Coccidioides DNA detection by PCR

General Information

Lab Name

Lab Code

COCDNA

Epic Ordering

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.

It has been declared a select agent by both the U.S. Department of Health and Human Services and the U.S. Department of Agriculture, and is considered a biosafety level 3 pathogen.

Coccidioides PCR detects Coccidioides immitis/posadasii with higher specificity and sensitivity than the broad-range fungal PCR. The analytical sensitivity is 1 genome per PCR reaction.

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

References

David J. DiCaudo Coccidioidomycosis: A review and update J Am Acad Dermatol 2006;55:929-42

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

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

Guidelines

Ordering & Collection

Specimen Type

Tissue (Fresh frozen or paraffin-embedded), Fluid (see Acceptable Specimens for details)

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)

Common acceptable body fluid examples: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.

Additional Acceptable Specimens

Sputum

Unacceptable Specimens

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

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, University of Washington Medical Center, 1959 NE Pacific street, Seattle, WA 98195

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?

Billing & Coding

CPT codes: 87801
LOINC: 48588-8
Interfaced Order Code: UOW4444