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HelpTest Code PNRP Pneumocystis jiroveci, Molecular Detection, PCR, Varies
Reporting Name
Pneumocystis PCRUseful For
Preferred test for detection of Pneumocystis
Method Name
Real-Time Polymerase Chain Reaction (PCR)
Performing Laboratory
Mayo Clinic Laboratories in Rochester
Specimen Type
VariesAdditional Testing Requirements
This test should always be performed in conjunction with fungal culture; order FGEN / Fungal Culture, Routine.
Shipping Instructions
Specimen must arrive within 7 days of collection; specimens older than 7 days will be rejected.
Necessary Information
Specimen source is required.
Specimen Required
The high sensitivity of amplification by polymerase chain reaction requires the specimen to be processed in an environment in which contamination of the specimen by Pneumocystis species DNA is unlikely.
Preferred Specimens: Pleural, respiratory (eg, bronchoalveolar lavage [BAL], bronchial washing, sputum), or fresh tissue
Acceptable Specimens: If no fresh specimen is available, digested respiratory specimens treated with N-acetyl-L-cysteine-sodium hydroxide (NALC/NaOH) are acceptable (eg, BAL, bronchial washing, respiratory fluid, sputum, or tracheal secretion)
Submit only 1 of the following specimens:
Preferred
Specimen Type: Body fluid
Sources: Pleural
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, tracheal secretions, 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: Respiratory
Container/Tube: Sterile container
Specimen Volume: 5-10 mm
Collection Instructions:
1. Submit fresh tissue.
2. Keep tissue moist with sterile water or sterile saline
Acceptable
Specimen Type: NALC/NaOH-digested respiratory specimens
Sources: BAL, 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 or nondigested respiratory specimen: 0.5 mL; Fresh tissue: 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 |
Reject Due To
| Body fluid other than pleural fluid Blood Bone Nonrespiratory tissue Bone marrow Organ tissues other than lung Paraffin-embedded tissue Specimen in anaerobe vial or viral transport medium Feces Swab Tissue in formalin fluid Urine |
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 |
|---|---|---|
| PNRP | Pneumocystis PCR | 89996-3 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| SRC63 | Specimen Source | 31208-2 |
| 81698 | Pneumocystis PCR, Result | 89996-3 |
| 24188 | Special Information | 48767-8 |
| 24189 | Report Status | No LOINC Needed |
Clinical Information
Pneumocystis pneumonia is an important cause of opportunistic infection in patients who are immunocompromised, particularly those with HIV. The causative agent, Pneumocystis jiroveci, cannot be cultured in vitro, and, therefore, laboratory detection has historically relied upon microscopic identification directly from patient specimens using fluorescent stains or antibodies. Stains often lack sensitivity and require expertise on the part of the reader to differentiate Pneumocystis jiroveci from staining artifacts and other fungi. This real-time polymerase chain reaction assay provides a sensitive and specific detection of Pneumocystis from bronchoalveolar lavage fluid and other respiratory specimens.
Interpretation
A positive result indicates the presence of Pneumocystis DNA.
A negative result indicates the absence of detectable Pneumocystis DNA.
Cautions
Test results should be used as an aid in diagnosis and should not be considered diagnostic in themselves. The literature indicates that Pneumocystis can cause asymptomatic colonization of healthy individuals and those who are immunocompromised. Therefore, test results should be correlated with patient symptoms and clinical presentation.
A negative result does not rule out the presence of Pneumocystis or active disease because the organism may be present at undetectable levels.
Method Description
Nucleic acids are extracted using the MagNA Pure LC Instrument (Roche). The extract is then amplified using the LightCycler real-time polymerase chain reaction (PCR) platform (Roche). The detection of amplicon is based on fluorescence resonance energy transfer (FRET), which utilizes hybridization probes. The presence of the specific organism nucleic acid is confirmed by performing a melting curve analysis of the amplicon.(Arcenas RC, Uhl JR, Buckwalter SP, et al: A real-time PCR assay for detection of Pneumocystis from bronchoalveolar lavage fluid. Diagn Microbiol Infect Dis. 2006 Mar;54(3):169-175)