Test Catalog

Test Id : PNRP

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Pneumocystis jiroveci, Molecular Detection, PCR, Varies

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Overview

Test Catalog

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

Preferred test for detection of Pneumocystis

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

Pneumocystis PCR

Specimen Type
Describes the specimen type validated for testing

Varies

Shipping Instructions

Specimen must arrive within 7 days of collection; specimens older than 7 days will be rejected.

Necessary Information

Specimen source is required.

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
SRC63 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 Pneumocystis species DNA is unlikely.

 

Submit only 1 of the following specimens:

 

Preferred 

Specimen Type: Body fluid

Sources: Pleural

Container/Tube: Sterile container

Specimen Volume: 1 mL

 

Specimen Type: Respiratory

Sources: Bronchoalveolar lavage, bronchial washing, tracheal secretions, or sputum

Container/Tube: Sterile container

Specimen Volume: 1 mL

 

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: Lavage fluid, bronchial washing, respiratory fluid, sputum, or tracheal secretion

Container/Tube: Sterile container

Specimen Volume: 2 mL

Collection Instructions:

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

0.5 mL

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

Other 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 Specimen >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

Preferred test for detection of Pneumocystis

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Pneumocystis pneumonia is an important cause of opportunistic infection in immunocompromised patients, 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. Unfortunately, stains often lack sensitivity and require expertise on the part of the reader in order to differentiate Pneumocystis jiroveci from staining artifacts and other fungi. This real-time PCR assay provides sensitive (21% more sensitive than direct detection using fluorescent calcofluor white stain), specific, and objective detection of Pneumocystis from bronchoalveolar lavage fluid and other specimens.

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 the presence of Pneumocystis DNA.

 

A negative result indicates the absence of detectable Pneumocystis DNA.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

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 and immunocompromised individuals. 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.

Supportive Data

A total of 221 bronchoalveolar lavage (BAL) fluid samples were evaluated for the presence of Pneumocystis DNA by the LightCycler and compared to fluorescent microscopy using calcofluor white staining. Of the 221, 24 were positive and 190 were negative by both detection methods. The remaining 7 were positive by PCR and negative by microscopy. The 7 specimens that were positive using LightCycler PCR alone were tested using another PCR assay targeting a second Pneumocystis gene. All 7 specimens were positive using the second target suggesting that they were true positives that were undetected using the microscopic method. The sensitivity, specificity, positive and negative predictive values of this real-time PCR assay is 100%, 96%, 77%, and 100%, respectively. The analytical sensitivity of the method is 5.6 copies/mcL of positive plasmid control or approximately 28 copies/reaction. The analytical sensitivity in spiked, pooled BAL specimens was found to be 56 targets/mcL using the positive control plasmid. PCR inhibition was tested by spiking 50 extracted negative respiratory specimens (including 10 BAL fluid specimens) with 100 copies of target/mcL using a positive control plasmid. No PCR inhibition was detected. The specificity of the PCR assay was determined by evaluating DNA extracted from pure cultures of a variety of bacteria and fungi. Extracted human DNA was analyzed as well. None of the microbial or human DNA was amplified by the Pneumocystis LightCycler assay indicating that the assay is specific for Pneumocystis species.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Cushion MT: Pneumocystis. In Manual of Clinical Microbiology. Eighth edition. Edited by PR Murray, EJ Baron, JH Jorgensen, et al: Washington, DC, ASM Press, 2003, pp 1712-1725

2. Maskell NA, Waine DJ, Lindley A, et al: Asymptomatic carriage of Pneumocystis jiroveci in subjects undergoing bronchoscopy: a prospective study. Thorax 2003;58(7):594-597

3. Miller RF, Ambrose HE, Wakefield AE: Pneumocystis carinii f. sp. hominis DNA in immunocompetent health care workers in contact with patients with P. carinii pneumonia. J Clin Microbiol 2001;39(11):3877-3882

4. Takahashi T, Goto M, Endo T, et al: Pneumocystis carinii carriage in immunocompromised patients with and without human immunodeficiency virus infection. J Med Microbiol 2002;51(7):611-614

5. Vargas SL, Hughes WT, Santolaya ME, et al: Search for primary infection by Pneumocystis carinii in a cohort of normal, healthy infants. Clin Infect Dis 2001;32(6):855-861

6. Wakefield AE, Lindley AR, Ambrose HE, et al: Limited asymptomatic carriage of Pneumocystis jiroveci in human immunodeficiency virus-infected patients. J Infect Dis 2003;187(6):901-908

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

Bronchoalveolar lavage fluid and sputum are liquefied using N-acetyl-L-cysteine. Following liquefication, cells are pelleted by centrifugation and resuspended in S.T.A.R. buffer (Roche). Nucleic acids are extracted using the MagNA Pure LC Instrument (Roche). The extract is then transferred to individual self-contained cuvettes for amplification using the LightCycler real-time PCR platform (Roche). 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 (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;54:169-175)

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
PNRP Pneumocystis PCR 89996-3
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.
SRC63 Specimen Source 31208-2
81698 Pneumocystis PCR, Result 89996-3
24188 Special Information 48767-8
24189 Report Status No LOINC Needed

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