Pneumocystis DNA detection by PCR
General Information
Lab Name
Pneumocystis DNA detection by PCR
Lab Code
PNEDNA
Epic Name
Pneumocystis DNA detection by PCR
Description
Detection of Pneumocystis jirovecii (previously Pneumocystis carinii) DNA.
Pneumocystis jirovecii (formerly Pneumocystis carinii) is an opportunistic fungal pathogen which can cause pneumonia in patients with impaired immune systems, such as those with AIDS or who are receiving immunosuppressive drugs. It is important to accurately identify the presence of Pneumocystis in immunocompromised patients for the implementation of proper therapy. Conventional diagnosis is based on direct microscopic examination of respiratory specimens, but these methods can often be difficult to interpret. PCR allows for more definitive detection of Pneumocystis in clinical specimens.
The UWMC Molecular Diagnosis laboratory utilizes a real-time PCR protocol with fluorescent probes targeted to the Kex-1 gene to identify Pneumocystis jirovecii in clinical specimens. Pneumocystis PCR detects Pneumocystis jirovecii with higher sensitivity than the broad-range fungal PCR. The analytic sensitivity is 6 genomes per PCR reaction.
Synonyms
molecular PCP, molecular PJP, molecular Pneumocystis, PCP, PCP detection, PCP identification, PCP PCR, PCP sequencing, PJP, PJP detection, PJP identification, PJP PCR, PJP sequencing, Pneumocystis carinii PCR, Pneumocystis detection, Pneumocystis identification, Pneumocystis jiroveci, Pneumocystis jirovecii PCR, Pneumocystis PCR, Pneumocystis sequencing, universal PCR
Components
Interpretation
Method
DNA extraction, nucleic acid purification, polymerase chain reaction (PCR), sequencing
Reference Range
See individual components
Guidelines
Ordering & Collection
Specimen Type
Collection
Acceptable specimens are listed below. Please see Molecular Microbiology Specimen Submission for complete specimen collection and handling instructions.
Shipping/Handling
- Fresh frozen tissue/fluid specimens should be collected into a DNA free container labeled with at least two identifiers and be submitted and maintained on dry ice.
- Formalin Fixed Paraffin-embedded tissues (FFPE, PET) can be sent ambient or with ice packs during warmer summer months to prevent melting.
Acceptable Specimens
- Fresh frozen tissue
- Fresh frozen fluid: any body fluid is acceptable if it is not listed under Unacceptable Specimens.
- Common examples include: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.
- Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides
- Sputum: acceptable - except for Bacterial PCR reflex NGS [BCTDNA]/Bacterial DNA Detection by PCR (without reflex to NGS) [NRBDNA], Fungal PCR reflex NGS [FUNDNA]/Fungal DNA Detection by PCR (without reflex to NGS) [NRFDNA], and Nontuberculous Mycobacteria DNA Detection [NTMDNA]* assays
- eSwabs**, UTM (universal transport media), body fluid/bone marrow in EDTA (not including blood)
- Sodium polyanethol sulfonate (SPS, Wampole Isolator Tubes) acceptable with disclaimer
*Mycobacterium avium complex DNA Detection [MAVDNA] can be ordered on sputum
**Fungal PCR reflex NGS [FUNDNA] and Fungal DNA Detection by PCR (without reflex to NGS) [NRFDNA] may have interference due to some lots of eSwabs which have been found to contain Saccharomyces cerevisiae DNA, resulting in false positive detection. Clinical correlation and/or retesting with a different collection method is advised. The detection of S. cerevisiae from eSwab specimens can interfere with our ability to rule out other fungal DNA.
Unacceptable Specimens
- Blood, serum, plasma, stool/rectal swabs
- No citrated or heparinized solutions
- Tissues floating in formalin
- Swab/fluid collected in tube containing agar
Optimal Quantity:
- Fresh Tissue: 0.3-1.0 cm^3
- Fluid: 0.2-1 mL
- Formalin Fixed Paraffin-embedded Tissue (FFPE/PET): blocks are preferred and will be sent back to client upon completion of testing
- Scrolls/unstained slides: cross-sectional area >1cm^2 send 10 sections of 10µm thickness, if <1cm^2 send 20 sections if available
Please note: We do not need a separate specimen aliquot for each test ordered. Only a single specimen aliquot or block of optimal quantity is necessary for performing multiple tests. If multiple aliquots or blocks of optimal quantity are sent, up to 2 will be pooled.
Forms & Requisitions
Molecular Microbiology Order Form
Handling Instructions
Please see Molecular Microbiology Specimen Submission for complete specimen collection and handling instructions.
Quantity
requested: See "Collection" for Optimal Quantity
minimum: Specimens below optimal quantity are acceptable for testing, however, diagnostic yield is generally proportional to specimen size.
Processing
UWMC/HMC: Store and send fresh tissue/fluid specimens refrigerated, if specimen storage and transport will exceed 8 hours, freeze at -20°C. Freeze all fresh tissue/fluid specimens at -20°C upon arrival in UW Molecular Microbiology.
Performance
LIS Dept Code
Micro Molecular Diag (MMD)
Performing Location(s)
| UW-MT |
Microbiology, Molecular Diagnostics
206-520-4600 ---------------------------------------- Shipping Address Attn: Molecular Microbiology Performing Lab Address Clinical Microbiology Lab, NW177 |
Contact Information Please e-mail us with any questions or comments you may have. Your inquiry will be answered as soon as possible. email: molmicdx@uw.edu The Molecular Microbiology lab is open from Monday-Friday, 7am-4pm PDT. Billing inquiries and requests for faxed reports can be made to our Client Services Department at (206) 520-4600 or (800) 713-5198. For results or other inquiries, we can be reached by phone at the following numbers:
For assistance during weekends, holidays and after hours, please contact Lab Medicine Resident at (206) 598-6190 |
|---|
Frequency
Fresh frozen tissues/fluids result in 2-3 business days after receipt of specimen. Formalin Fixed Paraffin-embedded tissues result in 3-4 business days after receipt of specimen.
Available STAT?
No