Arthroderma olidum, sp. nov. A new addition to theTrichophyton terrestrecomplex

Changes in fungal taxonomy: mycological rationale and clinical implications

Numerous fungal species of medical importance have been recently subjected to and will likely continue to undergo nomenclatural changes as a result of the application of molecular approaches to fungal classification together with abandonment of dual nomenclature. Here, we summarize those changes affecting key groups of fungi of medical importance, explaining the mycological (taxonomic) rationale that underpinned the changes and the clinical relevance/importance (where such exists) of the key nomenclatural revisions. Potential mechanisms to mitigate unnecessary taxonomic instability are suggested, together with approaches to raise awareness of important changes to minimize potential clinical confusion.

Name Changes for Fungi of Medical Importance, 2020 to 2021

The current article summarizes recent changes in nomenclature for fungi of medical importance published in the years 2020 to 2021, including new species and revised names for existing ones. Many of the revised names have been widely adopted without further discussion. However, those that concern common pathogens of humans may take longer to achieve general usage, with new and current names reported together to engender increasing familiarity with the correct taxonomic classification.

Phylogenetic and ecological reevaluation of the order Onygenales

The order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.

Keratinophilic and Keratinolytic Fungi in Cave Ecosystems: A Culture-Based Study of Brestovská Cave and Demänovská Ľadová and Slobody Caves (Slovakia)

Despite speleomycological research going back to the 1960s, the biodiversity of many specific groups of micromycetes in underground sites still remains unknown, including keratinolytic and keratinophilic fungi. These fungi are a frequent cause of infections in humans and animals. Since subterranean ecosystems are inhabited by various animals and are a great tourist attraction, the goal of our research was to provide the first report of keratinophilic and keratinolytic fungal species isolated from three caves in Tatra Mts., Slovakia (Brestovská, Demänovská Ľadová and Demänovská Slobody). Speleomycological investigation was carried out inside and outside the explored caves by combining culture-based techniques with genetic and phenotypic identifications. A total of 67 fungal isolates were isolated from 24 samples of soil and sediment using Vanbreuseghem hair bait and identified as 18 different fungal species. The study sites located inside the studied caves displayed much more fungal species (17 species) than outside the underground (3 species), and the highest values of the Shannon diversity index of keratinophilic and keratinolytic fungi were noted for the study sites inside the Demänovská Slobody Cave. Overall, Arthroderma quadrifidum was the most common fungal species in all soil and/or sediment samples. To the best of our knowledge, our research has allowed for the first detection of fungal species such as Arthroderma eboreum, Arthrodermainsingulare, Chrysosporiumeuropae, Chrysosporiumsiglerae, Keratinophytonwagneri, and Penicillium charlesii in underground sites. We also showed that the temperature of soil and sediments was negatively correlated with the number of isolated keratinophilic and keratinolytic fungal species in the investigated caves.

Three-gene phylogeny of the genus Arthroderma: Basis for future taxonomic studies

Arthroderma is the most diverse genus among dermatophytes encompassing species occurring in soil, caves, animal burrows, clinical material and other environments. In this study, we collected ex-type, reference and authentic strains of all currently accepted Arthroderma species and generated sequences of three highly variable loci (ITS rDNA, β-tubulin, and translation elongation factor 1-α). The number of accepted species was expanded to 27. One novel species, A. melbournense (ex-type strain CCF 6162T = CBS 145858T), is described. This species was isolated from toenail dust collected by a podiatrist in Melbourne, during an epidemiological study of four geographical regions of Eastern Australia. Trichophyton terrestre, Chrysosporium magnisporum, and Chrysosporium oceanitis are transferred to Arthroderma. Typification is provided for T. terrestre that is not conspecific with any of the supposed biological species from the former T. terrestre complex, that is, A. insingulare, A. lenticulare and A. quadrifidum. A multi-gene phylogeny and reference sequences provided in this study should serve as a basis for future phylogenetic studies and facilitate species identification in practice.

LAY ABSTRACT

The genus Arthroderma encompasses geophilic dermatophyte species that infrequently cause human and animal superficial infections. Reference sequences from three genetic loci were generated for all currently accepted Arthroderma species and phylogeny was constructed. Several taxonomic novelties are introduced. The newly provided data will facilitate species identification and future taxonomic studies.

She Loves Me, She Loves Me Not: On the Dualistic Asexual/Sexual Nature of Dermatophyte Fungi

Dermatophytes are ascomycetous fungi whose sexuality is greatly influenced by their ecology. Sexual reproduction is ubiquitous among soil-related geophiles and some animal-associated zoophiles. In contrast, anthropophiles are generally present as a single mating type in the population and appear to reproduce asexually. In this article, the current knowledge on the sexuality of dermatophytes including reproduction modes, mating conditions, mating type distributions and the mating type (MAT) locus is presented in the context of revised taxonomy and discussed from an evolutionary perspective.

A novel dermatophyte relative, Nannizzia perplicata sp. nov., isolated from a case of tinea corporis in the United Kingdom

A novel dermatophyte was isolated from skin scales of a female patient presenting with tinea corporis of the wrist and arm. Her principal risk factor was long-term corticosteroid use for underlying Lupus autoimmune syndrome. Microscopic examination of skin scales from lesions revealed hyphae consistent with dermatophyte infection, and a morphologically identical fungus grew in pure culture on all cultures of skin scales. Repeat isolation of the same organism from persistent lesions five months later confirmed the novel species as the causative agent. Microscopic examination revealed predominantly smooth, thin-walled macroconidia, with large numbers of unicellular aleuriospores of varied shapes and sizes. Since the isolate exhibited considerable microscopic pleomorphism, sharing morphological features consistent with several dermatophyte genera, it was subjected to multi-locus phylogenetic analyses employing a total of six different loci. Sequence analyses of all loci revealed that the isolate clustered with species within Nannizzia but diverged from all known members of the genus by 2 to 13% depending on locus analyzed. The isolate exhibited high minimum inhibitory concentrations for terbinafine in vitro, which might explain why the infection had failed to respond to two cycles of oral treatment with this antifungal agent. Interestingly, sequences in GenBank of an unnamed "Microsporum sp" isolated from leg skin of a patient in the Czech Republic showed greater than 99% identity across all of the loci analysed in common, indicating that this novel organism, which we describe here as Nannizzia perplicata sp. nov., is likely not restricted to the UK.

Rapid Identification of Clinically Relevant Members of the Genus Exophiala by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Description of Two Novel Species, Exophiala campbellii and Exophiala lavatrina

Exophiala is a ubiquitous pleomorphic genus comprising at least 40 species, many of which have been associated with superficial, visceral, or systemic infections in humans, other mammals, or cold-blooded animals. In this study, we investigated the potential of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) for the identification of Exophiala species. A total of 89 isolates (including 50 human and 4 animal clinical isolates) stored in the National Collection of Pathogenic Fungi were identified by PCR amplification and sequencing of internal transcribed spacer region 1. Eighty-three of the isolates corresponded to 16 known species within Exophiala/Rhinocladiella The remaining six isolates are shown by phylogenetic analyses based on four loci to represent two novel Exophiala species. Four isolates from domestic bathrooms which form a sister species with Exophiala lecanii-corni are described here as Exophiala lavatrina sp. nov. The remaining two isolates, both from subcutaneous infections, are distantly related to Exophiala oligosperma and are described here as Exophiala campbellii sp. nov. The triazoles and terbinafine exhibited low MICs against all Exophiala isolates in vitro MALDI-TOF MS successfully distinguished all 18 species and identified all isolates after appropriate reference spectra were created and added to commercial databases. Intraspecific mean log scores ranged from 1.786 to 2.584 and were consistently significantly higher than interspecific scores (1.193 to 1.624), with the exception of E. lecanii-corni and E. lavatrina, for which there was considerable log score overlap. In summary, MALDI-TOF MS allows the rapid and accurate identification of a wide range of clinically relevant Exophiala species.

Sexual Reproduction in Dermatophytes

Sexual reproduction is a rich source of genetic variation and commonly observed among fungi. Basically two different modes of sexual reproduction are observed in fungi, namely heterothallism where two compatible mating types are required to undergo mating and homothallism in which the organism is self-fertile. The genomic region governing the process of sexual reproduction and sex determination is called the mating type (MAT) locus. In filamentous ascomycetes including dermatophytes, the MAT locus harbors two different transcription factor genes in two different mating types. This review focuses on sexual reproduction and the structure of the MAT locus in dermatophytes. The reproductive modes and the observed mating types are summarized for different phylogenetic clades of dermatophytes. In addition, the question of whether or not unisexual reproduction, an interesting form of homothallism, may be the sexual reproduction mode especially in anthropophilic dermatophytes is raised.

Unusual Species of Dermatophytes: Rarely Identified or New?

Dermatophytes are causing superficial mycosis in animals and humans. Depending on the geophilic, zoophilic or anthropophilic origin of the fungus but also on the immunological status of the patient, symptomatology can widely differ. Nevertheless, each species is currently associated with typical clinical manifestations, even if atypical localizations and/or clinical pictures are sometimes also reported. Diagnostic tools applied to species identification have been changing since the last two decades with the more frequent use of molecular methods currently considered nowadays as reference methods for species identification. It becomes obvious that the algorithm used for the distinction of closely related species needs to combine phenotypic and genomic methods. All these different points are discussed, and the most recent novel species causing or involved in human dermatophytosis are reported.

Novel Taxa Associated with Human Fungal Black-Grain Mycetomas: Emarellia grisea gen. nov., sp. nov., and Emarellia paragrisea sp. nov

Eumycetoma is a debilitating, chronic, fungal infection that is endemic in India, Indonesia, and parts of Africa and South and Central America. It remains a neglected tropical disease in need of international recognition. Infections follow traumatic implantation of saprophytic fungi and frequently require radical surgery or amputation in the absence of appropriate treatment. Several fungal species can cause black-grain mycetomas, including Madurella spp. (Sordariales), Falciformispora spp., Trematosphaeria grisea, Biatriospora mackinnonii, Pseudochaetosphaeronema larense, and Medicopsis romeroi (all Pleosporales). We performed phylogenetic analyses based on five loci on 31 isolates from two international culture collections to establish the taxonomic affiliations of fungi that had been isolated from cases of black-grain mycetoma and historically classified as Madurella grisea Although most strains were well resolved to species level and corresponded to known agents of eumycetoma, six independent isolates, which failed to produce conidia under any conditions tested, were only distantly related to existing members of the Pleosporales Five of the six isolates shared >99% identity with each other and are described as Emarellia grisea gen. nov. and sp. nov; the sixth isolate represents a sister species in this novel genus and is described as Emarellia paragrisea. Several E. grisea isolates were present in both United Kingdom and French culture collections and had been isolated independently over 6 decades from cases of imported eumycetoma. Four of the six isolates involved patients that had originated on the Indian subcontinent. All isolates were all susceptible in vitro to the azole antifungals, but had elevated MICs with caspofungin.

Microsporum aenigmaticum sp. nov. from M. gypseum complex, isolated as a cause of tinea corporis

An undescribed Microsporum species was isolated from skin scales recovered from a 40-mm large, annular, scaling lesion on the wrist of a 46-year-old woman. The risk factors for dermatophyte infection in the patient were frequent work in the garden, hunting, and contact with dogs and horses. Direct microscopic examination of the scales revealed the presence of dermatophyte hyphae; when the samples were cultured, a morphologically similar fungus grew on all slants in pure culture. Both of these findings strongly suggested that the isolate was the true causal agent of infection. The possible geophilic nature of the species was based on phylogenetic analysis (internal transcribed spacer region of rDNA and β-tubulin gene) that placed it in between species of the M. gypseum complex. However, its divergencies from all other Microsporum species exceeded 4% base pairs. Based on β-tubulin phylogeny, the isolated species is a sister to M. gypseum. The species produces abundant chlamydospores and clumps of hyphae similar to those of ascomatal primordia but no conidia and ascospores. The species was unable to grow at 37°C and does not grow on T6 basal medium, which is unlike other Microsporum species; hair perforation and urease tests were positive. The addition of histidine to the T6 medium resulted in rapid growth of the fungus. The phylogenetic evidence, morphology, growth parameters, and physiology justified the proposal that the isolate is a new species, M. aenigmaticum, sp. nov.

Cutaneous mycosis in a Barbastelle bat (Barbastella barbastellus) caused by Hyphopichia burtonii

A rare barbastelle bat (Barbastella barbastellus) died shortly after being found in emaciated condition in Devon, England. The skin over the muzzle and face was grossly thickened, crusty, and in places was sloughing and ulcerated. There were numerous nodules up to 3 mm in diameter on both wings and ear pinnae. Histologically, multiple foci of epidermal hyperplasia, hyperkeratosis, and crateriform erosions containing masses of fungal spores and septate hyphae were found in the wing. Epidermal hyperplasia and follicular hyperkeratosis, with fungal masses within keratinized follicles and also in fissured stratum corneum, were found in the pinna. Hyphae did not invade the dermis, and there was no inflammation, but there was multifocal serous exudation and crusting. No parasites or other significant organisms were identified. Microscopic and multiple cultural analyses of face and wing lesions demonstrated (10/10) a fine, septate fungus bearing laterally oval to clavate conidia; morphologically and culturally this was entirely consistent with Hyphopichia burtonii, and polymerase chain reaction analysis and sequencing gave 100% identity with the type strain. The organism isolated was morphologically consistent with that repeatedly seen in histology sections and demonstrates that although H. burtonii has not previously been recognized as a dermatophyte, it clearly has the ability to invade the skin of live bats. Although not identical, the lesions in this case show similarity with those of white nose syndrome and therefore H. burtonii should be considered as a potential pathogen of bats.

[Taxonomy and biology of fungi causing human infection]

The advent of molecular techniques, mainly DNA sequencing, has led to important changes in the taxonomy of pathogenic fungi and a better understanding of the phylogenetic relationships among them. The number of fungal species potentially pathogenic for humans has increased dramatically. Most of them are cryptic species belonging to complex species that have replaced traditional single morphospecies. This has occurred in several genera of mucorales and particularly in different ascomycetous genera, such as Aspergillus, Fusarium, Sporothrix and Scedosporium, among others. The correct identification of these species is crucial for a better management of patients, since on many occasions those species show different virulence and different antifungal responses. This review summarises some of the most striking recent taxonomic changes produced in pathogenic fungi.