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In Africa,<jats:italic>Plasmodium falciparum<\/jats:italic>remains susceptible to artemisinin-based combination therapy (ACT), but the emergence of resistant parasites in multiple countries in Southeast Asia and concerns over emergence and\/or spread of resistant parasites in Africa warrants continuous monitoring. The World Health Organization recommends that surveillance for molecular markers of resistance be included within therapeutic efficacy studies (TES). The current study assessed molecular markers associated with resistance to Artemether\u2212lumefantrine (AL) and Dihydroartemisinin\u2212piperaquine (DP) from samples collected from children aged 6\u201359\u00a0months enrolled in a TES conducted in Siaya County, western Kenya from 2016 to 2017.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Three\u00a0hundred and twenty-three samples collected pre-treatment (day-0) and 110 samples collected at the day of recurrent parasitaemia (up to day 42) were tested for the presence of drug resistance markers in the<jats:italic>Pfk13<\/jats:italic>propeller domain, and the<jats:italic>Pfmdr1<\/jats:italic>and<jats:italic>Pfcrt<\/jats:italic>genes by Sanger sequencing. Additionally, the<jats:italic>Pfpm2<\/jats:italic>gene copy number was assessed by real-time polymerase chain reaction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>No mutations previously associated with artemisinin resistance were detected in the<jats:italic>Pfk13<\/jats:italic>propeller region. However, other non-synonymous mutations in the<jats:italic>Pfk13<\/jats:italic>propeller region were detected. The most common mutation found on day-0 and at day of recurrence in the<jats:italic>Pfmdr1<\/jats:italic>multidrug resistance marker was at codon 184<jats:bold>F<\/jats:bold>. Very few mutations were found in the<jats:italic>Pfcrt<\/jats:italic>marker (&lt;\u20095%). Within the DP arm, all recrudescent cases (8 sample pairs) that were tested for<jats:italic>Pfpm2<\/jats:italic>gene copy number had a single gene copy. None of the associations between observed mutations and treatment outcomes were statistically significant.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The results indicate absence of<jats:italic>Pfk13<\/jats:italic>mutations associated with parasite resistance to artemisinin in this area and a very high proportion of wild-type parasites for<jats:italic>Pfcrt<\/jats:italic>. Although the frequency of<jats:italic>Pfmdr1<\/jats:italic>184<jats:bold>F<\/jats:bold>mutations was high in these samples, the association with treatment failure did not reach statistical significance. As the spread of artemisinin-resistant parasites remains a possibility, continued monitoring for molecular markers of ACT resistance is needed to complement clinical data to inform treatment policy in Kenya and other malaria-endemic regions.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12936-020-03358-7","type":"journal-article","created":{"date-parts":[[2020,8,14]],"date-time":"2020-08-14T14:02:54Z","timestamp":1597413774000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Assessment of molecular markers of anti-malarial drug resistance among children participating in a therapeutic efficacy study in western Kenya"],"prefix":"10.1186","volume":"19","author":[{"given":"Winnie","family":"Chebore","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyong","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nelli","family":"Westercamp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kephas","family":"Otieno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya Ping","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheila B.","family":"Sergent","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelsey Anne","family":"Rondini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samaly Souza","family":"Svigel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benard","family":"Guyah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Venkatachalam","family":"Udhayakumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric S.","family":"Halsey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron M.","family":"Samuels","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0554-1976","authenticated-orcid":false,"given":"Simon","family":"Kariuki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,8,14]]},"reference":[{"key":"3358_CR1","volume-title":"World malaria report 2019","author":"WHO","year":"2019","unstructured":"WHO. 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