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.

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

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2025年12月19日

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Josephat Bungei,
Collins Ouma,
Daibin Zhong,
Job Oyweri,
Ming-Chieh Lee,
Guofa Zhou,
Harrysone Atieli,
John Githure,
Chloe Wang,
Guiyun Yan

摘要

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.