Updating the Taxonomy of Dermatophytes of the BCCM/IHEM Collection According to the New Standard: A Phylogenetic Approach

Tinea Capitis at Ibn Sina Hospital in Rabat, Morocco: Epidemiological and Etiological Study Over 25 Years (From 1997 to 2021)

Introduction/Objective In Morocco, tinea capitis is a common reason for consultation, especially in children. Our study aimed to determine the epidemiology of tinea capitis in the Central Laboratory of Parasitology and Mycology at the Ibn Sina University Hospital Center (UHC) in Rabat. Materials and methods This is a retrospective study conducted over 25 years (from 1997 to 2021). It included 247 patients with lesions suggestive of tinea capitis, who underwent a mycological examination. Results Among 594 requests for the diagnosis of tinea capitis, 247 cases were positive. A clear predominance of children (86.23%; n=213) as compared to adults (13.77%; n=34) was observed. The sex ratio (M/F) was 1.77. Hair parasitism was mainly dominated by the pure endothrix type 54.47% (n=122). The two most frequently isolated species were Trichophyton violaceum (51.24%; n=125) and Microsporum canis (36.06%; n=88). In children, these two species represented 47.42% (n=101) and 41.31% (n=88), respectively. In adults, Trichophyton violaceum was the predominant species, accounting for 77.42% (n=24); in females, it was 76.41% (n=68); and Microsporum canis was predominant in males (50.32%; n=78). Conclusion The epidemiology of this condition is in a constant state of flux, influenced by various lifestyle factors. Our research unveiled a notable upward trend in zoophilic species over the 25-year study period, while conversely, anthropophilic species demonstrated a discernible decline.

Culturable fungi from urban soils in China II, with the description of 18 novel species in Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes and Sordariomycetes)

As China's urbanisation continues to advance, more people are choosing to live in cities. However, this trend has a significant impact on the natural ecosystem. For instance, the accumulation of keratin-rich substrates in urban habitats has led to an increase in keratinophilic microbes. Despite this, there is still a limited amount of research on the prevalence of keratinophilic fungi in urban areas. Fortunately, our group has conducted in-depth investigations into this topic since 2015. Through our research, we have discovered a significant amount of keratinophilic fungi in soil samples collected from various urban areas in China. In this study, we have identified and characterised 18 new species through the integration of morphological and phylogenetic analyses. These findings reveal the presence of numerous unexplored fungal taxa in urban habitats, emphasising the need for further taxonomic research in urban China.

New taxonomic framework for Arthrodermataceae: a comprehensive analysis based on their phylogenetic reconstruction, divergence time estimation, phylogenetic split network, and phylogeography

The Arthrodermataceae, or dermatophytes, are a major family in the Onygenales and important from a public health safety perspective. Here, based on sequenced and downloaded from GenBank sequences, the evolutionary relationships of Arthrodermataceae were comprehensively studied via phylogenetic reconstruction, divergence time estimation, phylogenetic split network, and phylogeography analysis. These results showed the clades Ctenomyces, Epidermophyton, Guarromyces, Lophophyton, Microsporum, Paraphyton, and Trichophyton were all monophyletic groups, whereas Arthroderma and Nannizzia were polyphyletic. Among them, Arthroderma includes at least four different clades, Arthroderma I, III and IV are new clades in Arthrodermataceae. Nannizzia contains at least two different clades, Nannizzia I and Nannizzia II, but Nannizzia II was a new clade in Arthrodermataceae. The unclassified group, distributed in Japan and India, was incorrectly identified; it should be a new clade in Arthrodermataceae. The phylogenetic split network based on the ITS sequences provided strong support for the true relationships among the lineages in the reconstructed phylogenetic tree. A haplotype phylogenetic network based on the ITS sequences was used to visualize species evolution and geographic lineages relationships in all genera except Trichophyton. The new framework provided here for the phylogeny and taxonomy of Arthrodermataceae will facilitate the rapid identification of species in the family, which should useful for evaluating the results of preventive measures and interventions, as well as for conducting epidemiological studies.

Current Topics in Dermatophyte Classification and Clinical Diagnosis

Dermatophytes are highly infectious fungi that cause superficial infections in keratinized tissues in humans and animals. This group of fungi is defined by their ability to digest keratin and encompasses a wide range of species. Classification of many of these species has recently changed due to genetic analysis, potentially affecting clinical diagnosis and disease management. In this review, we discuss dermatophyte classification including name changes for medically important species, current and potential diagnostic techniques for detecting dermatophytes, and an in-depth review of Microsporum canis, a prevalent zoonotic dermatophyte. Fungal culture is still considered the “gold standard” for diagnosing dermatophytosis; however, modern molecular assays have overcome the main disadvantages of culture, allowing for tandem use with cultures. Further investigation into novel molecular assays for dermatophytosis is critical, especially for high-density populations where rapid diagnosis is essential for outbreak prevention. A frequently encountered dermatophyte in clinical settings is M. canis, which causes dermatophytosis in humans and cats. M. canis is adapting to its primary host (cats) as one of its mating types (MAT1-2) appears to be going extinct, leading to a loss of sexual reproduction. Investigating M. canis strains around the world can help elucidate the evolutionary trajectory of this fungi.

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.

Phylogeny, Antifungal Susceptibility, and Point Mutations of SQLE Gene in Major Pathogenic Dermatophytes Isolated From Clinical Dermatophytosis

Drug resistance is one of the major challenges to skin fungal infections, especially in tropical and subtropical infections caused by dermatophytes. This study aimed to determine the antifungal susceptibility of clinically dermatophytes and evaluate point mutations in terbinafine-resistant isolates. A total number of 123 clinical dermatophyte isolates in eight species were evaluated in terms of sensitivity to seven major antifungals. Furthermore, the point mutation in squalene epoxidase (SQLE) gene responsible for terbinafine resistance was studied. The dermatophytes species were identified by morphological characteristics and confirmed by the ITS sequencing. Also, the phylogenetic tree was drawn using the RAxML analyses for 123 dermatophytes isolates. A new XXIX genotype was also found in 4 Trichophyton mentagrophytes isolates. Based on the results obtained, terbinafine was the most effective antifungal drug followed by itraconazole and voriconazole. Trichophyton rubrum and Trichophyton tonsurans were the most susceptible species (MIC₅₀ = 0.01, 0.09 μg/ml), and T. mentagrophytes was the most resistant species (MIC₅₀ = 0.125 μg/ml) to terbinafine. Of the 123 dermatophytes isolates, six isolates showed reduced susceptibility to terbinafine, and only Trichophyton indotineae had a mutation in SQLE gene as a Phe397Leu substitution. Overall, the antifungal susceptibility test is necessary for managing dermatophytosis. These results help physicians to control the course of the disease and provide further insights to select effective drugs for patients with dermatophytosis, especially in tropical and subtropical regions of the world, where dermatophytosis is still a public health problem.

Re-discovery of Trichophyton bullosum in North Africa as a cause of severe dermatophytosis in donkeys

This article reports the first verified cases of infection by Trichophyton bullosum in Africa since the description of the fungus, isolated in 1933 from the coat of horses in Tunisia and Mali. We found the fungus in cutaneous samples obtained from donkeys suffering from severe dermatitis with areas of alopecia and scaling in the surroundings of Cairo (Egypt). Fungal elements (arthroconidia and hyphae) were seen at the microscopy of material collected by skin scraping and digested in NaOH. Fungal colonies grown on various culture media were identified through PCR and sequencing of the ITS rDNA region. Since the original report in Africa and the Middle East, only a few cases have been reported thus far in humans in France and two cases in horses in the Czech Republic and Japan. Trichophyton bullosum seems thus an infrequent cause of dermatophytosis. However, the actual prevalence of this pathogen may be underestimated due to the similarity with T. verrucosum, a predominant cause of infection in cattle, occasionally found on horses and donkeys. Indeed, the two fungi can be distinguished only via molecular methods, which are poorly employed in epidemiological studies on equine and bovine dermatophytosis. The present study results add to our knowledge on the ecology of this poorly explored dermatophyte, supporting the concept that equines are the primary hosts of T. bullosum and confirming the presence of this pathogen in Africa. At the same time, these are the first unequivocally documented infections in donkeys due to T. bullosum.

Atypical chlamydoconidium-producing Trichophyton tonsurans strains from Ceará State, Northeast Brazil: investigation of taxonomy by phylogenetic analysis and biofilm susceptibility

Chlamydoconidium-producing Trichophyton tonsurans strains isolated in Northeastern Brazil have morphological features different from the classic description of this dermatophyte species. This study investigated the phylogenetic relationship of chlamydoconidium-producing T. tonsurans strains isolated in Northeastern Brazil. Also, the effect of terbinafine and farnesol on mature biofilms of T. tonsurans strains was evaluated. The mass spectra of T. tonsurans strains were investigated by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The ITS and LSU loci regions of rDNA and the partial β-tubulin gene were sequenced and the phylogenetic tree was analysed. The effects of terbinafine and farnesol on mature T. tonsurans biofilms were evaluated through the analysis of metabolic activity, quantification of biomass and observation by scanning electron microscopy. MALDI-TOF MS spectra of the chlamydoconidium-producing T. tonsurans strains differed from the spectrum of the control strain (ATCC 28942), presenting an intense ion peak at m/z 4155 Da. Phylogenetic tree analysis showed that the chlamydoconidium-producing strains isolated in Northeastern Brazil are allocated to a single cluster, differing from strains isolated from other countries. As for mature T. tonsurans biofilms, farnesol reduced biomass and metabolic activity by 64.4 and 65.9 %, respectively, while terbinafine reduced the biomass by 66.5 % and the metabolic activity by 69 %. Atypical morphological characteristics presented by chlamydoconidium-producing T. tonsurans strains result from phenotypic plasticity, possibly for adaptation to environmental stressors. Also, farnesol had inhibitory activity against T. tonsurans biofilms, demonstrating this substance can be explored for development of promising anti-biofilm drugs against dermatophytes.

Human and Zoonotic Dermatophytoses: Epidemiological Aspects

Introduction

Dermatophytes are a group of molds characterized by the ability to produce keratinases, thereby carving out for themselves specific ecological niches. Their traditional division into three genera, Trichophyton, Microsporum, and Epidermophyton has been expanded to nine and the species in each genus were modified. Dermatophytes are among the most prevalent causes of human and animal mycoses. Their epidemiology is influenced by various factors. These factors may be evolutive such as the predilected environment of the fungus, namely, humans (anthropophilic), animals (zoophilic), or environment (geophilic), is evolutionary and thus may require centuries to develop. Many other factors, however, result from a variety of causes, affecting the epidemiology of dermatophytoses within a shorter time frame.

Objective

This review aims at summarizing the factors that have modified the epidemiology of dermatophytoses during the last decades.

Results

Geographic and climatic conditions, demography such as age and gender, migration, socio-economic conditions, lifestyle, and the environment have had an impact on changes in the epidemiology of dermatophytoses, as have changes in the pattern of human interaction with animals, including pets, farm, and wild animals. A typical example of such changes is the increased prevalence of Trichophyton tonsurans, which spread from Latin America to the United States and subsequently becoming a frequent etiological agent of tinea capitis in Africa, Middle East, and other areas.

Conclusion

The comprehension of the epidemiology of dermatophytoses has a major bearing on their prevention and treatment. Since it is undergoing continuous changes, periodic assessments of the most recent developments of this topic are required. This article aims at providing such an overview.

A Polyphasic Approach to Classification and Identification of Species within the Trichophyton benhamiae Complex

In recent years, considerable advances have been made in clearing up the phylogenetic relationships within the Arthrodermataceae family. However, certain closely related taxa still contain poorly resolved species boundaries. Here, we tried to elucidate the species composition of the Trichophyton benhamiae species complex using a combined approach consisting of multi-gene phylogenetic analysis based on internal transcribed spacer (ITS) and beta-tubulin (BT) gene regions, morphological analysis, and spectral comparison using MALDI-ToF. We confirmed the existence of 11 different monophyletic clades within the complex representing either species or genetically distinct groups within species. MALDI-ToF spectrometry analysis revealed that most of these clades were readily distinguishable from one another; however, some closely related sister clades, such as T. europaeum and T. japonicum, were often misidentified as their counterpart. The distinct “yellow” and “white” phenotypes of T. benhamiae do not have a clear genetic basis and should thus be considered as different morphotypes of the same species. Strains traditionally considered T. benhamiae can be divided into three main clades: (i) T. benhamiae, (ii) T. europaeum/T. japonicum, and (iii) the phylogenetically distant T. africanum. While T. europaeum and T. japonicum are distinguishable based on their genotype, spectral and morphological analysis did not provide clear delimiting characteristics.

Performance of the new ID-fungi plate using two types of reference libraries (Bruker and MSI) to identify fungi with the Bruker MALDI Biotyper

During the last decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the diagnosis of fungal infections. Recently, a new Conidia ID-fungi plate (IDFP) medium was introduced to facilitate growth and sampling of fungi. This study aimed to evaluate the IDFP for fungal MALDI-TOF MS identification by comparison with a standard fungal growth medium using two reference libraries. A total of 75 filamentous fungal isolates (including 32 dermatophytes) were inoculated on IDFP and Sabouraud-gentamicin-chloramphenicol (SGC) agar and identified by MALDI-TOF MS using formic acid/acetonitrile extraction. Both the commercially available Bruker library (version 2.0) and the public available MSI web application (version 2018) were applied. For 15% of the isolates, a faster growth was noticed on IDFP compared to SGC. IDFP enhanced the performance of fungal identification compared to SGC for both MSI (increase of 16% identifications to genus and 5% to species level) and Bruker library (increase of 22% identifications to genus and 8% to species level). In total, only 73% of the tested isolates were present in the Bruker library compared to 92% for MSI library. No significant difference (P = 0.46) in MALDI score between IDFP and SGC was observed for the MSI library, but scores were significantly (P = 0.03) higher for IDFP when using Bruker library, potentially explained by the prevention of agar contamination by using IDFP since the Bruker database was created from liquid media. IDFP is a promising alternative growth medium for MALDI-TOF MS fungal identification which would strongly benefit from optimizing the Bruker reference library.

Onygenalean Fungi as Major Human and Animal Pathogens

During the last two decades, many onygenalean pathogens were discovered, redefined, or re-classified from existing taxa into clusters of micro-species, among which the original genotypes often appeared to be uncommon and exceptional. The impact of these developments on the diagnosis and treatment of fungal diseases remains to be determined in most instances. This exciting collection of invited articles provides a full flavor of ongoing changes in the knowledge about taxonomy, genetics, ecology, epidemiology, and clinical spectra of human and animal pathogens classified in the order Onygenales. Recent developments have set the stage for an ambitious translational research agenda. Diagnostic mycology laboratories now need MALDI-TOF-MS spectra, PCR probes, and other specific tools to assist them in the rapid diagnosis of new species. Similarly, an educational set of type materials of new species needs to be readily available for enhanced expertise among the wider medical mycology community. As several new species were discovered retrospectively, it is crucial to expand the re-sampling to other fungal culture collections and archived paraffin tissues. Finally, clinical and laboratory investigations are needed to get an accurate assessment of the prevalence and impact of new pathogens as the cause of major fungal diseases.