Pneumocystis Jirovecii (Formerly Pneumocystis Carinii), Microscopic Detection


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Subject: Pneumocystis Jirovecii (Formerly Pneumocystis Carinii), Microscopic Detection

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  • Pneumocystis jirovecii, a fungal pathogen, is ubiquitous in nature, with low pathogenic potential. In severely immunocompromised patients, especially patients with AIDS, however, it is responsible for potentially fatal respiratory disease.


  • This test is used to detect infection with the fungal pathogen P. jirovecii in lower respiratory specimens. This test may be used to evaluate immunocompromised patients who present with severe atypical pneumonia.

  • Method:

    • Direct examination of respiratory specimens for P. jirovecii can be performed using several staining methods. Detection is based on the identification of organisms with typical morphology; different reagents may stain the “cyst” form, “trophozoite” form, or both.

    • Giemsa-based stains are convenient but may be difficult to read because of staining of background material. Sensitivity is approximately 50%. Stains using tagged monoclonal antibody reagents provide the highest sensitivity, approximately 91%. Calcofluor white staining has sensitivity approximately 74%. GMS staining provides sensitivity approximately 79%. Staining techniques have excellent specificity when interpreted by experienced microbiologists.

Special Collection and Transport Instructions

  • Acceptable specimens include material obtained by BAL or sputum induced using nebulized hypertonic saline.

    • Transbronchial or surgical biopsy specimens are acceptable specimens for Pneumocystis detection.

    • Expectorated sputum and respiratory secretions obtained by suction through an endotracheal tube or after percussive respiratory therapy are not acceptable for Pneumocystis testing.


  • The performance of tests for direct detection of P. jirovecii depends on numerous factors, including the prior probability of infection, type of specimen submitted, specimen processing, and staining method used.

  • Submission of expectorated sputum, tracheal aspirates, or specimens other than induced sputum, BAL, or biopsy specimens results in poor detection of P. jiroveci.

Suggested Readings

Cruciani  M, Marcati  P, Malena  M, et al. Meta-analysis of diagnostic procedures for Pneumocystis carinii pneumonia in HIV-1-infected patients. Eur Respir J.  2002;20:982–989.
Procop  GW, Haddad  S, Quinn  J, et al. Detection of Pneumocystis jiroveci in respiratory specimens by four staining methods. J Clin Microbiol.  2004;42(7):3333–3335.
Thomas  CF Jr, Limper  AH. Pneumocystis pneumonia. N Engl J Med.  2004;350:2487–2498.