DIVERSITY OF HOST SPECIES AND STRAINS OF PNEUMOCYSTIS-CARINII IS BASED ON RIBOSOMAL-RNA SEQUENCES

We have amplified by PCR Pneumocystis carinii cytoplasmic small-subuni t rRNA (variously referred to as 16S-like or 18S-like rRNA) genes from DNA extracted from bronchoalveolar lavage and induced sputum specimen s from patients positive for P. carinii and from infected ferret lung tissue. The amplification products were cloned into pUC18, and individ ual clones were sequenced. Comparison of the determined sequences with each other and with published rat and partial human P. carinii small- subunit rRNA gene sequences reveals that, although all P. carinii smal l-subunit rRNAs are closely related (similar to 96% identity), small-s ubunit rRNA genes isolated from different host species (human, rat, an d ferret) exhibit distinctive patterns of sequence variation. Two type s of sequences were isolated from the infected ferret lung tissue, one as a predominant species and the other as a minor species. There was 96% identity between the two types. In situ hybridization of the infec ted ferret lung tissue with oligonucleotide probes specific for each t ype revealed that there were two distinct strains of P. carinii presen t in the ferret lung tissue. Unlike the ferret P, carinii isolates, th e small-subunit rRNA gene sequences from different human P. carinii is olates have greater than 99% identity and are distinct from all rat an d ferret sequences so far inspected or reported in the literature. Sou thern blot hybridization analysis of PCR amplification products from s everal additional bronchoalveolar lavage or induced sputum specimens f rom P. carinii-infected patients, using a P-32-labeled oligonucleotide probe specific for human P. carinii, also suggests that all of the hu man P. carinii isolates are identical. These findings indicate that hu man P. carinii isolates may represent a distinct species of P. carinii distinguishable from rat and ferret P. carinii on the basis of charac terization of small-subunit rRNA gene sequences.