This study employs landscape genetics to investigate the environmental drivers of a deadly vector-borne disease, malaria caused by Plasmodium falciparum, in a more spatially comprehensive manner than any previous work. With 1804 samples from 44 sites collected in western Kenya in 2012 and 2013, we performed resistance surface analysis to show that Lake Victoria acts as a barrier to transmission between areas north and south of the Winam Gulf. In addition, Mantel correlograms clearly showed significant correlations between genetic and geographic distance over short distances (less than 70 km). In both cases, we used an identity-by-state measure of relatedness tailored to find highly related individual parasites in order to focus on recent gene flow that is more relevant to disease transmission. To supplement these results, we performed conventional population genetics analyses, including Bayesian clustering methods and spatial ordination techniques. These analyses revealed some differentiation on the basis of geography and elevation and a cluster of genetic similarity in the lowlands north of the Winam Gulf of Lake Victoria. Taken as a whole, these results indicate low overall genetic differentiation in the Lake Victoria region, but with some separation of parasite populations north and south of the Winam Gulf that is explained by the presence of the lake as a geographic barrier to gene flow. We recommend similar landscape genetics analyses in future molecular epidemiology studies of vector-borne diseases to extend and contextualize the results of traditional population genetics.

BACKGROUND: In sub-Saharan Africa, malaria, transmitted by the Anopheles mosquito, remains one of the foremost public health concerns. Anopheles gambiae, the primary malaria vector in sub-Saharan Africa, is typically associated with ephemeral, sunlit habitats; however, An. gambiae larvae often share these habitats with other anophelines along with other disease-transmitting and benign mosquito species. Resource limitations within habitats can constrain larval density and development, and this drives competitive interactions among and between species. METHODS: We used naturally occurring stable isotope ratios of carbon and nitrogen to identify resource partitioning among co-occurring larval species in microcosms and natural habitats in western Kenya. We used two and three source mixing models to estimate resource utilization (i.e. bacteria, algae, organic matter) by larvae. RESULTS: Laboratory experiments revealed larval δ13C and δ15N composition to reflect the food sources they were reared on. Resource partitioning was demonstrated between An. gambiae and Culex quinquefasciatus larvae sharing the same microcosms. Differences in larval δ13C and δ15N content was also evident in natural habitats, and Anopheles species were consistently more enriched in δ13C when compared to culicine larvae. CONCLUSIONS: These observations demonstrate inter-specific resource partitioning between Cx. quinquefasciatus and An. gambiae larvae in natural habitats in western Kenya. This information may be translated into opportunities for targeted larval control efforts by limiting specific larval food resources, or through bio-control utilizing competitors at the same trophic level.

Background

In African highland areas where endemicity of malaria varies greatly according to altitude and topography, parasitaemia accompanied by fever may not be sufficient to define an episode of clinical malaria in endemic areas. To evaluate the effectiveness of malaria interventions, age-specific case definitions of clinical malaria needs to be determined. Cases of clinical malaria through active case surveillance were quantified in a highland area in Kenya and defined clinical malaria for different age groups.

Methods

A cohort of over 1,800 participants from all age groups was selected randomly from over 350 houses in 10 villages stratified by topography and followed for two-and-a-half years. Participants were visited every two weeks and screened for clinical malaria, defined as an individual with malaria-related symptoms (fever [axillary temperature≥37.5°C], chills, severe malaise, headache or vomiting) at the time of examination or 1-2 days prior to the examination in the presence of a Plasmodium falciparum positive blood smear. Individuals in the same cohort were screened for asymptomatic malaria infection during the low and high malaria transmission seasons. Parasite densities and temperature were used to define clinical malaria by age in the population. The proportion of fevers attributable to malaria was calculated using logistic regression models.

Results

Incidence of clinical malaria was highest in valley bottom population (5.0% cases per 1,000 population per year) compared to mid-hill (2.2% cases per 1,000 population per year) and up-hill (1.1% cases per 1,000 population per year) populations. The optimum cut-off parasite densities through the determination of the sensitivity and specificity showed that in children less than five years of age, 500 parasites per μl of blood could be used to define the malaria attributable fever cases for this age group. In children between the ages of 5-14, a parasite density of 1,000 parasites per μl of blood could be used to define the malaria attributable fever cases. For individuals older than 14 years, the cut-off parasite density was 3,000 parasites per μl of blood.

Conclusion

Clinical malaria case definitions are affected by age and endemicity, which needs to be taken into consideration during evaluation of interventions.

Anopheles gambiae is the major malaria vector in Africa. Examining the molecular basis of A. gambiae traits requires knowledge of both genetic variation and genome-wide linkage disequilibrium (LD) map of wild A. gambiae populations from malaria-endemic areas. We sequenced the genomes of nine wild A. gambiae mosquitoes individually using next-generation sequencing technologies and detected 2,219,815 common single nucleotide polymorphisms (SNPs), 88% of which are novel. SNPs are not evenly distributed across A. gambiae chromosomes. The low SNP-frequency regions overlay heterochromatin and chromosome inversion domains, consistent with the lower recombinant rates at these regions. Nearly one million SNPs that were genotyped correctly in all individual mosquitoes with 99.6% confidence were extracted from these high-throughput sequencing data. Based on these SNP genotypes, we constructed a genome-wide LD map for wild A. gambiae from malaria-endemic areas in Kenya and made it available through a public Website. The average size of LD blocks is less than 40 bp, and several large LD blocks were also discovered clustered around the para gene, which is consistent with the effect of insecticide selective sweeps. The SNPs and the LD map will be valuable resources for scientific communities to dissect the A. gambiae genome.

Vector-borne diseases are among the diseases that have been linked with climate change (IPCC. 2001). Malaria is probably the deadliest climate sensitive vector-borne disease (Githeko et al. 2000). About 90% of the 300-500 million cases of the reported malaria cases worldwide come from Africa. In the late 80s to the 90s, malaria epidemics occurred frequently in western Kenya highlands, often taking the population by surprise. The epidemics were caused by Plasmodium falciparum and transmitted by Anopheles gambiae and Anopheles funestus. Epidemics were associated with high morbidity and mortality in all age groups, with prevalence of the disease rising from about 20% to about 60%. The case mortality in functional health facilities were estimated at about 7.5% (Githeko and Ndegwa 2001). The malaria transmission system involves a complex interaction between humans, mosquitoes, the plasmodium parasite, climate and the physical environment. Warming of the climate is expected to lead to latitudinal and altitudinal temperature increase. The temporal and spatial changes in temperature, precipitation and humidity that are expected to occur under different climate change scenarios will affect the biology and ecology of vectors and intermediate hosts and consequently the risk of disease transmission. The risk increases because, although arthropods can regulate their internal temperature by changing their behaviour, they cannot do so physiologically and are thus critically dependent on climate for their survival and development (Lindsay and Birley 1996). Temperature is inversely related to altitude, thus the high-elevation areas in Africa, or highlands, generally exhibit low ambient temperature, which restricts the development of vectors and parasites. Because malaria transmission rate is temperature-dependent, any factor that alters the temperature in the highland would reduce the duration of parasite development, larval development and increase the mosquito biting rates, and subsequently increase malaria transmission in the highlands.

Abstract Background Irrigated vegetable farms within the city of Kumasi, Ghana, create hotspots for the breeding of malaria vectors, which could lead to high transmission of malaria. This study investigated the abundance and productivity of mosquitoes in an irrigated vegetable farm in Kumasi, Ghana. Methods Adult mosquito productivity was estimated five days in a week in different irrigated scheme types (dug-out wells, furrows and footprints) for 12 weeks using emergence traps. Larval sampling was done five days a week to estimate the abundance of larvae from the different irrigated schemes types. Results Mosquito breeding in the irrigated vegetable field was confined to dug-out wells, furrows and human footprints. Mosquito productivity (m2/week) was highest in the dugout wells followed by the human footprints and the least was in the furrows (11.23, 5.07 and 4.34 An. gambiae/m2/week). Larval abundance for the late instars (3rd, 4th and pupae) also followed the same trend, with the dug-out wells having the highest larval abundance followed by the human footprints and then the furrows (13.24, 6.81, 5.87 larvae/week). Mosquito productivity and abundance was negatively correlated with rainfall (R2 = 0.209; P< 0.01). Conclusion This study showed that adult and larval mosquito abundance and larval survival were high in the irrigated fields in the irrigated vegetable farm. This therefore, contributed significantly to adult mosquito populations and hence malaria transmission in the city.

The impact of malaria intervention measures (insecticide-treated net use and artemisinin combination therapy) on malaria genetics was investigated at two sites in western Kenya: an endemic lowland and an epidemic highland. The genetic structure of the parasite population was assessed by using microsatellites, and the prevalence of drug-resistant mutations was examined by using the polymerase chain reaction-restriction fragment length polymorphism method. Two years after intervention, genetic diversity remained high in both populations. A significant decrease in the prevalence of quintuple mutations conferring resistance to sulfadoxine-pyrimethamine was detected in both populations, but the mutation prevalence at codon 1246 of the Plasmodium falciparum multidrug resistance 1 gene had increased in the highland population. The decrease in sulfadoxine-pyrimethamine-resistant mutants is encouraging, but the increase in P. falciparum multidrug resistance 1 gene mutations is worrisome because these mutations are linked to resistance to other antimalarial drugs. In addition, the high level of genetic diversity observed after intervention suggests transmission is still high in each population.

Abstract Background In sub-Saharan Africa, malaria, transmitted by the Anopheles mosquito, remains one of the foremost public health concerns. Anopheles gambiae, the primary malaria vector in sub-Saharan Africa, is typically associated with ephemeral, sunlit habitats; however, An. gambiae larvae often share these habitats with other anophelines along with other disease-transmitting and benign mosquito species. Resource limitations within habitats can constrain larval density and development, and this drives competitive interactions among and between species. Methods We used naturally occurring stable isotope ratios of carbon and nitrogen to identify resource partitioning among co-occurring larval species in microcosms and natural habitats in western Kenya. We used two and three source mixing models to estimate resource utilization (i.e. bacteria, algae, organic matter) by larvae. Results Laboratory experiments revealed larval δ13C and δ15N composition to reflect the food sources they were reared on. Resource partitioning was demonstrated between An. gambiae and Culex quinquefasciatus larvae sharing the same microcosms. Differences in larval δ13C and δ15N content was also evident in natural habitats, and Anopheles species were consistently more enriched in δ13C when compared to culicine larvae. Conclusions These observations demonstrate inter-specific resource partitioning between Cx. quinquefasciatus and An. gambiae larvae in natural habitats in western Kenya. This information may be translated into opportunities for targeted larval control efforts by limiting specific larval food resources, or through bio-control utilizing competitors at the same trophic level.