Dermatophytes: recognizing species of clonal fungi

Molecular diagnosis of dermatophyte infections

PURPOSE OF REVIEW

Recent advances in the molecular diagnostics of dermatophytosis may improve speed, specificities and sensitivities. This review provides an update on the current available molecular techniques for the diagnosis of dermatophytosis.

RECENT FINDINGS

Molecular diagnostics of dermatophytosis relate to the direct detection of dermatophyte DNA in clinical specimens. Important challenges have been associated with the DNA extraction procedures, which despite improvement still lack consensus, and the fact that phenotypic species classification not always translates into distinct molecular taxonomic entities. Molecular methods are divided into conventional PCR, real-time PCR and post-PCR techniques. The former benefits from simplicity and being less expensive to implement, real-time PCR is less laborious, may enable a broader spectrum of simultaneous species detections and the closed system reduces contamination risk, whereas post-PCR strategies may increase the number of species identified but prolong the turnaround time, and the processing of PCR products increases the laboratory contamination risk.

SUMMARY

Current molecular methods are on the verge of overcoming most of the early challenges regarding dermatophyte taxonomy, DNA extraction procedures and species specificity, and thus may lead to an increased adoption of such methods. This may point towards a novel consensus in which molecular methods supplement or even replace classical diagnosis of dermatophytosis.

Waterborne Exophiala species causing disease in cold-blooded animals

The majority of mesophilic waterborne species of the black yeast genus Exophiala (Chaetothyriales) belong to a single clade judging from SSU rDNA data. Most taxa are also found to cause cutaneous or disseminated infections in cold-blooded, water animals, occasionally reaching epidemic proportions. Hosts are mainly fish, frogs, toads, turtles or crabs, all sharing smooth, moist or mucous skins and waterborne or amphibian lifestyles; occasionally superficial infections in humans are noted. Cold-blooded animals with strictly terrestrial life styles, such as reptiles and birds are missing. It is concluded that animals with moist skins, i.e. those being waterborne and those possessing sweat glands, are more susceptible to black yeast infection. Melanin and the ability to assimilate alkylbenzenes are purported general virulence factors. Thermotolerance influences the choice of host. Exophiala species in ocean water mostly have maximum growth temperatures below 30 °C, whereas those able to grow until 33(−36) °C are found in shallow waters and occasionally on humans. Tissue responses vary with the phylogenetic position of the host, the lower animals showing poor granulome formation. Species circumscriptions have been determined by multilocus analyses involving partial ITS, TEF1, BT2 and ACT1.

Matings among three teleomorphs of Trichophyton mentagrophytes

Three genetically hybrid F1 progenies produced between a clinical isolate of Arthroderma simii (KMU4810) and a tester strain of A. vanbreuseghemii (RV27961) were crossed with two tester strains of A. vanbreuseghemii (RV27961 and RV27960) and a tester strain of A. benhamiae (RV30001), respectively. Three crossings yielded hybrid second progenies. Another interspecies crossing between A. simii (KMU4810) and a tester strain of A. benhamiae (RV26680) yielded one hybrid F1 progeny (Asb57). The second crossings of F1 progeny (Asb57) with A. vanbreuseghemii (RV27961) and A. benhamiae (RV30001) yielded many hybrid second progenies. Some hybrid second progenies produced between F1 progeny and A. vanbreuseghemii were confirmed to have genes from three species. The gene exchangeability among three Arthroderma species was shown and the meaning of these events discussed.

Successful mating of Trichophyton rubrum with Arthroderma simii

Crossing of Trichophyton rubrum with Arthroderma simii yielded many ascomata around the fluffy T. rubrum colonies. One of the 35 supposed ascospores isolated from matured ascoma was shown to be a hybrid of the two species. Hybrids were observed within the genotypes of four different genes, i.e., rRNA, actin, DNA topoisomerase II and cytochrome b. These results strongly suggest that T. rubrum is not an asexual or clonal species.

Real-time PCR and DNA sequencing for detection and identification of Trichophyton rubrum as a cause of culture negative chronic granulomatous dermatophytosis

A 31-year-old patient presented with a diagnosis of granulomatous dermatophytosis based on the clinical aspect of the lesions and the rare presence of hyphae on direct microscopic examination of clinical material. A chronic evolution and progression of the disease, its resistance to a wide range of antifungal agents, the occasional presence of hyphae on direct examination but consistently negative cultures over a 5-year period prompted the use of amplification-based DNA analyses of several successive swab samples or skin biopsies. DNA was extracted using a combination of two semi-automated DNA isolation methods (FastPrep preparation and NucliSENS lysis magnetic extraction method). Identification relied both on sequence analysis of amplicons after SYBR Green real-time PCR of the panfungal internal transcribed spacer 1 (ITS1) genetic target, as well as the unique amplicon melting curve profile of positive samples. Accordingly, Trichophyton rubrum was unambiguously identified in several clinical samples collected over a 7-month period. This case illustrates the contribution of DNA-based assays applied directly to sample biopsies for identifying causative agents in cases in which fungal pathogens are highly suspected but culture are repeatedly negative. It also pinpoints the benefit of combining semi-automated DNA preparation methods, analysis of ITS1 amplicon melting curve profiles and sequence analysis on repeated skin biopsy samples for unambiguous identification of the causative fungal species.

Organization and evolutionary trajectory of the mating type (MAT) locus in dermatophyte and dimorphic fungal pathogens

Sexual reproduction in fungi is governed by a specialized genomic region, the mating type (MAT) locus, whose gene identity, organization, and complexity are diverse. We identified the MAT locus of five dermatophyte fungal pathogens (Microsporum gypseum, Microsporum canis, Trichophyton equinum, Trichophyton rubrum, and Trichophyton tonsurans) and a dimorphic fungus, Paracoccidioides brasiliensis, and performed phylogenetic analyses. The identified MAT locus idiomorphs of M. gypseum control cell type identity in mating assays, and recombinant progeny were produced. Virulence tests in Galleria mellonella larvae suggest the two mating types of M. gypseum may have equivalent virulence. Synteny analysis revealed common features of the MAT locus shared among these five dermatophytes: namely, a small size ( approximately 3 kb) and a novel gene arrangement. The SLA2, COX13, and APN2 genes, which flank the MAT locus in other Ascomycota are instead linked on one side of the dermatophyte MAT locus. In addition, the transcriptional orientations of the APN2 and COX13 genes are reversed compared to the dimorphic fungi Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii. A putative transposable element, pogo, was found to have inserted in the MAT1-2 idiomorph of one P. brasiliensis strain but not others. In conclusion, the evolution of the MAT locus of the dermatophytes and dimorphic fungi from the last common ancestor has been punctuated by both gene acquisition and expansion, and asymmetric gene loss. These studies further support a foundation to develop molecular and genetic tools for dermatophyte and dimorphic human fungal pathogens.

Successful mating of a human isolate of Arthroderma simii with a tester strain of A. vanbreuseghemii

An isolate of Arthroderma simii was successfully mated with a tester strain of A. vanbreuseghemii cultured on the plate of simple agar with some hair on it at 27 degrees C. Confirmation of sexual reproduction was made by the detection of hybrids of two parental genotypes. The implications of this result are discussed from the viewpoint of a reevaluation of the species boundaries of dermatophytes.

Preclinical studies with 5,10,15-Tris(4-methylpyridinium)-20-phenyl-[21H,23H]-porphine trichloride for the photodynamic treatment of superficial mycoses caused by Trichophyton rubrum

Dermatophytes are fungi that cause infections of keratinized tissues. We have recently demonstrated the susceptibility of the dermatophyte Trichophyton rubrum to photodynamic treatment (PDT) with 5,10,15-Tris(4-methylpyridinium)-20-phenyl-[21H,23H]-porphine trichloride (Sylsens B) in 5 mm citric acid/sodium citrate buffer (pH 5.2, formulation I). In this work, we examined the penetration of Sylsens B in healthy and with T. rubrum infected skin and we investigated the susceptibility of T. rubrum to PDT using formulation I and UVA-1 radiation (340-550 nm). Skin penetration studies were performed with formulations I and II (Sylsens B in PBS, pH 7.4) applied on dermatomed skin, human stratum corneum (SC), disrupted SC by T. rubrum growth and SC pretreated with a detergent. No penetration was observed in healthy skin. Disruption of SC by preceding fungal growth caused Sylsens B penetration at pH 7.4, but not at pH 5.2. However, chemically damaged SC allowed Sylsens B to penetrate also at pH 5.2. UVA-1 PDT was applied ex vivo during two fungal growth stages of two T. rubrum strains (CBS 304.60 and a clinical isolate). Both strains could be killed by UVA-1 alone (40 J/cm(2)). Combined with formulation I (1 and 10 microm Sylsens B for, respectively, CBS 304.60 and the clinical isolate), only 18 J/cm(2) UVA-1 was required for fungal kill. Therefore, PDT with 10 microm Sylsens B (formulation I) and 18 J/cm(2) UVA-1 could be considered as effective and safe. This offers the possibility to perform clinical studies in future.

Hedgehog ringworm in humans and a dog

We report 3 related cases of human dermatophytosis and 1 dog dermatophytosis likely caused by contact with a European hedgehog. Trichophyton erinacei was isolated from stratum corneum samples. This type of zoophilic dermatophytosis is rare in south-east Belgium and probably in the rest of the country as well.

Pets as the main source of two zoonotic species of the Trichophyton mentagrophytes complex in Switzerland, Arthroderma vanbreuseghemii and Arthroderma benhamiae

In cases of highly inflammatory dermatophytosis in humans, it is important to identify the possible source of animal transmission in order to prevent recurrence, family outbreaks or rapidly progressing epidemics. A survey of dermatophytes in pets during a 14-month period in Switzerland revealed, in addition to Microsporum canis, two different species of the Trichophyton mentagrophytes complex, Arthroderma benhamiae and Arthroderma vanbreuseghemii, all causing inflammatory dermatophytoses. Arthroderma benhamiae was only and frequently isolated from guinea pigs. Arthroderma vanbreuseghemii was isolated mainly from European short hair cats, but also from dogs and in one case from a pure-bred cat. Ninety-three percent of the cats carrying A. vanbreuseghemii were hunters and all had skin lesions. In contrast, cats with skin lesions that were strictly indoors were found to be almost exclusively infected by M. canis. Therefore, it can be suspected that infection with A. vanbreuseghemii occurred during hunting and that the natural source of this dermatophyte is either soil or an animal other than the cat, most probably a rodent.

Identification of dermatophytes by sequence analysis of the rRNA gene internal transcribed spacer regions

Identification of dermatophytes using the traditional method is sometimes problematic because of atypical microscopic or macroscopic morphology. The aim of this study was to evaluate the feasibility of using sequencing of the ribosomal internal transcribed spacer (ITS)1 and ITS2 regions for identification of 17 dermatophyte species. The ITS regions of 188 strains (62 reference strains and 126 clinical isolates) were amplified by PCR and sequenced. Species identification was made by sequence comparison with an in-house database comprising ITS sequences of type or neotype strains or by blast searches for homologous sequences in public databases. Strains producing discrepant results between conventional methods and ITS sequence analysis were analysed further by sequencing the D1–D2 domain of the large-subunit rRNA gene for species clarification. The identification rates by ITS1 and ITS2 sequencing were higher than 97 %. Based on reference sequences of type or neotype strains, it was noted that most strains of Trichophyton mentagrophytes were misidentifications of Trichophyton interdigitale. In addition, barcode sequences were present in species of the Microsporum canis complex and Trichophyton rubrum complex. These barcode sequences are useful for species delineation when the results of ITS sequencing are ambiguous. In conclusion, ITS sequencing provides a very accurate and useful method for the identification of dermatophytes.

Rapid identification and differentiation of Trichophyton species, based on sequence polymorphisms of the ribosomal internal transcribed spacer regions, by rolling-circle amplification

DNA sequencing analyses have demonstrated relatively limited polymorphisms within the fungal internal transcribed spacer (ITS) regions among Trichophyton spp. We sequenced the ITS region (ITS1, 5.8S, and ITS2) for 42 dermatophytes belonging to seven species (Trichophyton rubrum, T. mentagrophytes, T. soudanense, T. tonsurans, Epidermophyton floccosum, Microsporum canis, and M. gypseum) and developed a novel padlock probe and rolling-circle amplification (RCA)-based method for identification of single nucleotide polymorphisms (SNPs) that could be exploited to differentiate between Trichophyton spp. Sequencing results demonstrated intraspecies genetic variation for T. tonsurans, T. mentagrophytes, and T. soudanense but not T. rubrum. Signature sets of SNPs between T. rubrum and T. soudanense (4-bp difference) and T. violaceum and T. soudanense (3-bp difference) were identified. The RCA assay correctly identified five Trichophyton species. Although the use of two "group-specific" probes targeting both the ITS1 and the ITS2 regions were required to identify T. soudanense, the other species were identified by single ITS1- or ITS2-targeted species-specific probes. There was good agreement between ITS sequencing and the RCA assay. Despite limited genetic variation between Trichophyton spp., the sensitive, specific RCA-based SNP detection assay showed potential as a simple, reproducible method for the rapid (2-h) identification of Trichophyton spp.

Atypical Microsporum canis variant in an immunosuppressed child

A 10-year old boy with X-chromosomal adrenoleukodystrophy presented with scaly patches on the scalp and diffuse effluvium. He was on immunosuppressive therapy because of a chronic graft-versus-host-reaction after allogenic bone marrow transplantation. At home he had been in contact with cats, rabbits and guinea pigs. Through Wood light and KOH examination, we confirmed the diagnosis of tinea capitis and started antimycotic therapy. The morphology of the culture first suggested Epidermophyton floccosum, Trichophyton mentagrophytes var. nodulare or Trichophyton tonsurans as possible causes for this infection. Further studies, however, revealed an atypical form of Microsporum canis infection.

Phylogenetic analysis of Trichophyton mentagrophytes human and animal isolates based on MnSOD and ITS sequence comparison

Dermatophytes are keratinophilic fungi able to infect keratinized tissues of human or animal origin. Among them, Trichophyton mentagrophytes is known to be a species complex composed of several species or variants, which occur in both human and animals. Since the T. mentagrophytes complex includes both anthropophilic and zoophilic pathogens, accurate molecular identification is a critical issue for comprehensive understanding of the clinical and epidemiological implications of the genetic heterogeneity of this complex. Here, 41 T. mentagrophytes isolates from either human patients (14 isolates) or animals (27 isolates) with dermatophytosis were prospectively isolated by culture and identified on morphological bases at the University Hospital Centres of Lille and Poitiers, and the Veterinary School of Alfort, respectively. The isolates were differentiated by DNA sequencing of the variable internal transcribed spacer (ITS) regions flanking the 5.8S rDNA, and of the housekeeping gene encoding the manganese-containing superoxide dismutase (MnSOD), an enzyme which is involved in defence against oxidative stress and has previously provided interesting insight into both fungal taxonomy and phylogeny. ITS1-ITS2 regions and MnSOD sequences successfully differentiate between members of the T. mentagrophytes complex and the related species Trichophyton rubrum. Whatever the phylogenetic marker used, members of this complex were classified into two major clades exhibiting a similar topology, with a higher variability when the ITS marker was used. Relationships between ITS/MnSOD sequences and host origin, clinical pattern and phenotypic characteristics (macroscopic and microscopic morphologies) were analysed.

Identification of dermatophyte species causing onychomycosis and tinea pedis by MALDI-TOF mass spectrometry

Identification of dermatophytes is currently performed based on morphological criteria and is increasingly supported by genomic sequence comparison. The present study evaluates an alternative based on the analysis of clinical fungal isolates by mass spectrometry. Samples originating from skin and nail were characterized morphologically and by sequencing the internal transcribed spacer 1 (ITS1), ITS2 and the 5.8S rDNA regions of the rDNA clusters. In a blind comparative study, samples were analyzed by matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF MS). The mass spectra were compared to a database comprising of the spectral data of reference strains by applying the saramis software package. All fungal isolates belonging to the taxa Trichophyton rubrum, T. interdigitale, T. tonsurans, Arthroderma benhamiae and Microsporum canis were correctly identified, irrespective of host origin and pathology. To test the robustness of the approach, four isolates were grown on five different media and analyzed. Although the resulting mass spectra varied in detail, a sufficient number of signals were conserved resulting in data sets exploitable for unequivocal species identification. Taken together, the usually widespread dermatophytes can be identified rapidly and reliably by mass spectrometry. Starting from pure cultures, MALDI-TOF MS analysis uses very simple sample preparation procedures, and a single analysis is performed within minutes. Costs for consumables as well as preparation time are considerably lower than for PCR analysis.

Identification of dermatophytes by an oligonucleotide array

Species of dermatophytes are classified into three anamorphic (asexual) genera, Epidermophyton, Microsporum, and Trichophyton. Conventional methods used to identify dermatophytes are often lengthy and may be inconclusive because of atypical microscopic or colony morphology. Based on the internal transcribed spacer 1 (ITS-1) and ITS-2 sequences of the rRNA genes, an oligonucleotide array was developed to identify 17 dermatophyte species. The method consisted of PCR amplification of the ITS regions using universal primers, followed by hybridization of the digoxigenin-labeled PCR products to an array of oligonucleotides (17- to 30-mers) immobilized on a nylon membrane. Of 198 dermatophyte strains and 90 nontarget strains tested, the sensitivity and specificity of the array were 99.5% and 97.8%, respectively. The only strain not identified (Microsporum audouinii LMA 597) was found to have a nucleotide insertion at the ITS-2 region where the probe was designed. Two nontarget strains, Microsporum equinum LMA 40396666 and Trichophyton gourvilii var. intermedium CBS 170.65, were misidentified as Microsporum canis and Trichophyton soudanense, respectively. Sequence analysis of the ITS regions revealed that the two misidentified strains displayed high sequence homology with the probes designed for M. canis and T. soudanense, respectively. The present method can be used as a reliable alternative to conventional identification methods and can be completed with isolated colonies within 24 h.

Microsatellite markers reveal geographic population differentiation in Trichophyton rubrum

A worldwide selection of more than 200 isolates of the anthropophilic dermatophyteTrichophyton rubrumwere analysed using seven microsatellite markers. Fifty-five multilocus genotypes were recognized, allowing a subdivision of the species into two populations. Both populations reproduced strictly clonally, showed a different predilection on the human host (scalp vs foot) and displayed geographic differentiation. Genotypes of one population originated predominantly from Africa, whilst the second population showed a worldwide distribution excluding the African continent. Genotypic diversity was highest in the African population, despite the lower number of strains analysed, suggesting thatT. rubrumis likely to have evolved in Africa. No diagnostic correlation was observed between multilocus genotypes and any of the phenotypical characteristics of the strains. The involvement of multiple strains in a single patient detected by workers using other typing methods was not supported by these microsatellite markers. Four of the developed microsatellite markers may be applied for diagnostic purposes.

Swimming pools and fungi: an environmental epidemiology survey in Italian indoor swimming facilities

A growing number of people attend swimming facilities for recreational activities, rehabilitative treatments, or sport. Filamentous fungi and yeast can be isolated from contaminated air, water and surfaces and may represent a biological risk for employees and users. Here we investigated the occurrence of mycotic species, in a sample of Italian swimming pools (n = 10). Detection and identification of isolated species were achieved by cultural and morphological methods. Results revealed moderate mycotic titres and a high biodiversity. Penicillium spp., Aspergillus spp., Cladosporium spp. and Alternaria sp., were constantly detected in air and surfaces sampled by the swimming area, while pathogenic yeast Candida albicans was never detected. Fusarium spp. was the most common taxon isolated from surfaces. For one facility, we typed the genotypic profiles and studied, by genetic typing, the spatial and temporal distribution of isolates. Phylogenetic relationships between species were analysed by alignment of small ribosomal subunit RNA sequences.

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.