Arthroderma chiloniense sp. nov. isolated from human stratum corneum: Description of a new Arthroderma species

Inopinatus corneliae sp. nov. gen. nov. isolated from human skin: A newly discovered keratinophilic hyphomycete, order Onygenales

BACKGROUND

Fungi clinically relevant to human skin comprise prevalent commensals and well-known pathogens. Only rarely human skin harbours fungi that evade identification.

OBJECTIVE

To characterise an enigmatic specimen isolated from a skin lesion.

METHODS

A comprehensive clinical and mycological workup including conventional methods for phenotypic characterisation and sequencing based on internal transcribed spacer (ITS) and large subunit (LSU) regions to infer a phylogenetic tree.

RESULTS

Cultures on common solid media were macroscopically inconspicuous initially until mycelial tufts developed on the surface, notably on potato dextrose agar. Polymorphous chlamydospores were detected but no aleurospores and ascomata. At 26°C, the isolate grew on standard agars, plant materials and garden soil and utilised peptone, keratins, lipids, inulin, erythrocytes and cellulose. It also grew at 5°C and at 37°C. Nucleotide sequences of its ITS region showed 93% similarity to sequences of different Malbranchea species. The closest matches among LSU rRNA sequences were obtained with the genera Amauroascus, Arthroderma, Auxarthronopsis and Malbranchea (93%-95%). A combined phylogenetic analysis placed the fungus in a sister clade to Neogymnomycetaceae, classified as incertae sedis in Onygenales, on a large distance to either Diploospora rosea or 'Amauroascus' aureus.

CONCLUSIONS

The genus Inopinatus gen. nov. (MB854685) with the species Inopinatus corneliae sp. nov. (MB854687) is introduced to accommodate our isolate (holotype: DSM 116806; isotypes: CBS 151104, IHEM 29063). Probably Inopinatus corneliae is a geophilic species that, although potentially harmful, was no relevant pathogen in our case. Its ecology, epidemiology and pathogenicity need to be further clarified.

Wild rodents harbour high diversity of Arthroderma

Arthroderma is the most diverse genus of dermatophytes, and its natural reservoir is considered to be soil enriched by keratin sources. During a study on the diversity of dermatophytes in wild small rodents in the Czech Republic, we isolated several strains of Arthroderma. To explore the diversity and ecological significance of these isolates from rodents (n = 29), we characterised the strains genetically (i.e., sequenced ITS, tubb and tef1α), morphologically, physiologically, and by conducting mating experiments. We then compared the rodent-derived strains to existing ITS sequence data from GenBank and the GlobalFungi Database to further investigate biogeography and the association of Arthroderma species with different types of environments. In total, eight Arthroderma species were isolated from rodents, including four previously described species (A. crocatum, A. cuniculi, A. curreyi, A. quadrifidum) and four new species proposed herein, i.e., A. rodenticum, A. simile, A. zoogenum and A. psychrophilum. The geographical distribution of these newly described species was not restricted to the Czech Republic nor rodents. Additional isolates were obtained from bats and other mammals, reptiles, and soil from Europe, North America, and Asia. Data mining showed that the genus has a diverse ecology, with some lineages occurring relatively frequently in soil, whereas others appeared to be more closely associated with live animals, as we observed in A. rodenticum. Low numbers of sequence reads ascribed to Arthroderma in soil show that the genus is rare in this environment, which supports the hypothesis that Arthroderma spp. are not soil generalists but rather strongly associated with animals and keratin debris. This is the first study to utilise existing metabarcoding data to assess biogeographical, ecological, and diversity patterns in dermatophytes. Citation: Moulíková Š, Kolařík M, Lorch JM, et al. 2022. Wild rodents harbour high diversity of Arthroderma. Persoonia 50: 27- 47. https://doi.org/10.3767/persoonia.2023.50.02.

Fungal Nomenclature: Managing Change is the Name of the Game

Fungal species have undergone and continue to undergo significant nomenclatural change, primarily due to the abandonment of dual species nomenclature in 2013 and the widespread application of molecular technologies in taxonomy allowing correction of past classification errors. These have effected numerous name changes concerning medically important species, but by far the group causing most concern are the Candida yeasts. Among common species, Candida krusei, Candida glabrata, Candida guilliermondii, Candida lusitaniae, and Candida rugosa have been changed to Pichia kudriavzevii, Nakaseomyces glabrata, Meyerozyma guilliermondii, Clavispora lusitaniae, and Diutina rugosa, respectively. There are currently no guidelines for microbiology laboratories on implementing changes, and there is ongoing concern that clinicians will dismiss or misinterpret laboratory reports using unfamiliar species names. Here, we have outlined the rationale for name changes across the major groups of clinically important fungi and have provided practical recommendations for managing change.

[Clinical picture, causative agents and diagnostics of dermatomycoses]

Dermatomycoses affect free skin, hairy scalp, fingernails and toenails. In addition, oral mucosa and genital mucosa can also be affected by fungal infections. The most common pathogens causing skin fungal infections are dermatophytes. They are responsible for, among others, tinea corporis, tinea capitis and onychomycosis (tinea unguium). Mainly anthropophilic dermatophytes are found as pathogens. In the case of tinea capitis-at least in Europe and in German-speaking countries-zoophilic skin fungi must also be considered. Rarely, geophilic dermatophytes can also be isolated. Yeast infections of the skin, mostly caused by Candida albicans, primarily affect the intertriginous skin areas, for example, the groin region, but also the submammary area and the spaces between the fingers and toes. Elderly patients are often affected, but also infants and, in particular, immunocompromised patients. These patient groups are also more frequently affected by oral mucosal infections caused by Candida albicans and other Candida species. Pseudomembranous candidiasis of the oral mucosa and tongue typically affects patients with HIV/AIDS. Mold infections in dermatology are relevant in onychomycosis of the big toenail. The causative agent is usually Scopulariopsis brevicaulis. Cutaneous mold infections are rare and only occur in immunocompromised patients. The mycological diagnosis of dermatomycoses is based on the microscopic, if possible fluorescence-optical detection of fungal hyphae and spores from skin scales, nail shavings and hair roots. The culture detection of dermatophytes, yeasts and molds allows the identification of the causative fungal species, but often fails, especially in patients who have already been treated with antifungal agents. In view of the high sensitivity and specificity of the molecular methods for fungal detection compared to culture, polymerase chain reaction (PCR) must realistically be regarded as the gold standard for dermatophytosis diagnostics. However, it should not be neglected that the three pillars of diagnostics-preparation, culture, PCR-currently deliver the best results.

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.

Two novel species of Arthroderma isolated from domestic cats with dermatophytosis in the United States

Dermatophytosis is a superficial fungal infection of keratinized tissues that can occur in humans and other animals. In domestic cats, the majority of cases are caused by Microsporum canis and can spread to other animals and humans via arthrospores. Between 2019 and 2021, 164 cases of suspected dermatophytosis were recorded in animals from a high-volume shelter in California. Samples (hair, nail, and skin scraping) were collected for routine screening from these individuals. One hundred and twenty-six of these were diagnosed as M. canis by culture and internal transcribed spacer (ITS) sequence. In four suspected dermatophytosis cases occurring in kittens in 2019, cultures grown at 20°C yielded fungi with colony morphology more similar to Arthroderma species than Microsporum. Morphologic and microscopic examinations were conducted, and gene segments for the ITS, β-tubulin, and translation elongation factor 1-alpha (TEF1) regions were sequenced from DNA extracted from these cultures. Sequences were aligned to other dermatophytes using maximum likelihood and neighbor-joining trees and were compared to previously described fungal species to assess nucleotide homology. We identified two previously undescribed fungal species, herein proposed as Arthroderma lilyanum sp. nov. and Arthroderma mcgillisianum sp. nov. M. canis co-cultured in two of the four cases. Other physiologic tests supported this diagnosis. These species have significance as potential pathogens and should be considered as rule-outs for dermatophytosis in cats. The potential for infection of other species, including humans, should be considered.

"Indian" strains of Trichophyton mentagrophytes with reduced itraconazole susceptibility in Germany

We use published reports and three of our own tinea cases as an opportunity to report on "Indian" strains of Trichophyton (T.) mentagrophytes with ITS genotype VIII and reduced susceptibility to itraconazole due to the mutation c.1342G>A in the SQLE gene in Germany. In vitro measurements of resistance revealed normal susceptibility to terbinafine, but markedly reduced susceptibility to itraconazole - although no valid breakpoints are currently defined and minimum inhibitory concentrations (MICs) depend on the methods used. Problems related to the determination and interpretation of MICs are outlined. Our cases show that azole-resistant "Indian" strains of T. mentagrophytes with ITS genotype VIII occurred in Germany as early as 2011, which is earlier than was previously assumed. This variant of the pathogen cannot be phenotypically distinguished from customary strains of T. mentagrophytes; its identification is based on genetics. The taxonomic classification is still under debate. This variant is anthropophilic and causes only mildly inflammatory tinea lesions with many fungal elements. Its further dissemination must therefore be expected. Prerequisites for rapid and valid antimycotic testing against dermatophytes need to be developed.

Identification of Zoophilic Dermatophytes Using MALDI-TOF Mass Spectrometry

Dermatophytoses represent a major health burden in animals and man. Zoophilic dermatophytes usually show a high specificity to their original animal host but a zoonotic transmission is increasingly recorded. In humans, these infections elicit highly inflammatory skin lesions requiring prolonged therapy even in the immunocompetent patient. The correct identification of the causative agent is often crucial to initiate a targeted and effective therapy. To that end, matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) represents a promising tool. The objective of this study was to evaluate the reliability of species identification of zoophilic dermatophytes using MALDI-TOF MS. The investigation of isolates from veterinary clinical samples suspicious of dermatophytoses suggests a good MALDI-TOF MS based identification of the most common zoophilic dermatophyte Microsporum canis. Trichophyton (T.) spp. usually achieved scores only around the cutoff value for secure species identification because of a small number of reference spectra. Moreover, these results need to be interpreted with caution due to the close taxonomic relationship of dermatophytes being reflected in very similar spectra. In our study, the analysis of 50 clinical samples of hedgehogs revealed no correct identification using the provided databases, nor for zoophilic neither for geophilic causative agents. After DNA sequencing, adaptation of sample processing and an individual extension of the in-house database, acceptable identification scores were achieved (T. erinacei and Arthroderma spp., respectively). A score-oriented distance dendrogram revealed clustering of geophilic isolates of four different species of the genus Arthroderma and underlined the close relationship of the important zoophilic agents T. erinacei, T. verrucosum and T. benhamiae by forming a subclade within a larger cluster including different dermatophytes. Taken together, MALDI-TOF MS proofed suitable for the identification of zoophilic dermatophytes provided fresh cultures are used and the reference library was previously extended with spectra of laboratory-relevant species. Performing independent molecular methods, such as sequencing, is strongly recommended to substantiate the findings from morphologic and MALDI-TOF MS analyses, especially for uncommon causative agents.

Name Changes for Fungi of Medical Importance, 2018 to 2019

The current article summarizes recent changes in nomenclature for fungi of medical importance published in the years 2018 to 2019, 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.

[Arthroderma crocatum on human skin]

We report on three cases in which Arthroderma (A.) crocatum was isolated from human skin in Germany. The characteristics and epidemiology of this rare geophilic and probably mostly apathogenic dermatophyte are described paying special attention to its gymnothecia. The combination of KOH mount, culture and genetic analysis is the foundation for clinically meaningful conclusions. It is likely that the prevalence of A. crocatum is currently underestimated.

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.

[Dynamic diversity of dermatophytes]

BACKGROUND

Many dermatologists do not understand the perpetual adjustments in the dermatophyte nomenclature.

OBJECTIVES

The aim is to explain the background and the development of methods that have led to previous and current changes of dermatophyte taxonomy and to the detection of new dermatophytes.

METHODS

In this article we evaluate the recent literature on this topic and our own results in the fields of dermatophyte identification, their detection, and of the associated taxonomic developments.

RESULTS

Today, the phylogenetic species concept is the basis of taxonomic classification, including that of dermatophytes. Genetic techniques have decisively advanced this and are state of the art nowadays. The detection of new dermatophyte species was often triggered by clinical observations and by morphologically conspicuous cultures that prompted their subsequent exact mycological characterization. Even today not all species of dermatophytes are unequivocally defined.

CONCLUSIONS

By exclusively using selected genetic characteristics for the construction of phylogenetic trees additional taxonomically relevant features are neglected. Therefore it is necessary to better integrate data derived from morphologic, physiologic, ecologic and pathophysiologic observations into phylogenetic analyses. Dermatologists are still asked to contribute such information.