Background In Mali, malaria is highly endemic and remains stable despite the implementation of various malaria control measures. genetic diversity, genetic differentiation and linkage disequilibrium. Results Of 156 qPCR-positive samples, complete genotyping of 112 samples was achieved. The parasite populations displayed high genetic diversity (mean He?=?0.77), which was consistent with a high level of malaria transmission in Mali. Genetic differentiation was low (FST?Rabbit polyclonal to AKR1A1 diversity and the pronounced gene flux amongst populations may represent an obstacle to control malaria. Indeed, Huperzine A results suggest that parasite populations are polymorphic enough to adapt to their host and to counteract interventions, such as anti-malarial vaccination. Additionally, the panmictic parasite population structure imply that resistance traits may disseminate freely from one area to another, making control measures performed at a local level ineffective. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1397-0) contains supplementary material, which is available to authorized users. malaria remains highly endemic; stable incidence of the disease has been reported in several malaria vaccine-testing sites, such as Bandiagara [2]. In contrast to the situation in Mali, recent studies have shown that in other countries of the Sahel region, such as Senegal [3C5], enhanced interventions have effectively reduced malaria transmission. The heterogeneous results of malaria control programmes highlight the complexity of malaria epidemiology and Huperzine A the necessity to adapt interventions to local epidemiological settings. In Mali, from the Sahara Desert to the Sudano-Guinean savannah, throughout the Sahel region, the variety of malaria transmission pattern is characterized by a north to south increasing gradient [6]. Malaria transmission is highly seasonal and peaks during the rainy season, but it has been shown that transmission can continue late into the dry season [6C9]. Assessing genetic diversity may be useful to elucidate the mechanisms of transmission persistence and rebound. Such studies would provide insight into human reservoirs of the parasites, including symptomatic cases and those of asymptomatic carriage [3, 8, 10] and human migration patterns associated with parasite flux [11C15]. Additionally, a clear understanding of genetic diversity would shed light on the characteristics of malaria burden and the expected difficulties hindering malaria control. Indeed, it has been shown that genetic diversity is indicative of the ability of malaria parasites to adapt to their hosts by selection of advantageous traits, such as drug resistance and antigenic variability [16]. genetic diversity can be assessed by analysing genetic polymorphism of the merozoite surface proteins (and and genes are under selective pressure and neutral markers such as microsatellites or Huperzine A single nucleotide polymorphism (SNPs) are better suited for population genetics assessment [19]. Highly polymorphic microsatellite markers have been widely used to study population genetics via multiple loci variable number of tandem repeats analysis (MLVA) [11C15, 20C23]. These studies provided insights into various population genetic features, including parasite migration and linkage disequilibrium. To date, microsatellite markers have never been assessed to study population genetics in Mali. In this study, MLVA was performed on Huperzine A DNA extracted from blood samples collected from four Malian study sites displaying various malaria transmission Huperzine A patterns. The four study sites were located along a 900-km long north to south axis and included the city of Bamako. Methods Study sites Blood samples were collected in Rharous (Timbuktu District), Bamako (Bamako District), Doneguebougou (Kati District), and Bougoula Hameau (Sikasso District) (Fig.?1). Each of the study sites represents a different pattern of malaria transmission as defined by previous Malian epidemiological reports [6, 24, 25]. According to these reports, malaria is hypo-endemic in the urban zone of Bamako, whereas the disease is sporadic with occasional epidemics in Rharous, which is located in the Sahara Desert. Malaria is hyper-endemic in Doneguebougou [a site located in the Sudano-Sahelian zone, where malaria is characterized by a short transmission season (3C4?months)] and Bougoula [which is located in the Sudano-Guinean zone, where the transmission season is longer (4C6?months)]. Fig.?1 Maps of Mali showing four study sites and four malaria epidemiological patterns [6, 24]. Annual isohyets (mm) separate each climatic zone. The climatic zones from north to south are as follows: Saharian zone (malaria transmission is sporadic to epidemic), … Study design A total of 648 blood samples were collected by finger.