Admixture in Humans of Two Divergent Plasmodium knowlesi Populations Associated with Different Macaque Host Species.

Paul C. S. Divis,Balbir Singh,Craig W. Duffy,Samuel A. Assefa,Clemens H. Kocken,Fread Anderios,Shamilah Hisam,Asmad Matusop,David J. Conway,Ananias A. Escalante

doi:10.1371/journal.ppat.1004888

Abstract

Human malaria parasite species were originally acquired from other primate hosts and subsequently became endemic, then spread throughout large parts of the world. A major zoonosis is now occurring with Plasmodium knowlesi from macaques in Southeast Asia, with a recent acceleration in numbers of reported cases particularly in Malaysia. To investigate the parasite population genetics, we developed sensitive and species-specific microsatellite genotyping protocols and applied these to analysis of samples from 10 sites covering a range of >1,600 km within which most cases have occurred. Genotypic analyses of 599 P. knowlesi infections (552 in humans and 47 in wild macaques) at 10 highly polymorphic loci provide radical new insights on the emergence. Parasites from sympatric long-tailed macaques (Macaca fascicularis) and pig-tailed macaques (M. nemestrina) were very highly differentiated (FST = 0.22, and K-means clustering confirmed two host-associated subpopulations). Approximately two thirds of human P. knowlesi infections were of the long-tailed macaque type (Cluster 1), and one third were of the pig-tailed-macaque type (Cluster 2), with relative proportions varying across the different sites. Among the samples from humans, there was significant indication of genetic isolation by geographical distance overall and within Cluster 1 alone. Across the different sites, the level of multi-locus linkage disequilibrium correlated with the degree of local admixture of the two different clusters. The widespread occurrence of both types of P. knowlesi in humans enhances the potential for parasite adaptation in this zoonotic system.

Highlights

The epidemiological emergence of infections can be traced by genotypic analyses, with a high level of resolution when pathogens have a high mutation rate, as illustrated by recently emerged viruses that have a massive impact on global public health [1,2]
Extraordinary phases of pathogen evolution may occur during an emerging zoonosis, potentially involving adaptation to human hosts, with changes in patterns of virulence and PLOS Pathogens | DOI:10.1371/journal.ppat
In a large population genetic survey, we show that the malaria parasite Plasmodium knowlesi in humans is an admixture of two highly divergent parasite populations, each associated with different forest-dwelling macaque reservoir host species

Summary

Introduction

The epidemiological emergence of infections can be traced by genotypic analyses, with a high level of resolution when pathogens have a high mutation rate, as illustrated by recently emerged viruses that have a massive impact on global public health [1,2]. Such analysis is more challenging for eukaryote pathogens with low mutation rate, it is clear that the major human malaria parasites Plasmodium falciparum and P. vivax have been endemic for many thousands of years after having been acquired as zoonotic infections from African apes [3,4]. Sequences of parasite mitochondrial genomes and a few nuclear gene loci indicate ongoing zoonotic infection, as human P. knowlesi genotypes share most alleles identified in parasites sampled from wild macaques [15,16,17]

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Conclusion