Examining Plasmodium falciparum and P. vivax clearance subsequent to antimalarial drug treatment in the Myanmar-China border area based on quantitative real-time polymerase chain reaction

BackgroundRecent emergence of artemisinin-resistant P. falciparum has posed a serious hindrance to the elimination of malaria in the Greater Mekong Subregion. Parasite clearance time, a measure of change in peripheral parasitaemia in a sequence of samples taken after treatment, can be used to reflect the susceptibility of parasites or the efficiency of antimalarials. The association of genetic polymorphisms and artemisinin resistance has been documented. This study aims to examine clearance time of P. falciparum and P. vivax parasitemia as well as putative gene mutations associated with residual or recurred parasitemia in Myanmar.MethodsA total of 63 P. falciparum and 130 P. vivax samples collected from two internally-displaced populations and one surrounding village were examined for parasitemia changes. At least four samples were taken from each patient, at the first day of diagnosis up to 3 months following the initial treatment. The amount of parasite gene copy number was estimated using quantitative real-time PCR based on a species-specific region of the 18S rRNA gene. For samples that showed residual or recurred parasitemia after treatment, microsatellites were used to identify the 'post-treatment' parasite genotype and compared such with the 'pre-treatment' genotype. Mutations in genes pfcrt, pfmdr1, pfatp6, pfmrp1 and pfK13 that are potentially associated with ACT resistance were examined to identify if mutation is a factor for residual or persistent parasitemia.ResultsOver 30% of the P. falciprium infections showed delayed clearance of parasitemia after 2-3 days of treatment and 9.5% showed recurred parasitemia. Mutations in codon 876 of the pfmrp1 corroborated significance association with slow clearance time. However, no association was observed in the variation in pfmdr1 gene copy number as well as mutations of various codonsinpfatp6, pfcrt, and pfK13 with clearance time. For P. vivax, over 95% of the infections indicated cleared parasitemia at days 2-3 of treatment. Four samples were found to be re-infected with new parasite strains based on microsatellite genotypes after initial treatment.ConclusionThe appearance of P.falciparum infected samples showing delayed clearance or recurred parasitemia after treatment raises concerns on current treatment and ACT drug resistance

Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum

Single nucleotide polymorphisms (SNPs) have been shown to be useful in revealing population structure with continental-and regional-scale samples. In epidemiological study, a careful selection of SNPs to track disease spread in local communities would provide an important addition to traditional disease surveillance. This study used SNPs and microsatellites to examine population structure of Plasmodium falciparum at fine- scale in malaria-endemic areas of Western Kenya. A set of high performance (HP) SNPs were selected from a large SNP panel based on BELS ranking, FST values and minor allele frequency criteria. The discriminative power and assignment accuracy of different SNP panels including nonsynonymous SNPs, silent SNPs, previously published barcode SNPs, and the HP SNPs were evaluated together with microsatellites. Among all SNP panels, HP SNPs showed the highest level of differentiation and self-assignment accuracy on average among sites. Clear distinction was observed between the northern and southern P. falciparum samples, whereas samples from the south were least diverged from one another. These results were comparable to those by microsatellites. Nonsynonymous, silent, and barcode SNPs all showed similar levels of genetic variability to one another and weaker structure than the HP SNPs. We described here the procedure of selecting a set of HP SNPs from a large panel of SNPs that resolve population structure of P. falciparum between the northern and southern regions of Western Kenya. This procedure is recommended in future study to screen and select HP SNPs that can trace Plasmodium spread among local communities of finer geographical scales

Frequent Spread of Plasmodium vivax Malaria Maintains High Genetic Diversity at the Myanmar-China Border, Without Distance and Landscape Barriers

BackgroundIn Myanmar, civil unrest and the establishment of internally displaced person (IDP) settlements along the Myanmar-China border have impacted malaria transmission.MethodsMicrosatellite markers were used to examine source-sink dynamics for Plasmodium vivax between IDP settlements and surrounding villages in the border region. Genotypic structure and diversity were compared across the 3 years following the establishment of IDP settlements, to infer demographic history. We investigated whether human migration and landscape heterogeneity contributed to P. vivax transmission.ResultsP. vivax from IDP settlements and local communities consistently exhibited high genetic diversity within populations but low polyclonality within individuals. No apparent genetic structure was observed among populations and years. P. vivax genotypes in China were similar to those in Myanmar, and parasite introduction was unidirectional. Landscape factors, including distance, elevation, and land cover, do not appear to impede parasite gene flow.ConclusionsThe admixture of P. vivax genotypes suggested that parasite gene flow via human movement contributes to the spread of malaria both locally in Myanmar and across the international border. Our genetic findings highlight the presence of large P. vivax gene reservoirs that can sustain transmission. Thus, it is important to reinforce and improve existing control efforts along border areas

Landscape Genetics of African Malaria Parasite and Its Vectors

During a time of intensive antimalarial campaigns, it is crucial to understand the effects these campaigns have on the population genetics of malaria parasites and mosquitoes, particularly with respect to genes associated with drug and insecticide resistance. In addition, as countries approach malaria elimination, it will be critically important to understand the underlying factors that cause malaria epidemics or help to sustain malaria transmission in order to effectively control malaria and achieve elimination. Therefore, my dissertation research aims to A) evaluate the impact that public health interventions have on the population genetics of malaria parasites and mosquitoes; and B) assess the relative impact that key ecological factors have on the dispersal, measured through gene flow, of malaria parasites and vectors. To address these aims, I collected malaria parasite and mosquito samples in Kenya and genotyped them for molecular markers associated with drug and insecticide resistance, as well as neutral markers to infer gene flow. I tested the link between key ecological factors (temperature, precipitation, vegetation index, topographic wetness index, human population density, and distance to roads) and spatial genetic structure between populations using landscape genetic analytic methods. I found a recent increase in drug resistance markers associated with the antimalarial drug used to prevent malaria in pregnancy, as well as an increase in polymorphisms associated with increased tolerance to the partner drug of the first-line treatment for malaria. I found a key mutation to be associated with insecticide resistance in Anopheles arabiensis in Kenya, as well as that this mutation is common throughout Western Kenya. Finally, I found that high human population density promotes dispersal of An. gambiae s.s., high temperatures and low vegetation indices promote dispersal of An. arabiensis, and that physical barriers to human travel, such as lakes, may prevent dispersal of P. falciparum in Kenya. These findings allow us to identify areas susceptible to the introduction of malaria parasites and malaria vectors, as well as drug and insecticide resistance

Landscape Genetics of African Malaria Parasite and Its Vectors

During a time of intensive antimalarial campaigns, it is crucial to understand the effects these campaigns have on the population genetics of malaria parasites and mosquitoes, particularly with respect to genes associated with drug and insecticide resistance. In addition, as countries approach malaria elimination, it will be critically important to understand the underlying factors that cause malaria epidemics or help to sustain malaria transmission in order to effectively control malaria and achieve elimination. Therefore, my dissertation research aims to A) evaluate the impact that public health interventions have on the population genetics of malaria parasites and mosquitoes; and B) assess the relative impact that key ecological factors have on the dispersal, measured through gene flow, of malaria parasites and vectors. To address these aims, I collected malaria parasite and mosquito samples in Kenya and genotyped them for molecular markers associated with drug and insecticide resistance, as well as neutral markers to infer gene flow. I tested the link between key ecological factors (temperature, precipitation, vegetation index, topographic wetness index, human population density, and distance to roads) and spatial genetic structure between populations using landscape genetic analytic methods. I found a recent increase in drug resistance markers associated with the antimalarial drug used to prevent malaria in pregnancy, as well as an increase in polymorphisms associated with increased tolerance to the partner drug of the first-line treatment for malaria. I found a key mutation to be associated with insecticide resistance in Anopheles arabiensis in Kenya, as well as that this mutation is common throughout Western Kenya. Finally, I found that high human population density promotes dispersal of An. gambiae s.s., high temperatures and low vegetation indices promote dispersal of An. arabiensis, and that physical barriers to human travel, such as lakes, may prevent dispersal of P. falciparum in Kenya. These findings allow us to identify areas susceptible to the introduction of malaria parasites and malaria vectors, as well as drug and insecticide resistance

Landscape Genetics: A Toolbox for Studying Vector-Borne Diseases

Landscape genetics aims to quantify the effect of landscape on gene flow. Broadly, the approach involves measuring genetic variation, quantifying landscape heterogeneity, and statistically testing the link between both genetic variation and landscape heterogeneity. This approach has been widely used by conservation biologists, for example to identify barriers restricting movement in threatened populations. More recently, landscape genetics has been used to study the epidemiology of infectious diseases, such as chronic wasting disease, raccoon rabies, and malaria. This method can be useful in identifying potential hotspot areas of disease movement for targeted public health interventions and containment of disease and drug resistance. However, vector-borne disease epidemiology is particularly complex, as it is affected by the movement of both the vector and human or vertebrate host. This feature could potentially inhibit the ability to detect the effect of landscape on gene flow, since the ecology of vectors and hosts are likely different and potentially conflicting. Here, we provide a summary of the latest innovations in the field of landscape genetics with a focus on those that could help increase the power to detect landscape effects in vector-borne human disease studies. We also provide a recommended framework for studying vector-borne diseases using a landscape genetics approach. Landscape genetics has the potential to be a powerful tool for the field of vector-borne disease epidemiology but has so far been underutilized. The provided synthesis of tools and considerations for conducting a landscape genetics study of a vector-borne disease aim to bridge the gap between the two disciplines