Plasmodium falciparum anti-malarial drug resistance in The Gambia:Identification of potential genetic markers by retrospective whole genome approaches

Malaria disease from infection with the parasite Plasmodium falciparum remains an important global health problem. More information is needed to continue developing new ways of controlling the disease which infects predominantly impoverished endemic countries in sub Saharan Africa. Some of this includes information on genetic differences between different types of the parasites, particularly those that don't respond to the drugs presently used for treatment. Malaria has developed resistance to previously available cheap drugs like chloroquine and Fansidar. Due to this strong ability to develop new ways of evading drugs and continuing transmission of infection and cause disease in other individuals, it now requires the use of new drug combinations containing the compound artemisinin (ART) to treat infections. These new drug combinations (ACTs) are more expensive and represent the only most effective treatment of malaria infections in sub saharan Africa. However, there are indications that some infections with malaria in South East Asia are not treated as effectively as expected with these new drug combinations indicating that the parasites may already be developing new mechanisms to resist the effect of these drug combinations. If this alarming development were to continue and spread to Africa it will be a big blow to the efforts to reduce the burden of malaria in the continent that bears 90% of the malaria burden. For the scientific community to be ready for such an eventuality, it is important to start looking at factors that will enable these parasites that resist drug action to develop and spread in affected sub Saharan Arican populations. Some of these factors include the the ability of some parasites to tolerate drug concentrations that will normally kill them. The challenge in gaining understanding of the complex processes in the parasite that create the conditions for drug resistance is the requirement for large amount of data from populations where these drugs have been used for some time. Aquiring such information can now be possible by advancements in technologies for rapidly analysing the quantity and quality of genetic differences between infections before and since ACT adoption in Africa. This project therefore seeks a better understanding of the processes that lead to antimalarial drug resistance by taking advantage of advances in new technologies to comprehensively study genetic differences in the parasites from the period before ACTs through five years of its use in the West African state, The Gambia. Use of drugs and the low level of transmission in this region is favorable for parasites to develp resistance. This information will enable the identification of genetics determinants of drug resistance and communities in which parasites that donot respond to drug are transmitted. The study will then employ methods in the lab to determine the sensitivity of these parasites to drugs being used. Those that are resistant to drugs will be analysed using genetics tools. The study will also look at how parasites will be cleared from infected people being treated with ACTs. Communities with parasites that fail to clear from blood during treatment will be the focus of further genetic analysis to determine if genetic changes are responsible for this kind of behaviour. This project will make use of excellent collaboration between MRC Unit, The Gambia and Northern partners (UK and US) for analysis and technology transfer. The study will last for a period of 48 months and will build capacity for future population genetic research in the African sub region given the different vaccine, drug and vector interventions being implimented. The findings from the project should also inform policy makers on developing new intervention strategies that will incorporate the percularities of populations studied. It will enable the developmeent of my research career in this field as an independent genomics scientist in West Africa.

Reports of decreasing malaria endemicity are countered by the emergence of parasite strains resistant to new artermisinin-based drug combinations. The threat of artemisinin resistance may be a major threat for the effort to eliminate malaria, particularly in Africa where the burden is the highest. The main goal of this proposal is therefore to identify and determine the distribution of drug resistant markers in a West African population, The Gambia, following five years of implementation of ACT. In the past few years we have developed molecular methods to study the genetics, population genomic diversity and evolution of malaria parasites in West Africa. The published genomic data and current preliminary retrospective data enable us to propose new approachees on molecular epidemiology of malaria. The specific aims are to 1.) Characterize variation in microsatellite and single nucleotide polymorphisms in malaria infections following the implementation of ACT in The Gambia, 2.) Determine the prevalence of resistance markers in endemic communities and 3.) Determine the association of these polymorphisms with treatment failure and reduce drug sensitivity. The study will employ hybrid select and Illumina sequencing of retrospective isolates in collaboration with the Broad Institute, US. High resolution drug sensitivity phenotyping of field isolates will employ new flow cytometric techniques that allow determination of the effects of artemisinin derivatives on early developmental stages of parasites. The genomes of parasites from ex vivo and in vivo studies will be genotyped in collaboration with the Wellcome Trust Sanger institute, UK. The project will be of public health benefit in identifying and combating drug-resistant malaria, potentially enhancing the drive towards malaria elimination in the Gambia. The genomic data will be vital in studies charaterising malaria diversity. It will empower me and my research team on advanced genome informatics and statistics.

This proposal seeks to maximize the economic and social impact of the research through meetings and communication strategies designed to maximize engagement with stakeholders and communities by ensuring relevance and access to data. Since it will provide vital information on drug responses in malaria, a disease of significant public health importance in impoverished sub Saharan Africa (an estimated 215 million cases and 655,000 deaths in 2010 alone worldwide), the heaviest impact will be in the domain of public health. Emergence or spread of artemisinin resistance to Africa will significantly increase the malaria burden, particularly because there are no alternative drugs with equal efficacy. The information on the prevalence of infections and the infective forms of malaria from different communities is vital for guiding decision on specific or enhanced interventions targeting the study communities in The Gambia. Hence the project will engage a platform of continuous interaction with the national malaria control programme including bi-annual meetings and seminars to assess mutual interests and develop action plans for data exploitation. We will generate of map of molecular drug resistance in the Gambia by the end of the second year of the project. Such data will inform needs for therapeutic vigilance and help guide intervention strategies in areas most affected. Participants in the study will benefit from free medical consultation and health care during the study. This generally should improve the health status of the study communities as malaria constitutes a major source of poor health. The Gambia is visited yearly by thousands of tourists from European countries including the UK. Hence travel malaria is a potential risk to the UK. In the short term, surveys planned in this studies will update, advance and positively impact knowledge on the fundamental mechanisms of drug resistance and diversity of infections. Identified genetic markers will be translated into molecular procedures that will be transferred to the national public health labs for disease and resistance surveillance through training. As genomics research is yet to be established in much of sub Saharan Africa, this project will provide opportunities for the PI and local collaborators at MRC, The Gambia, to develop skills in genome data management, analysis and cutting edge technologies. This will be done in collaboration with LSHTM, a well known institution in the field of tropical communicable diseases research. Collaboration will also include two genome sequencing centres, the Wellcome Trust Sanger Institute and the BI, which are at the forefront of technological development in pathogen genome sequencing and analysis. This will improve the local expertise in technology, analysis and communication of molecular epidemiology research findings. The requested instrumentations for the MRC unit, The Gambia, will provide opportunities for cutting edge computation and bioinformatics. This will allow for buidling capacity in populations genetics and genomics of malaria and other infectious pathogens in The Gambia and the West African sub-region. These studies will provide information on resistance to antimalarial combination therapies that could be important in the treatment of imported malaria cases to the UK. It will also provide more ground for studies on disease epidemiology as it will assess for the first time information from archival specimens to determine changes in parasite populations under varying drug pressure. Data and tools generated in the course of this work will be available not only to malaria researchers but also to the wider biology research community, as well as teachers and students at several levels. Data in the public database will be available for exploitation in testing theories on epidemiology and molecular evolution of natural malaria infections.