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Pneumocystis jirovecii (formerly Pneumocystis carinii) is a common, atypical opportunistic fungal pathogen, causing a severe, life-threatening disease called Pneumocystis pneumonia (PCP) in patient’s immunosuppressed by HIV infection, malignancy, transplantation, or therapeutic immunosuppression (Saric et al., 1994; Aderaye et al., 2003). PCP is associated with substantial morbidity, and mortality rates range from 10% to 40%. The diagnosis of PCP relies on the microscopic detection of P. jirovecii in stained clinical samples. Polymerase chain reaction (PCR) may provide better sensitivity than microscopy; therefore, evaluation and implementation of PCR assays are required for the detection of Pneumocystis infection. P. jirovecii is not cultivatable, therefore molecular tools are used for characterizing P. jirovecii genotypes; common targets are the dihydropteroate synthase (DHPS) and mitochondrial large subunit rRNA (mtLSU rRNA) genes. DHPS is a therapeutic target; mutations may be associated with co-trimoxazole prophylaxis and treatment failure. Polymorphisms in mtLSUrRNA have been used for phylogenetic studies.
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