Fungal Molecular Diagnostics

Currently Available Molecular Diagnostics for Fungi

February 2011

Currently there are a limited number of molecular diagnostic tests available for the detection and identification of fungi in the clinical laboratory. For fungal isolates growing in pure culture, nucleic acid hybridization probes, DNA sequencing, peptide nucleic acid fluorescence in situ hybridization (or PNA FISH) probes, and laboratory-developed polymerase chain reaction (or PCR) tests are available. Molecular methods used in the direct detection and identification of fungi from patient specimens are even further limited to a handful of laboratory-developed PCR tests targeting specific fungal agents. There are several diagnostics companies who have developed or who are developing PCR, array-based, and other molecular tests for fungi but, in large part, these have not yet entered into routine clinical laboratory use at this time.

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Currently Available Fungi Diagnostics

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Jump to section:

• Introduction
• Objectives
• Traditional Methods of Fungal Diagnostics
• Traditional Methods
• Potential Advantages of Fungal Molecular Diagnostics
• Currently Available Molecular Diagnostics for Fungi
• Nucleic Acid Hybridization Probes³
• Nucleic Acid Hybridization Probes
• Nucleic Acid Hybridization Probes for Fungi
• Nucleic Acid Hybridization Probes
• DNA Sequencing for Fungi
• Ribosomal Structure: Fungi
• Traditional Sequencing Workflow
• Sequence Analysis
• Current Applications of D2 Fungal Sequencing at the Mayo Clinic
• Rapid, Direct Identification of Yeast from Blood Cultures
• PNA-FISH Basics
• PNA FISH for Candida spp—Direct Detection from Blood
• Yeast Identification Timeline from Positive Blood Bottle
• Potential Advantages of Direct Detection
• Fungal PCR Assays at Mayo Clinic
• Real-time PCR Workflow
• Pneumocystis PCR
• Pneumocystis LC-PCR Melt Curves
• Concordance of the Pneumocystis LightCycler PCR Assay and Calcofluor White Stain for BAL Fluid
• Coccidioides species Real-time PCR
• Melt-curve Analysis of Coccidioides spp Grown in Culture
• Utility of Coccidioides PCR Testing in the Clinical Setting⁴
• Meningeal Coccidioidomycosis Diagnosed by Real-Time PCR Analysis of Cerebrospinal Fluid⁵
• Histoplasma capsulatum/Blastomyces dermatitidis Real-Time PCR
• What lies in the future for fungal molecular diagnostics?
• Mass Spectrometric Identification Of Fungi
• Summary
• References
• Questions?
• Disclosure