Fungal Molecular Diagnostics
Sequence Analysis
February 2011
The DNA sequence from the patient-derived isolate is then compared to fungal sequence libraries containing well-characterized sequences. Libraries searched include the MicroSeq library from Applied Biosystems and a laboratory-specific custom library that we have developed over the last decade. Finally, if neither of these databases provides a good matching sequence, the NCBI GenBank database can be searched using the BLAST tool. Caution should be used when matches are achieved against the GenBank database since it is not curated and therefore may contain inaccurate sequences or organism identifications. Before using a GenBank sequence, we make certain the sequence is an exact match to the unknown isolate, that it is of a good length and quality score, that it was deposited by a reputable, experienced group or individual, that it has been published in a peer-reviewed journal, and that the phenotypic description in the journal matches the unknown isolate before considering reporting it as a match. The DNA sequence can be obtained in as little as 8 hours after an organism has grown in culture providing a very rapid turnaround time as compared with many phenotypic identification methods.
Sequence Analysis |
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
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