Chitin synthase 1 gene of Arthroderma benhamiae isolates in Japan

A Comparative Description of Dermatophyte Genomes: A State-of-the-Art Review

The nomenclature and phylogeny of dermatophytes is currently based on the nucleotide sequence polymorphisms of a few genomic regions. However, the limitations of this multilocus sequence-based approach makes dermatophyte species identification difficult. Variation and adaptation are key to the persistence of species. Nevertheless, this heterogeneity poses a genuine problem for the classification and nomenclature of dermatophytes. The relatively high intra-species and low inter-species polymorphisms of this keratinophilic group of fungi hampers both species delineation and identification. Establishing the taxonomic boundaries of dermatophyte species complexes remains controversial. Furthermore, until recently, knowledge of molecular biology, genetics and genomics remained limited. This systematic review highlights the added value of whole genome sequencing and analysis data in dermatophyte classification that might enhance identification and, consequently, the diagnosis and management of dermatophytoses. Our approach consisted in describing and comparing the dermatophyte mitochondrial genomes, secretomes (Adhesins, LysM domains, proteases) and metabolic pathways, with the aim to provide new insights and a better understanding of the phylogeny and evolution of dermatophytes.

Phylogenetic analysis of dermatophyte species using DNA sequence polymorphism in calmodulin gene

Use of phylogenetic species concepts based on rDNA internal transcribe spacer (ITS) regions have improved the taxonomy of dermatophyte species; however, confirmation and refinement using other genes are needed. Since the calmodulin gene has not been systematically used in dermatophyte taxonomy, we evaluated its intra- and interspecies sequence variation as well as its application in identification, phylogenetic analysis, and taxonomy of 202 strains of 29 dermatophyte species. A set of primers was designed and optimized to amplify the target followed by bilateral sequencing. Using pairwise nucleotide comparisons, a mean similarity of 81% was observed among 29 dermatophyte species, with inter-species diversity ranging from 0 to 200 nucleotides (nt). Intraspecies nt differences were found within strains of Trichophyton interdigitale, Arthroderma simii, T. rubrum and A. vanbreuseghemii, while T. tonsurans, T. violaceum, Epidermophyton floccosum, Microsporum canis, M. audouinii, M. cookei, M. racemosum, M. gypseum, T. mentagrophytes, T schoenleinii, and A. benhamiae were conserved. Strains of E. floccosum/M. racemosum/M. cookei, A. obtosum/A. gertleri, T. tonsurans/T. equinum and a genotype of T. interdigitale had identical calmodulin sequences. For the majority of the species, tree topology obtained for calmodulin gene showed a congruence with coding and non-coding regions including ITS, BT2, and Tef-1α. Compared with the phylogenetic tree derived from ITS, BT2, and Tef-1α genes, some species such as E. floccosum and A. gertleri took relatively remote positions. Here, characterization and obtained dendrogram of calmodulin gene on a broad range of dermatophyte species provide a basis for further discovery of relationships between species. Studies of other loci are necessary to confirm the results.

Molecular epidemiology, phylogeny and evolution of dermatophytes

Dermatophytes are fungi that invade and propagate in the keratinized skin of mammals, including humans, often causing contagious infections. The species of medical concern belong to the genera Microsporum, Trichophyton, Epidermophyton (in their anamorphic state) and Arthroderma (in their telomorphic state), which were traditionally identified based on their morphology and biochemical characters. Nonetheless, limitations linked to the differentiation of closely related agents at species and strains level have been recently overcome by molecular studies. Indeed, an accurate identification of dermatophytes is pivotal for the establishment of effective control and prevention programs as well as for determining the most appropriate and effective antifungal therapies to be applied. This article reviews the DNA techniques and the molecular markers used to identify and to characterize dermatophyte species, as well as aspects of their phylogeny and evolution. The applications of typing molecular strain to both basic and applied research (e.g., taxonomy, ecology, typing of infection, antifungal susceptibility) have also been discussed.

Identification of the Trichophyton mentagrophytes complex species using MALDI-TOF mass spectrometry

Dermatophytes are fungi capable of invading keratinized tissues and are responsible for the most common fungal infection worldwide: dermatophytosis. Identification of these organisms to the species level is often necessary for the correct treatment of these infections, and is always recommended from an epidemiological point of view. Since the identification of dermatophytes is sometimes problematic, we assessed whether Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) could provide a useful tool to identify dermatophytes of the Trichophyton mentagrophytes complex. A reference database was constructed with 17 strains of six different species belonging to this complex. A total of 54 dermatophyte strains of the Belgian co-ordinated collections of micro-organisms, Scientific Institute of Public Health, Brussels, Belgium (BCCM™/IHEM) collection were used to challenge this database; 89% of the tested strains (not used as reference strains in the database) could readily be identified. When incorrect identifications were encountered, the confusion was always between phylogenetically closely related taxa which indicates that observations made by MALDI-TOF MS correlate with phylogenetic data. To assess this observation, a dendrogram outlining the similarities between the obtained spectra was constructed. Strikingly, the relationships found in this dendrogram were highly similar to the ones observed in the phylogenetic tree recently reported by Beguin and co-workers. In conclusion, MALDI-TOF MS is a fast and reliable tool for the identification of dermatophytes, since it can even discriminate between the closely related species of the T. mentagrophytes complex. Moreover, our data indicate that the data obtained by MALDI-TOF MS correlate with phylogenetic data.

Molecular identification and phylogenesis of dermatophytes isolated from rabbit farms and rabbit farm workers

Little information is available on the molecular epidemiology of dermatophytoses in rabbit farms and farm workers. A total of 117 isolates belonging to the Trichophyton mentagrophytes complex and 21 isolates of Microsporum canis were collected from rabbits with or without skin lesions, air samples of farms known to harbour these pathogens, and from farm workers with skin lesions, and molecularly characterized. Sequencing of amplicons from the T. mentagrophytes complex and M. canis isolates revealed the presence of one sequence-type for both partial chitin synthase-1 gene (pchs-1) and ribosomal internal transcribed spacer (ITS+), respectively. On the basis of comparative sequence analyses, isolated representing the T. mentagrophytes complex were molecularly identified as Trichophyton interdigitale (zoophilic) Priestley. The M. canis and T. interdigitale pchs-1 sequences herein analysed were 100% homologous to known sequences from different hosts (i.e., cats, dogs, humans and rabbits). Conversely, the ITS+ sequences of T. interdigitale from dogs, pigs and mice were identical, but displayed up to 8.6% difference with those from humans, guinea pigs and rabbits. The results of this study suggest that environmental and clinical isolates of T. interdigitale (zoophilic) and M. canis might share a common origin. Interestingly, the close phylogenetic relationship between T. interdigitale (zoophilic) strains and isolates from dogs, pigs and mice might indicate that these animals represented a reservoir of dermatophyte infection in rabbit farms. These animal species should therefore be considered when setting up control protocols to prevent infections by dermatophytes and their zoonotic transmission.

Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes

Background

Dermatophytes are fungi that cause superficial infections of the skin, hair, and nails. They are the most common agents of fungal infections worldwide. Dermatophytic fungi constitute three genera, Trichophyton, Epidermophyton, and Microsporum, and the evolutionary relationships between these genera are epidemiologically important. Mitochondria are considered to be of monophyletic origin and mitochondrial sequences offer many advantages for phylogenetic studies. However, only one complete dermatophyte mitochondrial genome (E. floccosum) has previously been determined.

Results

The complete mitochondrial DNA sequences of five dermatophyte species, T. rubrum (26,985 bp), T. mentagrophytes (24,297 bp), T. ajelloi (28,530 bp), M. canis (23,943 bp) and M. nanum (24,105 bp) were determined. These were compared to the E. floccosum sequence. Mitochondrial genomes of all 6 species were found to harbor the same set of genes arranged identical order indicating that these dermatophytes are closely related. Genome size differences were largely due to variable lengths of non-coding intergenic regions and the presence/absence of introns. Phylogenetic analyses based on complete mitochondrial genomes reveals that the divergence of the dermatophyte clade was later than of other groups of pathogenic fungi.

Conclusion

This is the first systematic comparative genomic study on dermatophytes, a highly conserved and recently-diverged lineage of ascomycota fungi. The data reported here provide a basis for further exploration of interrelationships between dermatophytes and will contribute to the study of mitochondrial evolution in higher fungi.