Pneumocystis Jirovecii Pneumonia

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PatientPlus articles are written by UK doctors and are based on research evidence, UK and European Guidelines. They are designed for health professionals to use, so you may find the language more technical than the condition leaflets.

See also: Antibiotics written for patients

Synonym: pneumocystosis

Pneumocystis pneumonia (PCP) is a major cause of morbidity and mortality among immunocompromised people. It remains a leading AIDS-defining opportunistic infection in HIV-infected individuals.[1] Pneumocystis is primarily a pulmonary pathogen but the incidence of extrapulmonary disease has been estimated at 0.06-2.5% of cases.[2] 

Pneumocystis organisms from different host species have very different DNA sequences, indicating multiple species. Because of the genetic and functional distinctness, the organism that causes human PCP (formerly known as Pneumocystis carinii) is now named Pneumocystis jirovecii.[3] 

P. jirovecii is a unicellular eukaryote which shares characteristics with both protozoa and fungi.

  • DNA studies suggest that P. jirovecii is frequently found in healthy adults in the normal community. It can cause a transient infection in an immunocompetent host.[4] 
  • A UK study of reported cases in England between 2000-2010 showed an increase of laboratory-confirmed cases of 7% per year. These were principally non-HIV infected cases, mainly in immunocompromised transplant recipients or patients with haematological malignancy.[5] 
  • The introduction of highly active antiretroviral therapy (HAART) dramatically reduced the incidence of PCP in HIV-positive individuals.[6] It fell from 4.9 cases per 100 person-years before March 1995 to 0.3 cases per 100 person-years after March 1998.[7] 
  • In the developing world, rates of PCP are lower, possibly due to poor survival with HIV, underdiagnosis and prior pulmonary infection with tuberculosis and other organisms.[8] 

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Risk factors[9][10] 

  • PCP tends to affect HIV-positive patients who have a CD4 count below 200 cells/mm3.
  • HIV patients with oral thrush or fever, or AIDS-defining diagnosis.
  • Patients taking steroids or other immunosuppressants.
  • Patients with haematological malignancy.
  • Organ transplant recipients.
  • Connective tissue diseases such as rheumatoid arthritis.
  • Congenital immune deficiency - eg, thymic aplasia, severe combined immune deficiency (SCID), hypogammaglobulinaemia.
  • Severe malnutrition (poor nutrition in HIV-positive individuals increases risk).
  • Pre-existing lung disease.
  • Cough is usually non-productive but productive cough may occur in up to a third of patients.
  • Exertional dyspnoea.
  • Fever.
  • Tachypnoea.
  • Chest pain.
  • There may be signs of AIDS such as thrush, oral hairy leukoplakia or Kaposi's sarcoma.
  • Respiratory examination is highly variable and often normal. Scattered crackles and wheeze may be present, or (rarely) signs of focal consolidation.
  • Pulse oximetry may show low SaO2 at rest.
  • Extrapulmonary disease may manifest as hepatosplenomegaly, lymphadenopathy or ocular disease.

Blood tests

  • Elevated lactate dehydrogenase is indicative of the diagnosis but not highly specific or sensitive.
  • Arterial blood gases may show hypoxia and hypocarbia due to hyperventilation.
  • The alveolar-arterial oxygen tension gradient may be increased.
  • The use of serum (1→3) beta-D-glucan levels (high in PCP) is being investigated as a diagnostic test.[12]
  • PCR can be used for early diagnosis of PCP in HIV-infected patients.[13]


  • CXR can be normal or show perihilar fluffy shadows or pneumothorax.
  • Standard CT imaging shows ground glass infiltrates but has low sensitivity and specificity.
  • High-resolution CT, however, has a sensitivity of 100% and a specificity of 89%.[14]
  • Gallium scanning is highly sensitive but with low and variable specificity.


  • The organism cannot be routinely cultured and is detected by staining of the cyst wall or trophozoite in sputum samples, usually with silver-based stains. Repeated samples may need to be taken to confirm the diagnosis.
  • Sputum may be collected following inhalation of nebulised saline and/or chest physiotherapy and should also be sent for routine and mycobacterial culture.
  • If sputum is negative but PCP is still suspected, then bronchoscopy with bronchoalveolar lavage or transbronchial biopsy may detect the organism.
  • Open lung biopsy may occasionally be employed.

Pulmonary function tests

  • May show a modest reduction in the vital capacity (VC) and the total lung capacity (TLC).
  • The most consistent abnormality is a decrease in the single-breath diffusing capacity for carbon monoxide (DLCO), which has a sensitivity of 89%.


  • Breathlessness on mild exercise, which may be associated with cough and sweats.
  • Arterial blood gases and oxygen saturation at rest, on air: PaO2 >11 kPa; SaO2 >96%.
  • CXR: normal or minor perihilar infiltrates.


  • Breathlessness on minimal exercise, fever (with or without sweats).
  • Arterial blood gases and oxygen saturation at rest, on air: PaO2 8-11 kPa; SaO2 91-96%.
  • CXR: diffuse interstitial shadowing.


  • Breathlessness at rest, persistent fever and cough.
  • Arterial blood gases and oxygen saturation at rest, on air: PaO2 <8 kPa; SaO2 <91%.
  • CXR: extensive interstitial shadowing, with or without alveolar shadowing.
  • Early diagnosis greatly aids successful therapy.
  • It is important to consider the diagnosis in patients who are HIV-negative but have other risk factors.[17] 
  • Mild cases may be treated with oral medication, as outpatients. Moderate-to-severe cases usually require hospitalisation and intravenous therapy.
  • Treating empirically without confirmation of the diagnosis may be necessary but is best avoided if possible, due to the danger of missing other causes for the symptoms.
  • Patients often deteriorate 3-5 days after starting treatment. This is thought to be due to inflammation caused by dead pneumocystis organisms.
  • A favourable response to treatment may take 7 days or more.

Mild-to-moderate disease

  • High-dose co-trimoxazole (trimethoprim-sulfamethoxazole) is the drug of choice. Concomitant host disease influences susceptibility to adverse drug reactions. HIV increases the risk of toxicity with many drugs including co-trimoxazole. Adverse effects and hypersensitivity reactions are common in such patients and include fever and maculopapular rash. Co-trimoxazole is usually well tolerated in immunocompetent patients but should be avoided in those with severe hepatic or renal dysfunction and porphyria.[18] It is also best avoided during pregnancy and breast-feeding. Side-effects are numerous and include nausea, vomiting, skin reactions, neutropenia, thrombocytopenia, hepatitis and cholestatic jaundice.[18] 
  • Alternatives if the patient is unable to tolerate co-trimoxazole are:
    • Atovaquone suspension - this has similar efficacy as pentamidine and is better tolerated than parenteral pentamidine, co-trimoxazole or dapsone. However, oral atovaquone has limited and unpredictable bioavailability.[10] 
    • Dapsone with trimethoprim - dapsone is given intravenously or occasionally in nebulised form in the treatment of PCP.
    • Clindamycin with primaquine (unlicensed use in the UK) - clindamycin is associated with the development of antibiotic-associated colitis and treatment must be immediately discontinued if diarrhoea develops.
    • Aerosolised pentamidine isetionate is no longer recommended because it is associated with increased frequency of relapse.[19] 

Severe disease

  • Intravenous high-dose co-trimoxazole is first-line treatment but toxic effects mean it may not be tolerated.
  • Pentamidine isetionate:
    • Given by intravenous infusion, is used for patients who either cannot tolerate co-trimoxazole or who have not responded to it.
    • Can cause severe hypotension during or immediately after infusion; blood pressure and glucose should be carefully monitored.
  • Oral prednisolone or parenteral hydrocortisone:
    • Steroids are an important adjunctive therapy for patients with moderate-to-severe infections associated with HIV infection.
    • Steroids are usually given in high dosage for 5-7 days and then the dose is reduced and continued for a further two weeks.
    • Steroid treatment should be started at the same time as the antimicrobial therapy and withdrawn before antimicrobial treatment is complete.

Trimethoprim and dapsone may be used in combination for mild-to-moderate PCP, although unlicensed.[18] An alternative regimen should be used in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency.[18]

Prior to the HIV epidemic, co-trimoxazole was rarely used in developed countries due to concerns regarding toxicity. Resistance to co-trimoxazole in such countries was therefore very low. However, since the use of co-trimoxazole and dapsone for the treatment and long-term prophylaxis of PCP and toxoplasmosis, increased levels of resistance have been detected.[20] 

A number of single base polymorphisms have been demonstrated in the P. jirovecii nucleotide sequence that codes for dihydropteroate synthetase. These mutations may affect substrate binding and be associated with the emergence of resistance to sulfonamides and dapsone.[21] Mutations in the cytochrome b gene have been demonstrated in atovaquone-resistant P. jirovecii isolates, which are likely to represent mechanisms of resistance.[22] 

Findings linking mortality rates to the acquisition of the mutated P. jirovecii organism are inconsistent, which is not surprising, since survival in HIV-positive patients depends on many other factors. However, it does make assessment of the impact of drug resistance in such patients difficult and more research is required to develop strategies to prevent the emergence of further resistance strains.[23]

Before the introduction of HAART, the two-year probability of developing PCP in HIV-positive patients was 40%. HAART has reduced the rate of opportunistic infections and so the absolute benefit of prophylactic treatment in those taking HAART is less significant. Recent studies have suggested that in HIV patients taking HAART with CD4 T-cell counts above 200 cells/mm3, discontinuation of prophylaxis does not increase the incidence of PCP. Current guidelines recommend that persons who meet these criteria can discontinue PCP prophylaxis and remain off prophylaxis as long as the CD4 T-cell count remains above 200 cells/mm3.[19] For more information see separate article Antiretroviral Agents.

New drugs against P. jirovecii are in development. Caspofungin, an echinocandin which inhibits beta-glucan synthesis, has been used in America as a salvage drug in severe cases. It is not always effective and is not currently licensed in the UK.[24] Sordarin derivatives and novel types of azoles have shown promising activity against PCP.[25] The promise of future new targets is expected with the annotation of the pneumocystis genome.[26] 

Drug prophylaxis reduces the incidence of PCP and lengthens the disease-free intervals between episodes.

  • It should be considered for:
    • All patients with a history of the pneumocystis infection.
    • Severely immunocompromised patients.
    • All HIV-positive individuals once their CD4 T-cell count falls below 200 cells/mm3.
  • Prophylaxis should continue until immunity recovers sufficiently.
  • Oral co-trimoxazole by mouth is the drug of choice.
  • Dapsone and atovaquone have also been used for prophylaxis.
  • Patients (particularly children) who start HAART and attain low HIV viral load and improved CD4 counts may have prophylactic therapy safely discontinued.
  • Respiratory failure.
  • Acute respiratory distress syndrome.
  • Worsening of condition after starting therapy.
  • Pulmonary cyst formation.
  • Pneumothorax.
  • Haematogenous spread.
  • Extrapulmonary infection (typically affecting the bone marrow, liver, spleen, lymph nodes, gut and eyes).

The use of HAART has made significant changes to the prognosis of HIV-related pulmonary infections. Currently, the most common HIV-related pulmonary infection diagnosed in developed countries is bacterial pneumonia, and in developing countries, tuberculosis.[14] An American study of hospitalised patients reported a mortality rate of 10.3%. Mortality is about 10-20% in mild-to-moderate cases, rising to 65% in patients who require artificial ventilation.[14] Due to restricted access to optimal medical care, PCP remains a common AIDS-defining illness in developed nations and is associated with significant morbidity and mortality.[27] 

Further reading & references

  • Fong S, Daly KR, Tipirneni R, et al; Antibody responses against Pneumocystis jirovecii in health care workers over time. Emerg Infect Dis. 2013 Oct;19(10):1612-9. doi: 10.3201/eid1910.121836.
  • Cisse OH, Pagni M, Hauser PM; De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient. MBio. 2012 Dec 26;4(1):e00428-12. doi: 10.1128/mBio.00428-12.
  1. Miller RF, Huang L, Walzer PD; Pneumocystis pneumonia associated with human immunodeficiency virus. Clin Chest Med. 2013 Jun;34(2):229-41. doi: 10.1016/j.ccm.2013.02.001. Epub 2013 Apr 8.
  2. Anuradha, Sinha A; Extrapulmonary Pneumocystis carinii infection in an AIDS patient: a case report. Acta Cytol. 2007 Jul-Aug;51(4):599-601.
  3. Calderon EJ; Pneumocystis infection: seeing beyond the tip of the iceberg. Clin Infect Dis. 2010 Feb 1;50(3):354-6. doi: 10.1086/649870.
  4. Medrano FJ, Montes-Cano M, Conde M, et al; Pneumocystis jirovecii in general population. Emerg Infect Dis. 2005 Feb;11(2):245-50.
  5. Maini R, Henderson KL, Sheridan EA, et al; Increasing Pneumocystis pneumonia, England, UK, 2000-2010. Emerg Infect Dis. 2013 Mar;19(3):386-92. doi: 10.3201/eid1903.121151.
  6. Llibre JM, Revollo B, Vanegas S, et al; Pneumocystis jirovecii pneumonia in HIV-1-infected patients in the late-HAART era in developed countries. Scand J Infect Dis. 2013 Aug;45(8):635-44. doi: 10.3109/00365548.2013.777778. Epub 2013 Apr 3.
  7. Morris A, Lundgren JD, Masur H, et al; Current epidemiology of Pneumocystis pneumonia. Emerg Infect Dis. 2004 Oct;10(10):1713-20.
  8. Lowe DM, Rangaka MX, Gordon F, et al; Pneumocystis jirovecii pneumonia in tropical and low and middle income countries: a systematic review and meta-regression. PLoS One. 2013 Aug 2;8(8):e69969. doi: 10.1371/journal.pone.0069969. Print 2013.
  9. Pneumocystis jirovecii pneumonia (PCP) prevention; Press release, Public Health England, 2013
  10. Rodriguez M, Fishman JA; Prevention of infection due to Pneumocystis spp. in human immunodeficiency virus-negative immunocompromised patients. Clin Microbiol Rev. 2004 Oct;17(4):770-82, table of contents.
  11. Cisse OH, Pagni M, Hauser PM; De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient. MBio. 2012 Dec 26;4(1):e00428-12. doi: 10.1128/mBio.00428-12.
  12. Onishi A, Sugiyama D, Kogata Y, et al; Diagnostic accuracy of serum 1,3-beta-D-glucan for pneumocystis jiroveci pneumonia, invasive candidiasis, and invasive aspergillosis: systematic review and meta-analysis. J Clin Microbiol. 2012 Jan;50(1):7-15. doi: 10.1128/JCM.05267-11. Epub 2011 Nov 9.
  13. Chawla K, Martena S, Gurung B, et al; Role of PCR for diagnosing Pneumocystis jirovecii pneumonia in HIV-infected individuals in a tertiary care hospital in India. Indian J Pathol Microbiol. 2011 Apr-Jun;54(2):326-9. doi: 10.4103/0377-4929.81624.
  14. Benito N, Moreno A, Miro JM, et al; Pulmonary infections in HIV-infected patients: an update in the 21st century. Eur Respir J. 2012 Mar;39(3):730-45. doi: 10.1183/09031936.00200210. Epub 2011 Sep 1.
  15. Spiro S et al; Grading Severity of Pneumocystis jirovecii Pneumonia, Clinical Respiratory Medicine, 2012
  16. Treatment of opportunistic infection in HIV-seropositive individuals; British HIV Association (2011)
  17. McKinnell JA, Cannella AP, Kunz DF, et al; Pneumocystis pneumonia in hospitalized patients: a detailed examination of symptoms, management, and outcomes in human immunodeficiency virus (HIV)-infected and HIV-uninfected persons. Transpl Infect Dis. 2012 Oct;14(5):510-8. doi: 10.1111/j.1399-3062.2012.00739.x. Epub 2012 May 1.
  18. British National Formulary
  19. Guidelines for Prevention and Treatment of Opportunistic Infections in HIV-Infected Adults and Adolescents; AIDSinfo, 2013
  20. Harris JR, Marston BJ, Sangrujee N, et al; Cost-effectiveness analysis of diagnostic options for pneumocystis pneumonia (PCP). PLoS One. 2011;6(8):e23158. doi: 10.1371/journal.pone.0023158. Epub 2011 Aug 15.
  21. Friaza V, Morilla R, Respaldiza N, et al; Pneumocystis jiroveci dihydropteroate synthase gene mutations among colonized individuals and Pneumocystis pneumonia patients from Spain. Postgrad Med. 2010 Nov;122(6):24-8. doi: 10.3810/pgm.2010.11.2219.
  22. Baggish AL, Hill DR; Antiparasitic agent atovaquone. Antimicrob Agents Chemother. 2002 May;46(5):1163-73.
  23. Huang L, Morris A, Limper AH, et al; An Official ATS Workshop Summary: Recent advances and future directions in pneumocystis pneumonia (PCP). Proc Am Thorac Soc. 2006 Nov;3(8):655-64.
  24. Kim T, Hong HL, Lee YM, et al; Is caspofungin really an effective treatment for Pneumocystis jirovecii pneumonia in immunocompromised patients without human immunodeficiency virus infection? Experiences at a single center and a literature review. Scand J Infect Dis. 2013 Jun;45(6):484-8. doi: 10.3109/00365548.2012.760842. Epub 2013 Jan 15.
  25. Lorand T, Kocsis B; Recent advances in antifungal agents. Mini Rev Med Chem. 2007 Sep;7(9):900-11.
  26. Ma L, Huang DW, Cuomo CA, et al; Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis. FASEB J. 2013 May;27(5):1962-72. doi: 10.1096/fj.12-224444. Epub 2013 Feb 7.
  27. Morrow BM, Samuel CM, Zampoli M, et al; Pneumocystis pneumonia in South African children diagnosed by molecular methods. BMC Res Notes. 2014 Jan 10;7(1):26. doi: 10.1186/1756-0500-7-26.

Disclaimer: This article is for information only and should not be used for the diagnosis or treatment of medical conditions. EMIS has used all reasonable care in compiling the information but make no warranty as to its accuracy. Consult a doctor or other health care professional for diagnosis and treatment of medical conditions. For details see our conditions.

Original Author:
Dr Colin Tidy
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Peer Reviewer:
Prof Cathy Jackson
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