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Test ID: CIMRP Coccidioides immitis/posadasii, Molecular Detection, PCR, Varies

Reporting Name

Coccidioides PCR

Useful For

Rapid detection of Coccidioides DNA, preferred method


An aid in diagnosing coccidioidomycosis

Clinical Information

Coccidioidomycosis is caused by the dimorphic fungi, Coccidioides immitis and Coccidioides posadasii. These organisms are endemic to the southwestern regions of the United States, northern Mexico, and areas of Central and South America. The illness commonly manifests as a self-limited upper respiratory tract infection, but can also result in disseminated disease that may be refractory to treatment.(1) Clinical onset generally occurs 10 to 16 days following inhalation of coccidioidal spores (arthroconidia).(2) Disease progression may be rapid in previously healthy or immunosuppressed individuals.


At present, the gold standard for the diagnosis of coccidioidomycosis is culture of the organism from clinical specimens. Culture is highly sensitive and, with the implementation of DNA probe assays for confirmatory testing of culture isolates, yields excellent specificity.(3) However, growth in culture may take up to several weeks. This often delays the diagnosis and treatment of infected individuals. In addition, the propagation of Coccidioides species in the clinical laboratory is a significant safety hazard to laboratory personnel, serving as an important cause of laboratory-acquired infections if the organism is not quickly identified and handled appropriately (ie, in a Biosafety Level 3 facility). Serological tests including immunodiffusion and complement fixation are widely used for the detection of antibody against Coccidioides. Serology for Coccidioides can be limited by delays in antibody development or nonspecificity due to cross-reactions with other fungi. In addition, immunodiffusion and complement fixation tests are highly labor intensive and are generally limited to reference laboratories.


Molecular methods can identify Coccidioides species directly from clinical specimens, allowing for a more rapid diagnosis. Fungal culture should also be performed since the isolate may be needed for antifungal susceptibility testing.


A positive result indicates presence of Coccidioides DNA.


A negative result indicates absence of detectable Coccidioides DNA.

Report Available

1 to 3 days

Day(s) Performed

Monday through Sunday

Clinical Reference

1. Chiller TM, Galgiani JN, Stevens DA: Coccidioidomycosis. Infect Dis Clin North Am 2003;17:41-57

2. Feldman BS, Snyder LS: Primary pulmonary coccidioidomycosis. Semin Respir Infect 2001;16:231-237

3. Padhye AA, Smith G, Standard PG, et al: Comparative evaluation of chemiluminescent DNA probe assays and exoantigen tests for rapid identification of Blastomyces dermatitis and Coccidioides immitis. J Clin Microbiol 1994;32:867-870

4. Inoue T, Nabeshima K, Kataoka H, Koono M: Feasibility of archival non-buffered formalin-fixed and paraffin-embedded tissues for PCR amplification: an analysis of resected gastric carcinoma. Pathol Int 1996;46:997-1004

5. Binnicker MH, Popa AS, Catania J, et al: Meningeal coccidioidomycosis diagnosed by real-time polymerase chain reaction analysis of cerebrospinal fluid. Mycopathologia 2011;171:285-289

6. Vucicevic D, Blair JE, Binnicker MJ, et al: The utility of Coccidioides polymerase chain reaction testing in the clinical setting. Mycopathologia 2010;170:345-351

Method Name

Real-Time Polymerase Chain Reaction (PCR)

Specimen Type


Shipping Instructions

Specimen must arrive within 7 days of collection; specimen >7 days will be rejected.

Necessary Information

Specimen source is required.

Specimen Required

The high sensitivity of amplification by PCR requires the specimen to be processed in an environment in which contamination of the specimen by Coccidioides species DNA is unlikely.


Preferred Specimens: Body fluid, cerebrospinal fluid (CSF), ocular fluid, respiratory (eg, bronchoalveolar lavage [BAL], bronchial washing, sputum), fresh tissue, or bone


Acceptable Specimens: If no fresh specimen is available, digested respiratory specimens treated with N-acetyl-L-cysteine (NALC)/NaOH are acceptable (eg, bronchoalveolar lavage fluid, bronchial washing, respiratory fluid, sputum, or tracheal secretion)


Submit only 1 of the following specimens:


Specimen Type: Body fluid

Sources: Body, ocular, or CSF

Container/Tube: Sterile container

Specimen Volume: 1 mL

Additional Information: Only fresh, non-NALC/NaOH-digested body fluid is acceptable.


Specimen Type: Respiratory

Sources: BAL, bronchial washing, or sputum

Container/Tube: Sterile container

Specimen Volume: 1 mL if only PCR ordered or 3 mL if PCR ordered with smear and culture


Specimen Type: Tissue

Sources: Fresh tissue or bone

Container/Tube: Sterile container

Specimen Volume: 5-10 mm

Collection Instructions: Keep moist with sterile water or sterile saline

Additional Information: Only fresh, non-NALC/NaOH-digested tissue is acceptable.



Specimen Type: NALC/NaOH-digested respiratory specimens

Sources: Lavage fluid, bronchial washing, respiratory fluid, sputum, or tracheal secretion

Container/Tube: Sterile container

Specimen Volume: 2 mL

Collection Instructions:

1. Submit digested specimen treated with NALC/NaOH.

2. Clearly indicate on container and order form that specimen is a digested specimen.

Specimen Minimum Volume

Body fluid: 0.5 mL; Respiratory specimen nondigested: 0.5 mL; Fresh tissue or bone: 5 mm; NALC-NaOH-digested specimen: 1 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Refrigerated (preferred) 7 days
  Frozen  7 days

Reference Values

Not applicable

Test Classification

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information


LOINC Code Information

Test ID Test Order Name Order LOINC Value
CIMRP Coccidioides PCR 48588-8


Result ID Test Result Name Result LOINC Value
SRC64 Coccidioides PCR, Specimen Source 31208-2
88804 Coccidioides PCR, Result 48588-8

Testing Algorithm

See Meningitis/Encephalitis Panel Algorithm in Special Instructions.


If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.

Mayo Clinic Laboratories | Microbiology and Infectious Disease Catalog Additional Information:

mml-mbid-cnsinfections, mml-respiratoryinfections