Test Catalog

Test Id : CIMRP

Coccidioides immitis/posadasii, Molecular Detection, PCR, Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

Rapid detection of Coccidioides DNA, preferred method

 

An aid in diagnosing coccidioidomycosis

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

See Meningitis/Encephalitis Panel Algorithm in Special Instructions.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

Real-Time Polymerase Chain Reaction (PCR)

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Coccidioides PCR

Aliases
Lists additional common names for a test, as an aid in searching

Cocci

Cocci PCR

San Joaquin Valley Fever

Valley Fever

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

See Meningitis/Encephalitis Panel Algorithm in Special Instructions.

Specimen Type
Describes the specimen type validated for testing

Varies

Shipping Instructions

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

Necessary Information

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
SRC64 Coccidioides PCR, Specimen Source

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete 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 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.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Forms

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

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

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

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

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 Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

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

Useful For
Suggests clinical disorders or settings where the test may be helpful

Rapid detection of Coccidioides DNA, preferred method

 

An aid in diagnosing coccidioidomycosis

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

See Meningitis/Encephalitis Panel Algorithm in Special Instructions.

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, allowing for a more rapid diagnosis. Fungal culture should also be performed since the isolate may be needed for antifungal susceptibility testing.

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 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.

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 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.

Clinical Reference
Recommendations for 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 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

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

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)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Monday through Sunday

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

1 to 3 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

7 days

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

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 instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

87798

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

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

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports