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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\n                      <jats:italic>Plasmodium falciparum<\/jats:italic>\n                      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.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Up to 270 dried blood spot samples (214 in Dangassa and 56 in Nioro-du-Sahel) were collected from\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      positive patients in 2016. Samples were analysed on the Agena MassARRAY\n                      <jats:sup>\u00ae<\/jats:sup>\n                      iPLEX platform. Specific codons were targeted in\n                      <jats:italic>Pfcrt<\/jats:italic>\n                      ,\n                      <jats:italic>Pfmdr1<\/jats:italic>\n                      ,\n                      <jats:italic>Pfdhfr<\/jats:italic>\n                      , and\n                      <jats:italic>Pfdhps, Pfarps10, Pfferredoxin, Pfexonuclease<\/jats:italic>\n                      and\n                      <jats:italic>Pfmdr2<\/jats:italic>\n                      genes. The Sanger\u2019s 101-SNPs-barcode method was used to assess the genetic diversity of\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      and to determine the parasite species.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The\n                      <jats:italic>Pfcrt<\/jats:italic>\n                      _76\n                      <jats:underline>T<\/jats:underline>\n                      chloroquine-resistance genotype was found at a rate of 64.4% in Dangassa and 45.2% in Nioro-du-Sahel (\n                      <jats:italic>p\u2009<\/jats:italic>\n                      =\u20090.025). The\n                      <jats:italic>Pfdhfr_51I<\/jats:italic>\n                      -\n                      <jats:italic>59R<\/jats:italic>\n                      -\n                      <jats:italic>108N<\/jats:italic>\n                      pyrimethamine-resistance genotype was 14.1% and 19.6%, respectively in Dangassa and Nioro-du-Sahel. Mutations in the\n                      <jats:italic>Pfdhps<\/jats:italic>\n                      <jats:italic>_S436<\/jats:italic>\n                      -\n                      <jats:italic>A437<\/jats:italic>\n                      -\n                      <jats:italic>K540<\/jats:italic>\n                      -\n                      <jats:italic>A581<\/jats:italic>\n                      -\n                      <jats:italic>613A<\/jats:italic>\n                      sulfadoxine-resistance gene was significantly more prevalent in Dangassa as compared to Nioro-du-Sahel (\n                      <jats:italic>p\u2009<\/jats:italic>\n                      =\u20090.035). Up to 17.8% of the isolates from Dangassa\n                      <jats:italic>vs<\/jats:italic>\n                      7% from Nioro-du-Sahel harboured at least two codon substitutions in this haplotype. The amodiaquine-resistance\n                      <jats:italic>Pfmdr1<\/jats:italic>\n                      _N86Y mutation was identified in only three samples (two in Dangassa and one in Nioro-du-Sahel). The lumefantrine-reduced susceptibility\n                      <jats:italic>Pfmdr1_Y184F<\/jats:italic>\n                      mutation was found in 39.9% and 48.2% of samples in Dangassa and Nioro-du-Sahel, respectively. One piperaquine-resistance\n                      <jats:italic>Exo<\/jats:italic>\n                      <jats:italic>_E415G<\/jats:italic>\n                      mutation was found in Dangassa, while no artemisinin resistance genetic-background were identified. A high\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      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 (\n                      <jats:italic>p\u2009<\/jats:italic>\n                      =\u20090.04) and Real McCOIL (\n                      <jats:italic>p\u2009<\/jats:italic>\n                      =\u20090.02) methods relative to Nioro-du-Sahel.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      was observed. These observations suggest that the use of artemisinins is relevant in both Dangassa and Nioro-du-Sahel.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12936-019-2986-5","type":"journal-article","created":{"date-parts":[[2019,11,12]],"date-time":"2019-11-12T06:03:37Z","timestamp":1573538617000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1193-6501","authenticated-orcid":false,"given":"Seidina A. 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