Panfungal PCR on formalin-fixed, paraffin-embedded tissue: to proceed or not proceed?

Area of Science:

• Medical Mycology
• Molecular Diagnostics
• Pathology

Background:

• Invasive fungal disease (IFD) diagnosis using panfungal PCR on formalin-fixed, paraffin-embedded (FFPE) tissue presents challenges in interpreting results.
• Differentiating true pathogens from colonizers/contaminants is crucial for accurate IFD diagnosis.

Purpose of the Study:

• To evaluate the clinical utility and cost-effectiveness of panfungal PCR-DNA sequencing assays on FFPE tissues.
• To compare PCR performance based on the presence or absence of fungal elements visualized via histopathology.

Main Methods:

• A retrospective audit of FFPE tissue specimens undergoing panfungal PCR from January 2021 to August 2022.
• Comparison of panfungal PCR results with histopathology findings (presence or absence of fungal elements).
• Calculation of the cost per clinically significant positive result in both groups.

Main Results:

• Fungal forms were observed in 18.1% of FFPE samples via histopathology.
• Panfungal PCR yielded clinically significant results in 35.6% of histopathology-positive samples versus 3.0% of histopathology-negative samples.
• The cost per clinically significant result was substantially lower (AUD 258.13) when fungal elements were seen on histopathology compared to when they were not (AUD 3,105.22).

Conclusions:

• Panfungal PCR demonstrates limited clinical utility in FFPE tissues when no fungal elements are visible on histopathology.
• Utilizing panfungal PCR primarily on histopathology-positive samples enhances result interpretation and optimizes laboratory resource allocation.
• Targeted use of panfungal PCR on FFPE tissues improves diagnostic yield and cost-effectiveness for invasive fungal disease detection.