Identification of Fungal Pathogens in Tissue Samples from Patients with Proven Invasive Infection by Fluorescence In Situ Hybridization

  • Ilka McCormick Smith
  • Volker RickertsEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1508)


Identification of fungal pathogens in clinical samples by hybridization with short oligonucleotide probes is increasingly used in the diagnosis of invasive fungal infections. Rapid and specific fungal identification has been documented in different diagnostic settings allowing for specific patient management. Identification of fungal pathogens in formalin-fixed, paraffin-embedded tissue samples appears to be rewarding as these materials are stored in pathology archives offering an insight into the etiology of deep fungal infections that is often not achieved by non-molecular tests. In contrast to PCR based methods, amplification of target sequences is unnecessary limiting the potential for contamination and localization within infected tissue is possible helping to distinguish between colonization and infection.

Key words

FISH Invasive fungal infection Formalin-fixed Paraffin-embedded tissue Candidiasis Aspergillosis 


  1. 1.
    Amann R, Fuchs BM (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6(5):339–348Google Scholar
  2. 2.
    Kempf VAJ, Trebesius K, Autenrieth IB (2000) Fluorescent in situ hybridization allows rapid identification of microorganisms in blood cultures. J Clin Microbiol 38(2):830–838PubMedPubMedCentralGoogle Scholar
  3. 3.
    Da Silva RM Jr et al (2015) Fluorescent in situ hybridization of pre-incubated blood culture material for the rapid diagnosis of histoplasmosis. Med Mycol 53(2):160–164CrossRefPubMedGoogle Scholar
  4. 4.
    Da Silva RM Jr et al (2015) Evaluation of fluorescence in situ hybridisation (FISH) for the detection of fungi directly from blood cultures and cerebrospinal fluid from patients with suspected invasive mycoses. Ann Clin Microbiol Antimicrob 14:6CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Wilson DA et al (2005) Multicenter evaluation of a Candida albicans peptide nucleic acid fluorescent in situ hybridization probe for characterization of yeast isolates from blood cultures. J Clin Microbiol 43(6):2909–2912Google Scholar
  6. 6.
    Martins ML et al (2010) Direct and specific identification of Cryptococcus neoformans in biological samples using fluorescently labelled DNA probes. Eur J Clin Microbiol Infect Dis 29(5):571–576Google Scholar
  7. 7.
    Montone KT, Guarner J (2013) In situ hybridization for rRNA sequences in anatomic pathology specimens, applications for fungal pathogen detection: a review. Adv Anat Pathol 20(3):168–174Google Scholar
  8. 8.
    Rickerts V (2015) Identification of fungal pathogens in formalin-fixed, paraffin-embedded tissue samples by molecular methods. Fungal Biology 2016; 120(2):279–287Google Scholar
  9. 9.
    Rickerts V et al (2011) Comparison of quantitative real time PCR with sequencing and ribosomal RNA-FISH for the identification of fungi in formalin fixed, paraffin-embedded tissue specimens. BMC Infect Dis 11:202CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Fredricks DN et al (2000) Rhinosporidium seeberi: a human pathogen from a novel group of aquatic protistan parasites. Emerg Infect Dis 6(3):273–282CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Rickerts V et al (2013) Deciphering the aetiology of a mixed fungal infection by broad-range PCR with sequencing and fluorescence in situ hybridisation. Mycoses 2013;56(6):681–686Google Scholar
  12. 12.
    Behrens S et al (2003) In situ accessibility of small-subunit rRNA of members of the domains bacteria, archaea, and eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microbiol 69(3):1748–1758Google Scholar
  13. 13.
    Inacio J et al (2003) In situ accessibility of Saccharomyces cerevisiae 26S rRNA to Cy3-labeled oligonucleotide probes comprising the D1 and D2 domains. Appl Environ Microbiol 69(5):2899–2905Google Scholar
  14. 14.
    Fredricks DN, Relman DA (2001) Localization of Tropheryma whippelii rRNA in tissues from patients with Whipple's disease. J Infect Dis 183(8):1229–1237Google Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.FG 16: Erreger von Pilz-, und Parasiteninfektionen und MykobakteriosenRobert Koch-InstitutBerlinGermany

Personalised recommendations