The prevalence of Pneumocystis carinii pneumonia (PCP) in humans caused by more than a single genotype has been reported to range from 10 to 67%, depending on the method used for detection (3, 19). Most coinfections were associated with primary rather than recurrent disease. To better understand the factors influencing the development of coinfections, the time periods between inoculations and the genotype of the infecting organisms were evaluated in the chronically immunosuppressed-inoculated rat model of PCP. P. carinii f. sp. carinii infecting rats differentiated by karyotypic profiles exhibit the same low level of genetic divergence manifested by organisms infecting humans. P. carinii f. sp. carinii karyotype forms 1, 2, and 6 were inoculated into immunosuppressed rats, individually and in dual combinations, spaced 0, 10, and 20 days apart. Infections comprised of both organism forms resulted from admixtures inoculated at the same time. In contrast, coinfections did not develop in most rats, where a 10-or 20-day gap was inserted between inoculations; only the first organism form inoculated was detected by pulsed-field gel electrophoresis in the resultant infection. Organism burdens were reduced with combinations of forms 1 and 2 spaced 20 days apart but not in rats inoculated with forms 1 and 6. A role for the host response in the elimination of the second population and in reduction of the organism burden was suggested by the lack of direct killing of forms 1 and 2 in an in vitro ATP assay, by reduction of the burden by autoclaved organisms, and by the specific reactions of forms 1 and 2 but not forms 1 and 6. These studies showed that the time between inoculations was critical in establishing coinfections and P. carinii f. sp. carinii karyotype profiles were associated with differences in biological responses. This model provides a useful method for the study of P. carinii coinfections and their transmission in humans.Organisms termed Pneumocystis carinii were placed in the Fungal kingdom more than 10 years ago on the basis of gene sequence comparisons (14, 29), yet much of their basic biological processes remains poorly understood, due in large part to their poor growth outside the mammalian lung environment (11). Recent genetic comparisons (32), as well as animal inoculation studies (16) and antigenic analyses (2, 15), provide strong evidence that "P. carinii" is actually a family of organisms that, although related, exhibit species specificity among its mammalian hosts.Comparisons at five genetic loci suggest three levels of genetic divergence are present among P. carinii organism populations (30). The highest level of divergence, class III, was observed among Pneumocystis populations isolated from different mammalian hosts and ranged from 5 to 50% divergence in nucleotide sequence at these selected loci, with the internal transcribed sequence (ITS) regions being most divergent. Class II divergence ranged from 4 to 7% for all genes, with a 20 to 30% difference at the ITS regions. Organisms demonstrating ...