Evolution of the human pathogenic lifestyle in fungi

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  • Blackwell, M. The fungi: 1, 2, 3… 5.1 million species? Am. J. Bot. 98, 426–438 (2011).

    PubMed 
    Article 

    Google Scholar 

  • Hawksworth, D. L. & Lucking, R. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.FUNK-0052-2016 (2017).

  • Stop neglecting fungi. Nat. Microbiol. https://doi.org/10.1038/nmicrobiol.2017.120 (2017).

  • Fungus focus. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-018-0721-1 (2018).

  • Denning, D. W. Calling upon all public health mycologists: to accompany the country burden papers from 14 countries. Eur. J. Clin. Microbiol. Infect. Dis. 36, 923–924 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Konopka, J., Casadevall, A., Taylor, J., Heitman, J. & Cowen, L. One Health: Fungal Pathogens of Humans, Animals, and Plants (American Academy of Microbiology, 2019).

  • Bongomin, F., Gago, S., Oladele, R. O. & Denning, D. W. Global and multi-national prevalence of fungal diseases-estimate precision. J. Fungi 3, 57 (2017).

    Article 

    Google Scholar 

  • Latge, J. P. & Chamilos, G. Aspergillus fumigatus and aspergillosis in 2019. Clin. Microbiol. Rev. https://doi.org/10.1128/CMR.00140-18 (2019).

  • Fisher, M. C. et al. Threats posed by the fungal kingdom to humans, wildlife, and agriculture. mBio 11, e00449-20 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Chang, C. C. & Levitz, S. M. Fungal immunology in clinical practice: magical realism or practical reality? Med. Mycol. 57, S294–S306 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Gow, N. A. & Netea, M. G. Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge. Philos. Trans. R. Soc. B 371, 20150462 (2016).

    Article 
    CAS 

    Google Scholar 

  • Romani, L. Immunity to fungal infections. Nat. Rev. Immunol. 11, 275–288 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Fisher, M. C., Hawkins, N. J., Sanglard, D. & Gurr, S. J. Worldwide emergence of resistance to antifungal drugs challenges human health and food security. Science 360, 739–742 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Robbins, N., Caplan, T. & Cowen, L. E. Molecular evolution of antifungal drug resistance. Annu. Rev. Microbiol. 71, 753–775 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • James, T. Y., Stajich, J. E., Hittinger, C. T. & Rokas, A. Toward a fully resolved fungal tree of life. Annu. Rev. Microbiol. 74, 291–313 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Li, Y. et al. A genome-scale phylogeny of the kingdom Fungi. Curr. Biol. 31, 1653–1665 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wijayawardene, N. N. et al. Outline of fungi and fungus-like taxa. Mycosphere 11, 1060–1456 (2020).

    Article 

    Google Scholar 

  • Rokas, A., Mead, M. E., Steenwyk, J. L., Oberlies, N. H. & Goldman, G. H. Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity. PLoS Pathog. 16, e1008315 (2020).

  • Mead, M. E. et al. An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi. Genetics 218, iyab066 (2021).

    PubMed 
    Article 

    Google Scholar 

  • Mead, M. E. et al. Characterizing the pathogenic, genomic, and chemical traits of Aspergillus fischeri, a close relative of the major human fungal pathogen Aspergillus fumigatus. mSphere 4, e00018-19 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Steenwyk, J. L., Shen, X. X., Lind, A. L., Goldman, G. H. & Rokas, A. A robust phylogenomic time tree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium. mBio 10, e00925-19 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Garcia Garces, H., Hamae Yamauchi, D., Theodoro, R. C. & Bagagli, E. PRP8 intein in onygenales: distribution and phylogenetic aspects. Mycopathologia 185, 37–49 (2020).

    CAS 
    PubMed 

    Google Scholar 

  • Hassan, M. I. A. & Voigt, K. Pathogenicity patterns of mucormycosis: epidemiology, interaction with immune cells and virulence factors. Med. Mycol. 57, S245–S256 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Gabaldon, T., Naranjo-Ortiz, M. A. & Marcet-Houben, M. Evolutionary genomics of yeast pathogens in the Saccharomycotina. FEMS Yeast Res. 16, fow064 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Opulente, D. A. et al. Pathogenic budding yeasts isolated outside of clinical settings. FEMS Yeast Res. 19, foz032 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Singh-Babak, S. D., Babak, T., Fraser, H. B. & Johnson, A. D. Lineage-specific selection and the evolution of virulence in the Candida clade. Proc. Natl Acad. Sci. USA 118, e2016818118 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hagen, F. et al. Importance of resolving fungal nomenclature: the case of multiple pathogenic species in the cryptococcus genus. mSphere https://doi.org/10.1128/mSphere.00238-17 (2017).

  • Kwon-Chung, K. J. et al. The case for adopting the ‘Species Complex’ nomenclature for the etiologic agents of cryptococcosis. mSphere https://doi.org/10.1128/mSphere.00357-16 (2017).

  • Sugui, J. A. et al. Genetic relatedness versus biological compatibility between Aspergillus fumigatus and related species. J. Clin. Microbiol. 52, 3707–3721 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Grice, E. A. & Dawson, T. L. Jr Host–microbe interactions: Malassezia and human skin. Curr. Opin. Microbiol. 40, 81–87 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Van Dyke, M. C. C., Teixeira, M. M. & Barker, B. M. Fantastic yeasts and where to find them: the hidden diversity of dimorphic fungal pathogens. Curr. Opin. Microbiol. 52, 55–63 (2019).

    PubMed 
    Article 

    Google Scholar 

  • de Hoog, G. S. et al. Toward a novel multilocus phylogenetic taxonomy for the dermatophytes. Mycopathologia 182, 5–31 (2017).

    PubMed 
    Article 

    Google Scholar 

  • Hirakawa, M. P. et al. Genetic and phenotypic intra-species variation in Candida albicans. Genome Res. 25, 413–425 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wang, J. M. et al. Intraspecies transcriptional profiling reveals key regulators of Candida albicans pathogenic traits. mBio https://doi.org/10.1128/mBio.00586-21 (2021).

  • Kowalski, C. H. et al. Fungal biofilm morphology impacts hypoxia fitness and disease progression. Nat. Microbiol. 4, 2430–2441 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Kowalski, C. H. et al. Heterogeneity among isolates reveals that fitness in low oxygen correlates with Aspergillus fumigatus virulence. mBio https://doi.org/10.1128/mBio.01515-16 (2016).

  • Ries, L. N. A. et al. Nutritional heterogeneity among Aspergillus fumigatus strains has consequences for virulence in a strain- and host-dependent manner. Front. Microbiol. 10, 854 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Dos Santos, R. A. C. et al. Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis. Front. Genet. 11, 459 (2020).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Beale, M. A. et al. Genotypic diversity is associated with clinical outcome and phenotype in cryptococcal meningitis across Southern Africa. PLoS Negl. Trop. Dis. https://doi.org/10.1371/journal.pntd.0003847 (2015).

  • Ventoulis, I. et al. Bloodstream infection by Saccharomyces cerevisiae in two COVID-19 patients after receiving supplementation of Saccharomyces in the ICU. J. Fungi https://doi.org/10.3390/jof6030098 (2020).

  • Hoenigl, M. et al. Sinusitis and frontal brain abscess in a diabetic patient caused by the basidiomycete Schizophyllum commune: case report and review of the literature. Mycoses 56, 389–393 (2013).

    PubMed 
    Article 

    Google Scholar 

  • Nanno, S. et al. Disseminated Hormographiella aspergillata infection with involvement of the lung, brain, and small intestine following allogeneic hematopoietic stem cell transplantation: case report and literature review. Transpl. Infect. Dis. 18, 611–616 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Ioannou, P., Vamvoukaki, R. & Samonis, G. Rhodotorula species infections in humans: a systematic review. Mycoses 62, 90–100 (2019).

    PubMed 
    Article 

    Google Scholar 

  • Seyedmousavi, S. et al. Fungal infections in animals: a patchwork of different situations. Med. Mycol. 56, 165–187 (2018).

    PubMed 
    Article 

    Google Scholar 

  • Rodrigues, A. M., de Hoog, G. S. & de Camargo, Z. P. Sporothrix species causing outbreaks in animals and humans driven by animal–animal transmission. PLoS Pathog. 12, e1005638 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Han, B., Pan, G. & Weiss, L. M. Microsporidiosis in humans. Clin. Microbiol. Rev. https://doi.org/10.1128/CMR.00010-20 (2021).

  • Cushion, M. T. Are members of the fungal genus Pneumocystis (a) commensals; (b) opportunists; (c) pathogens; or (d) all of the above? PLoS Pathog. 6, e1001009 (2010).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Romo, J. A. & Kumamoto, C. A. On commensalism of Candida. J. Fungi https://doi.org/10.3390/jof6010016 (2020).

  • Bensasson, D. et al. Diverse lineages of Candida albicans live on old oaks. Genetics 211, 277–288 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Taylor, L. H., Latham, S. M. & Woolhouse, M. E. Risk factors for human disease emergence. Philos. Trans. R. Soc. B 356, 983–989 (2001).

    CAS 
    Article 

    Google Scholar 

  • Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Tekaia, F. & Latge, J. P. Aspergillus fumigatus: saprophyte or pathogen? Curr. Opin. Microbiol. 8, 385–392 (2005).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Casadevall, A. Cards of virulence and the global virulome for humans. Microbe 1, 359–364 (2006).

    Google Scholar 

  • Gostincar, C. et al. Fungi between extremotolerance and opportunistic pathogenicity on humans. Fungal Diversity 93, 195–213 (2018).

    Article 

    Google Scholar 

  • Egidi, E. et al. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat. Commun. 10, 2369 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Robert, V., Cardinali, G. & Casadevall, A. Distribution and impact of yeast thermal tolerance permissive for mammalian infection. BMC Biol. 13, 18 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Yamamoto, N. et al. Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air. ISME J. 6, 1801–1811 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Chung, H. & Lee, Y. H. Hypoxia: a double-edged sword during fungal pathogenesis? Front. Microbiol. 11, 1920 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Magwene, P. M. et al. Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 108, 1987–1992 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Novohradska, S., Ferling, I. & Hillmann, F. Exploring virulence determinants of filamentous fungal pathogens through interactions with soil amoebae. Front. Cell. Infect. Microbiol. 7, 497 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Bloom, A. L. M. et al. Thermotolerance in the pathogen Cryptococcus neoformans is linked to antigen masking via mRNA decay-dependent reprogramming. Nat. Commun. 10, 4950 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Findley, K. et al. Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the Tremellales. Eukaryot. Cell 8, 353–361 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • White, T. C. et al. Fungi on the skin: dermatophytes and Malassezia. Cold Spring Harb. Perspect. Med. https://doi.org/10.1101/cshperspect.a019802 (2014).

  • Rodrigues, A. M. et al. The threat of emerging and re-emerging pathogenic Sporothrix species. Mycopathologia 185, 813–842 (2020).

    PubMed 
    Article 

    Google Scholar 

  • Steenbergen, J. N., Shuman, H. A. & Casadevall, A. Cryptococcus neoformans interactions with amoebae suggest an explanation for its virulence and intracellular pathogenic strategy in macrophages. Proc. Natl Acad. Sci. USA 98, 15245–15250 (2001).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Casadevall, A., Fu, M. S., Guimaraes, A. J. & Albuquerque, P. The ‘Amoeboid Predator-Fungal Animal Virulence’ hypothesis. J. Fungi https://doi.org/10.3390/jof5010010 (2019).

  • Magditch, D. A., Liu, T. B., Xue, C. & Idnurm, A. DNA mutations mediate microevolution between host-adapted forms of the pathogenic fungus Cryptococcus neoformans. PLoS Pathog. 8, e1002936 (2012).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Fu, M. S. et al. Amoeba predation of Cryptococcus neoformans results in pleiotropic changes to traits associated with virulence. mBio https://doi.org/10.1128/mBio.00567-21 (2021).

  • Albuquerque, P. et al. A hidden battle in the dirt: soil amoebae interactions with Paracoccidioides spp. PLoS Negl. Trop. Dis. 13, e0007742 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Sil, A. & Andrianopoulos, A. Thermally dimorphic human fungal pathogens–polyphyletic pathogens with a convergent pathogenicity trait. Cold Spring Harb. Perspect. Med. 5, a019794 (2014).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Boyce, K. J. & Andrianopoulos, A. Fungal dimorphism: the switch from hyphae to yeast is a specialized morphogenetic adaptation allowing colonization of a host. FEMS Microbiol. Rev. 39, 797–811 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Strope, P. K. et al. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome Res. 25, 762–774 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Raffa, N. & Keller, N. P. A call to arms: mustering secondary metabolites for success and survival of an opportunistic pathogen. PLoS Pathog. 15, e1007606 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Munoz, J. F., McEwen, J. G., Clay, O. K. & Cuomo, C. A. Genome analysis reveals evolutionary mechanisms of adaptation in systemic dimorphic fungi. Sci. Rep. 8, 4473 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Mixao, V. & Gabaldon, T. Hybridization and emergence of virulence in opportunistic human yeast pathogens. Yeast 35, 5–20 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Maxwell, C. S. et al. Gene exchange between two divergent species of the fungal human pathogen, Coccidioides. Evolution 73, 42–58 (2019).

    PubMed 
    Article 

    Google Scholar 

  • Gusa, A. et al. Transposon mobilization in the human fungal pathogen Cryptococcus is mutagenic during infection and promotes drug resistance in vitro. Proc. Natl Acad. Sci. USA 117, 9973–9980 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Bennett, R. J., Forche, A. & Berman, J. Rapid mechanisms for generating genome diversity: whole ploidy shifts, aneuploidy, and loss of heterozygosity. Cold Spring Harb. Perspect. Med. https://doi.org/10.1101/cshperspect.a019604 (2014).

  • Steenwyk, J. L., Soghigian, J. S., Perfect, J. R. & Gibbons, J. G. Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. BMC Genomics 17, 700 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Cisse, O. H. et al. Genomic insights into the host specific adaptation of the Pneumocystis genus. Commun. Biol. 4, 305 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ianiri, G. et al. HGT in the human and skin commensal Malassezia: a bacterially derived flavohemoglobin is required for NO resistance and host interaction. Proc. Natl Acad. Sci. USA 117, 15884–15894 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Sun, S., Hoy, M. J. & Heitman, J. Fungal pathogens. Curr. Biol. 30, R1163–R1169 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Taylor, J. W. Evolutionary perspectives on human fungal pathogens. Cold Spring Harb. Perspect. Med. https://doi.org/10.1101/cshperspect.a019588 (2014).

  • Steenwyk, J. L. et al. Variation among biosynthetic gene clusters, secondary metabolite profiles, and cards of virulence across aspergillus species. Genetics 216, 481–497 (2020).

  • Jackson, A. P. et al. Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans. Genome Res. 19, 2231–2244 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Carroll, S. B. Evolution at two levels: on genes and form. PLoS Biol. 3, e245 (2005).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Sorrells, T. R. & Johnson, A. D. Making sense of transcription networks. Cell 161, 714–723 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Fisher, K. J. & Lang, G. I. Experimental evolution in fungi: an untapped resource. Fungal Genet. Biol. 94, 88–94 (2016).

    PubMed 
    Article 

    Google Scholar 

  • Forche, A. et al. Rapid phenotypic and genotypic diversification after exposure to the oral host niche in Candida albicans. Genetics 209, 725–741 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • de Crecy, E., Jaronski, S., Lyons, B., Lyons, T. J. & Keyhani, N. O. Directed evolution of a filamentous fungus for thermotolerance. BMC Biotechnol. 9, 74 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Tso, G. H. W. et al. Experimental evolution of a fungal pathogen into a gut symbiont. Science 362, 589–595 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Hu, G. et al. Microevolution during serial mouse passage demonstrates FRE3 as a virulence adaptation gene in Cryptococcus neoformans. mBio 5, e00941–00914 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ene, I. V. et al. Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen. Proc. Natl Acad. Sci. USA 115, E8688–E8697 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Forche, A. et al. Selection of Candida albicans trisomy during oropharyngeal infection results in a commensal-like phenotype. PLoS Genet. 15, e1008137 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lucking, R. et al. Fungal taxonomy and sequence-based nomenclature. Nat. Microbiol. 6, 540–548 (2021).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Cao, C., Xi, L. & Chaturvedi, V. Talaromycosis (Penicilliosis) due to Talaromyces (Penicillium) marneffei: insights into the clinical trends of a major fungal disease 60 years after the discovery of the pathogen. Mycopathologia 184, 709–720 (2019).

    PubMed 
    Article 

    Google Scholar 

  • Fishman, J. A. Pneumocystis jiroveci. Semin. Respir. Crit. Care Med. 41, 141–157 (2020).

    PubMed 
    Article 

    Google Scholar 

  • Gabaldon, T. & Carrete, L. The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata. FEMS Yeast Res. 16, fov110 (2016).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Grigoriev, I. V. et al. MycoCosm portal: gearing up for 1,000 fungal genomes. Nucleic Acids Res. 42, D699–D704 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Shen, X. X. et al. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Sci. Adv. 6, eabd0079 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Shen, X. X. et al. Tempo and mode of genome evolution in the budding yeast subphylum. Cell 175, 1533–1545 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Robert, V. et al. MycoBank gearing up for new horizons. IMA Fungus 4, 371–379 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Nguyen, N. H. et al. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).

    Article 

    Google Scholar 

  • Wang, F. et al. Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments. Nat. Microbiol. 6, 1066–1081 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Zhao, S., Ge, W., Watanabe, A., Fortwendel, J. R. & Gibbons, J. G. Genome-wide association for itraconazole sensitivity in non-resistant clinical isolates of Aspergillus fumigatus. Front. Fung. Biol. 1, 617338 (2021).

    Article 

    Google Scholar 

  • Barber, A. E. et al. Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection. Nat. Microbiol. 6, 1526–1536 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Smith, S. D., Pennell, M. W., Dunn, C. W. & Edwards, S. V. Phylogenetics is the new genetics (for most of biodiversity). Trends Ecol. Evol. 35, 415–425 (2020).

    PubMed 
    Article 

    Google Scholar 

  • Mazi, P. B., Rauseo, A. M. & Spec, A. Blastomycosis. Infect. Dis. Clin. North Am. 35, 515–530 (2021).

    PubMed 
    Article 

    Google Scholar 

  • Pappas, P. G., Lionakis, M. S., Arendrup, M. C., Ostrosky-Zeichner, L. & Kullberg, B. J. Invasive candidiasis. Nat. Rev. Dis. Prim. 4, 18026 (2018).

    PubMed 
    Article 

    Google Scholar 

  • Van Dyke, M. C. C., Thompson, G. R., Galgiani, J. N. & Barker, B. M. The rise of Coccidioides: forces against the dust devil unleashed. Front. Immunol. 10, 2188 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Maziarz, E. K. & Perfect, J. R. Cryptococcosis. Infect. Dis. Clin. North Am. 30, 179–206 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Schwartz, I. S. et al. Emergomyces: the global rise of new dimorphic fungal pathogens. PLoS Pathog. 15, e1007977 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Batista, B. G., Chaves, M. A., Reginatto, P., Saraiva, O. J. & Fuentefria, A. M. Human fusariosis: an emerging infection that is difficult to treat. Rev. Soc. Bras. Med. Trop. 53, e20200013 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Bahr, N. C., Antinori, S., Wheat, L. J. & Sarosi, G. A. Histoplasmosis infections worldwide: thinking outside of the Ohio River valley. Curr. Trop. Med. Rep. 2, 70–80 (2015).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ruan, Y. et al. The largest meta-analysis on the global prevalence of microsporidia in mammals, avian and water provides insights into the epidemic features of these ubiquitous pathogens. Parasites Vectors 14, 186 (2021).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Prakash, H. & Chakrabarti, A. Global epidemiology of mucormycosis. J. Fungi https://doi.org/10.3390/jof5010026 (2019).

  • Martinez, R. New trends in paracoccidioidomycosis epidemiology. J. Fungi https://doi.org/10.3390/jof3010001 (2017).

  • Brown, L., Leck, A. K., Gichangi, M., Burton, M. J. & Denning, D. W. The global incidence and diagnosis of fungal keratitis. Lancet Infect. Dis. 21, e49–e57 (2021).

    PubMed 
    Article 

    Google Scholar 

  • Plaignaud, M. Obervation sur un fongus du sinus maxillaire. J. de Chirugie 87, 244–251 (1791).

  • Knoke, M. & Bernhardt, H. The first description of an oesophageal candidosis by Bernhard von Langenbeck in 1839. Mycoses 49, 283–287 (2006).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Chander, J. Textbook of Medical Mycology 4th edn, 534–596 (Jaypee Brothers Medical Publishers Ltd., 2018).

  • Dawson, T. L. Jr Malassezia: the forbidden kingdom opens. Cell Host Microbe 25, 345–347 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Hirschmann, J. V. The early history of coccidioidomycosis: 1892–1945. Clin. Infect. Dis. 44, 1202–1207 (2007).

    PubMed 
    Article 

    Google Scholar 

  • Bradsher, R. W.Jr The endemic mimic: blastomycosis an illness often misdiagnosed. Trans. Am. Clin. Climatol. Assoc. 125, 188–203 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Freij, J. B. & Freij, B. J. The earliest account of human cryptococcosis (Busse–Buschke Disease) in a woman with chronic osteomyelitis of the tibia. Pediatr. Infect. Dis. J. 34, 1278 (2015).

    PubMed 
    Article 

    Google Scholar 

  • Lopes-Bezerra, L. M. et al. Sporotrichosis between 1898 and 2017: the evolution of knowledge on a changeable disease and on emerging etiological agents. Med. Mycol. 56, 126–143 (2018).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Benard, G. Pathogenesis and classification of paracocidioidomycosis: new insights from old good stuff. Open Forum Infect. Dis. 8, ofaa624 (2021).

    PubMed 
    Article 

    Google Scholar 

  • Collins, R. D. Dr William DeMonbreun: description of his contributions to our understanding of histoplasmosis and analysis of the significance of his work. Hum. Pathol. 36, 453–464 (2005).

    PubMed 
    Article 

    Google Scholar 

  • Walzer, P. D. The ecology of Pneumocystis: perspectives, personal recollections, and future research opportunities. J. Eukaryot. Microbiol. 60, 634–645 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Schneider, E. et al. A coccidioidomycosis outbreak following the Northridge, Calif, earthquake. JAMA 277, 904–908 (1997).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Gremiao, I. D., Miranda, L. H., Reis, E. G., Rodrigues, A. M. & Pereira, S. A. Zoonotic epidemic of sporotrichosis: cat to human transmission. PLoS Pathog. 13, e1006077 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Stephen, C., Lester, S., Black, W., Fyfe, M. & Raverty, S. Multispecies outbreak of cryptococcosis on southern Vancouver Island, British Columbia. Can. Vet. J. 43, 792–794 (2002).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Chang, D. C. et al. Multistate outbreak of Fusarium keratitis associated with use of a contact lens solution. JAMA 296, 953–963 (2006).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Neblett Fanfair, R. et al. Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011. N. Engl. J. Med. 367, 2214–2225 (2012).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Vaux, S. et al. Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen. mBio https://doi.org/10.1128/mBio.02309-14 (2014).

  • Larone, D. H. & Walsh, T. J. Exserohilum rostratum: anatomy of a national outbreak of fungal meningitis. Clin. Microbiol. Newsl. 35, 185–193 (2013).

    Article 

    Google Scholar 

  • Hoenigl, M. Invasive fungal disease complicating Coronavirus disease 2019: when it rains, it spores. Clin. Infect. Dis. 73, e1645–e1648 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Hubka, V. et al. Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens capable of interspecific hybridization. Persoonia 41, 142–174 (2018).

  • Knowles, S. L. et al. Mapping the fungal battlefield: using in situ chemistry and deletion mutants to monitor interspecific chemical interactions between fungi. Front. Microbiol. 10, 285 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Oberlies, N. H. et al. Droplet probe: coupling chromatography to the in situ evaluation of the chemistry of nature. Nat. Prod. Rep. 36, 944–959 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lamoth, F. Aspergillus fumigatus-related species in clinical practice. Front. Microbiol. 7, 683 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Cox, M. J., Loman, N., Bogaert, D. & O’Grady, J. Co-infections: potentially lethal and unexplored in COVID-19. Lancet Microbe 1, e11 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Crum-Cianflone, N. F. Invasive aspergillosis associated with severe influenza infections. Open Forum Infect. Dis. 3, ofw171 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Ezeokoli, O. T., Gcilitshana, O. & Pohl, C. H. Risk factors for fungal co-infections in critically ill COVID-19 patients, with a focus on immunosuppressants. J. Fungi https://doi.org/10.3390/jof7070545 (2021).

  • Koehler, P. et al. COVID-19 associated pulmonary aspergillosis. Mycoses 63, 528–534 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Alanio, A., Delliere, S., Fodil, S., Bretagne, S. & Megarbane, B. Prevalence of putative invasive pulmonary aspergillosis in critically ill patients with COVID-19. Lancet Respir. Med. 8, e48–e49 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Prattes, J. et al. Diagnosis and treatment of COVID-19 associated pulmonary apergillosis in critically ill patients: results from a European confederation of medical mycology registry. Intensive Care Med. https://doi.org/10.1007/s00134-021-06471-6 (2021).

  • Arastehfar, A. et al. COVID-19 associated pulmonary aspergillosis (CAPA)—from immunology to treatment. J. Fungi https://doi.org/10.3390/jof6020091 (2020).

  • John, T. M., Jacob, C. N. & Kontoyiannis, D. P. When uncontrolled diabetes mellitus and severe COVID-19 converge: the perfect storm for mucormycosis. J. Fungi 7, 298 (2021).

    CAS 
    Article 

    Google Scholar 

  • Steenwyk, J. L. et al. Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus. Microbiol. Spectr. https://doi.org/10.1128/Spectrum.00010-21 (2021).

  • Casadevall, A. The pathogenic potential of a microbe. mSphere https://doi.org/10.1128/mSphere.00015-17 (2017).

  • Keizer, E. M. et al. Variation of virulence of five Aspergillus fumigatus isolates in four different infection models. PLoS ONE 16, e0252948 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cramer, R. A. & Kowalski, C. H. Is it time to kill the survival curve? A case for disease progression factors in microbial pathogenesis and host defense research. mBio https://doi.org/10.1128/mBio.03483-20 (2021).

  • Garcia-Solache, M. A. & Casadevall, A. Global warming will bring new fungal diseases for mammals. mBio 1, e00061-10 (2010).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Nnadi, N. E. & Carter, D. A. Climate change and the emergence of fungal pathogens. PLoS Pathog. 17, e1009503 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rhodes, J. & Fisher, M. C. Global epidemiology of emerging Candida auris. Curr. Opin. Microbiol. 52, 84–89 (2019).

    PubMed 
    Article 

    Google Scholar 

  • Chow, N. A. et al. Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses. mBio 11, e03364-19 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lockhart, S. R. et al. Simultaneous emergence of multidrug-resistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clin. Infect. Dis. 64, 134–140 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Casadevall, A., Kontoyiannis, D. P. & Robert, V. Environmental Candida auris and the global warming emergence hypothesis. mBio https://doi.org/10.1128/mBio.00360-21 (2021).

  • Arora, P. et al. Environmental isolation of Candida auris from the Coastal Wetlands of Andaman Islands, India. mBio https://doi.org/10.1128/mBio.03181-20 (2021).

  • Taylor, J. W. et al. Sources of fungal genetic variation and associating it with phenotypic diversity. Microbiol Spectr. https://doi.org/10.1128/microbiolspec.FUNK-0057-2016 (2017).

  • Kim, N.-S. The genomes and transposable elements in plants: are they friends or foes? Gene. Genom. 39, 359–370 (2017).

  • Cortés-Ortiz, L., Roos, C. & Zinner, D. Introduction to special issue on primate hybridization and hybrid zones. Int. J. Primatol. 40, 1–8 (2019).

  • Gogarten, J. P. & Townsend, J. P. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3, 679–687 (2005).

  • Shastry, B. S. SNPs in disease gene mapping, medicinal drug development and evolution. J. Hum. Genet. 52, 871–880 (2007).

  • Powell, R. V., Willett, C. R., Goertzen, L. R. & Rashotte, A. M. Lineage specific conservation of cis-regulatory elements in Cytokinin Response Factors. Sci. Rep. 9, 13387 (2019).

  • Campbell, M. A., Buser, T. J., Alfaro, M. E. & López, J. A. Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships. PeerJ 8, e9389 (2020).

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