Coccidioides DNA detection by PCR
General Information
- Lab Name
- Coccidioides DNA detection by PCR
- Lab Code
- COCDNA
- Epic Name
- Coccidioides DNA detection by PCR
- Description
Detection of Coccidioides immitis or Coccidioides posadasii DNA
Coccidioides immitis is a pathogenic fungus that resides in the soil in certain parts of the Southwestern United States and Northern Mexico. C. immitis and a closely related species Coccidioides posadasii, can cause a disease called coccidioidomycosis, and it is also a rare cause of meningitis, mostly in immunocompromised persons. The illness commonly manifests as a self-limited, upper respiratory tract infection, but it can also result in disseminated disease that may be refractory to treatment.
The Molecular Microbiology laboratory designed a specific primer mix that can amplify both Coccidioides immitis and Coccidioides posadasii. These specific primers are used in a nested PCR following amplification of the ITS2 region. More recently the laboratory has designed FRET probes specific for detecting Coccidioides immitis and Coccidioides posadasii.
- References
David J. DiCaudo Coccidioidomycosis: A review and update J Am Acad Dermatol 2006;55:929-42
- Forms & Requisitions
- Synonyms
- Coccidioides detection, Coccidioides identification, Coccidioides PCR, Coccidioides sequencing, Coccidioidiomycosis PCR, Fungal sequencing, molecular Coccidioides, universal PCR, Valley Fever
- Components
-
Interpretation
- Guidelines
- Method
DNA extraction, nucleic acid purification, polymerase chain reaction (PCR), sequencing
- Reference Range
- See individual components
- References
David J. DiCaudo Coccidioidomycosis: A review and update J Am Acad Dermatol 2006;55:929-42
Ordering & Collection
- Specimen Type
- Tissue (Fresh frozen or paraffin-embedded), Fluid (see Acceptable Specimens for details)
- Collection
-
Acceptable specimens are listed below. Please see Molecular Microbiology Specimen Submission for complete specimen collection and handling instructions.
Shipping/Handling
- Fresh frozen tissue/fluid specimens should be collected into a DNA free container labeled with at least two identifiers and 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.
Acceptable Specimens
- Fresh frozen tissue
- Fresh frozen fluid: any body fluid is acceptable if it is not listed under Unacceptable Specimens.
- Common examples include: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.
- Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides. Note that fresh tissue is considered the optimal specimen of choice, as it reduces the chance of introducing exogenous DNA templates or microorganisms during embedding/fixation, and because formalin fixation dramatically reduces the sensitivity of molecular assays due to reduced template yield and quality.
- Sputum: acceptable - except for Bacterial PCR reflex NGS [BCTDNA]/Bacterial DNA Detection by PCR (without reflex to NGS) [NRBDNA], Fungal PCR reflex NGS [FUNDNA]/Fungal DNA Detection by PCR (without reflex to NGS) [NRFDNA], and Nontuberculous Mycobacteria DNA Detection [NTMDNA]* assays
- eSwabs**, UTM (universal transport media), body fluid/bone marrow in EDTA (not including blood)
- Sodium polyanethol sulfonate (SPS, Wampole Isolator Tubes) acceptable with disclaimer
*Mycobacterium avium complex DNA Detection [MAVDNA] can be ordered on sputum
**Fungal PCR reflex NGS [FUNDNA] and Fungal DNA Detection by PCR (without reflex to NGS) [NRFDNA] may have interference due to some lots of eSwabs which have been found to contain Saccharomyces cerevisiae DNA, resulting in false positive detection. Clinical correlation and/or retesting with a different collection method is advised. The detection of S. cerevisiae from eSwab specimens can interfere with our ability to rule out other fungal DNA.
Unacceptable Specimens
- Blood, serum, plasma, stool/rectal swabs
- No citrated or heparinized solutions
- Tissues floating in formalin
- Swab/fluid collected in tube containing agar
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 over scrolls/unstained slides 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.
Fresh tissue is the optimal specimen of choice, as it reduces the chance of introducing exogenous DNA templates or microorganisms during embedding/fixation. Formalin fixation dramatically reduces the sensitivity of the assays due to reduced template yield and quality.
- Forms & Requisitions
- Handling Instructions
Please see Molecular Microbiology Specimen Submission for complete specimen collection and handling instructions.
- Quantity
-
Requested: See "Collection" for Optimal Quantity
Minimum: Specimens below optimal quantity are acceptable for testing, however, diagnostic yield is generally proportional to specimen size.
Processing
- Receiving Instructions
UWMC/HMC: Store and send fresh tissue/fluid specimens refrigerated, if specimen storage and transport will exceed 8 hours, freeze at -20°C. Freeze all fresh tissue/fluid specimens at -20°C upon arrival in UW Molecular Microbiology.
- Misc Sendout
Performance
- Lab Department
- Micro Molecular Diag(MMD)
- 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
- Performing Location(s)
-
UW-MT Microbiology, Molecular Diagnostics
206-520-4600----------------------------------------
Shipping Address
Attn: Molecular Microbiology
UW CLSPS
1601 Lind Ave SW Room 117
Renton, WA 98057
Phone: 206-520-4600
Alternate phone: 206-598-6147Performing Lab Address
Clinical Microbiology Lab, NW177
University of Washington Medical Center
1959 NE Pacific Street
Seattle, WA 98195
Phone: 206-598-5735
Alternate phone: 206-598-6147Contact Information
Please e-mail us with any questions or comments you may have. Your inquiry will be answered as soon as possible.
email: molmicdx@uw.edu
The Molecular Microbiology lab is open from Monday-Friday, 7am-4pm PDT.
Billing inquiries and requests for faxed reports can be made to our Client Services Department at (206) 520-4600 or (800) 713-5198.
For results or other inquiries, we can be reached by phone at the following numbers:
- Phone: (206) 598-5735
- Alternate phone: (206) 598-6147
- FAX: (206) 520-4903
For assistance during weekends, holidays and after hours, please contact Lab Medicine Resident at (206) 598-6190
Billing & Coding
- CPT Codes
- 87801
- LOINC
- 48588-8
- Interfaced Order Code
- UOW4444