Genomic profiling of drug resistance markers in Plasmodium falciparum samples from the Democratic Republic of the Congo (2017) and Tanzania (2020-2021).

BACKGROUND: Molecular surveillance is essential to detect emerging artemisinin partial resistance (ART-R) and partner drug resistance in Sub-Saharan Africa. OBJECTIVES: To describe the prevalence of Plasmodium falciparum resistance markers in two high-burden countries using artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL): the Democratic Republic of the Congo (DRC) and Tanzania. METHODS: A total of 1254 day-0 P. falciparum-positive samples were analysed: 837 from four sentinel sites of a therapeutic efficacy study (TES) in the DRC (2017) and 417 from an intermittent preventive treatment in schoolchildren (IPTsc) trial in Handeni and Kilindi districts, Tanga Region, Tanzania (2020-2021). Pfkelch13, Pfcrt and Pfmdr1 were analysed by Illumina MiSeq amplicon sequencing. RESULTS: Reliable sequences were obtained for 1193 isolates. The Pfkelch13 wild-type allele predominated (98.4%); none of the four non-synonymous mutations detected (N489Y, K568T, A578S, V589I) are classified as validated, candidate or potential ART-R markers, and the validated markers R561H, P441L and C469Y reported elsewhere in East Africa were absent. Pfcrt K76T was found in 23.3% of Tanzanian and 26.3% of DRC isolates, with substantial between-site variation in the DRC (4.3% to 93.6% at Rutshuru). Pfmdr1 haplotype profiles differed between countries: NFSND predominated in Tanzania (71.5%) while NYSND remained the most frequent in the DRC (60.9%); 86Y was twice as frequent in the DRC (11.1%) as in Tanzania (6.2%). CONCLUSIONS: No validated ART-R marker was detected, but partner-drug haplotype distributions reflected the first-line ACTs used in each country. Continued molecular surveillance is needed to track these signatures alongside the recent emergence of ART-R.