An overview of using fungal DNA for the diagnosis of invasive mycoses

Introduction Fungal PCR has undergone considerable standardization and, together with the availability of commercial assays, external quality assessment schemes, and extensive performance validation data, is ready for widespread use for the screening and diagnosis of invasive fungal disease (IFD). Areas Covered Drawing on the experience and knowledge of the leads of the various working parties of the Fungal PCR initiative, this review will address general considerations concerning the use of molecular tests for the diagnosis of IFD, before focusing specifically on the technical and clinical aspects of molecular testing for the main causes of IFD and recent technological developments. Expert Opinion For infections caused by Aspergillus, Candida, and Pneumocystis jirovecii, PCR testing is recommended, and combination with serological testing will likely enhance the diagnosis. For other IFD (e.g. mucormycosis), molecular diagnostics represent the only non-classical mycological approach toward diagnoses, and continued performance validation and standardization have improved confidence in such testing. The emergence of antifungal resistance can be diagnosed, in part, through molecular testing. Next-generation sequencing has the potential to significantly improve our understanding of fungal phylogeny, epidemiology, pathogenesis, mycobiome/microbiome, and interactions with the host, while identifying novel and existing mechanisms of antifungal resistance and novel diagnostic/therapeutic targets.

Automated summary

Fungal PCR has been standardized and is ready for widespread use in the screening and diagnosis of invasive fungal disease (IFD). PCR testing is recommended for infections caused by Aspergillus, Candida, and Pneumocystis jirovecii, and combination with serological testing can enhance the diagnosis. Molecular diagnostics represent a non-classical approach for other IFD and have improved confidence in testing through continued validation and standardization. Molecular testing can also diagnose antifungal resistance, and next-generation sequencing has the potential to improve our understanding of fungal phylogeny, epidemiology, and resistance mechanisms.