Application of PCR to the identification of dermatophyte fungi

Species-identification of dermatophytes Trichophyton, Microsporum and Epidermophyton by PCR and PCR-RFLP targeting of the DNA topoisomerase II genes

BACKGROUND

We have focused on the DNA topoisomerase II genes of pathogenic fungi and have previously applied polymerase chain reaction (PCR)-based identification of several species including the some of the major dermatophyte species.

OBJECTIVE

To identify the dermatophytes (18 species) to a species level by PCR and PCR-restriction fragment length polymorphism (RFLP) techniques, without determining the nucleotide sequence.

METHODS

The genomic DNAs of the dermatophytes (ten species of Trichophyton, seven species of Microsporum, and Epidermaphyton floccosum) were amplified by PCR using a common primer set (dPsD1) for the dermatophytes, followed by nested PCR using other primer sets (dPsD2, PsT and PsME) that contained primers specific for the DNA topoisomerase II genes of the dermatophytes. PCRs using PsT and PsME were used for the species-identification of Trichophyton, Microsporum and E. floccosum. The PCR products generated by dPsD2 were digested with restriction enzymes (Hinc II, Hinf, Afl II and PflM I), and the restriction profiles were analyzed.

RESULTS

Of the eighteen species of dermatophytes, five species (T. rubrum, T. violaceum, M. canis, M. gypseum and E. floccosum) were specifically identified by the PCR using PsT and PsME to the species level, and the remaining species were identified by the unique restriction profiles for each species in the PCR-RFLP analysis, except that the restriction profile of T. mentagrophytes var. interdigitale was identical to that of T. mentagrophytes var. quinckeanum.

CONCLUSION

PCR and PCR-RFLP techniques targeting the DNA topoisomerase II gene are simple and rapid, and quite useful as tools for the identification of dermatophytes to the species level.

The role of molecular biology and nucleic Acid technology in the study of human infection and epidemiology

OBJECTIVE

In this review, we will focus on recent molecular typing methods that can be applied to different pathogens and assess their values and limitations.

BACKGROUND

Resistant subgroups within a species of pathogenic organisms often emerge as dominant strains under the selective pressures of antibiotics, vaccinations, and new health care practices. The emergence of resistant organisms has added to the burden and cost of health care-related infections. Pathogens derived from a common ancestry are often difficult to distinguish by conventional methods, and the practice of clinical microbiology and infectious disease epidemiology must adapt to this problem.

DISCUSSION

Conventional strain typing methods provide a limited means of distinguishing epidemic from endemic or sporadic isolates of pathogens. Nucleic acid-based methods complement conventional and serologic methods of organism isolation and typing. Often, these genomic methods offer more discrimination and details than the phenotype-based conventional methods.

RESULTS AND CONCLUSIONS

Highly sensitive molecular techniques are capable of detecting single base pair substitutions and resolving the mechanism of underlying complex variation.

PCR-based identification of common dermatophyte species using primer sets specific for the DNA topoisomerase II genes

BACKGROUND

We have determined nucleotide sequences of the DNA topoisomerase II genes of the dermatophyte species, and conducted a PCR-based identification system using species-specific primers for the nucleotide sequences.

OBJECTIVE

To identify the major dermatophytes, Trichophyton rubrum, T. mentagrophytes, T. violaceum, M. gypseum, M. canis and E. floccosum, by PCR amplifications at the species level, without determining the nucleotide sequence.

METHODS

For PCR-based identification of the major dermatophyte species, a common primer set (dPsD1) for these species and species-specific primer sets (PsT and PsME) for each species were designed based on the genomic sequences of the DNA topoisomerase II genes of the dermatophytes, and tested for their specificities in PCR amplifications. The method consisted of amplification of the genomic DNA topoisomerase II gene by the common primer set, followed by a second PCR with the primer sets consisting of species-specific primers for each dermatophyte species.

RESULTS

Using dPsD1, a DNA fragment of 3390 bp was amplified from the genomic DNA of all the dermatophyte species. In the subsequent nested PCR using species-specific primer sets (PsT and PsME), both sets amplified unique sizes of PCR products, all of which corresponded to a species of the dermatophytes even in the presence of other fungal DNA.

CONCLUSION

We demonstrate that the PCR-based identification targeting the DNA topoisomerase II gene is rapid and simple, and is available as a tool for the identification of the major dermatophyte species.

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.

A specific PCR assay for the dermatophyte fungus Microsporum canis

A DNA fragment of approximately 1.2 kb, generated from the common dermatophyte Microsporum canis by arbitrarily primed polymerase chain reaction (PCR) using random primer OPU13, was cloned and sequenced. Based on the resulting sequencing data, a forward primer (MC1F) and a reverse primer (MC1R) have been designed and assessed by PCR for their usefulness in the improved identification of M. canis. The results obtained suggest that these primers are specific for M. canis, as a band of 900 bp was amplified in PCR with genomic DNA from M. canis only, and not from any of the other dermatophyte species or varieties, other fungi or common bacteria examined. Combining this PCR technique with a rapid mini-preparation method for fungal DNA, a definitive diagnosis of M. canis can be achieved within a day from the primary cultures. Future refinement of a DNA purification protocol from clinical specimens would further enhance the potential of the PCR based test for improved detection and identification of M. canis.