Maximizing Yield and Speed of Fungal Pathogen Identification with Molecular Testing Performed Directly on Patient Specimens

Purpose of Review Molecular assays for fungal pathogen detection directly in patient specimens represent valuable diagnostic tools, with the potential to increase sensitivity and reduce turnaround time. This review highlights existing and emerging molecular methods for the diagnosis of fungal infections, their clinical performance, limitations, and knowledge gaps. Recent Findings Broad-range PCR and metagenomic sequencing detect diverse pathogens but have not replaced traditional methods. Limitations are cost, availability, and limited real-world performance data. Multi-target panels and organism-specific assays can provide increased sensitivity and, frequently, speed. Some single- or multi-target assays are commercially available to many clinical laboratories. Summary Molecular diagnostic methods for fungal pathogens are diverse; complement culture, stains, and biomarkers; and increasingly fulfill case definitions. To maximize yield, assay selection should be guided by suspected organisms and patient-specific risk factors. Collaboration between patient-facing providers and laboratorians/pathologists promotes optimal testing strategies and the deployment of more rapid and specific assays.