[en] Pneumocystis fungi are opportunistic parasites of mammalian lungs whose evolution, ecology and host specificity
in natural host populations remain poorly understood and controversial. Using an extensive collection of 731
lung samples from 27 rodent species sampled in five Southeast Asian countries, and nested PCR amplification of
mitochondrial and nuclear genes, we investigated the host specificity and genetic structure of Pneumocystis
lineages infecting wild rodents. We also identified the rodent species playing a central role in the transmission of
these parasites using network analysis and centrality measurement and we characterized the environmental
conditions allowing Pneumocystis infection in Southeast Asia using generalized linear mixed models.
Building upon an unprecedented Pneumocystis sampling from numerous rodent species belonging to closely
related genera, our findings provide compelling evidence that the host specificity of Pneumocystis lineages
infecting rodents is not restricted to a single host species or genus as often presented in the literature but it
encompasses much higher taxonomic levels and more distantly related rodent host species. The phylogenetic
species status at both mitochondrial and nuclear genetic markers of at least three new Pneumocystis lineages,
highly divergent from Pneumocystis species currently described, is also suggested by our data. Our models show
that the probability of Pneumocystis infection in rodent hosts is positively correlated to environmental variables
reflecting habitat fragmentation and landscape patchiness. Synanthropic and habitat-generalist rodents
belonging to the Rattus, Sundamys and Bandicota genera played a role of bridge host species for Pneumocystis
spreading in these heterogeneous habitats, where they can reach high population densities. These are critical findings improving our understanding of the ecology of these enigmatic parasites and the role played bycospeciation and host switches in their evolution. Our results also confirmed the role of land-use change and habitat fragmentation in parasite amplification and spillover in rodents.
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