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

ABSTRACT

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.

KEYWORDS:

• Invasive fungal disease
• fungal PCR
• candida PCR
• aspergillus PCR
• PCP PCR
• mucorales PCR

Article highlights

• Standardization of methods and the availability of commercial PCR tests for a range of fungal pathogens allows fungal PCR tests to be performed in generic molecular diagnostic facilities, outside of specialist mycology reference centers.

• Molecular tests to aid in the diagnosis of invasive fungal disease are performed under quality control regulations comparable to other biomarker assays, permitting inclusion in the routine diagnostic repertoire of mycological tests and international definitions.

• Molecular tests provide a non-culture alternative for the identification of fungal strains/species resistant to antifungal therapy.

• Combining serological and molecular testing provides an optimal strategy for the diagnosis of a range of fungal pathogens.

• Next-generation sequencing has the potential to enhance our knowledge of substantial areas of medical mycology, but significant methodological hurdles must be overcome before the benefits are widely available.

Declaration of Interest

PL White has performed diagnostic evaluations and received meeting sponsorship from Associates of Cape Cod, Bruker, Dynamiker, and Launch Diagnostics; speaker fees, expert advice fees, and meeting sponsorship from Gilead; and speaker and expert advice fees from F2G. A Alanio has received personal fees from Pfizer and Gilead and travel grant from Astellas. M Lackner has received grants from F2G Ltd. L Millon has received speaker fees from Gilead and Pfizer and travel grants from Gilead, Pfizer Basilea, and MSD. RR Richardson has received speaker honoraria from Astellas Pharma, Gilead Sciences, and Pfizer and research funding from Associates of Cape Cod. JP Donnelly has received personal fees from F2G Ltd, Gilead Sciences, and Pfizer. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Reviewer disclosures

Peer reviewers of this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This paper was not funded.