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

Pathology. 2023 Aug;55(5):669-672. doi: 10.1016/j.pathol.2023.03.011. Epub 2023 May 23.


Performance of panfungal PCR-DNA sequencing assays for diagnosis of invasive fungal disease on formalin-fixed, paraffin-embedded tissue (FFPE) is influenced by many variables. Interpretation of a positive result can be challenging due to the need to differentiate colonisers and contaminants from clinically significant pathogens. We conducted a retrospective audit on FFPE tissue specimens that underwent panfungal PCR from January 2021 to August 2022. Panfungal PCR results from samples where fungal elements were visualised on histopathology were compared with results from samples where no fungal elements were visualised. The cost per clinically significant positive sample in each group was calculated. Of the 248 FFPE tissues sampled, 18.1% (45/248) had fungal forms seen on histopathology. Panfungal PCR was positive in 22/45 samples (48.9%), with 16 (35.6%) results deemed clinically significant. For the remaining 203 specimens, panfungal PCR was positive in 19 (9.4%) samples with only six (3.0%) clinically significant. The average cost per clinically significant result was AUD 258.13 in the histopathology positive group and AUD 3,105.22 in the histopathology negative group. Our data suggest panfungal PCR has limited clinical utility in FFPE tissue when no fungal elements are seen. Restricting the assay to only those samples that are positive on histopathological examination aids interpretation of PCR positive results and conserves laboratory resources.

Keywords: Panfungal PCR; diagnostic stewardship; formalin-fixed; fungi; paraffin-embedded.

MeSH terms

  • Formaldehyde
  • Humans
  • Invasive Fungal Infections* / diagnosis
  • Paraffin Embedding
  • Polymerase Chain Reaction / methods
  • Retrospective Studies
  • Tissue Fixation


  • Formaldehyde