Test ID: CIMRP
Coccidioides immitis/posadasii, Molecular Detection, PCR
Secondary ID 
A test code used for billing and in test definitions created prior to November 2011
NY State Approved Indicates the status of NY State approval and if the test is orderable for NY State clients.
Useful For Suggests clinical disorders or settings where the test may be helpful
Rapid detection of Coccidioides
An aid in diagnosing coccidioidomycosis
Method Name A short description of the method used to perform the test
Real-Time Polymerase Chain Reaction (PCR)
(PCR is utilized pursuant to a license agreement with Roche Molecular Systems, Inc.)
Reporting Name A shorter/abbreviated version of the Published Name for a test; an abbreviated test name
Aliases Lists additional common names for a test, as an aid in searching
Valley Fever
Cocci
Cocci PCR
Specimen Type Describes the specimen type needed for testing
Specimen Required Defines the optimal specimen. This field describes the type of specimen required to perform the test and the preferred volume to complete testing. The volume allows automated processing, fastest throughput and, when indicated, repeat or reflex testing.
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 not likely.
Forms: If not ordering electronically, submit a Microbiology Request Form (Supply T244) with the specimen.
Acceptable Specimens: Body fluid, cerebrospinal fluid, respiratory (eg, bronchoalveolar lavage fluid, bronchial washing, sputum), tissue (fresh or paraffin block) or bone
Unacceptable Specimens: Blood, bone marrow, specimen in anaerobe vial or viral transport medium (including but not limited to M4, M5, BD viral transport media, thioglycolate broth), stool, swab, tissue in formalin fluid, urine, specimen >7 days old (with the exception of paraffin tissue)
Specimen must arrive within 7 days of collection; specimen >7 days will be rejected.
Specimen source is required.
Submit only 1 of the following specimens:
Specimen Type: Body fluid
Sources: Body fluid or cerebrospinal fluid
Container/Tube: Sterile container
Specimen Volume: 1 mL
Specimen Stability Information: Refrigerated (preferred) 7 days/Ambient 7 days/Frozen 7 days
Specimen Type: Respiratory
Sources: Bronchoalveolar lavage fluid, bronchial washing, or sputum
Container/Tube: Sterile container
Specimen Volume: 1 mL
Specimen Stability Information: Refrigerated (preferred) 7 days/Ambient 7 days/Frozen 7 days
Specimen Type: Tissue
Sources: Fresh, paraffin, or bone
Container/Tube:
Preferred: Sterile container
Acceptable: Biopsy specimen of tissue fixed with formalin in a paraffin block
Specimen Volume: 5-10 mm
Collection Instructions: Block must be sent for sectioning.
Specimen Stability Information:
Fresh tissue: Refrigerated (preferred) 7 days/Ambient 7 days/Frozen 7 days
Fixed tissue (paraffin): Ambient (preferred)
Specimen Minimum Volume Defines the amount of specimen required to perform an assay once, including instrument and container dead space. Submitting the minimum specimen volume makes it impossible to repeat the test or perform confirmatory or perform reflex testing. In some situations, a minimum specimen volume may result in a QNS (quantity not sufficient) result, requiring a second specimen to be collected.
Reject Due To Identifies specimen types and conditions that may cause the specimen to be rejected
| Hemolysis | NA |
| Lipemia | NA |
| Icterus | NA |
| 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), stool, swab, tissue in formalin fluid, urine, specimen >7 days old (with the exception of paraffin tissue) |
Specimen Stability Information Provides a description of the temperatures required to transport a specimen to the laboratory. Alternate acceptable temperature(s) are also included.
| Specimen Type | Temperature | Time |
|---|---|---|
| Varies | Varies | |
Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test
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, avoiding the need for culture and allowing for a more rapid and safer diagnosis.
Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.
Not applicable
Interpretation Provides information to assist in interpretation of the test results
A positive result indicates presence of Coccidioides DNA.
A negative result indicates absence of detectable Coccidioides DNA.
Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances
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 the Coccidioides immittis and Coccidioides posadasii.
Formalin-fixed, paraffin-embedded tissue is not an optimal source for PCR analysis as formalin fixation has been demonstrated to decrease the sensitivity of PCR.(4) Therefore, a negative PCR result from fixed tissue should be interpreted with caution if the clinical presentation is suggestive of coccidioidomycosis.
Supportive Data
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 samples was 73.4% and 100% respectively.
The limit of detection of the assay was determined to be between 1 and 10 copies of target/microliters (<50 copies of target/reaction). The analytic specificity of the assay was determined by performing a 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.
Clinical Reference Provides recommendations for further in-depth reading of a clinical nature
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, 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
Method Description Describes how the test is performed and provides a method-specific reference
Following specimen processing, nucleic acids are extracted using the MagNa Pure Compact (Roche Applied Sciences). 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)
Day(s) and Time(s) Test Performed Outlines the days and times the test is performed. This field reflects the day and time the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time required before the test is performed. Some tests are listed as continuously performed, which means assays are performed several times during the day.
Varies 3 times per week
Analytic Time Defines the amount of time it takes the laboratory to setup and perform the test. This is defined in number of days. The shortest interval of time expressed is "same day/1 day," which means the results may be available the same day that the sample is received in the testing laboratory. One day means results are available 1 day after the sample is received in the laboratory.
Maximum Laboratory Time Defines the maximum time from specimen receipt at Mayo Medical Laboratories until the release of the test result
Specimen Retention Time Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded
Performing Laboratory Location The location of the laboratory that performs the test
Test Classification Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer's instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR), Investigation Use Only (IUO) product, or a Research Use Only (RUO) product.
CPT Code Information Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Medical Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.
87798
LOINC® Code Information Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the result codes returned for this test or profile.
| Result ID | Reporting Name | LOINC Code |
|---|---|---|
| SRC64 | Specimen Source | 31208-2 |
| 88804 | Result | 48588-8 |
| 28288 | Special Information | 48767-8 |
| 28289 | Report Status | N/A |
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