Blackwell, M. The fungi: 1, 2, 3… 5.1 million species? Am. J. Bot. 98, 426–438 (2011).
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).
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).
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).
Chang, C. C. & Levitz, S. M. Fungal immunology in clinical practice: magical realism or practical reality? Med. Mycol. 57, S294–S306 (2019).
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).
Romani, L. Immunity to fungal infections. Nat. Rev. Immunol. 11, 275–288 (2011).
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).
Robbins, N., Caplan, T. & Cowen, L. E. Molecular evolution of antifungal drug resistance. Annu. Rev. Microbiol. 71, 753–775 (2017).
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).
Li, Y. et al. A genome-scale phylogeny of the kingdom Fungi. Curr. Biol. 31, 1653–1665 (2021).
Wijayawardene, N. N. et al. Outline of fungi and fungus-like taxa. Mycosphere 11, 1060–1456 (2020).
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).
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).
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).
Garcia Garces, H., Hamae Yamauchi, D., Theodoro, R. C. & Bagagli, E. PRP8 intein in onygenales: distribution and phylogenetic aspects. Mycopathologia 185, 37–49 (2020).
Hassan, M. I. A. & Voigt, K. Pathogenicity patterns of mucormycosis: epidemiology, interaction with immune cells and virulence factors. Med. Mycol. 57, S245–S256 (2019).
Gabaldon, T., Naranjo-Ortiz, M. A. & Marcet-Houben, M. Evolutionary genomics of yeast pathogens in the Saccharomycotina. FEMS Yeast Res. 16, fow064 (2016).
Opulente, D. A. et al. Pathogenic budding yeasts isolated outside of clinical settings. FEMS Yeast Res. 19, foz032 (2019).
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).
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).
Grice, E. A. & Dawson, T. L. Jr Host–microbe interactions: Malassezia and human skin. Curr. Opin. Microbiol. 40, 81–87 (2017).
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).
de Hoog, G. S. et al. Toward a novel multilocus phylogenetic taxonomy for the dermatophytes. Mycopathologia 182, 5–31 (2017).
Hirakawa, M. P. et al. Genetic and phenotypic intra-species variation in Candida albicans. Genome Res. 25, 413–425 (2015).
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).
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).
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).
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).
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).
Ioannou, P., Vamvoukaki, R. & Samonis, G. Rhodotorula species infections in humans: a systematic review. Mycoses 62, 90–100 (2019).
Seyedmousavi, S. et al. Fungal infections in animals: a patchwork of different situations. Med. Mycol. 56, 165–187 (2018).
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).
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).
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).
Taylor, L. H., Latham, S. M. & Woolhouse, M. E. Risk factors for human disease emergence. Philos. Trans. R. Soc. B 356, 983–989 (2001).
Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012).
Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).
Tekaia, F. & Latge, J. P. Aspergillus fumigatus: saprophyte or pathogen? Curr. Opin. Microbiol. 8, 385–392 (2005).
Casadevall, A. Cards of virulence and the global virulome for humans. Microbe 1, 359–364 (2006).
Gostincar, C. et al. Fungi between extremotolerance and opportunistic pathogenicity on humans. Fungal Diversity 93, 195–213 (2018).
Egidi, E. et al. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat. Commun. 10, 2369 (2019).
Robert, V., Cardinali, G. & Casadevall, A. Distribution and impact of yeast thermal tolerance permissive for mammalian infection. BMC Biol. 13, 18 (2015).
Yamamoto, N. et al. Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air. ISME J. 6, 1801–1811 (2012).
Chung, H. & Lee, Y. H. Hypoxia: a double-edged sword during fungal pathogenesis? Front. Microbiol. 11, 1920 (2020).
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).
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).
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).
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).
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).
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).
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).
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).
Sil, A. & Andrianopoulos, A. Thermally dimorphic human fungal pathogens–polyphyletic pathogens with a convergent pathogenicity trait. Cold Spring Harb. Perspect. Med. 5, a019794 (2014).
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).
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).
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).
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).
Mixao, V. & Gabaldon, T. Hybridization and emergence of virulence in opportunistic human yeast pathogens. Yeast 35, 5–20 (2018).
Maxwell, C. S. et al. Gene exchange between two divergent species of the fungal human pathogen, Coccidioides. Evolution 73, 42–58 (2019).
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).
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).
Cisse, O. H. et al. Genomic insights into the host specific adaptation of the Pneumocystis genus. Commun. Biol. 4, 305 (2021).
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).
Sun, S., Hoy, M. J. & Heitman, J. Fungal pathogens. Curr. Biol. 30, R1163–R1169 (2020).
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).
Carroll, S. B. Evolution at two levels: on genes and form. PLoS Biol. 3, e245 (2005).
Sorrells, T. R. & Johnson, A. D. Making sense of transcription networks. Cell 161, 714–723 (2015).
Fisher, K. J. & Lang, G. I. Experimental evolution in fungi: an untapped resource. Fungal Genet. Biol. 94, 88–94 (2016).
Forche, A. et al. Rapid phenotypic and genotypic diversification after exposure to the oral host niche in Candida albicans. Genetics 209, 725–741 (2018).
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).
Tso, G. H. W. et al. Experimental evolution of a fungal pathogen into a gut symbiont. Science 362, 589–595 (2018).
Hu, G. et al. Microevolution during serial mouse passage demonstrates FRE3 as a virulence adaptation gene in Cryptococcus neoformans. mBio 5, e00941–00914 (2014).
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).
Forche, A. et al. Selection of Candida albicans trisomy during oropharyngeal infection results in a commensal-like phenotype. PLoS Genet. 15, e1008137 (2019).
Lucking, R. et al. Fungal taxonomy and sequence-based nomenclature. Nat. Microbiol. 6, 540–548 (2021).
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).
Fishman, J. A. Pneumocystis jiroveci. Semin. Respir. Crit. Care Med. 41, 141–157 (2020).
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).
Grigoriev, I. V. et al. MycoCosm portal: gearing up for 1,000 fungal genomes. Nucleic Acids Res. 42, D699–D704 (2014).
Shen, X. X. et al. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Sci. Adv. 6, eabd0079 (2020).
Shen, X. X. et al. Tempo and mode of genome evolution in the budding yeast subphylum. Cell 175, 1533–1545 (2018).
Robert, V. et al. MycoBank gearing up for new horizons. IMA Fungus 4, 371–379 (2013).
Nguyen, N. H. et al. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).
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).
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).
Barber, A. E. et al. Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection. Nat. Microbiol. 6, 1526–1536 (2021).
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).
Mazi, P. B., Rauseo, A. M. & Spec, A. Blastomycosis. Infect. Dis. Clin. North Am. 35, 515–530 (2021).
Pappas, P. G., Lionakis, M. S., Arendrup, M. C., Ostrosky-Zeichner, L. & Kullberg, B. J. Invasive candidiasis. Nat. Rev. Dis. Prim. 4, 18026 (2018).
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).
Maziarz, E. K. & Perfect, J. R. Cryptococcosis. Infect. Dis. Clin. North Am. 30, 179–206 (2016).
Schwartz, I. S. et al. Emergomyces: the global rise of new dimorphic fungal pathogens. PLoS Pathog. 15, e1007977 (2019).
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).
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).
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).
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).
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).
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).
Hirschmann, J. V. The early history of coccidioidomycosis: 1892–1945. Clin. Infect. Dis. 44, 1202–1207 (2007).
Bradsher, R. W.Jr The endemic mimic: blastomycosis an illness often misdiagnosed. Trans. Am. Clin. Climatol. Assoc. 125, 188–203 (2014).
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).
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).
Benard, G. Pathogenesis and classification of paracocidioidomycosis: new insights from old good stuff. Open Forum Infect. Dis. 8, ofaa624 (2021).
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).
Walzer, P. D. The ecology of Pneumocystis: perspectives, personal recollections, and future research opportunities. J. Eukaryot. Microbiol. 60, 634–645 (2013).
Schneider, E. et al. A coccidioidomycosis outbreak following the Northridge, Calif, earthquake. JAMA 277, 904–908 (1997).
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).
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).
Chang, D. C. et al. Multistate outbreak of Fusarium keratitis associated with use of a contact lens solution. JAMA 296, 953–963 (2006).
Neblett Fanfair, R. et al. Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011. N. Engl. J. Med. 367, 2214–2225 (2012).
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).
Hoenigl, M. Invasive fungal disease complicating Coronavirus disease 2019: when it rains, it spores. Clin. Infect. Dis. 73, e1645–e1648 (2021).
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).
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).
Lamoth, F. Aspergillus fumigatus-related species in clinical practice. Front. Microbiol. 7, 683 (2016).
Cox, M. J., Loman, N., Bogaert, D. & O’Grady, J. Co-infections: potentially lethal and unexplored in COVID-19. Lancet Microbe 1, e11 (2020).
Crum-Cianflone, N. F. Invasive aspergillosis associated with severe influenza infections. Open Forum Infect. Dis. 3, ofw171 (2016).
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).
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).
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).
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).
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).
Nnadi, N. E. & Carter, D. A. Climate change and the emergence of fungal pathogens. PLoS Pathog. 17, e1009503 (2021).
Rhodes, J. & Fisher, M. C. Global epidemiology of emerging Candida auris. Curr. Opin. Microbiol. 52, 84–89 (2019).
Chow, N. A. et al. Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses. mBio 11, e03364-19 (2020).
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).
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).