Molecular identification of dermatophytes isolated in Sfax-Tunisia

A Comparative Study on the Phenotypic Versus Molecular Identification of Clinical Dermatophytes

Dermatophytosis is the superficial infection of keratinized tissue like skin, hair, and nails, in humans and animals, by a group of closely related fungi known as dermatophytes. Phenotypic identification of dermatophytes, especially through classical methods can be difficult and uncertain at times, especially when differentiating species with overlapping characteristics. Alternative identification methods based on amplification and sequence analysis of the highly polymorphic internal transcribed spacer (ITS) sequences flanking the 5.8S ribosomal RNA gene has proven to be quite sensitive and reliable. The objective of our study was to compare the phenotypic and the ITS sequencing-based methods for the identification of clinically isolated dermatophyte specimens from Puducherry, India. A total of 13 clinical samples from 39 suspected cases were found positive for dermatophytes using KOH/DMSO preparations. Specimens were subsequently cultured in Sabouraud dextrose agar (SDA) supplemented with chloramphenicol, gentamicin, and cycloheximide. Dermatophytes were identified based on culture characteristics and microscopic examination in lactophenol cotton blue preparations. ITS sequencing was additionally performed after PCR amplification for species identification. Identification based on phenotype through microscopy and culture methods confirmed infections with Trichophyton mentagrophytes (n = 11), T. rubrum (n = 1), and Microsporum gypseum (n = 1). The strains were confirmed by ITS sequencing without any discrepancy with phenotypic identification. Identification of common dermatophytes based on phenotypic characteristics may be used as a reliable method of diagnosis where sophisticated methods like ITS sequencing and PCR are unavailable.

A Comparative Study on Phenotypic versus ITS-Based Molecular Identification of Dermatophytes Isolated in Dakar, Senegal

Classically, dermatophytes are identified by phenotypic methods even if these methods, sometimes, remain difficult or uncertain. On the other hand, nucleotide sequence analysis of internal transcribed spacers (ITS) of rDNA has proved to be a useful method for identification of dermatophytes. The objective of this study was to compare the phenotypic method with DNA sequencing of the ITS regions for identification of dermatophyte species isolated in Dakar, Senegal. A collection of thirty-two strains of dermatophytes were isolated from patients suffering from dermatophytosis. Mycological identification revealed Trichophyton soudanense (n = 13), T. interdigitale (n = 10), Microsporum audouinii (n = 5), and one strain for each of the following species: T. rubrum, T. mentagrophytes, and M. canis and one unidentified strain. For comparison, ITS-based PCR and DNA sequencing were applied for identification of the isolated dermatophytes. ITS sequences showed, in BLAST search analysis, 99-100% of similarity. Identification of dermatophyte isolates by conventional methods was confirmed by DNA sequencing of the ITS regions in 84% of cases. Discrepancies concern mostly T. rubrum misidentified as T. interdigitale. PCR sequencing provided an excellent tool for identifying dermatophyte strains that do not present typical morphological characteristics. It was also able to give correct identification of an atypical strain of M. audouinii responsible of mycetoma of the scalp.

Multiplex PCR assay for the detection of common dermatophyte nail infections

Onychomycosis is one of the most prevalent dermatophytic diseases. Mycological methods used in the conventional diagnosis may not be optimal. Multiplex (MX) PCR was reported as a reliable alternative. Dermatophyte gene sequence records were used to design a MX PCR for detection and identification of dermatophytes in nail specimens. A MX PCR method based on the amplification of the chitin synthase 1 and internal transcribed spacer genes was developed. The study included 93 strains of dermatophytes and non-dermatophytic fungi, six dermatophytic reference strains and 201 nail specimens from patients with dermatophytic onyxis. DNA extraction directly from nail samples was carried out by using the QIAamp DNA extraction kit (Quiagen). A set of primers was designed and their specificity was assessed. MX PCR detected the causal agent in specimens from which Trichophyton rubrum and T. interdigitale grew in culture and also identified a dermatophyte species in an additional 32 specimens that were negative in microscopy and culture. None of the investigated non-dermatophytic strains was positive. Sensitivity of MX PCR was higher as compared to mycological examination (97% vs. 81.1%). MX PCR for direct detection of dermatophytes from nail samples yielded mixed flora in 32.8% of samples. MX PCR proved sensitive and adequate for the diagnosis of dermatophytic onychomycosis. It is much adapted to cases where culture is negative or contaminated by overgrowing moulds, which makes the identification of the causal agent problematic.