Genetic profile of P. falciparum strains in villages around Soum irrigation Dam, Burkina Faso: insights from targeted sequencing of drug resistance markers in Pfkelch13, Pfubp1, Pfcoronin, Pfcrt, Pfmdr1, Pfdhps and Pfdhfr genes

Abstract Hydro-agricultural settings may sustain high and prolonged malaria transmission and increase antimalarial drug use, potentially intensifying selection pressure on P. falciparum strains. Molecular surveillance in these settings is essential to detect changes in markers associated with resistance to artemisinin, Sulfadoxine-Pyrimethamine (SP), and Artemisinin-Based Combination Therapy (ACT) partner drugs. This study characterized the genetic profile and seasonal distribution of P. falciparum strains circulating in villages surrounding the Soum irrigation dam in Burkina Faso. A prospective monitoring approach was implemented through monthly repeated cross-sectional household surveys in five villages around the Soum dam in the Nanoro health district from March 2022 to February 2023. Dried blood spots from microscopy-positive samples were randomly selected by village and transmission season. Illumina technology was used to sequence molecular markers of partial resistance to artemisinin ( Pfkelch13 , Pfcoronin , Pfubp1 ), Sulfadoxine-Pyrimethamine ( Pfdhfr , Pfdhps ), and Artemisinin-Based Combination therapy (ACT) partner drugs ( Pfmdr1 , Pfcrt ). Allele and haplotype prevalences were compared across villages, transmission seasons, and age groups using chi-square or Fisher’s exact tests, as appropriate. A total of 712 P. falciparum -positive samples were selected for the sample size for molecular analysis. No validated or candidate mutations associated with artemisinin partial resistance were detected in Pfkelch13 and Pfcoronin. Pfubp1 D1525E and E1528D mutations, suspected to be associated with delayed parasite clearance, were each detected at 18.5% and 19.1%, respectively. Mutant alleles of Pfdhfr , including 51 I (73.7%), 59 R (88.6%) and 108 N (91.4%), were highly prevalent. In Pfdhps , the mutant 437 G allele was highly detected (88.4%), whereas 431 V , 540 E and 581 G occurred at low frequencies (< 2%). No significant variation was found between villages and transmission season for Pfdhfr and Pfdhps ( p > 0.05). The wildtype 86 N allele of Pfmdr1 was predominant (95.2%), while mutant allele 184 F (49.31%) was higher and differed significantly between villages ( p = 0.029) with the highest frequency in Séguédin (57.4%) and the lowest in Soala (40.5%). The Pfcrt wildtype CVMNK haplotype (97.4%) remained dominant. This study found no validated Pfkelch13 mutation and no candidate Pfcoronin mutation associated with artemisinin partial resistance. However, the emergence of D1525E and E1528D mutations of Pfubp1 may suggest early signals adaptation of P. falciparum to artemisinin in the study area. The relatively high and expected frequency of Pfdhfr and Pfdhps without significant variations between villages and transmission period suggests homogeneous circulation of these mutations across the study area and reflects continued pressure of SP. The emerging Pfdhps 431 V and 540 E and high frequency of Pfmdr1 184 F allele reinforced the need for regular surveillance to anticipate any resistance of SP and Lumefantrine.