In the last decade, tremendous progress has been made in the fight against malaria. Between 2000 and 2012, the global malaria mortality rate was reduced by 45%. This is an impressive achievement but these gains are threatened by emerging resistance to the frontline antimalarial drug, artemisinin.
Artemisinin combination therapy (ACT)—a combination of artemisinin with partner drugs—is the best available treatment for malaria and has been a key factor in reducing the number of malaria deaths. When first introduced, ACTs were universally effective and capable of killing malaria parasites very rapidly, in a matter of hours. But over the past few years it has become apparent in Southeast Asia that ACTs are taking longer to kill Plasmodium falciparum, the species of parasite that is responsible for most malaria deaths worldwide. This phenomenon, known as slow parasite clearance rate, is the first sign of parasites developing artemisinin resistance.
Drug resistance has dogged efforts to control and eliminate malaria for more than a century. Each time a new antimalarial drug has been introduced, the parasites have evolved resistance to it. In many cases, these successive waves of drug resistance first emerged in the same part of Southeast Asia, the Lower Mekong region, and then spread to other malaria endemic areas.
Since clinical artemisinin resistance was first reported in Western Cambodia in 2009, it has been confirmed in four countries in the region: Thailand, Cambodia, Viet Nam, and Myanmar. “We’re now seeing treatment failure rates to ACT of up to 30% in western Cambodia and the Thai-Myanmar border,” reports Dr Elizabeth Ashley, Tracking Resistance to Artemisinin Collaboration (TRAC) Project Manager.
If these treatments were to fail in Africa, where mortality rates are highest, it could trigger a public health crisis. “Artemisinin resistance is the biggest urgency in malaria. From an operational viewpoint, losing artemisinin would be a disaster,” says Dr Olivo Miotto, CGGH Senior Informatics Fellow. “You have to protect the drugs.”
Integrating genomics into a large multi-centre clinical study
In response to this emerging threat, the Tracking Resistance to Artemisinin Collaboration (TRAC) was formed in 2011 to assess the susceptibility of malaria parasites to artemisinin at multiple sites in Asia and Africa using the phenotype of slow parasite clearance as an indicator. TRAC is a large multi-centre collaboration coordinated by Mahidol Oxford Tropical Medicine Research Unit (MORU) in Bangkok, and comprises a range of research institutions as well as National Malaria Control Programmes and the World Health Organization (WHO).
Between May 2011 and April 2013, this ambitious project collected samples from 1,200 patients with uncomplicated malaria at their 15 study sites in 10 countries—representing the most extensive and detailed study of early parasitological responses to artemisinin ever conducted.
While TRAC is mapping clinical responses to ACTs, leveraging on these data to unravel the genetics of artemisinin resistance is a natural extension of this project. As the TRAC study sites were selected to target areas of emerging resistance, samples will include parasites that are artemisinin resistant alongside sensitive parasites—those that are more easily killed off by the drug. This provides scientists with a unique opportunity to compare resistant and sensitive parasites to look for genetic differences that may be contributing to the resistant parasites’ ability to tolerate the drug.
Ultimately, the goals are to develop cost-effective genetic tools to determine whether a patient is carrying parasites that are drug resistant; to map the emergence of resistance; to understand the mechanisms and routes of spread of resistance; and to plan the most effective strategy to control and eliminate the problem.
The CGGH is leading this area of analysis by integrating the clinical data with genome sequencing data on 1,000 parasite samples collected by the study. This large genetic data set is being generated through a partnership between Wellcome Trust Sanger Institute and MalariaGEN.
As a part of this arrangement, it’s been agreed that sequence data will be integrated into the large, global set of genetic data produced by the MalariaGEN P. falciparum Community Project and released with user-friendly web tools to maximise the value of these findings for the scientific community.
The potential of this project impressed the Bill and Melinda Gates Foundation, which provided funding for the genetic analysis, while the Wellcome Trust has financed all sequencing work.
Progress towards a deeper understanding of artemisinin resistance
Genome sequencing of the TRAC clinical samples has now been completed, generating terabytes of data that were processed by the sequence-analysis pipeline team led by Jim Stalker, to produce quality-controlled information about many thousands of variants for each sample.
This large data set provides the starting point for the population genetic analysis team—Miotto who is based at MORU in Bangkok, together with Dr Roberto Amato and Jacob Almagro-Garcia who are based in Oxford—to analyse the genetic factors that correlate with artemisinin resistance.
The team expect to release their first results this year, but caution that these analyses are anything but straightforward. “We’re studying the parasite population structure extensively. The reality is that artemisinin resistance is a very complex problem from an epidemiological point of view. There are clear patterns that we’ve observed but all sorts of confounding factors come into play,” says Miotto.
This field of research is moving forward extremely rapidly. Last year saw publications in Nature Genetics by Miotto and colleagues about multiple strains of artemisinin-resistant parasites in Cambodia, and in Nature by Dr. Frédéric Ariey and colleagues from Institut Pasteur identifying a molecular marker of artemisinin resistance. The World Health Organization (WHO) recently released an update on the state of artemisinin confirming that parasites collected in Laos were positive for the newly-discovered markers for artemisinin resistance.
While these are clearly big steps forward, there is much work left to do. “We need to understand the mechanism of resistance but also to understand what causes resistance to emerge in some places and not others. That way you can look for the potential spread of artemisinin resistance rather than just describing where it’s at right now,” says Miotto.
A microcosm of the original vision for the CGGH, this collaboration connects the on-the-ground realities of malaria control efforts to the high-tech infrastructure of large-scale genomics. “It’s amazing to see studies going on at multiple locations in the Mekong region, where precise clinical measurements are being made in patients undergoing treatment for malaria, and within a few months these clinical data are connected to genome sequence data on the parasites,” says Professor Dominic Kwiatkowski, CGGH Director, as he reflects on the strength of the collaboration with TRAC.
While their analyses are ongoing, Miotto and his team are optimistic that this rich data set will add depth to our understanding of artemisinin resistance emerging in Southeast Asia—and help to inform ongoing efforts to track and stem its spread.
The Tracking Resistance to Artemisinin Collaboration (TRAC) was formed in 2011 to assess the susceptibility of malaria parasites to artemisinin at multiple sites in Asia and Africa. TRAC is a large-scale collaboration coordinated by the Mahidol Oxford Tropical Medicine Research Unit (MORU) in Bangkok, and comprises research groups and National Malaria Control Programmes in each of the study-site countries, along with the London School of Hygiene and Tropical Medicine (LSHTM), the Liverpool School of Tropical Medicine (LSTM), the WorldWide Antimalarial Resistance Network (WWARN) and the Global Malaria Programme of the World Health Organization (WHO GMP).
- Miotto O, Amato R, Ashley EA et al. Nature Genetics, 2015; Jan 19: AOP
Ex vivo susceptibility of Plasmodium falciparum to antimalarial drugs in western, northern, and eastern Cambodia, 2011-2012: association with molecular markersLim P, Dek D, Try V et al. Antimicrob Agents Chemother, 2013; Nov;57(11): 5277-83.
- Miotto O, Almagro-Garcia J, Manske M et al. Nature Genetics, 2013; Jun;45(6): 648-55.