Coccidioides DNA detection by PCR

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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

Molecular Microbiology Order Form

Synonyms
Coccidioides detection, Coccidioides identification, Coccidioides PCR, Coccidioides sequencing, Coccidioidiomycosis PCR, Fungal sequencing, molecular Coccidioides, universal PCR, Valley Fever
Components
Code Name
COCRS Coccidioides PCR: Detection, nested ITS
COCID Coccidioides PCR: Identification, nested ITS
COCSI Coccidioides PCR: Specimen Description
COCSPI Coccidioides PCR: External Identifier
COCSR Coccidioides PCR: Special Requests
COCSC Coccidioides PCR: Specimen Comments
COCNAE Coccidioides PCR: Specimen DNA Extractio
COCREV Coccidioides PCR: Pathologist Review
COCME Coccidioides PCR: Method Note

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

*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

    Molecular Microbiology Order Form

    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

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    Shipping Address

    Attn: Molecular Microbiology
    UW CLSPS
    1601 Lind Ave SW Room 117
    Renton, WA 98057
    Phone: 206-520-4600
    Alternate phone: 206-598-6147

    Performing Lab Address

    Clinical Microbiology Lab, NW177
    University of Washington Medical Center
    1959 NE Pacific Street
    Seattle, WA 98195
    Phone: 206-598-5735
    Alternate phone: 206-598-6147

    Contact 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