Fungal DNA Detection by PCR
General Information
Lab Name
Fungal DNA Detection by PCR
Lab Code
FUNDNA
Epic Name
Fungal DNA detection by PCR
Description
In many specimens, fungal elements can be seen by microscopy of tissue sections but are very difficult to grow due to their fastidious nature, or are not viable as a result of antifungal therapy.
Some specimens may never reveal the presence of a fungal pathogen because of low abundance and/or lack of viability. Often, fungal elements are seen on paraffin embedded tissue when a fresh tissue specimen is no longer available.
The use of PCR technology to detect fungal DNA within the total DNA extracted directly from clinical specimens facilitates the identification of these pathogens. Using both fungal 28S and Internal Transcribed Spacer sequence (ITS) DNA as targets we have set up PCR assays to detect fungal pathogens. Sequences of amplified DNA are analyzed to identify the fungal pathogen present in the specimen.
REFLEXIVE TESTING: When suspected pathogen microorganisms are detected, identification procedures are performed, as appropriate for the organism and specimen.
COCDNA (Coccidioidies PCR)
CRYDNA (Cryptococcus PCR)
MUCDNA (Mucorales PCR)
HISDNA (Histoplasma PCR)
PNEDNA (Pneumocystis PCR)
Incidental Finding Reflexes:
AMBPCR (Acanthamoeba and Balamuthia PCR)
LSHDNA (Leishmania PCR)
TOXDNA (Toxoplasma PCR)
Multiple Template Reflexes, if requested by ordering physician:
NGSITS (Fungal detection by ITS NGS)
For more information on this test, to download a requisition form, and for a list of acceptable and unacceptable specimens, please refer to: Molecular Diagnosis Microbiology Section Website
Synonyms
28s PCR, 28S sequencing, broad range fungal PCR, broad range fungi PCR, fungal 28S, fungal identification, fungal ITS, Fungal PCR, fungal sequencing, fungi identification, Fungi PCR, fungi sequencing, ITS PCR, ITS sequencing, molecular fungal, molecular fungi, universal fungal PCR, universal fungi PCR
Components
| Code | Name |
|---|---|
| FU28RS | Fungal PCR: Detection, 28S rDNA |
| FU28ID | Fungal PCR: 28S Identification |
| FUITRS | Fungal PCR: Detection, ITS rDNA |
| FUITID | Fungal PCR: ITS Identification |
| FUSI | Fungal PCR: Specimen Description |
| FUSPI | Fungal PCR: External Identifier |
| FUSR | Fungal PCR: Special Requests |
| FUSC | Fungal PCR: Specimen Comments |
| FUNAE | Fungal PCR: Specimen DNA Extraction |
| FUREV | Fungal PCR: Pathologist Review |
| FUME | Fungal PCR: Method Note |
Interpretation
Method
DNA extraction, nucleic acid purification, polymerase chain reaction (PCR), sequencing
Reference Range
See individual components
Guidelines
Ordering & Collection
Specimen Type
Collection
Acceptable specimens are listed below. Please see this page for complete specimen collection and handling instructions.
Specimens should be collected into a DNA free container labeled with at least two identifiers.
Acceptable Specimens
- Fresh frozen tissue
- Fresh frozen fluid: any body fluid is acceptable if it is not listed under Unacceptable Specimens. See common examples below.
- Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides are acceptable
- eSwabs* and UTM (universal transport media)
*Some lots of eSwabs have been found to contain Saccharomyces cerevisiae DNA, resulting in false postive detection. The detection of S. cerevisiae from eSwab specimens can interfere with our ability to rule out other fungal DNA. Clinical corrrelation and/or retesting with a different collection method will be advised.
Common acceptable body fluid examples: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.
Unacceptable Specimens
- Sputum, blood, serum, plasma, stool
- No citrated or heparinized solutions
- No SPS (Sodium Polyanethole Sulfonate) e.g. Wampole Isolator Tubes
- Tissues floating in formalin
- Swab/fluid collected in tube containing agar
Handling Instructions
Fresh frozen tissue/fluid specimens should be submitted and maintained on dry ice.
Formalin Fixed Paraffin-embedded tissues (FFPE, PET) can be sent ambient or with ice packs during warmer summer months to prevent melting.
Optimal Quantity:
- Fresh Tissue: 0.3-1.0 cm^3
- Fluid: 0.2-1 mL
- Formalin Fixed Paraffin-embedded Tissue (FFPE/PET): blocks are preferred and will be sent back to client upon completion of testing
- Scrolls/unstained slides: cross-sectional area >1cm^2 send 10 sections of 10µm thickness, if <1cm^2 send 20 sections if available
Please note: We do not need a separate specimen aliquot for each test ordered. Only a single specimen aliquot or block of optimal quantity is necessary for performing multiple tests. If multiple aliquots or blocks of optimal quantity are sent, up to 2 will be pooled.
Quantity
requested: See Optimal Quantity above
minimum: Specimens below optimal quantity are acceptable for testing, however, diagnostic yield is generally proportional to specimen size.
Processing
UWMC/HMC – store and send specimen refrigerated and freeze specimens at -20°C upon arrival in UW-ML Microbiology. If specimen storage and transport will exceed 8 hours, freeze at -20°C.
Freeze specimens at -20°C upon arrival
Outside Laboratories: Freeze specimens in sterile containers at -20°C. Transport all specimens on dry ice.
Performance
LIS Dept Code
Micro Molecular Diag (MMD)
Performing Location(s)
| UW-MT |
Microbiology, Molecular Diagnostics
206-520-4600 Clinical Lab, Room # NW177, |
|---|
Frequency
Fresh frozen tissues/fluids result in 2-3 business days after receipt of specimen. Formalin Fixed Paraffin-embedded tissues result in 3-4 business days after receipt of specimen.
Available STAT?
No