Pneumocystis jirovecii - Pneumocystis Pneumonia

Pneumocystis jirovecii is a fungal organism that causes pneumonia predominantly in immunocompromised patients. PCR is the preferred testing method for immunocompromised patients who do not have HIV.

  • Diagnosis
  • Background
  • Lab Tests
  • References
  • Related Topics

Indications for Testing

  • Fever, shortness of breath, and cough in immunocompromised patients, particularly those at risk or positive for HIV

Laboratory Testing

  • Pneumocystis pneumonia (PCP) diagnosis and testing (CDC)
  • Polymerase chain reaction (PCR) – more sensitive than direct fluorescent antibody (DFA) staining
    • Preferred test for immunocompromised patients who do not have HIV – microscopy staining of fluids’ yield is low in these patients
    • Specimens include bronchoalveolar lavage (BAL), sputum, nasopharyngeal wash
  • DFA staining using monoclonal antibodies on induced sputum or BAL
  • Grocott-Gomori methenamine-silver stain or Giemsa stain on lung tissue specimen
  • Culture – cannot be easily cultured
  • Cytopathologic examination of Pap-stained BAL fluid
  • (1,3)-beta-D-glucan assay
    • Up to 30% false-positive rate
    • Not as well studied in P. jirovecii as other fungi


  • Immunohistochemistry – P. jirovecii stain

Imaging Studies

  • Chest x-ray
    • Bilateral symmetrical ground-glass opacities
    • 10-25% are normal
  • High resolution computed tomography (CT) – ground-glass opacities

Differential Diagnosis


  • Incidence
    • In AIDS patients – <1/100
    • In solid organ transplant patients not taking prophylactic antibiotics – 5-10/100
  • Sex – M:F equal (except in HIV-positive individuals, where M>F)
  • Transmission – airborne droplets


  • Classified as a fungus because RNA is homologous to fungal RNA
  • Four morphological forms – trophozoites, cysts, precysts, sporozoites
  • Cyst is diagnostic form – stains with Giemsa and methenamine silver
  • Formerly known as Pneumocystis carinii, sp hominis

Risk Factors

  • Immunocompromised status
    • Autoimmune disease on multiple drug therapies
    • Primary immunodeficiencies
  • AIDS (CD4+ <200 cells/µL)
  • Organ transplantation
    • Most transplant patients receive Pneumocystis pneumonia (PCP) prophylaxis
    • Heart/lung transplant patients infected with cytomegalovirus (CMV)
    • Solid organ more common

Clinical Presentation

  • Subacute- to acute-onset pneumonia – non-HIV immunocompromised patients more likely to have acute presentation
  • Dyspnea, tachypnea, tachycardia, cyanosis (hypoxemia), nonproductive cough, fever
  • Coinfection with CMV may occur
  • Complications
    • Acute respiratory failure
    • Pneumothorax/pneumomediastinum
    • Dissemination disease
      • Almost exclusively in patients with HIV
      • Most common in lymph nodes, spleen, kidney, liver, thyroid, bone marrow
Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

Pneumocystis jirovecii by PCR 2006254
Method: Qualitative Polymerase Chain Reaction

Pneumocystis jirovecii DFA with Reflex to Pneumocystis jirovecii by PCR 2009226
Method: Direct Fluorescent Antibody Stain/Qualitative Polymerase Chain Reaction


Sensitivity dependent on patient population and specimen type

Negative result does not exclude possibility of infection; false-negative results may occur due to sampling errors or low number of organisms in specimen

Pneumocystis jirovecii DFA 0060052
Method: Direct Fluorescent Antibody Stain


Sensitivity dependent on patient population and specimen type

Negative result does not exclude possibility of infection; false-negative results may occur due to sampling errors or low number of organisms in specimen

Special Stain, Grocott's Methenamine Silver (GMS) 2005945
Method: Special Stain

(1,3)-Beta-D-Glucan (Fungitell) 2002434
Method: Semi-Quantitative Colorimetry


Does not detect fungal species that produce very low levels of (1-3)-beta-D-glucan (eg, Cryptococcus)

Does not detect Zygomycetes (eg, AbsidiaMucorRhizopus)

Yeast phase of Blastomyces dermatitidis may not be detected

Explify Respiratory Pathogens by Next Generation Sequencing 2013694
Method: Massively Parallel Sequencing

General References

Calderón EJ, Gutiérrez-Rivero S, Durand-Joly I, Dei-Cas E. Pneumocystis infection in humans: diagnosis and treatment. Expert Rev Anti Infect Ther. 2010; 8(6): 683-701. PubMed

Catherinot E, Lanternier F, Bougnoux M, Lecuit M, Couderc L, Lortholary O. Pneumocystis jirovecii Pneumonia. Infect Dis Clin North Am. 2010; 24(1): 107-38. PubMed

Fujii T, Nakamura T, Iwamoto A. Pneumocystis pneumonia in patients with HIV infection: clinical manifestations, laboratory findings, and radiological features. J Infect Chemother. 2007; 13(1): 1-7. PubMed

Gilroy SA, Bennett NJ. Pneumocystis pneumonia. Semin Respir Crit Care Med. 2011; 32(6): 775-82. PubMed

Reid AB, Chen SC, Worth LJ. Pneumocystis jirovecii pneumonia in non-HIV-infected patients: new risks and diagnostic tools. Curr Opin Infect Dis. 2011; 24(6): 534-44. PubMed

Theel ES, Doern CD. β-D-glucan testing is important for diagnosis of invasive fungal infections. J Clin Microbiol. 2013; 51(11): 3478-83. PubMed

Medical Reviewers

Last Update: November 2017