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HelpTest Code CIMT Coccidioides immitis/posadasii, Molecular Detection, PCR, Paraffin, Tissue
Reporting Name
Coccidioides PCR, FFPEUseful For
Rapid detection of Coccidioides DNA
Aiding in the diagnosis of coccidioidomycosis using paraffin-embedded tissue specimens
Method Name
Real-Time Polymerase Chain Reaction (PCR)
Performing Laboratory
Mayo Clinic Laboratories in Rochester
Specimen Type
Tissue, ParaffinNecessary Information
Specimen source is required.
Specimen Required
Preferred Paraffin-embedded tissue block:
Supplies: Tissue Block Container (T553)
Specimen Type: Formalin-fixed, paraffin-embedded tissue block (FFPE)
Sources: Body tissue
Container/Tube: Tissue block
Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block to be cut and returned.
Acceptable Paraffin-embedded tissue block:
Specimen Type: Formalin-fixed, paraffin-embedded tissue block (FFPE)
Sources: Body tissue
Container/Tube: Sterile container for each individual cut section (scroll).
Collection Instructions: Perform microtomy and prepare five separate 10-micron sections. Each section (scroll) must be placed in a separate sterile container for submission.
Specimen Minimum Volume
See Specimen Required.
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Tissue, Paraffin | Ambient (preferred) | ||
| Refrigerated | |||
Reject Due To
| Any non-FFPE tissue blocks FFPE bone marrow FFPE slides FFPE body fluids | Reject |
Reference Values
Not applicable
Day(s) Performed
Monday through Sunday
CPT Code Information
87798
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| CIMT | Coccidioides PCR, FFPE | 95913-0 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| CIRR | Coccidioides PCR, FFPE, Result | 95913-0 |
| SRCCI | Coccidioides PCR, FFPE, Source | 31208-2 |
Disease States
- 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, with recent literature suggests the geographic area of endemicity may be expanding over time.
The gold standard for the diagnosis of coccidioidomycosis is culture of the organism from clinical specimens due to its high sensitivity. However, growth in culture may take up to several weeks, which can delay diagnosis and treatment. In addition, the propagation of Coccidioides species in the clinical laboratory is a significant safety hazard to laboratory personnel.
This polymerase chain reaction method can identify Coccidioides species directly from clinical specimens, allowing for a rapid diagnosis, and should be used in conjunction with culture. For specimen types such as formalin-fixed, paraffin-embedded tissue, culture is not possible, but the molecular test may provide useful information.
Interpretation
A positive result indicates presence of Coccidioides DNA.
A negative result indicates absence of detectable Coccidioides DNA.
An inhibition result indicates that the detection of Coccidioides DNA is inhibited in this specimen. A new specimen can be resubmitted under a new order, if desired.
Cautions
This rapid polymerase chain reaction (PCR) assay detects Coccidioides nucleic acid and, therefore, does not distinguish between viable, disease-related 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.
Formalin fixation has been demonstrated to decrease the sensitivity of PCR. Therefore, a negative PCR result from fixed tissue should be interpreted with caution if the clinical presentation is suggestive of coccidioidomycosis.
Supportive Data
The sensitivity and specificity of the assay testing 148 formalin-fixed, 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
1. Vucicevic D, Blair JE, Binnicker MJ, et al: The utility of Coccidioides polymerase chain reaction testing in the clinical setting. Mycopathologia. 2010 Nov;170(5):345-351
2. Hartmann CA, Aye WT, Blair JE: Treatment considerations in pulmonary coccidioidomycosis. 2016 Oct;10(10):1079-1091
Method Description
Following specimen processing, nucleic acids are extracted, and the extract transferred to individual self-contained cuvettes for amplification using the LightCycler real-time polymerase chain reaction (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)