Molecular and Phenotypic Characterization of Nannizzia (Arthrodermataceae)

Phylogenetic studies of the family Arthrodermataceae have revealed seven monophyletic dermatophyte clades representing the genera Trichophyton, Epidermophyton, Nannizzia, Lophophyton, Paraphyton, Microsporum, and Arthroderma. Members of the genus Nannizzia are geo- or zoophiles that occasionally infect humans. With the newly proposed taxonomy, the genus Nannizzia comprises thirteen species, i.e., Nannizzia aenigmatica, N. corniculata, N. duboisii, N. fulva, N. graeserae, N. gypsea, N. nana, N. incurvata, N. perplicata, N. persicolor, N. praecox, and two novel species. Nannizzia polymorpha sp. nov. was isolated from a skin lesion of a patient from French Guiana. For the strain originally described as Microsporum racemosum by Borelli in 1965, we proposed Nannizzia lorica nom. nov. The species are fully characterized with five sequenced loci (ITS, LSU, TUB2, RP 60S L1 and TEF3), combined with morphology of the asexual form and physiological features. A key to the species based on phenotypic and physiological characters is provided.

PRP8 intein in dermatophytes: Evolution and species identification

Dermatophytes are keratinophilic fungi belonging to the family Arthrodermataceae. Despite having a monophyletic origin, its systematics has always been complex and controversial. Sequencing of nuclear ribosomal ITS and D1/D2 rDNA has been proposed as an efficient tool for identifying species in this group of fungi, while multilocus analyses have been used for phylogenetic species recognition. However, the search for new markers, with sequence and size variation, which enable species identification in only one polymerase chain reaction (PCR) step, is very attractive. Inteins seems to fulfill these characteristics. They are self-splicing genetic elements present within housekeeping coding genes, such as PRP8, that codify the most important protein of the spliceosome. The PRP8 intein has been described for Microsporum canis in databases but has not been studied in dermatophytes in any other published work. Thus, our aim was to determine the potential of this intervening element for establishing phylogenetic relationships among dermatophytes and for identifying species. It was found that all studied species have a full-length PRP8 intein with a Homing Endonuclease belonging to the family LAGLIDADG. Phylogenetic analyses were consistent with other previous phylogenies, confirming Epidermophyton floccosum in the same clade of the Arthroderma gypseum complex, Microsporum audouinii close to M. canis, differentiating A. gypseum from Arthroderma incurvatum, and in addition, better defining the Trichophyton interdigitale and Trichophyton rubrum species grouping. Length polymorphism in the HE region enables identification of the most relevant Microsporum species by a simple PCR-electrophoresis assay. Intein PRP8 within dermatophytes is a powerful additional tool for identifying and systematizing dermatophytes.

Molecular analysis of dermatophytes suggests spread of infection among household members

Dermatophyte infection from the same strains may be an important route for transmission of dermatophytoses within a household. In this study, we used molecular methods to identify dermatophytes in members of dermatophyte-infected households and evaluated variables associated with the spread of infection. Fungal species were identified by polymerase chain reaction (PCR) using primers targeting the internal transcribed spacer (ITS) regions (ITS1 and ITS4). For strain differentiation, fungal DNA was probed with a ribosomal DNA-specific probe (containing ITS1, 5.8S ribosomal DNA, and ITS2) to detect restriction fragment length polymorphisms (RFLPs). Associations between the spread of a dermatophyte infection and fungal/host variables were determined using χ² and logistic regression analyses. Among the 50 households enrolled in this study, 18 included multiple infected members (MIMs). Trichophyton rubrum was the most commonly isolated dermatophyte species, followed by Trichophyton mentagrophyts and Epidermophyton floccosum. Sixteen T rubrum strains (TR-A to TR-P) were identified, with spread of infection detected in 8 MIM households. Factors that were significantly (P<.05) associated with the spread of infection included the presence of strains TR-B or TR-D, a history of concomitant tinea pedis and onychomycosis, and plantar scaling and/or nail discoloration. This study is unique in that it used molecular evidence to demonstrate the association of certain strains with the spread of dermatophyte infection among members of the same household.

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.

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

In the present study, the nucleotide sequences of the CHS1 gene from dermatophytes and related fungi in the genera Chrysosporium, Epidermophyton, Microsporum and Trichophyton were investigated using molecular methods. About 440-bp genomic DNA fragments of the CHS1 gene from 21 species were amplified by polymerase chain reaction (PCR) and sequenced. The CHS1 nucleotide sequences of these fungi showed more than 83% similarity. The molecular taxonomy of the CHS1 gene sequences revealed that Microsporum was genetically distinct from Chrysosporium and Trichophyton, as classified by morphological characteristics.

Application of PCR to distinguish common species of dermatophytes

This report describes the application of PCR fingerprinting for the identification of species and varieties of common dermatophytes and related fungi utilizing as a single primer the simple repetitive oligonucleotide (GACA)(4). The primer was able to amplify all the strains, producing species-specific profiles for Microsporum canis, Microsporum gypseum, Trichophyton rubrum, Trichophyton ajelloi, and Epidermophyton floccosum. Intraspecific variability was not observed for these species. Instead, three different profiles were observed in the Trichophyton mentagrophytes group.

Phylogenetic relation of Epidermophyton floccosum to the species of Microsporum and Trichophyton in chitin synthase 1 (CHS1) gene sequences

The Nucleotide sequence of the chitin synthase 1 (CHS1) gene of Epidermophyton floccosum, an anthrophophilic dermatophyte which is the type species of the genus Epidermophyton was analyzed to determine its phylogenetic relation to eight other dermatophyte species belonging to the genera Microsporum and Trichophyton, which were sequenced in our previous studies. A genomic DNA fragment about 620 bp in length of the CHS1 gene was amplified from E. floccosum by polymerase chain reaction (PCR) and was sequenced. The CHS1 nucleotide sequence showed more than 85% similarity with sequences derived from the other dermatophytes. Phylogenetic analyses of the sequences from E. floccosum revealed that the genus Epidermophyton may be genetically distinct from Microsporum and Trichophyton.

Identification of several clinical isolates of dermatophytes based on the nucleotide sequence of internal transcribed spacer 1 (ITS 1) in nuclear ribosomal DNA

Nucleotide sequences of internal transcribed spacer 1 (ITS 1) in nuclear ribosomal DNA from seven morphologically unidentified dermatophyte isolates were determined. The sequences were compared with those of typical isolates of Trichophyton (T.) mentagrophytes var. interdigitale, T. rubrum, and Epidermophyton floccosum. Two of the isolates were classified as T. rubrum and the other five as T. mentagrophytes var. interdigitale. The results did not conflict with identifications using other molecular techniques, including random amplification of polymorphic DNA (RAPD) analysis and restriction enzyme analysis of mitochondrial DNAs. Thus, the nuclotide sequence of ITS 1 is possibly a good molecular marker for identification of these major anthropophilic dermatophyte species.

Phylogenetic classification and species identification of dermatophyte strains based on DNA sequences of nuclear ribosomal internal transcribed spacer 1 regions

The mutual phylogenetic relationships of dermatophytes of the genera Trichophyton, Microsporum, and Epidermophyton were demonstrated by using internal transcribed spacer 1 (ITS1) region ribosomal DNA sequences. Trichophyton spp. and Microsporum spp. form a cluster in the phylogenetic tree with Epidermophyton floccosum as an outgroup, and within this cluster, all Trichophyton spp. except Trichophyton terrestre form a nested cluster (100% bootstrap support). Members of dermatophytes in the cluster of Trichophyton spp. were classified into three groups with ITS1 homologies, with each of them being a monophyletic cluster (100% bootstrap support). The Arthroderma vanbreuseghemii-Arthroderma simii group consists of A. vanbreuseghemii, A. simii, Trichophyton mentagrophytes isolates from humans, T. mentagrophytes var. quinckeanum, Trichophyton tonsurans, and Trichophyton schoenleinii. Arthroderma benhamiae, T. mentagrophytes var. erinacei, and Trichophyton verrucosum are members of the Arthroderma benhamiae group. Trichophyton rubrum and Trichophyton violaceum form the T. rubrum group. This suggests that these "species" of dermatophytes have been overclassified. The ITS1 sequences of 11 clinical isolates were also determined to identify the species, and all strains were successfully identified by comparison of their base sequences with those in the ITS1 DNA sequence database.

Random amplification of polymorphic DNA is useful for the differentiation of several anthropophilic dermatophytes

The efficacy of random amplification of polymorphic DNA (RAPD) analysis, a polymerase chain reaction (PCR)-based technology, as a tool for differentiation of several anthropophilic dermatophytes, that is, Trichophyton mentagrophytes var. interdigitale, T. rubrum and Epidermophyton floccosum, was examined. Total cellular DNA extracted by a mini-preparation method were used as template DNAs and PCRs were performed using five primers, all of which were synthesized 10-mers. All of the primers generated PCR products and their electrophoresed profiles were characteristic for each of the species. Since these anthropophilic dermatophyte species could be differentiated clearly by the RAPD analysis, this method may be useful for identification of these species. Minimal intraspecies polymorphisms were observed between the isolates of T. mentagrophytes var. interdigitale. The banding patterns were reproducible using template DNAs prepared at different times from each of stock cultures.

Phylogeny of Epidermophyton floccosum and other dermatophytes

Eleven strains of Epidermophyton floccosum were compared with 5 Microsporum and 5 Trichophyton species with respect to the restriction fragment length polymorphism (RFLP) of the mitochondrial DNA to reveal their phylogenetic relationships. The phylogeny of 11 species showed that the three dermatophyte genera could not be separated from each other and could be considered to be congeneric. This result is not inconsistent with the results from ribosomal RNA sequences.