Molecular taxonomy of dermatophytes and related fungi by chitin synthase 1 (CHS1) gene sequences

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.

Phenotypic and Genotypic Identification of Dermatophytes from Mexico and Central American Countries

Dermatophytes are fungi included in the genera Trichophyton, Microsporum, Epidermophyton, Nannizzia, Paraphyton, Lophophyton, and Arthroderma. Molecular techniques have contributed to faster and more precise identification, allowing significant advances in phylogenetic studies. This work aimed to identify clinical isolates of dermatophytes through phenotypic (macro- and micromorphology and conidia size) and genotypic methods (sequences of ITS regions, genes of β tubulin (BT2), and elongation factor α (Tef-1α)) and determine the phylogenetic relationships between isolates. Ninety-four dermatophyte isolates from Costa Rica, Guatemala, Honduras, Mexico, and the Dominican Republic were studied. The isolates presented macro- and micromorphology and conidia size described for the genera Trichophyton, Microsporum, and Epidermophyton. Genotypic analysis classified the isolates into the genera Trichophyton (63.8%), Nannizzia (25.5%), Arthroderma (9.6%), and Epidermophyton (1.1%). The most frequent species were T. rubrum (26 isolates, 27.6%), T. interdigitale (26 isolates, 27.6%), and N. incurvata (11 isolates, 11.7%), N. gypsea and A. otae (nine isolates, 9.6%), among others. The genotypic methods clarified the taxonomic status of closely related species. For instance, the ITS and BT2 markers of T. rubrum/T. violaceum did not differ but the Tef-1α gene did. On the other hand, the three markers differed in T. equinum/T. tonsurans. Therefore, the ITS, BT2, and Tef-1α genes are useful for typing in phylogenetic analyses of dermatophytes, with Tef-1α being the most informative locus. It should be noted that isolate MM-474 was identified as T. tonsurans when using ITS and Tef-1α, but when using BT2, it was identified as T. rubrum. On the other hand, no significant difference was found when comparing the methods for constructing phylogenies, as the topologies were similar.

The unprecedented epidemic-like scenario of dermatophytosis in India: II. Diagnostic methods and taxonomical aspects

Trichophyton (T.) mentagrophytes now accounts for an overwhelming majority of clinical cases in India, a new "Indian genotype" (T. mentagrophytes ITS genotype VIII) having been isolated from skin samples obtained from cases across a wide geographical distribution in this country. The conventional diagnostic methods, like fungal culture, are, however, inadequate for diagnosing this agent. Thus, molecular methods of diagnosis are necessary for proper characterization of the causative agent. The shift in the predominant agent of dermatophytosis from T. rubrum to T. mentagrophytes, within a relatively short span of time, is without historic parallel. The apparent ease of transmission of a zoophilic fungus among human hosts can also be explained by means of mycological phenomena, like anthropization.

Recent advances in the diagnosis of dermatophytosis

Dermatophytosis is a disease of global significance caused by pathogenic keratinolytic fungi called dermatophytes in both animals and humans. The recent taxonomy of dermatophytes classifies them into six pathogenic genera, namely Microsporum, Trichophyton, Epidermophyton, Nannizzia, Lophophyton and Arthroderma. It is because of the delayed diagnostic nature and low accuracy of dermatophyte detection by conventional methods that paved the path for the evolution of molecular diagnostic techniques, which provide the accurate and rapid diagnosis of dermatophytosis for an appropriate, timely antifungal therapy that prevents the nonspecific over-the-counter self-medication. This review focuses on the importance of rapid and accurate diagnosis of dermatophytosis, limitations of conventional methods, selection of targets in diagnosis, and factors affecting sensitivity and specificity of various molecular diagnostic technologies in the diagnosis of dermatophytosis. Generally, all the molecular techniques have a significant edge over the conventional methods of culture and microscopy in the dermatophytosis diagnosis. However, in mycology laboratory, the suitability of any molecular diagnostic technique in the diagnosis of dermatophytosis is driven by the requirement of time, economy, complexity, the range of species spectrum detected and the scale of diagnostic output required. Thus, various choices involved in the pursuit of a diagnosis of dermatophytosis are determined by the available conditions and the facilities in the laboratory.

Epidermophyton floccosum: nucleotide sequence analysis and antifungal susceptibility testing of 40 clinical isolates

Purpose. Epidermophyton floccosum is an anthropophilic dermatophyte species, which is one of the common causative agents of dermatophytosis in different parts of the world. The aim of the present investigation was to evaluate the genetic diversity of E. floccosum strains isolated from different parts of Iran and to define the in vitro susceptibility profiles of seven antifungal drugs against these clinical isolates.Methodology. Forty clinical strains of E. floccosum isolated from 40 patients with dermatophytosis were subjected to DNA extraction and PCR amplification of the ITS rDNA region using universal primers ITS1 and ITS4. The in vitro activities of griseofulvin, itraconazole, voriconazole, posaconazole, caspofungin, ketoconazole and terbinafine were determined using a broth microdilution method according to the CLSI-M-38A2 protocol.Results. A mean genetic similarity of 99.5 % was found between E. floccosum strains, with intraspecies differences ranging from 0 to 3 nt. The geometric mean (GM) MICs and minimum effective concentrations (MECs) across all isolates were, in increasing order, as follows: terbinafine (GM=0.018 mg l^-1), posaconazole (GM=0.022 mg l^-1), itraconazole (GM=0.034 mg l^-1) and voriconazole (GM=0.045 mg l^-1), which had low MICs against all tested strains, whereas caspofungin (GM=0.22 mg l^-1), ketoconazole (GM=0.41 mg l^-1) and griseofulvin (GM=0.62 mg l^-1) demonstrated higher MICs.Conclusion. Our study showed low intraspecies variation within strains of E. floccosum. Furthermore, terbinafine, posaconazole, itraconazole and voriconazole were shown to be the most potent antifungal drugs against E. floccosum strains.

Clinical application of a molecular assay for the detection of dermatophytosis and a novel non-invasive sampling technique

The dermatophytoses are the most common superficial fungal infections worldwide. Clinical diagnosis is not reliable as there are many differentials, and laboratory diagnosis is required to gain access to treatment in more severe disease. Traditional diagnostic methods are limited by suboptimal sensitivity, specificity and prolonged turnaround times. Molecular methods are being used increasingly in the diagnostic algorithm in the clinical microbiology laboratory. The aim of this study was to evaluate a real-time polymerase chain reaction (RT-PCR) targeting the chitin synthase 1 gene (CHS1) of dermatophytes for analytical specificity, and to assess its clinical application by comparing it to the current methods of microscopy and culture. We also assessed a novel non-invasive sample collection technique involving adhesive tape impressions of suspected lesions. The PCR was highly specific, being able to discern between cultures of dermatophytes and other microorganisms. It also proved to be more sensitive than traditional methods at detecting dermatophytes in clinical samples. Similar sensitivities were seen on the samples assessed by the adhesive tape technique. An internal control system allowed for the detection of inhibition in certain culture and clinical specimens. This rapid and cost-effective technique could be incorporated into the initial diagnostic algorithm for dermatophytosis in Australian laboratories.

Diagnosis of Dermatophytosis Using Molecular Biology

Identification of fungi in dermatological samples using PCR is reliable and provides significantly improved results in comparison with cultures. It is possible to identify the infectious agent when negative results are obtained from cultures. In addition, identification of the infectious agent can be obtained in 1 day. Conventional and real-time PCR methods used for direct fungus identification in collected samples vary by DNA extraction methods, targeted DNA and primers, and the way of analysing the PCR products. The choice of a unique method in a laboratory is complicated because the results expected from skin and hair sample analysis are different from those expected in cases of onychomycosis. In skin and hair samples, one dermatophyte among about a dozen possible species has to be identified. In onychomycosis, the infectious agents are mainly Trichophyton rubrum and, to a lesser extent, Trichophyton interdigitale, but also moulds insensitive to oral treatments used for dermatophytes, which renders fungal identification mandatory. The benefits obtained with the use of PCR methods for routine analysis of dermatological samples have to be put in balance with the relative importance of getting a result in a short time, the price of molecular biology reagents and equipment, and especially the time spent conducting laboratory manipulations.

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.

Translation elongation factor 1-α gene as a potential taxonomic and identification marker in dermatophytes

Intra- and interspecies variations of the translation elongation factor 1-α (Tef-1α) gene were evaluated as a new identification marker in a wide range of dermatophytes, which included 167 strains of 30 species. An optimized pan-dermatophyte primer pair was designed, and the target was sequenced. Consensus sequences were used for multiple alignment and phylogenetic tree analysis and the levels of intra- and interspecific nucleotide polymorphism were assessed. Between species, the analyzed part of the Tef-1α gene varied in length from 709 to 769 nucleotides. Significant numbers of species including Trichophyton rubrum, T. tonsurans, T. schoenleinii, T. concentricum, T. violaceum, Epidermophyton floccosum, Microsporum ferrugineum, M. canis, M. audouinii, T. equinum, T. eriotrephon, and T. erinacei were invariant in Tef-1α and had sufficient barcoding distance with neighboring species. Although overall consistency was found between ITS phylogeny as the current molecular marker of dermatophytes and Tef-1α, a higher discriminatory power of Tef-1α appeared particularly useful in some clades of closely related species such as the A. vanbreuseghemii, T. rubrum, A. benhamiae, and A. otae complexes. Nevertheless, we stress that a single gene can not specify species borderlines among dermatophytes and multiple lines of evidence based on a multilocus inquiry may ascertain an incontrovertible evaluation of kinship.

Molecular diagnosis of onychomycosis

Onychomycosis is a frequent cause of nail infections due to dermatophytes. Molds and yeast may also be responsible of these pathologies. Antifungal treatments are frequently given without a mycological diagnosis, partly because of the requisite time for obtaining the biological results. The mycological diagnosis requires a direct microscopic examination and a culture in order to accurately identify the fungal genus and species. Nevertheless, this conventional diagnosis is often time consuming due to the delay of fungal cultures and presents disadvantages that make it not sufficient enough to give a precise and confident response to the clinicians. Therefore additional tests have been developed to help distinguish onychomycosis from other nail disorders. Among them, molecular biology techniques offer modern and rapid tools to improve traditional microbiological diagnosis. In this review, we first present the conventional diagnosis methods for onychomycosis and then we describe the main molecular biology tools and the currently available commercial kits that allow a rapid detection of the pathology.

Restriction analysis of β-tubulin gene for differentiation of the common pathogenic dermatophytes

BACKGROUND

Identification of dermatophytes at the species level, relying on macro- and microscopic properties of the colonies is time-consuming, questioned in many circumstances, and requires considerable expertise. In this study, we examined the potency of a new genetic marker, β-tubulin (BT2) gene, for differentiation of dermatophytes in an in silico and experimental restriction fragment length polymorphism (RFLP) profile.

METHODS

The BT2 sequences of dermatophyte species were retrieved from GenBank and analyzed using bioinformatics softwares to choose suitable restriction enzyme(s). Forty reference culture collections and 100 clinical isolates were PCR-amplified using the primers T1 and Bt2b and consequently subjected to virtual RFLP analysis. The dermatophytes were identified according to specific lengths of bands in agarose gel electrophoresis.

RESULTS

After digestion of partially amplified β-tubulin gene with the restriction enzyme FatI, three dermatophyte species, that is, Microsporum gypseum, M. canis, and Trichophyton verrucosum yielded unique restriction maps while the remaining species including T. interdigitale, T. rubrum, T. tonsurans, T. schoenleinii, and T. violaceum, were identified by further restriction digestion by Alw21I, MwoI, and HpyCH4V endonucleases. The length of RFLP products was same as of those expected by computer analysis.

CONCLUSION

The two-step BT2 restriction mapping used in this study is an effective tool for reliable differentiation of the clinically relevant species of dermatophytes.

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.

An improved molecular diagnostic assay for canine and feline dermatophytosis

The few studies attempting to specifically characterize dermatophytes from hair samples of dogs and cats using PCR-based methodology relied on sequence-based analysis of selected genetic markers. The aim of the present investigation was to establish and evaluate a PCR-based approach employing genetic markers of nuclear DNA for the specific detection of dermatophytes on such specimens. Using 183 hair samples, we directly compared the test results of our one-step and nested-PCR assays with those based on conventional microscopy and in vitro culture techniques (using the latter as the reference method). The one step-PCR was highly accurate (AUC > 90) for the testing of samples from dogs, but only moderately accurate (AUC = 78.6) for cats. A nested-PCR was accurate (AUC = 93.6) for samples from cats, and achieved higher specificity (94.1 and 94.4%) and sensitivity (100 and 94.9%) for samples from dogs and cats, respectively. In addition, the nested-PCR allowed the differentiation of Microsporum canis from Trichophyton interdigitale (zoophilic) and geophilic dermatophytes (i.e., Microsporum gypseum or Trichophyton terrestre), which was not possible using the one step-assay. The PCRs evaluated here provide practical tools for diagnostic applications to support clinicians in initiating prompt and targeted chemotherapy of dermatophytoses.

The evolution of sex: a perspective from the fungal kingdom

Sex is shrouded in mystery. Not only does it preferentially occur in the dark for both fungi and many animals, but evolutionary biologists continue to debate its benefits given costs in light of its pervasive nature. Experimental studies of the benefits and costs of sexual reproduction with fungi as model systems have begun to provide evidence that the balance between sexual and asexual reproduction shifts in response to selective pressures. Given their unique evolutionary history as opisthokonts, along with metazoans, fungi serve as exceptional models for the evolution of sex and sex-determining regions of the genome (the mating type locus) and for transitions that commonly occur between outcrossing/self-sterile and inbreeding/self-fertile modes of reproduction. We review here the state of the understanding of sex and its evolution in the fungal kingdom and also areas where the field has contributed and will continue to contribute to illuminating general principles and paradigms of sexual reproduction.

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.

Trichophyton mentagrophytes sive interdigitale? A dermatophyte in the course of time

Originally, the Trichophyton (T.) mentagrophytes complex distinguished between the anthropophilic subspecies T. mentagrophytes var. interdigitale, T. mentagrophytes var. nodulare (synonym T. krajdenii), and T. mentagrophytes var. goetzii and the zoophilic subspecies T. mentagrophytes var. granulosum (rodents), T. mentagrophytes var. erinacei (hedgehog), and T. mentagrophytes var. quinckeanum (mice). In addition, two sexual species (teleomorph) of this complex are known. These are Arthroderma (A.) benhamiae Ajello and Cheng 1967 and Arthroderma vanbreuseghemii Takashio 1973. According to recent molecular studies,the species T.mentagrophytes is synonymous with only the zoophilic subspecies T.mentagrophytes var. quinckeanum which is rare in Western Europe. The anthropophilic subspecies of T. mentagrophytes, as well as many of the zoophilic strains, formerly differentiated as var. mentagrophytes or var. granulosum, are indistinguishable and are now designated T.interdigitale. The morphological differentiation between anthropophilic and zoophilic T. interdigitale strains by classical microscopical and biochemical methods is often problematic. In particular, it is impossible to differentiate between the zoophilic strains of T. interdigitale, T. mentagrophytes, and the Trichophyton anamorph of A. benhamiae. In these cases, molecular identification methods may be applied to answer epidemiological, taxonomical and therapeutic questions.

ITS barcodes forTrichophyton tonsuransandT. equinum

Early molecular biosystematic studies of dermatophytes created considerable confusion about the taxonomic status of the horse-associated Trichophyton equinum vis-à-vis the anthropophilic T. tonsurans. Though this matter has recently been clarified, routine identification of these species based on the commonly used ribosomal internal transcribed spacer (ITS) sequence has been impractical. This is because, in the available sequences attributed to the species in GenBank, a clear species-level distinction does not appear to exist. In the present study, resequencing the ITS regions of several anomalous isolates is shown to eliminate this problem, which was mainly based on read errors in older sequences. Newly generated sequences and recent GenBank additions are analysed to show that T. equinum appears to be uniform in ITS sequence worldwide, while T. tonsurans is also uniform, excepting a single-base change found in one otherwise typical strain. Analysis also reveals a distinct, as yet incompletely classified Asian genotype that may belong to one or the other of these species. Standard ITS 'barcode sequences' are proposed for T. tonsurans and T. equinum, and a taxonomic neotype is designated to anchor the latter species. T. equinum var. autotrophicum is further evidenced as very closely related to T. equinum var. equinum, and the anomaly of its plesiomorphous phenotype is discussed in a population genetics context.

The complete DNA sequence of the mitochondrial genome of the dermatophyte fungus Epidermophyton floccosum

We report here the complete nucleotide sequence of the 30.9-kb mitochondrial genome of the dermatophyte fungus Epidermophyton floccosum. All genes are encoded on the same DNA strand and include seven subunits of the reduced nicotinamide adenine dinucleotide ubiquinone oxireductase (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), three subunits of cytochrome oxidase (cox1, cox2, and cox3), apocytochrome b (cob), three subunits of ATP synthase (atp6, atp8, and atp9), the small and large ribosomal RNAs (rns and rnl), and 25 tRNAs. A ribosomal protein gene (rps5) is present as an intronic ORF in the large ribosomal subunit. The genes coding for cob and cox1 carry one intron and nad5 carries two introns with ORFs. The mtDNA of E. floccosum has the same gene order as Trichophyton rubrum mtDNA, with the exception of some tRNA genes. Maximum likelihood phylogenetic analysis confirms T. rubrum as a close relative of E. floccosum. This is the first complete mitochondrial sequence of a species of the order Onygenales. This sequence is available under GenBank accession number AY916130.