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Validation of Dermatophyte PCR

28 May 2020

Faster turnaround times and improved sensitivity and predictive values of dermatophyte detection using a new nucleic acid testing (NAT) method.  This is what Dr Sarah Kidd and her team from SA Pathology’s National Mycology Reference Centre found in their recently published study.

Dermatophytes, the group of fungi that commonly cause skin, hair and nail infections, have traditionally been diagnosed by microscopy and fungal culture, a process that lacks sensitivity and takes as long as four weeks to provide a result. The nucleic acid testing technology allows the laboratory to amplify targeted sequences of fungal DNA in the patient sample, to allow for specific identification of the fungus.

The TGA-approved assay, which is manufactured by Australian company AusDiagnostics, uses Multiplex Tandem PCR (MT-PCR) technology with melt-curve analysis to accurately detect Trichophyton rubrum complex, Trichophyton mentagrophytes complex, Epidermophyton floccosum, Microsporum canis, Nannizzia gypsea (previously Microsporum gypseum) as well as other Trichophyton and Microsporum species, and Candida species.

Dr Kidd’s study, which was recently published in the RCPA Pathology journal, validated this assay against traditional microscopy and culture methods, using samples from more than 260 patients. When the MT-PCR was used alone sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were high (88.4%, 89.1%, 90% and 87.4%, respectively) compared to microscopy and culture.  However, when PCR was used in combination with microscopy, these values improved further to 99.1% sensitivity, 89.1% specificity, 91% PPV, and 98.9% NPV, highlighting the ongoing relevance of microscopy in laboratory practice. 

MT-PCR melt-curve analysis reveals detection of the Trichophyton rubrum complex in a patient sample.

The MT-PCR results are typically available within 2-5 days of receiving the sample, significantly faster than the 4 weeks allowed for culture. Faster result and improved sensitivity enables earlier intervention by clinicians with antifungal drugs, or exclusion of infection with fewer repeat tests.

SA Pathology has now replaced dermatophyte culture methods with the MT-PCR, but retained fungal microscopy due to its proven utility, not only for dermatophyte detection, but also for yeast (e.g. pityriasis versicolor) and parasite detection. The move to NAT for fungal pathogen detection and identification is the first in the state and is representative of the dedication that Dr Kidd and her team display to ensure the health and wellbeing of all South Australians.