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Detecting Candida auris in skin and nasal swabs by PCR

June 18 2020

Candida auris is a multi-drug-resistant potentially invasive species of Candida linked to extensive hospital outbreaks (Kenters et al, 2019). It is a halophilic species (salt tolerant) and so most often identified in the axilla or groin of patients, rather than in the stool as for Candida albicans or tropicalis. Recent advice has been to screen patients by culture and a new commercial agar has been produced to facilitate culture and immediate identification - CHROMagarTM Candida Plus (Borman et al, 2020). An alternative approach is via PCR detection.

Michael Malczynski and colleagues from Northwestern Memorial Hospital in Chicago developed a specific PCR for C. auris and assessed different DNA extraction system. Patient swabs using ESwabs (Copan) were collected and the swab liquid transport medium Amies was found to completely inhibit the PCR. Re-suspension of the pellet after centrifugation in PBS-BSA buffer allowed full PCR amplification. PCR and culture were positive in 38 of 1414 samples from 15 patients, with 100% concordance. The sensitivity of the PCR  was greatly reduced by the extraction system used – both the QIAamp kit and QIAsymphony tissue kit were markedly inferior to a labour intensive manual extraction method. Cultures initially grew other species in 6 samples until the PCR showed C. auris and mixed cultures with a minority C. auris population was found on repeat culture.

Eradicating a hospital outbreak of C. auris requires extensive screening, although if endemic as in some institutions in South Africa and India, this is problematic. These data clearly indicate how important both culture methodology is and also the details of the sample collection system and DNA extraction methodology to any PCR method. While one commercial C. auris assay is available, its utility in screening skin and nasal samples has yet to be validated.