Rapid detection of Coccidioides DNA, preferred method
An aid in diagnosing coccidioidomycosis
See Meningitis/Encephalitis Panel Algorithm in Special Instructions.
Real-Time Polymerase Chain Reaction (PCR)
Cocci
Cocci PCR
San Joaquin Valley Fever
Valley Fever
See Meningitis/Encephalitis Panel Algorithm in Special Instructions.
Varies
Specimen must arrive within 7 days of collection; specimen >7 days will be rejected.
Question ID | Description | Answers |
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SRC64 | Coccidioides PCR, Specimen Source |
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.
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.
If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.
Body fluid: 0.5 mL; Respiratory specimen nondigested: 0.5 mL; Fresh tissue or bone: 5 mm; NALC-NaOH-digested specimen: 1 mL
Other | Blood Bone marrow Specimen in anaerobe vial or viral transport medium (including but not limited to M4, M5, BD viral transport media, thioglycolate broth) Feces Swabs Tissues in formalin fluid Urine Specimens >7 days old |
Specimen Type | Temperature | Time | Special Container |
---|---|---|---|
Varies | Refrigerated (preferred) | 7 days | |
Frozen | 7 days |
Rapid detection of Coccidioides DNA, preferred method
An aid in diagnosing coccidioidomycosis
See Meningitis/Encephalitis Panel Algorithm in Special Instructions.
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.
Not applicable
A positive result indicates presence of Coccidioides DNA.
A negative result indicates absence of detectable Coccidioides DNA.
This test should always be performed in conjunction with fungal culture.
This rapid PCR assay detects Coccidioides nucleic acid and, therefore, does not distinguish between viable, disease-related organisms and transient colonizing organisms or nucleic acid persisting from old disease. Test results should be correlated with patient symptoms and clinical presentation before a definitive diagnosis is made.
A negative result does not rule out the presence of Coccidioides or active disease because the organism may be present at levels below the limit of detection for this assay.
This test does not distinguish between Coccidioides immitis and Coccidioides posadasii.
Analysis of 266 respiratory specimens (bronchoalveolar lavage, sputum, induced sputum, bronchial wash, pleural fluid) by LightCycler PCR for Coccidioides species detection demonstrated 100% sensitivity and 98.4% specificity compared with culture. Analysis of 66 fresh tissue specimens yielded 92.9% sensitivity and 98.1% specificity compared with culture. The sensitivity and specificity of the assay testing 148 paraffin-embedded tissue specimens was 73.4% and 100% respectively.
The limit of detection of the assay was determined to be between 1 and 10 copies of target/microliter (<50 copies of target/reaction). The analytic specificity of the assay was determined by performing a Basic Local Alignment Search Tool (BLAST) search of the primer and probe sequences on the National Center for Biotechnology Information website (http://www.ncbi.nml.nig.gov). In addition, an extensive panel of nucleic acid extracted from 114 potentially cross-reacting organisms including fungi, bacteria, mycobacteria, viruses, and human DNA was tested. The assay did not demonstrate cross-reactivity with any of the organisms included in the specificity panel.
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
Following specimen processing, nucleic acids are extracted and the extract is then transferred to individual self-contained cuvettes for amplification using the LightCycler real-time PCR platform (Roche Applied Sciences). The LightCycler is an automated instrument that amplifies and monitors the development of target nucleic acid (amplicon) after each cycle of PCR. The detection of amplicon is based on fluorescence resonance energy transfer, which utilizes hybridization probes. The presence of the specific organism nucleic acid is confirmed by performing a melting curve analysis of the amplicon.(Binnicker MJ, Buckwalter SP, Eisberner JJ, et al: Detection of Coccidioides species in clinical specimens by real-time PCR. J Clin Microbiol 2007; 45:173-178)
Monday through Sunday
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.
87798
Test Id | Test Order Name | Order LOINC Value |
---|---|---|
CIMRP | Coccidioides PCR | 48588-8 |
Result Id | Test Result Name |
Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
|
---|---|---|
SRC64 | Coccidioides PCR, Specimen Source | 31208-2 |
88804 | Coccidioides PCR, Result | 48588-8 |