title: Temporal trends in prevalence of Plasmodium falciparum molecular markers selected for by artemether-lumefantrine treatment in pre-ACT and post-ACT parasites in western Kenya.
abstract: Artemether-lumefantrine (AL) became the first-line treatment for uncomplicated malaria in Kenya in 2006. Studies have shown AL selects for SNPs in pfcrt and pfmdr1 genes in recurring parasites compared to the baseline infections. The genotypes associated with AL selection are K76 in pfcrt and N86, 184F and D1246 in pfmdr1. To assess the temporal change of these genotypes in western Kenya, 47 parasite isolates collected before (pre-ACT; 1995-2003) and 745 after (post-ACT; 2008-2014) introduction of AL were analyzed. In addition, the associations of parasite haplotype against the IC50 of artemether and lumefantrine, and clearance rates were determined. Parasite genomic DNA collected between 1995 and 2014 was analyzed by sequencing or PCR-based single-base extension on Sequenom MassARRAY. IC50s were determined for a subset of the samples. One hundred eighteen samples from 2013 to 2014 were from an efficacy trial of which 68 had clearance half-lives. Data revealed there were significant differences between pre-ACT and post-ACT genotypes at the four codons (chi-square analysis; p < 0.0001). The prevalence of pfcrt K76 and N86 increased from 6.4% in 1995-1996 to 93.2% in 2014 and 0.0% in 2002-2003 to 92.4% in 2014 respectively. Analysis of parasites carrying pure alleles of K + NFD or T + YYY haplotypes revealed that 100.0% of the pre-ACT parasites carried T + YYY and 99.3% of post-ACT parasites carried K + NFD. There was significant correlation (p = 0.04) between lumefantrine IC50 and polymorphism at pfmdr1 codon 184. There was no difference in parasite clearance half-lives based on genetic haplotype profiles. This study shows there is a significant change in parasite genotype, with key molecular determinants of AL selection almost reaching saturation. The implications of these findings are not clear since AL remains highly efficacious. However, there is need to closely monitor parasite genotypic, phenotypic and clinical dynamics in response to continued use of AL in western Kenya.
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Angela O
authors.initials: AO
authors.lastname: Achieng
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya ; Department of Biochemistry, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
authors.forename: Peninah
authors.initials: P
authors.lastname: Muiruri
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Luicer A
authors.initials: LA
authors.lastname: Ingasia
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Benjamin H
authors.initials: BH
authors.lastname: Opot
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Juma
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Redemptah
authors.initials: R
authors.lastname: Yeda
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya ; Institute of Tropical Medicine and Infectious Diseases, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
authors.forename: Bidii S
authors.initials: BS
authors.lastname: Ngalah
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Bernhards R
authors.initials: BR
authors.lastname: Ogutu
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Ben
authors.initials: B
authors.lastname: Andagalu
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Hoseah M
authors.initials: HM
authors.lastname: Akala
authors.affiliation: Department of Emerging Infectious Diseases, United States Army Medical Research Unit-Kenya/Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Edwin
authors.initials: E
authors.lastname: Kamau
mesh_terms: D000077611:Artemether, Lumefantrine Drug Combination; D037621:Artemisinins / Q000494:pharmacology* / Q000627:therapeutic use*; D015415:Biomarkers; D004338:Drug Combinations; D004983:Ethanolamines / Q000494:pharmacology* / Q000627:therapeutic use*; D005449:Fluorenes / Q000494:pharmacology* / Q000627:therapeutic use*; D005786:Gene Expression Regulation / Q000187:drug effects; D006239:Haplotypes; D006801:Humans; D007630:Kenya / Q000453:epidemiology; D016778:Malaria, Falciparum / Q000188:drug therapy / Q000453:epidemiology / Q000469:parasitology*; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism; D027425:ATP-Binding Cassette, Sub-Family C Proteins / Q000235:genetics / Q000378:metabolism; D010963:Plasmodium falciparum / Q000187:drug effects / Q000378:metabolism*; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism; D012641:Selection, Genetic; D013997:Time Factors
chemical_list: D000077611:Artemether, Lumefantrine Drug Combination; D037621:Artemisinins; D015415:Biomarkers; D004338:Drug Combinations; D004983:Ethanolamines; D005449:Fluorenes; D026901:Membrane Transport Proteins; D027425:ATP-Binding Cassette, Sub-Family C Proteins; D015800:Protozoan Proteins; C513498:Mdr1 protein, Plasmodium falciparum; C416369:PfCRT protein, Plasmodium falciparum
keywords: Africa; Artemether–lumefantrine; Artemisinin-based combination therapies; Chloroquine; Drug-resistance; Genetics; Molecular markers; Western Kenya