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Background  The ability of  Plasmodium falciparum  parasites to develop resistance to widely used anti-malarials threatens malaria control and elimination efforts. Regular drug efficacy monitoring is essential for ensuring effective treatment policies. In low transmission settings where therapeutic efficacy studies are often not feasible, routine surveillance for molecular markers associated with anti-malarial resistance provides an alternative for the early detection of emerging resistance. Such a longitudinal survey of changes in the prevalence of selected molecular markers of resistance was conducted in the malaria-endemic regions of Mpumalanga Province, South Africa, where malaria elimination at a district-level is being pursued.    Methods  Molecular analyses to determine the prevalence of alleles associated with resistance to lumefantrine ( mdr 86N,  crt 76K and  mdr1  copy number variation) and sulfadoxine–pyrimethamine ( dhfr  triple,  dhps  double, SP quintuple) were conducted between 2001 and 2018, while artemisinin resistance markers ( kelch13  mutations) were assessed only in 2018.    Results  Parasite DNA was successfully amplified from 1667/2393 (70%) of malaria-positive rapid diagnostic tests routinely collected at primary health care facilities. No artemisinin resistance-associated  kelch13  mutations nor amplification of the  mdr1  gene copy number associated with lumefantrine resistance were observed. However, prevalence of both the  mdr 86N and  crt 76K alleles increased markedly over the study period, with all isolates collected in 2018 carrying these markers. SP quintuple mutation prevalence increased steadily from 14% in 2001 to 96% in 2018. Mixed alleles at any of the codons assessed were rare by 2018.    Conclusion  No  kelch13  mutations confirmed or suspected to be associated with artemisinin resistance were identified in 2018. Although parasites carrying the  mdr 86N and  crt 76K alleles associated with reduced lumefantrine susceptibility were strongly selected for over the study period, nearing fixation by 2018, the marker for lumefantrine resistance, namely increased  mdr1  copy number, was not observed in this study. The increase in  mdr 86N and  crt 76K allele prevalence together with intense regional artemether–lumefantrine drug pressure, raises concern regarding the sustained artemether–lumefantrine efficacy. Regular, rigorous anti-malarial resistance marker surveillance across all three South African malaria-endemic provinces to inform case management is recommended.

malaria journal

Absence of kelch13 artemisinin resistance markers but strong selection for lumefantrine-tolerance molecular markers following 18 years of artemisinin-based combination therapy use in Mpumalanga Province, South Africa (2001–2018)