Heterogeneity and compartmentalization of Pneumocystis carinii f. sp hominis genotypes in autopsy lungs

The extent and importance of genotype heterogeneity of Pneumocystis carinii L sp. hominis within lungs have not previously been investigated. Two hund red forty PCR clones obtained from respiratory specimens and lung segments from three patients with fatal P. carinii pneumonia were investigated to de tect genetic diversity in the internal transcribed spacer (ITS) region of t he nuclear rRNA operon, the mitochondrial large-subunit (mtLSU) rRNA gene, and the dihydropteroate synthase-encoding gene. For two of the three examin ed patients, a mixture of different mtLSU rRNA and ITS genotypes was observ ed. Not all genotypes present in the lungs at autopsy were detected in the diagnostic respiratory samples. Compartmentalization of specific ITS and mt LSU rRNA sequence types was observed in different lung segments. In conclus ion, the interpretation of genotype data and in particular ITS sequence typ es in the assessment of epidemiological questions should be cautious since genotyping done on respiratory samples cannot a priori be assumed to repres ent all genotypes present within the lung.