ArticleBMC infectious diseases2011
Comparison of quantitative real time PCR with Sequencing and ribosomal RNA-FISH for the identification of fungi in formalin fixed, paraffin-embedded tissue specimens.
Article in BMC infectious diseases, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it, 101 citations in OpenAlex.
- Diagnostic performance of panfungal PCR on tissue specimens for the diagnosis of invasive fungal diseases: a systematic review and meta-analysis of the Fungal PCR Initiative (FPCRI).Journal of clinical microbiology · 2026Pooled it
- Setting higher standards for reports of microbial species in human cancers.Nature cancer · 2026Review
- Molecular diagnostics in cancer patients with suspected respiratory mold infections.Journal of clinical microbiology · 2025Article
- Aspergillus fumigatus promotes tumor angiogenesis via SLC7A11 on myeloid-derived suppressor cells.EMBO reports · 2025Article
- Challenges and predictive value of morphologic features in panfungal sequencing of formalin-fixed, paraffin-embedded tissues: A 5-year retrospective study.American journal of clinical pathology · 2025Article
- Animal Histoplasmosis in Europe: Review of the Literature and Molecular Typing of the Etiological Agents.Journal of fungi (Basel, Switzerland) · 2022Article
- Comparison Approach for Identifying Missed Invasive Fungal Infections in Formalin-Fixed, Paraffin-Embedded Autopsy Specimens.Journal of fungi (Basel, Switzerland) · 2022Article
- Exclusion of Mucorales Co-Infection in a Patient withJournal of fungi (Basel, Switzerland) · 2022Article
- Identification of Mucormycosis by Fluorescence In Situ Hybridization Targeting Ribosomal RNA in Tissue Samples.Journal of fungi (Basel, Switzerland) · 2022Article
- Splenic rupture and fungal endocarditis in a pediatric patient with invasive fusariosis after allogeneic hematopoietic stem cell transplantation for aplastic anemia: A case report.Frontiers in pediatrics · 2022Article
- Comprehensive Assessment of the Virulence FactorsJournal of fungi (Basel, Switzerland) · 2021Article
- Rapid Diagnosis of Central Nervous System Scedosporiosis by Specific Quantitative Polymerase Chain Reaction Applied to Formalin-Fixed, Paraffin-Embedded Tissue.Journal of fungi (Basel, Switzerland) · 2021Article
- Identification ofJournal of fungi (Basel, Switzerland) · 2021Article
- Molecular Techniques for Genus and Species Determination of Fungi From Fresh and Paraffin-Embedded Formalin-Fixed Tissue in the Revised EORTC/MSGERC Definitions of Invasive Fungal Infection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- The Evolving Landscape of Fungal Diagnostics, Current and Emerging Microbiological Approaches.Journal of fungi (Basel, Switzerland) · 2021Review
- Bovine Abortions Revisited-Enhancing Abortion Diagnostics by 16S rDNA Amplicon Sequencing and FluorescenceFrontiers in veterinary science · 2021Article
- Emergomycosis, an Emerging Systemic Mycosis in Immunocompromised Patients: Current Trends and Future Prospects.Frontiers in medicine · 2021Review
- Biosensors and Diagnostics for Fungal Detection.Journal of fungi (Basel, Switzerland) · 2020Review
- Detection of Histoplasma DNA from Tissue Blocks by a Specific and a Broad-Range Real-Time PCR: Tools to Elucidate the Epidemiology of Histoplasmosis.Journal of fungi (Basel, Switzerland) · 2020Article
- A Collaborative Tale of Diagnosing and Treating Chronic Pulmonary Aspergillosis, from the Perspectives of Clinical Microbiologists, Surgical Pathologists, and Infectious Disease Clinicians.Journal of fungi (Basel, Switzerland) · 2020Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentification of the causative agents of invasive fungal infections (IFI) is critical for guiding antifungal therapy. Cultures remain negative in a substantial number of IFI cases. Accordingly, species identification from formalin fixed, paraffin embedded (FFPE) tissue specimens by molecular methods such as fluorescence in situ hybridisation (FISH) and PCR provides an appealing approach to improve management of patients.
methodsWe designed FISH probes targeting the 28S rRNA of Aspergillus and Candida and evaluated them with type strains. Fluorescence microscopy (FM), using FISH probes and quantitative broad-range fungal PCR targeting the rRNA gene were applied to FFPE tissue specimens from patients with proven IFI in order to explore benefits and limitations of each approach.
resultsPCR followed by sequencing identified a broad spectrum of pathogenic fungi in 28 of 40 evaluable samples (70%). Hybridisation of FISH probes to fungal rRNA was documented in 19 of 40 tissue samples (47.5%), including 3 PCR negative samples with low fungal burden. The use of FISH was highly sensitive in invasive yeast infections, but less sensitive for moulds. In samples with hyphal elements, the evaluation of hybridisation was impaired due to autofluorescence of hyphae and necrotic tissue background.
conclusionsWhile PCR appears to be more sensitive in identifying the causative agents of IFI, some PCR negative and FISH positive samples suggest that FISH has some potential in the rapid identification of fungi from FFPE tissue samples.
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