Phylogeny of Pneumocystis carinii from 18 primate species confirms host specificity and suggests coevolution

Abstract

Primates are regularly infected by fungal organisms identified as Pneumocystis carinii. They constitute a valuable population for the confirmation of P. carinii host specificity. In this study, the presence of P. carinii was assessed by direct examination and nested PCR at mitochondrial large subunit (mtLSU) rRNA and dihydropteroate synthetase (DHPS) genes in 98 lung tissue samples from captive or wild nonhuman primates. Fifty-nine air samples corresponding to the environment of different primate species in zoological parks were also examined. Cystic forms of P. carinii were detected in smears from 7 lung tissue samples corresponding to 5 New World primate species. Amplifications at the mtLSU rRNA gene were positive for 29 lung tissue samples representing 18 different primate species or subspecies and 2 air samples corresponding to the environment of two simian colonies. Amplifications at the DHPS gene were positive for 8 lung tissue samples representing 6 different primate species. Direct sequencing of nested PCR products demonstrated that a specific mtLSU rRNA and DHPS sequence could be attributed to each primate species or subspecies. No nonhuman primate harbored the human type of P. carinii (P. carinii f. sp. hominis). Genetic divergence in primate-derived P. carinii organisms varied in terms of the phylogenetic divergence existing among the corresponding host species, suggesting coevolution.

FIG. 1

Phylogenetic relationships of P. carinii organisms from primate species inferred from mtLSU rRNA sequences. The phylogram presented resulted from bootstrapped data sets (20) obtained by using parsimony analysis (heuristic search option in PAUP 4.0). This tree was identical to the consensus of 18 most-parsimonious trees generated from the branch and bound algorithm in PAUP 4.0. The percentages above the branches are the frequencies with which a given branch appeared in 500 bootstrap replications. Bootstrap values below 50% are not displayed. The position of the squirrel monkey (S. sciureus)-derived P. carinii was not firmly established (dotted line). Branch lengths correspond to the total nucleotide changes assigned to each branch by PAUP 4.0. P. carinii from rat (P. carinii f. sp. carinii, GenBank no. U42914) and from mouse (P. carinii f. sp. muris, GenBank no. U20169) were chosen as outgroups.

FIG. 2

Phylogenetic relationships of P. carinii organisms from primate species inferred from DHPS sequences. The presented phylogram resulted from bootstrapped data sets (20) obtained by using parsimony analysis (heuristic search option in PAUP 4.0). This tree was identical to the consensus of three most-parsimonious trees generated from the branch and bound algorithm in PAUP 4.0. The percentages above the branches are the frequencies with which a given branch appeared in 500 bootstrap replications. Bootstrap values below 50% are not displayed. Branch lengths correspond to the total nucleotide changes assigned to each branch by PAUP 4.0. P. carinii from mouse (P. carinii f. sp. muris, GenBank no. U66283) was chosen as the outgroup.