Pneumocystis DNA detection by PCR

General Information

Lab Name

Lab Code

PNEDNA

Epic Ordering

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.

For more information on this test, to download a requisition form, and for a list of acceptable and unacceptable specimens, please refer to: Molecular Diagnosis Microbiology Section Website

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

Code	Name
PNERS	Pneumocystis PCR: Detection, Kex1
PNEID	Pneumocystis PCR: Identification, Kex1
PNESI	Pneumocystis PCR: Specimen Description
PNESPI	Pneumocystis PCR: External Identifier
PNESR	Pneumocystis PCR: Special Requests
PNESC	Pneumocystis PCR: Specimen Comments
PNENAE	Pneumocystis PCR: Specimen DNA Extraction
PNEREV	Pneumocystis PCR: Pathologist Review
PNEME	Pneumocystis PCR: Method Note

Interpretation

Method

DNA extraction, nucleic acid purification, polymerase chain reaction (PCR), sequencing

Reference Range

See individual components

Guidelines

Specialty testing for Molecular Microbiology

Ordering & Collection

Specimen Type

Tissue (Fresh frozen or paraffin-embedded), Fluid (see Acceptable Specimens for details)

Collection

Acceptable specimens are listed below. Please see this page for complete specimen collection and handling instructions.

Specimens should be collected into a DNA free container labeled with at least two identifiers.

Acceptable Specimens

Fresh frozen tissue
Fresh frozen fluid: any body fluid is acceptable if it is not listed under Unacceptable Specimens. See common examples below.
Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides are acceptable
eSwabs and UTM (universal transport media)

Common acceptable body fluid examples: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.

Additional Acceptable Specimens

Sputum

Unacceptable Specimens

Blood, serum, plasma, stool
No citrated or heparinized solutions
No SPS (Sodium Polyanethole Sulfonate) e.g. Wampole Isolator Tubes
Tissues floating in formalin
Swab/fluid collected in tube containing agar

Handling Instructions

Fresh frozen tissue/fluid specimens should 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.

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.

Quantity

requested: See Optimal Quantity above
minimum: Specimens below optimal quantity are acceptable for testing, however, diagnostic yield is generally proportional to specimen size.

Processing

Processing: UWMC/HMC – store and send specimen refrigerated and freeze specimens at -20°C upon arrival in UW-ML Microbiology. If specimen storage and transport will exceed 8 hours, freeze at -20°C.

Freeze specimens at -20°C upon arrival

Outside Laboratories: Freeze specimens in sterile containers at -20°C. Transport all specimens on dry ice.

Performance

LIS Dept Code

Micro Molecular Diag (MMD)

Performing Location(s)

UW-MT	Microbiology, Molecular Diagnostics 206-520-4600 Clinical Lab, Room # NW177, University of Washington Medical Center, 1959 NE Pacific street, Seattle, WA 98195

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?

Billing & Coding

CPT codes: 87798
LOINC: 6521-9
Interfaced Order Code: UOW4454