Comparative molecular surveillance of polymorphisms in chloroquine resistance transporter, multidrug resistance 1, and Kelch 13 genes associated with antimalarial drug resistance in Plasmodium falciparum isolates from Western Kenya.

BACKGROUND: Malaria treatment interventions play a central role in the prevention and control of Plasmodium falciparum infections worldwide. However, the emergence and spread of resistant P. falciparum parasites pose a serious public health challenge, as they reduce the effectiveness of antimalarial drugs and contribute to an increased global malaria burden. This study conducted a comparative molecular surveillance of antimalarial drug resistance in P. falciparum isolates from the Lake endemic and highland epidemic-prone regions of western Kenya.

METHODS: A cross-sectional study design was employed to screen patients presenting with malaria-associated symptoms among residents of the lake-endemic region of Nyando sub-County in Kisumu County and the highland epidemic-prone region of Marani sub-County in Kisii County. Single-nucleotide polymorphisms (SNPs) were genotyped in the chloroquine resistance transporter (Pfcrt), multidrug resistance 1 (Pfmdr1), and Kelch 13 (Pfk13) genes to identify validated molecular markers associated with resistance to chloroquine, artemisinin derivatives, and artemisinin partner drugs. A comparative analysis was conducted to assess mutation frequencies, genetic diversity, and selection pressure on molecular markers associated with antimalarial drug resistance between the Lake-endemic region and the highland epidemic-prone region.

RESULTS: Genotyping of molecular markers detected M74I, N75E, and K76T mutations each at a frequency of 5.4% in Pfcrt, N146I (0.9%), Y184F (48.2%), and D1246Y (3.6%) in Pfmdr1, and S522C (0.9%), R561H (0.9%), and A675V (12.8%) in Pfk13. Comparative analysis revealed a significant prevalence of the Pfcrt M74I, N75E, and K76T alleles (11.5%) and the Pfk13 A675V allele (27.5%) in the Kisii region (p < 0.05). Pfcrt CVIET (5.4%), Pfmdr1 NFD (46.7%), and Pfk13 SRV (12.8%) were the dominant haplotypes. Additionally, a novel Pfmdr1 N146I mutation and rare Pfk13 S522C and R561H mutations were detected in the Kisumu region. Although the Kisii region presented greater genetic diversity of Pfk13, neutrality statistics, Tajima's D (-1.8474, p < 0.05), Fu's Fs (-3.835), and Fu and Li's F (-3.5041, p < 0.02), suggest significant population expansion in the Kisumu region, potentially driven by the emergence of the rare S522C and R561H alleles.

CONCLUSION: Our findings reveal the persistence of the Pfcrt CVIET haplotype and elevated Pfk13 A675V mutation in Kisii, with a moderate prevalence of Pfmdr1 Y184F mutation in both regions. Crucially, we detected emerging novel Pfmdr1 N146I and rare Pfk13 S522C and R561H mutations in Kisumu. Given that artemether-lumefantrine is Kenya's first-line treatment, continuous molecular surveillance is essential to elucidate the selection pressures driving the spread of resistant P. falciparum in western Kenya.