PNRP - Clinical: Pneumocystis jiroveci, Molecular Detection, PCR

Test Catalog

Test Name

Test ID: PNRP    
Pneumocystis jiroveci, Molecular Detection, PCR

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