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In 2017\u20132019, we conducted a large-scale, cluster-randomised trial (LLINEUP) to evaluate long-lasting insecticidal nets (LLINs) treated with a pyrethroid insecticide plus PBO (PBO LLINs), as compared to conventional, pyrethroid-only LLINs across 104 health sub-districts (HSDs) in Uganda. In LLINEUP, and similar trials in Tanzania, PBO LLINs were found to provide greater protection against malaria than conventional LLINs, reducing parasitaemia and vector density. In the LLINEUP trial, we conducted cross-sectional household entomological surveys at baseline and then every 6\u00a0months for two years, which we use here to investigate longitudinal changes in mosquito infection rate and genetic markers of resistance. Overall, 5395 female <jats:italic>Anopheles<\/jats:italic> mosquitoes were collected from 5046 households. The proportion of mosquitoes infected (PCR-positive) with <jats:italic>Plasmodium falciparum<\/jats:italic> did not change significantly over time, while infection with non-<jats:italic>falciparum<\/jats:italic> malaria decreased in <jats:italic>An. gambiae<\/jats:italic> s.s., but not <jats:italic>An. funestus<\/jats:italic>. The frequency of genetic markers associated with pyrethroid resistance increased significantly over time, but the rate of change was not different between the two LLIN types. The knock-down resistance (<jats:italic>kdr<\/jats:italic>) mutation <jats:italic>Vgsc<\/jats:italic>-995S declined over time as <jats:italic>Vgsc<\/jats:italic>-995F, the alternative resistance mutation at this codon, increased. <jats:italic>Vgsc<\/jats:italic>-995F appears to be spreading into Uganda. Distribution of LLINs in Uganda was previously found to be associated with reductions in parasite prevalence and vector density, but here we show that the proportion of infective mosquitoes remained stable across both PBO and non-PBO LLINs, suggesting that the potential for transmission persisted. The increased frequency of markers of pyrethroid resistance indicates that LLIN distribution favoured the evolution of resistance within local vectors and highlights the potential benefits of resistance management strategies.<\/jats:p><jats:p><jats:italic>Trial registration<\/jats:italic>: This study is registered with ISRCTN, ISRCTN17516395. Registered 14 February 2017, <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.isrctn.com\/ISRCTN17516395\">http:\/\/www.isrctn.com\/ISRCTN17516395<\/jats:ext-link>.<\/jats:p>","DOI":"10.1038\/s41598-024-65050-z","type":"journal-article","created":{"date-parts":[[2024,6,24]],"date-time":"2024-06-24T11:03:19Z","timestamp":1719226999000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["LLIN Evaluation in Uganda Project (LLINEUP)\u2013effects of a vector control trial on Plasmodium infection prevalence and genotypic markers of insecticide resistance in Anopheles vectors from 48 districts of Uganda"],"prefix":"10.1038","volume":"14","author":[{"given":"Amy","family":"Lynd","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Gonahasa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah G.","family":"Staedke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ambrose","family":"Oruni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Maiteki-Sebuguzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Penelope A.","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin","family":"Knight","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grant","family":"Dorsey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jimmy","family":"Opigo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adoke","family":"Yeka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agaba","family":"Katureebe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary","family":"Kyohere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet","family":"Hemingway","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moses R.","family":"Kamya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"McDermott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric R.","family":"Lucas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin J.","family":"Donnelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,6,24]]},"reference":[{"key":"65050_CR1","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature15535","volume":"526","author":"S Bhatt","year":"2015","unstructured":"Bhatt, S. et al. 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