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Background  Described here is the first population genetic study of  Plasmodium malariae , the causative agent of quartan malaria. Although not as deadly as  Plasmodium falciparum ,  P. malariae  is more common than previously thought, and is frequently in sympatry and co-infection with  P. falciparum , making its study increasingly important. This study compares the population parameters of the two species in two districts of Malawi with different malaria transmission patterns - one seasonal, one perennial - to explore the effects of transmission on population structures.    Methods  Six species-specific microsatellite markers were used to analyse 257  P. malariae  samples and 257  P. falciparum  samples matched for age, gender and village of residence. Allele sizes were scored to within 2 bp for each locus and haplotypes were constructed from dominant alleles in multiple infections. Analysis of multiplicity of infection (MOI), population differentiation, clustering of haplotypes and linkage disequilibrium was performed for both species. Regression analyses were used to determine association of MOI measurements with clinical malaria parameters.    Results  Multiple-genotype infections within each species were common in both districts, accounting for 86.0% of  P. falciparum  and 73.2% of  P. malariae  infections and did not differ significantly with transmission setting. Mean MOI of  P. falciparum  was increased under perennial transmission compared with seasonal (3.14 vs 2.59, p = 0.008) and was greater in children compared with adults. In contrast,  P. malariae  mean MOI was similar between transmission settings (2.12 vs 2.11) and there was no difference between children and adults. Population differentiation showed no significant differences between villages or districts for either species. There was no evidence of geographical clustering of haplotypes. Linkage disequilibrium amongst loci was found only for  P. falciparum  samples from the seasonal transmission setting.    Conclusions  The extent of similarity between  P. falciparum  and  P. malariae  population structure described by the high level of multiple infection, the lack of significant population differentiation or haplotype clustering and lack of linkage disequilibrium is surprising given the differences in the biological features of these species that suggest a reduced potential for out-crossing and transmission in  P. malariae . The absence of a rise in  P. malariae  MOI with increased transmission or a reduction in MOI with age could be explained by differences in the duration of infection or degree of immunity compared to  P. falciparum .

Comparative population structure of Plasmodium malariae and Plasmodium falciparum under different transmission settings in Malawi