TYPING OF PNEUMOCYSTIS-CARINII STRAINS THAT INFECT HUMANS BASED ON NUCLEOTIDE-SEQUENCE VARIATIONS OF INTERNAL TRANSCRIBED SPACERS OF RIBOSOMAL-RNA GENES

Small portions of the 18S and the 26S rRNA genes, the entire 5.8S rRNA gene, and internal transcribed spacers ITS1 and ITS2 (located between the 18S and 5.8S rRNA genes and between the 5.8S and 26S rRNA genes, respectively) of Pneumocystis carinii that infect humans were cloned a nd sequenced. The nucleotide sequences of the 18S, 5.8S, and 26S rRNA genes determined in the study were approximately 90% homologous to tho se of P. carinii that infect rats, while the sequences of ITS1 and ITS 2 of P. carinii from the two different hosts were only 60% homologous. The 18S, 5.8S, and 26S rRNA gene sequences of P. carinii from 15 pati ent specimens were determined and were found to be identical to each o ther, whereas the ITS sequences were found to be variable. With the ob served sequence variation, it was possible to classify the ITS1 sequen ces into two types and the ITS2 sequences into three types. P. carinii strains that had the same type of ITS1 sequence could have a differen t type of ITS2, sequence. On the basis of the sequence types of the tw o ITS regions, P. carinii from the 15 patients were classified into fo ur groups. P. carinii from three patient specimens were found to conta in two different ITS sequence patterns. More surprisingly, one additio nal specimen was found to have one ITS sequence typical of P. carinii isolates that infect humans and another typical of P. carinii Isolates that infect rats. The studies indicate that it is possible to type P. carinii strains on the basis of their ITS sequences and that more tha n one ITS sequence pattern may be demonstrated in P. carinii from one patient, suggesting that coinfection with more than one strain of P. c arinii may occur in the same patient.