Identification of fungal pathogens in Formalin-fixed, Paraffin-embedded tissue samples by molecular methods

Fungal Biol. 2016 Feb;120(2):279-87. doi: 10.1016/j.funbio.2015.07.002. Epub 2015 Jul 17.


The etiology of invasive fungal infections (IFI) is incompletely understood due to diagnostic limitations including insensitivity of cultures and failure of histopathology to discriminate between different species. This diagnostic gap precludes the optimal use of antifungals, leading to adverse patient outcomes. The identification of fungal pathogens from Formalin-fixed, Paraffin-embedded tissue (FFPE) blocks by molecular methods is emerging as an alternative approach to study the etiology of IFI. PCR assays, including species specific- and broadrange fungal tests are used with FFPE samples from patients with proven IFI. Fungal species identification is achieved in 15-90% of the samples. This heterogeneity may be explained by the samples studied. However, comparison of different studies is impaired, as controls ruling out false positive-, false negative test results or PCR inhibition are frequently not reported. Studies using in situ hybridization also vary in the clinical samples included and the targeted fungi. In addition, target sequences, the probe chemistry and the detection of hybridization signals also account for the differences in diagnostic sensitivity. Using both approaches in parallel yields additive insights, potentially leading to a superior identification of fungal etiology and awareness of the limitations of both molecular diagnostic approaches.

Keywords: FFPE; FISH; Invasive fungal infection; PCR.

MeSH terms

  • DNA, Fungal / genetics
  • Formaldehyde / chemistry
  • Fungi / chemistry
  • Fungi / genetics
  • Fungi / isolation & purification*
  • Humans
  • Mycoses / diagnosis
  • Mycoses / microbiology*
  • Mycoses / pathology
  • Paraffin Embedding
  • Pathology, Molecular
  • Polymerase Chain Reaction


  • DNA, Fungal
  • Formaldehyde