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The aim of this study was to assess the current prevalence of molecular markers of drug resistance in\n                      <jats:italic>Plasmodium falciparum<\/jats:italic>\n                      in the four provinces with the highest malaria burden in Pakistan, after introducing artemether\u2013lumefantrine as first-line treatment in 2017.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Samples were collected during routine malaria surveillance in Punjab, Sindh, Baluchistan, and Khyber Pakhtunkhwa provinces of Pakistan between January 2018 and February 2019.\n                      <jats:italic>Plasmodium falciparum<\/jats:italic>\n                      infections were confirmed by rapid diagnostic test or microscopy.\n                      <jats:italic>Plasmodium falciparum<\/jats:italic>\n                      positive isolates (n\u2009=\u2009179) were screened by Sanger sequencing for single nucleotide polymorphisms (SNPs) in the\n                      <jats:italic>P<\/jats:italic>\n                      <jats:italic>. falciparum kelch 13<\/jats:italic>\n                      (\n                      <jats:italic>pfk13)<\/jats:italic>\n                      propeller domain and in\n                      <jats:italic>P. falciparum coronin<\/jats:italic>\n                      (\n                      <jats:italic>pfcoronin<\/jats:italic>\n                      ). SNPs in\n                      <jats:italic>P. falciparum multidrug resistance 1 (pfmdr1)<\/jats:italic>\n                      N86Y, Y184F, D1246Y and\n                      <jats:italic>P. falciparum chloroquine resistance transporter<\/jats:italic>\n                      (\n                      <jats:italic>pfcrt)<\/jats:italic>\n                      K76T were genotyped by PCR-restriction fragment length polymorphism.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      No artemisinin resistance associated SNPs were identified in the\n                      <jats:italic>pfk13<\/jats:italic>\n                      propeller domain or in\n                      <jats:italic>pfcoronin<\/jats:italic>\n                      . The\n                      <jats:italic>pfmdr1<\/jats:italic>\n                      N86, 184F, D1246 and\n                      <jats:italic>pfcrt<\/jats:italic>\n                      K76 alleles associated with reduced lumefantrine sensitivity were present in 83.8% (150\/179), 16.9% (29\/172), 100.0% (173\/173), and 8.4% (15\/179) of all infections, respectively. The chloroquine resistance associated\n                      <jats:italic>pfcrt<\/jats:italic>\n                      76T allele was present in 98.3% (176\/179) of infections.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      This study provides an update on the current prevalence of molecular markers associated with reduced\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      sensitivity to artemether and\/or lumefantrine in Pakistan, including a first baseline assessment of polymorphisms in\n                      <jats:italic>pfcoronin<\/jats:italic>\n                      . No mutations associated with artemisinin resistance were observed in\n                      <jats:italic>pfk13<\/jats:italic>\n                      or\n                      <jats:italic>pfcoronin<\/jats:italic>\n                      . However, the prevalence of the\n                      <jats:italic>pfmdr1<\/jats:italic>\n                      N86 and D1246 alleles, that have been associated with decreased susceptibility to lumefantrine, remain high. Although clinical and molecular data suggest that the current malaria treatment guidelines for\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      are presently effective in Pakistan, close monitoring for artemisinin and lumefantrine resistance will be critical to ensure early detection and enhanced containment of emerging ACT resistance spreading across from Southeast Asia.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12936-020-03276-8","type":"journal-article","created":{"date-parts":[[2020,6,8]],"date-time":"2020-06-08T08:05:46Z","timestamp":1591603546000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Surveillance of genetic markers associated with Plasmodium falciparum resistance to artemisinin-based combination therapy in Pakistan, 2018\u20132019"],"prefix":"10.1186","volume":"19","author":[{"given":"Abdul Qader","family":"Khan","sequence":"first","affiliation":[]},{"given":"Leyre","family":"Pernaute-Lau","sequence":"additional","affiliation":[]},{"given":"Aamer Ali","family":"Khattak","sequence":"additional","affiliation":[]},{"given":"Sanna","family":"Luijcx","sequence":"additional","affiliation":[]},{"given":"Berit","family":"Aydin-Schmidt","sequence":"additional","affiliation":[]},{"given":"Mubashir","family":"Hussain","sequence":"additional","affiliation":[]},{"given":"Taj Ali","family":"Khan","sequence":"additional","affiliation":[]},{"given":"Farees Uddin","family":"Mufti","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4734-5754","authenticated-orcid":false,"given":"Ulrika","family":"Morris","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,6,8]]},"reference":[{"key":"3276_CR1","unstructured":"WHO. 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