Co-evolution of the parasitic fungi Pneumocystis and their Muridae rodent hosts in Southeast Asia

Pneumocystis species are opportunistic and airborne-transmitted fungi that infect the lungs of numerous mammalian species. These highly diversified fungi are characterized by strong host specificity, probably associated with co-speciation. In this study, we investigate the Pneumocystis genetic diversity and infection rate in Muridae rodents of Southeast Asia in relation to environmental habitats. A total of 445 wild rodents belonging to 18 Southeast Asian Muridae species were tested for the presence of Pneumocystis in their lungs through PCR amplification of two Pneumocystis mitochondrial genes (mtLSU rRNA and mtSSU rRNA).
Pneumocystis DNA was detected in 215 (48.3%) out of these 445 rodents. Eight highly divergent Pneumocystis lineages were retrieved in our phylogenetic tree. Three of these lineages correspond to the described species Pneumocystis murina (infecting Mus species), P. carinii (infecting Rattus species) and P. wakefieldiae (also infecting Rattus species). Three individuals belonging to Rattus norvegicus were found co-infected by both P. carinii and P. wakefieldiae. The five remaining lineages may correspond to several new undescribed Pneumocystis species and infect the lungs of Cannomys (lineage 1), Bandicota (lineage 2), Berylmys (lineage 3), Rattus (lineage 4) and Maxomys, Niviventer and Leopoldamys (lineage 5) Muridae genera. The congruence between phylogenies of Pneumocystis and their rodent hosts has been tested using co-phylogenetic analyses and the number of inferred co-speciation events is significantly greater than expected by chance. Rodent species, age and sex have no influence on the Pneumocystis infection rate among Muridae rodents but individuals trapped close to human settlements in patchy habitat were more likely infected by Pneumocystis parasites.