakaguchi A, Sakai K, Gonoi T. Global gene expression reveals stress-responsive genes in Aspergillus fumigatus mycelia. BMC Genomics. 2017;18:942.PubMedPubMedCentralGoogle Scholar
  194. Tautz D. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 1989;17:6463–71.PubMedPubMedCentralGoogle Scholar
  195. Tavanti A, Davidson AD, Gow NAR, Maiden MCJ, Odds FC. Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III. J Clin Microbiol. 2005;43:284–92.PubMedPubMedCentralGoogle Scholar
  196. Tavares AH, Fernandes L, Bocca AL, Silva-Pereira I, Felipe MS. Transcriptomic reprogramming of genus Paracoccidioides in dimorphism and host niches. Fungal Genet Biol. 2015;81:98–109.PubMedGoogle Scholar
  197. Taylor JW. Evolutionary perspectives on human fungal pathogens. Cold Spring Harb Perspect Med. 2014;5:a019588.PubMedGoogle Scholar
  198. Taylor JW, Ellison CE. Mushrooms: morphological complexity in the fungi. Proc Natl Acad Sci U S A. 2010;107:11655–6.PubMedPubMedCentralGoogle Scholar
  199. Taylor JW, Geiser DM, Burt A, Koufopanou V. The evolutionary biology and population genetics underlying fungal strain typing. Clin Microbiol Rev. 1999;12:126–46.PubMedPubMedCentralGoogle Scholar
  200. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol. 2000;31:21–32.PubMedGoogle Scholar
  201. Taylor JW, Turner E, Townsend JP, Dettman JR, Jacobson D. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philos Trans R Soc Lond Ser B Biol Sci. 2006;361:1947–63.Google Scholar
  202. Taylor JW, Hann-Soden C, Branco S, Sylvain I, Ellison CE. Clonal reproduction in fungi. Proc Natl Acad Sci U S A. 2015;112:8901–8.PubMedPubMedCentralGoogle Scholar
  203. Teixeira MM, Barker BM. Use of population genetics to assess the ecology, evolution, and population structure of Coccidioides. Emerg Infect Dis. 2016;22:1022–30.PubMedPubMedCentralGoogle Scholar
  204. Teixeira MM, Theodoro RC, De Carvalho MJ, Fernandes L, Paes HC, Hahn RC, Mendoza L, Bagagli E, San-Blas G, Felipe MS. Phylogenetic analysis reveals a high level of speciation in the Paracoccidioides genus. Mol Phylogenet Evol. 2009;52:273–83.PubMedGoogle Scholar
  205. Teixeira MDM, Theodoro RC, Derengowski Lda S, Nicola AM, Bagagli E, Felipe MS. Molecular and morphological data support the existence of a sexual cycle in species of the genus Paracoccidioides. Eukaryot Cell. 2013;12:380–9.PubMedCentralGoogle Scholar
  206. Teixeira MDM, 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. 2014a;52:19–28.Google Scholar
  207. Teixeira MM, Theodoro RC, Nino-Vega G, Bagagli E, Felipe MS. Paracoccidioides species complex: ecology, phylogeny, sexual reproduction, and virulence. PLoS Pathog. 2014b;10:e1004397.PubMedPubMedCentralGoogle Scholar
  208. Teixeira MDM, Patane JS, Taylor ML, Gomez BL, Theodoro RC, De Hoog S, Engelthaler DM, Zancope-Oliveira RM, Felipe MS, Barker BM. Worldwide phylogenetic distributions and population dynamics of the genus Histoplasma. PLoS Negl Trop Dis. 2016;10:e0004732.PubMedCentralGoogle Scholar
  209. Theodoro RC, Teixeira Mde M, Felipe MS, Paduan Kdos S, Ribolla PM, San-Blas G, Bagagli E. Genus paracoccidioides: species recognition and biogeographic aspects. PLoS One. 2012;7:e37694.PubMedPubMedCentralGoogle Scholar
  210. Tsao S, Rahkhoodaee F, Raymond M. Relative contributions of the Candida albicans ABC transporters Cdr1p and Cdr2p to clinical azole resistance. Antimicrob Agents Chemother. 2009;53:1344–52.PubMedPubMedCentralGoogle Scholar
  211. Turissini DA, Gomez OM, Teixeira MM, McEwen JG, Matute DR. Species boundaries in the human pathogen Paracoccidioides. Fungal Genet Biol. 2017;106:9–25.PubMedGoogle Scholar
  212. Turner SA, Butler G. The Candida pathogenic species complex. Cold Spring Harb Perspect Med. 2014;4:a019778.PubMedPubMedCentralGoogle Scholar
  213. Untereiner WA, Scott JA, Naveau FA, Sigler L, Bachewich J, Angus A. The Ajellomycetaceae, a new family of vertebrate-associated Onygenales. Mycologia. 2004;96:812–21.PubMedGoogle Scholar
  214. Vallabhaneni S, Kallen A, Tsay S, Chow N, Welsh R, Kerins J, Kemble SK, Pacilli M, Black SR, Landon E, Ridgway J, Palmore TN, Zelzany A, Adams EH, Quinn M, Chaturvedi S, Greenko J, Fernandez R, Southwick K, Furuya EY, Calfee DP, Hamula C, Patel G, Barrett P, MSD, Lafaro P, Berkow EL, Moulton-Meissner H, Noble-Wang J, Fagan RP, Jackson BR, Lockhart SR, Litvintseva AP, Chiller TM. Investigation of the first seven reported cases of Candida auris, a globally emerging invasive, multidrug-resistant fungus – United States, May 2013-August 2016. MMWR Morb Mortal Wkly Rep. 2016;65:1234–7.PubMedGoogle Scholar
  215. Vite-Garin T, Estrada-Barcenas DA, Cifuentes J, Taylor ML. The importance of molecular analyses for understanding the genetic diversity of Histoplasma capsulatum: an overview. Rev Iberoam Micol. 2014;31:11–5.PubMedGoogle Scholar
  216. Vos P, Hogers R, Bleeker M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995;23:4407–14.PubMedPubMedCentralGoogle Scholar
  217. 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. 2017a;60:310–9.PubMedGoogle Scholar
  218. Wang RJ, Miller RF, Huang L. Approach to fungal infections in human immunodeficiency virus-infected individuals: Pneumocystis and beyond. Clin Chest Med. 2017b;38:465–77.PubMedPubMedCentralGoogle Scholar
  219. Webster RH, Sil A. Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum. Proc Natl Acad Sci U S A. 2008;105:14573–8.PubMedPubMedCentralGoogle Scholar
  220. Whaley SG, Berkow EL, Rybak JM, Nishimoto AT, Barker KS, Rogers PD. Azole antifungal resistance in Candida albicans and emerging non-albicans Candida species. Front Microbiol. 2016;7:2173.PubMedGoogle Scholar
  221. Whiston E, Taylor JW. Genomics in Coccidioides: insights into evolution, ecology, and pathogenesis. Med Mycol. 2014;52:149–55.PubMedGoogle Scholar
  222. Whiston E, Taylor JW. Comparative phylogenomics of pathogenic and nonpathogenic species. G3 (Bethesda). 2015;6:235–44.Google Scholar
  223. Whiston E, Zhang Wise H, Sharpton TJ, Jui G, Cole GT, Taylor JW. Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp. PLoS One. 2012;7:e41034.PubMedPubMedCentralGoogle Scholar
  224. White TC. Increased mRNA levels of ERG16, CDR, and MDR1 correlate with increases in azole resistance in Candida albicans isolates from a patient infected with human immunodeficiency virus. Antimicrob Agents Chemother. 1997;41:1482–7.PubMedPubMedCentralGoogle Scholar
  225. White TJ, Bruns TD, Lee SB, Taylor JW. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide to methods and applications. Cambridge: Academic Press; 1990.Google Scholar
  226. Wiley EO. The evolutionary species concept reconsidered. Syst Biol. 1978;27:17–26.Google Scholar
  227. Wilker E, Yaffe MB. 14-3-3 proteins – a focus on cancer and human disease. J Mol Cell Cardiol. 2004;37:633–42.PubMedGoogle Scholar
  228. Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990;18:6531–5.PubMedPubMedCentralGoogle Scholar
  229. Yan Z, Hull CM, Sun S, Heitman J, Xu J. The mating type-specific homeodomain genes SXI1 alpha and SXI2a coordinately control uniparental mitochondrial inheritance in Cryptococcus neoformans. Curr Genet. 2007;51:187–95.PubMedGoogle Scholar
  230. Yu J, Cleveland TE, Nierman WC, Bennett JW. Aspergillus flavus genomics: gateway to human and animal health, food safety, and crop resistance to diseases. Rev Iberoam Micol. 2005;22:194–202.PubMedGoogle Scholar
  231. Zakikhany K, Naglik JR, Schmidt-Westhausen A, Holland G, Schaller M, Hube B. In vivo transcript profiling of Candida albicans identifies a gene essential for interepithelial dissemination. Cell Microbiol. 2007;9:2938–54.PubMedGoogle Scholar
  232. Zhu W, Filler SG. Interactions of Candida albicans with epithelial cells. Cell Microbiol. 2010;12:273–82.PubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Daniel Raymond Kollath
    • 1
  • Marcus de Melo Teixeira
    • 1
  • Bridget Marie Barker
    • 1
    Email author
  1. 1.The Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffUSA

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