This organism is thought to be a sporozoan parasite with some similarities to Toxoplasma. Clinical infection is very frequent in patients who are immunocompromised and is rare otherwise. However, immunocompromise is selective; predominantly conditions that decrease T4 lymphocyte number or function (e.g., HIV-1 and HTLV-I infection, childhood acute lymphoblastic leukemia, and cyclosporin or corticosteroid therapy). About 70% of patients with AIDS eventually develop pneumocystis disease (range, 35%-80%), almost always confined to the lungs and with T4 lymphocyte counts below 200mm3. Infections present as pneumonia that rapidly becomes bilateral, with an x-ray pattern of the interstitial type with or without an alveolar component. At present, tissue culture is necessary for culture diagnosis. Currently, the most common means of diagnosis are nonimmunologic special stains performed on material from one of the following sources: lung transbronchial biopsies, with about 85% detected (range, 35%-98%); bronchial lavage, about 85%-90% detected (range, 59%-100%); bronchial brushing, about 40% detected (range, 12%-57%); aerosol-induced sputum, about 57% detected (range, 55%-79%); open lung biopsy, about 65% detected, and lung needle aspiration. Ordinary (noninduced) sputum is not considered an adequate source material. Sensitivity of these methods depends not only on the method but also on technique and the way the organisms are visualized (type of stain, antibody used, etc.). There are advocates for rapid staining techniques using touch preparations and stains such as toluidine blue O and also for the much more time-consuming silver stains such as methenamine silver. Each stain has been reported to detect as many as 75%-85% of cases. However, such statistics depend to a considerable extent on how the specimen was obtained and the experience of the institution. Toluidine blue O stain is much faster than silver strain but in general requires significantly more experience to interpret. Both toluidine blue O and silver methods stain pneumocystic cyst walls. Yeast cells are about the same size as pneumocystic cysts, and also stain with cyst wall stains. Differentiation between yeast and pneumocystic cysts may sometimes be difficult, especially if there are only a few organisms. Gram stain, Giemsa, or Wright’s stain used on smears can demonstrate pneumocystic trophozoites within cysts; the cyst wall does not stain. Trophozoite detection requires considerable experience and is much more time-consuming and less sensitive (in most laboratories) than cyst wall stains.

Immunofluorescent commercial kits using either direct (applied to specimen or slides) or indirect (liquid specimen) are available, and several evaluations found their sensitivity equal to or somewhat better than various histologic stains (85%-90% sensitivity; range, 27%-97%). One study using nucleic acid probes with PCR amplification reported sensitivity of 70% compared to the IFA sensitivity of 52% on induced sputum. Another study reported 100% sensitivity.