Oropharyngeal samples for genotyping and monitoring response to treatment in AIDS patients with Pneumocystis carinii pneumonia

A nested PCR, amplifying a portion of the gene encoding the mitochondrial l arge subunit ribosomal RNA (mt LSU rRNA) of Pneumocystis carinii sp, f. hom inis was applied to oropharyngeal samples obtained on repeated occasions fr om 12 HIV-infected patients with P. carinii pneumonia (PCP) to monitor resp onse to anti-P. carinii treatment. Genotyping of P. carinii sp. f. hominis was also performed on paired samples of oropharyngeal and broncho-alveolar lavage samples before the start of treatment, and on oropharyngeal samples during the course of treatment, by analysis of sequence variation at the in ternal transcribed spacer (ITS) regions of the nuclear rRNA operon, When a simple dilutional method was used, a reduction in the amount of amplificati on product was observed in samples from all patients during the course of t reatment. In eight of the 12 patients, a single ITS sequence type was found in the oropharyngeal samples and also in the paired broncho-alveolar lavag e sample. A mixed infection was identified in the samples from three patien ts. In eight patients, the ITS sequence types identified in the oropharynge al sample were the same as in the broncho-alveolar lavage sample. Nested PC R amplifying the mt LSU rRNA on oropharyngeal samples provides a non-invasi ve method of monitoring response to treatment of PCP, ITS sequence typing o f P. carinii sp. f. hominis from oropharyngeal samples appears to be a reli able alternative to broncho-alveolar lavage samples and provides a non-inva sive tool for further epidemiological studies.