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In 1988, DNA analysis showed that Pneumocystis is a fungus and not a protozoan. In 2001, further DNA analysis showed that Pneumocystis is species specific to the host it infects. Therefore, the species infecting humans has been renamed Pneumocystis jeroveci (pronounced “yee row vet zee”) in honor of the Czech parasitologist, Otto Jirovec who initially described the organism in humans. According to the International Code of Botanical Nomenclature, it is no longer correct to refer to the human Pneumocystis organism as P. carinii. Pneumocystis jiroveci is a causative agent of pneumonia in immunocompromised individuals, especially those infected with HIV.

Traditionally, pneumocystis has been detected in respiratory specimens by means of special staining, either by the Gomori methenamine silverstain (GMS) or fluorescent antibody (DFA). The Gomori methenamine silver stain is specific for cyst walls. Trophozoites do not stain. Positive smears show darkly staining cysts, usually in clumps, against a green background. The organisms must be differentiated from yeast cells and occasional white and red blood cells, which also stain brown to black. The disadvantages of special stains are lack of sensitivity, expertise required for interpretation, and labor intensiveness of the process.

Real time polymerase chain reaction (PCR) assay for detection of Pneumocystis has proven to be much more sensitive than special stains. PCR is now the preferred method to detect this organism. Bronchoalveolar lavage fluid (0.5 mL minimum) is the preferred specimen. Induced sputum, bronchial washings, and tracheal aspirates are also acceptable.

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