Evaluation of an in-house pan-Malassezia quantitative PCR in human clinical samples.

ABSTRACT

Althought Malassezia spp. have been involved in various pathologies, they are an integral part of the cutaneous, gut, oral, ears, nose and throat (ENT) mycobiota. Since Malassezia are difficult to grow in culture, unexhaustive molecular biology methods have been developed to detect them. The aim of the study was to evaluate an in-house pan-Malassezia quantitative polymerase chain reaction (panM-qPCR) on various clinical human samples and determine Malassezia burden in various human mycobiota. The panM-qPCR was designed to target the repeated 28S rDNA gene from all Malassezia species. We used the assay to quantify the Malassezia burden on 361 samples from 161 subjects (80 skin swabs from 10 healthy volunteers (HV), 13 samples from 2 seborrheic dermatitis patients (SD), 90 skin samples from 19 burned patients, 119 stool samples from 89 immunocompromised patients, 59 ENT samples from 41 patients). For HV, the amount of Malassezia was different according to the swabbed areas. Quantification cycle (Cq) in SD is lower than in HV. In burned patients, Cq was significantly lower compared to HV. In stool samples, 6.7% were positive for Malassezia spp. with a high Cq. For the ENT area, a higher proportion of positive specimens were detected in ear samples than in nose samples. Our findings emphasized the importance of qPCR, confirming elevated Malassezia spp. levels on individuals' faces and scalps, increased burden in SD patients and in severely burnt patients than in HV. The pan-MqPCR appears to be a promising tool for studying Malassezia in various human mycobiota.

Malassezia species are ubiquitous members of various human microbiomes, including cutaneous and mucosal sites. While these fungi have been implicated in several pathologies, their presence as commensals complicates their study, especially due to difficulties in culturing them in vitro. This has necessitated the development of molecular techniques to detect and quantify Malassezia species directly from clinical samples. In this study, we report on the development and application of an in-house pan-Malassezia quantitative PCR (panM-qPCR) assay. This assay targets the conserved 28S rDNA gene across all known Malassezia species, allowing for a broad-spectrum detection approach. We applied this panM-qPCR to a diverse set of clinical samples, totaling 361 specimens from 161 subjects, encompassing healthy individuals, patients with seborrheic dermatitis, burn victims, and immunocompromised individuals. Our results indicate variable Malassezia loads on different skin sites of healthy volunteers, with significantly lower quantification cycle (Cq) values observed in seborrheic dermatitis patients, suggesting an increased fungal burden. Burn patients also showed a marked increase in Malassezia spp. levels compared to healthy individuals. Stool samples demonstrated a low prevalence (6.7%) of Malassezia spp., but with high Cq values when present. Notably, ear samples revealed a higher positivity rate compared to nasal samples. The findings highlight the practicality and sensitivity of qPCR for elucidating the Malassezia burden across various human samples. This molecular approach confirms the differential colonization of Malassezia spp. in different clinical contexts. The panM-qPCR offers a promising approach for comprehensive mycobiota research, particularly in conditions where culture-based methods fall short.