Antimalarial drug resistance molecular makers of Plasmodium falciparum isolates from Sudan during 2015-2017

Background Current malaria control and elimination strategies rely mainly on efficacious antimalarial drugs. However, drug resistance is a major threat facing malaria control programs. Determination of drug resistance molecular markers is useful in the monitoring and surveillance of malaria drug efficacy. This study aimed to determine the mutations and haplotypes frequencies of different genes linked with antimalarial drug resistance in certain areas in Sudan. Methods A total of 226 dried blood spots (DBS) of microscopically diagnosedP.falciparumisolates were collected from Khartoum and three other areas in Sudan during 2015-2017.Plasmodium falciparumconfirmation and multiplicity of infection was assessed using the Sanger's 101 SNPs-barcode and speciation was confirmed using regions of the parasite mitochondria. Molecular genotyping of drug resistance genes (Pfcrt,Pfmdr1,Pfdhfr,Pfdhps,exonuclease,Pfk13, parasite genetic background (PGB) (Pfarps10,ferredoxin,Pfcrt,Pfmdr2)) was also performed. All genotypes were generated by selective regions amplicon sequencing of the parasite genome using the Illumina MiSeq platform at the Wellcome Sanger Institute, UK then genotypes were translated into drug resistance haplotypes and species determination. Findings In total 225 samples were confirmed to beP.falciparum. A higher proportion of multiplicity of infection was observed in Gezira (P<0.001) based on the Sanger 101 SNPs -barcode. The overall frequency of mutant haplotypePfcrt72-76 CVIET was 71.8%. ForPfmdr1, N86Y was detected in 53.6%, Y184F was observed in 88.1% and D1246Y was detected in 1.5% of the samples. The most frequently observed haplotype was YFD 47.4%. ForPfdhfr(codons 51, 59,108,164), the ICNI haplotype was the most frequent (80.7%) while forPfdhps(codons 436, 437, 540, 581, 613) the (SGEAA) was most frequent haplotype (41%). The Quadruple mutation (dhfrN51I, S108N +dhpsA437G, K540E) was the highest frequent combined mutation (33.9%). InPfkelch13gene, 18 non-synonymous mutations were detected, 7 of them were detected in other African countries. The most frequentPfk13mutation was E433D detected in four samples. All of thePfk13mutant alleles have not been reported to belong to mutations associated with delayed parasite clearance in Southeast Asia. PGB mutations were detected only inPfcrtN326S\I (46.3%) andPfcrtI356T (8.2%). Theexonucleasemutation was not detected. There was no significant variation in mutant haplotypes between study areas. Conclusions There was high frequency of mutations inPfcrt,PfdhfrandPfdhpsin this study. These mutations are associated with chloroquine and sulfadoxine-pyrimethamine (SP) resistance. Many SNPs inPfk13not linked with delayed parasite clearance were observed. TheexonucleaseE415G mutation which is linked with piperaquine resistance was not reported.