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Molecular detection of fungi in clinical specimens

Principal investigator: Volker Rickerts

Diverse fungi are widely spread in the environment. While permanently exposed to fungi, most humans are protected against invasive fungal infections by their defense systems. However, a growing number of immunocompromised hosts are susceptible for deep fungal infections.

The identification of the causative agents of invasive fungal infections is increasingly relevant for treatment decisions. Antifungal therapy is more likely to be effective when guided by the knowledge of the underlying pathogen. However, determining the etiology of invasive fungal infections by the cultivation of causative fungi is frequently not successful in clinical practice.

We use molecular biological methods, including PCR with sequencing and Fluorescence in situ hybridization (FISH) to identify the etiologic agents of invasive mycoses from tissue biopsies of patients with proven invasive fungal infections and respiratory secretions. This approach allows for a sensitive identification of fungal DNA by PCR and the localization to the infectious process by FISH, a prerequisite to inferring a causal relationship between the fungus and the disease.

Fluorescence-in-situ-hybridization (FISH) of fungal pathogens in a spiked bronchoalveolar lavage sample (BAL). Source: Jasmin Gerkrath (2016)/RKIFluorescence-in-situ-hybridization (FISH) of fungal pathogens in a spiked bronchoalveolar lavage sample (BAL). From left to right: Visualization of double stranded DNA in fungi and host cells with DAPI (blue), hybridization with unspecific eukaryotic probe (green), - with specific probe Mucorales (Magenta), - with specific probe for Aspergillus (orange), overlay of all channels documents the presence of diverse fungi Source: Jasmin Gerkrath (2016)/RKI

The combination of molecular techniques to identify the causative agents of deep fungal infections may lead to an improved knowledge of the etiology of invasive mycoses. In this way antimycotic therapies may be used in the best possible manner and hence the prognosis of these infections may be improved.

Co-worker:

  • Ilka McCormick Smith
  • Jasmin Gerkrath
  • Dunja Wilmes

Sub-projects:

  • rRNA-FISH for the identification of fungi in bronchoalveolar lavage
  • Identification of fungi in formalin-fixed tissue sections by broad-range PCR and sequencing
  • Molecular detection of pathogens in sputum of patients with cystic fibrosis

Further information

Date: 15.03.2024

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Publications

  • Dalimot JJ, Mc Cormick Smith I, Gerkrath J, Hartmann S, Cornely OA, Lee SC, Heitman J, Rickerts V (2022): Identification of Mucormycosis by Fluorescence In Situ Hybridization Targeting Ribosomal RNA in Tissue Samples.
    J of Fungi 8: 289. doi: 10.3390/jof8030289. more

  • Kessel J, Hogardt M, Aspacher L, Wichelhaus TA, Gerkrath J, Rosenow E, Springer J, Rickerts V (2022): Exclusion of Mucorales Co-Infection in a Patient with Aspergillus flavus Sinusitis by Fluorescence In Situ Hybridization (FISH).
    J. Fungi 8: 306. doi: 10.3390/jof8030306. more

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  • Lauerer RJ, Rosenow E, Beschorner R, Hempel J-M, Naros G, Hofmann A, Berger K, Sartor-Pfeiffer J, Mengel A, Ziemann U, Rickerts V, Feil K (2022): Rapid diagnosis of central nervous system scedosporiosis by specific quantitative polymerase chain reaction applied to formalin-fixed, paraffin-embedded tissue.
    J. Fungi 8 (1): 19. Epub 2021 Dec 27. doi: 10.3390/jof8010019. more

  • Wilmes D, McCormick-Smith I, Lempp C, Mayer U, Schulze AB, Theegarten D, Hartmann S, Rickerts V (2020): Detection of histoplasma DNA from tissue blocks by a specific and a broad-range real-time PCR: tools to elucidate the epidemiology of histoplasmosis.
    J. Fungi 6 (4): 319. Epub Nov 27. doi: 10.3390/jof6040319. more

  • Rooms I, Mugisha P, Gambichler T, Hadaschik E, Esser S, Rath PM, Haase G, Wilmes D, McCormick-Smith I, Rickerts V (2019): Disseminated emergomycosis in a person with HIV infection, Uganda.
    Emerg. Infect. Dis. 25 (9): 1750–1751. doi: 10.3201/eid2509.181234. more

  • Springer J, McCormick Smith I, Hartmann S, Winkelmann R, Wilmes D, Cornely O, Kessel J, Löffler J, Rickerts V (2018): Identification of Aspergillus and Mucorales in formalin-fixed, paraffin-embedded tissue samples: Comparison of specific and broad-range fungal qPCR assays
    Med. Mycol.: Epub Jun 19. doi: 10.1093/mmy/myy041. more

  • Brandt C, Roehmel J, Rickerts V et al. (2017): Aspergillus bronchitis in patients with cystic fibrosis
    Mycopathologia: Epub Aug 17. doi: 10.1007/s11046-017-0190-0. more

  • McCormick Smith I, Rickerts V (2016): Identification of fungal pathogens in tissue samples from patients with proven invasive infection by fluorescence in situ hybridization
    In: Lion T (eds), Human Fungal Pathogen Identification – Methods and Protocols. Methods in Molecular Biology vol. 1508. New York: Humana Press/Springer Nature, pp. 281–288. Epub Nov 12. doi: 10.1007/978-1-4939-6515-1_16. more

  • Rickerts V (2016): Identification of fungal pathogens in Formalin-fixed, Paraffin-embedded tissue samples by molecular methods
    Fungal Biol. 120 (2): 279–287. Epub 2015 Jul 17. doi: 10.1016/j.funbio.2015.07.002. more