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Pneumocystis jirovecii by Polymerase Chain Reaction (PCR)

Technical Brief

Pneumocystis jirovecii by Polymerase Chain Reaction (PCR)

Test Name

Pneumocystis jirovecii PCR (PCPPCR)

CPT Codes



Polymerase Chain Reaction (PCR)

Turnaround Time

3–5 days

Specimen Requirements

Specimen Type:
Bronchoalveolar lavage (BAL)
Sputum, Induced or Expectorated
Tracheal Lavage/Wash
Tissue, Lung

2 mL

Minimum Volume:
1 mL

Collection Container:
Sterile specimen container

Transport Temperature:


24 hours

Refrigerated (2° – 8° C):
7 days

Frozen (-20° – -70° C):
30 days

Background Information

Pneumocystis jirovecii is an atypical fungus that causes Pneumocystis pneumonia (PCP) in patients with a compromised immune system. Transplant recipients and those with poorly controlled HIV are at highest risk, but those receiving chemotherapy for malignant diseases and others with immunosuppression may also develop the disease. PCP is an important cause of morbidity and mortality in immunocompromised patients.

The diagnosis of PCP is a challenge since the microorganism does not grow in conventional culture. However, prompt and accurate detection of PCP is critically important for patient care, since the therapeutic agent used to treat patients with this infection is different from those employed for community-acquired pneumonia. Therefore, without an accurate diagnosis, the patient may be receiving inappropriate therapy.

Although direct examination of respiratory specimens has been used for years for the detection of Pneumocystis, these methods lack sensitivity or specificity. Cleveland Clinic Laboratories’ Molecular Pathology section and others have demonstrated that nucleic acid detection using Pneumocystis-specific primers and the polymerase chain reaction (PCR) is superior to conventional morphologic detection with respect to both sensitivity and specificity. Therefore, we now offer this method for the detection of Pneumocystis in respiratory specimens from patients at risk for this disease.

Clinical Indications

PCP is an opportunistic infection that can cause a lung infection in individuals with a weakened immune system, including those taking medications that may affect the immune system. The symptoms of PCP include breathing difficulties, fever, and a dry cough. Other symptoms include fatigue, night sweats, weight loss, and chest tightness.

Antibiotics are usually recommended for those with mild, moderate or severe PCP. The key to surviving PCP is early treatment.

DNA PCR is useful in detecting the organism, tracking the course of infection, and monitoring response to treatment.[1]


Amplification and detection of the specimen using real-time, qualitative PCR comparing DNA taken from bronchial samples or sputum.


The test results should aid in the diagnosis of pneumocystosis.

When “rare” quantities are detected, then the possibilities of early infection, resolving infection, or transient colonization should be considered.

Although a negative result does not entirely rule out the presence of PCP, the negative predictive value of this test is very high.


A positive result indicates the presence of Pneumocystis DNA.

A negative result indicates the absence of detectable Pneumocystis DNA.


1. Cushion MT: Pneumocystis. In Manual of Clinical Microbiology. 8th edition. Edited by PR Murray, EJ Baron, JH Jorgensen, et al. Washington, DC, ASM Press, 2003; pp 1712-1725.

2. 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.

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

4. Aliouat-Denis, C-M., et al. (2008). Pneumocystis species, co-evolution and pathogenic power. Infection, Genetics & Evolution 8 (5): 708–726. doi:10.1016/j.meegid.2008.05.0.001. PMID. 18565802.

5. Ponce CA, Gallo M, Bustamante R, Vargas SL (2010). Pneumocystis colonization is highly prevalent in the autopsied lungs of the general population. Clin Infect Dis 50 (3): 347353. doi:10.1086/649868. PMID 20047487.

6. 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. March 2001;32(6):855-861.