Abstract:
Background: Drug resistance is one of the greatest challenges of malaria control programme in Mali. Recent
advances in next-generation sequencing (NGS) technologies provide new and effective ways of tracking drug-resistant
malaria parasites in Africa. The diversity and the prevalence of Plasmodium falciparum drug-resistance molecular
markers were assessed in Dangassa and Nioro-du-Sahel in Mali, two sites with distinct malaria transmission patterns.
Dangassa has an intense seasonal malaria transmission, whereas Nioro-du-Sahel has an unstable and short seasonal
malaria transmission.
Methods: Up to 270 dried blood spot samples (214 in Dangassa and 56 in Nioro-du-Sahel) were collected from P. falciparum
positive patients in 2016. Samples were analysed on the Agena MassARRAY ® iPLEX platform. Specific codons
were targeted in Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps, Pfarps10, Pfferredoxin, Pfexonuclease and Pfmdr2 genes. The Sanger’s
101-SNPs-barcode method was used to assess the genetic diversity of P. falciparum and to determine the parasite
species.
Results: The Pfcrt_76T chloroquine-resistance genotype was found at a rate of 64.4% in Dangassa and 45.2% in
Nioro-du-Sahel (p = 0.025). The Pfdhfr_51I-59R-108N pyrimethamine-resistance genotype was 14.1% and 19.6%,
respectively in Dangassa and Nioro-du-Sahel. Mutations in the Pfdhps_S436-A437-K540-A581-613A sulfadoxine-resistance
gene was significantly more prevalent in Dangassa as compared to Nioro-du-Sahel (p = 0.035). Up to 17.8% of
the isolates from Dangassa vs 7% from Nioro-du-Sahel harboured at least two codon substitutions in this haplotype.
The amodiaquine-resistance Pfmdr1_N86Y mutation was identified in only three samples (two in Dangassa and one
in Nioro-du-Sahel). The lumefantrine-reduced susceptibility Pfmdr1_Y184F mutation was found in 39.9% and 48.2%
of samples in Dangassa and Nioro-du-Sahel, respectively. One piperaquine-resistance Exo_E415G mutation was
found in Dangassa, while no artemisinin resistance genetic-background were identified. A high P. falciparum diversity
was observed, but no clear genetic aggregation was found at either study sites. Higher multiplicity of infection was
observed in Dangassa with both COIL (p = 0.04) and Real McCOIL (p = 0.02) methods relative to Nioro-du-Sahel.
Conclusions: This study reveals high prevalence of chloroquine and pyrimethamine-resistance markers as well as
high codon substitution rate in the sulfadoxine-resistance gene. High genetic diversity of P. falciparum was observed.
These observations suggest that the use of artemisinins is relevant in both Dangassa and Nioro-du-Sahel.
