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In response to this threat nets have been developed that incorporate the synergist, piperonyl butoxide (PBO), which inhibits the activity of cytochrome P450s which is one main mechanisms of insecticide resistance, allowing resistance to pyrethroids to be reversed. However, data on the value and cost effectiveness of these nets is lacking. A large-scale cluster randomised trial of conventional LLINs and PBO-LLINs was conducted in Uganda in 104 health sub-districts (HSDs) in 2017\u20132019. Prior to the mass distribution of LLINs, a baseline entomological survey was carried out, the results of which are reported herein. Ten households from each HSD were randomly selected for entomological surveillance at baseline which included household mosquito collections.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Prior to LLIN distribution entomological collections were carried out in 1029 houses across the 104 HSDs. <jats:italic>Anopheles gambiae<\/jats:italic> (<jats:italic>s.l.<\/jats:italic>) was the principal vector in all but 9 of the 71 HSDs that yielded vector species. Molecular analysis found <jats:italic>An. gambiae<\/jats:italic> (<jats:italic>s.s.<\/jats:italic>) to be the predominant vector collected. <jats:italic>Plasmodium falciparum<\/jats:italic> was detected in 5.5% of <jats:italic>An. gambiae<\/jats:italic> (<jats:italic>s.s.<\/jats:italic>) and in 4.0% of <jats:italic>An. funestus<\/jats:italic> (<jats:italic>s.s.<\/jats:italic>) examined. Infection rates of other plasmodium species (<jats:italic>P. vivax<\/jats:italic>, <jats:italic>P. ovale and P. malariae<\/jats:italic>) were lower with infection rates of 1.2% and 1.7% for <jats:italic>An. gambiae<\/jats:italic> (<jats:italic>s.s.<\/jats:italic>) and <jats:italic>An. funestus<\/jats:italic> (<jats:italic>s.s.<\/jats:italic>), respectively. The knockdown resistance (<jats:italic>kdr)<\/jats:italic> mutation <jats:italic>Vgsc<\/jats:italic>-L1014S was found at very high frequency in <jats:italic>An. gambiae<\/jats:italic> (<jats:italic>s.s.<\/jats:italic>) with the <jats:italic>Vgsc<\/jats:italic>-L1014F mutation at low frequency and the wild-type allele virtually absent. In <jats:italic>An. arabiensis<\/jats:italic> the wild-type allele was predominant. The resistance-associated alleles, <jats:italic>Cyp4j5<\/jats:italic>-L43F and <jats:italic>Coeae1d<\/jats:italic> were found at moderate frequencies which varied across the study site. <jats:italic>Vgsc<\/jats:italic>-N1575Y mutation was not found in any samples examined.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>No significant differences between planned intervention arms was observed in vector densities, sporozoite infection rate or insecticide resistance marker frequency across the study site prior to the distribution of LLINs. Very high levels of <jats:italic>kdr<\/jats:italic> resistance were observed in all areas; however, the resistance-associated markers <jats:italic>Cyp4j5<\/jats:italic>-L43F and <jats:italic>Coeae1d<\/jats:italic> were found at varying frequencies across the study site which may have implications for the effectiveness of standard LLINs.<\/jats:p>\n                <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>\n              <\/jats:sec>","DOI":"10.1186\/s13071-019-3353-7","type":"journal-article","created":{"date-parts":[[2019,3,13]],"date-time":"2019-03-13T18:03:38Z","timestamp":1552500218000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["LLIN Evaluation in Uganda Project (LLINEUP): a cross-sectional survey of species diversity and insecticide resistance in 48 districts of Uganda"],"prefix":"10.1186","volume":"12","clinical-trial-number":[{"clinical-trial-number":"isrctn17516395","registry":"10.18810\/isrctn"}],"author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6054-0525","authenticated-orcid":false,"given":"Amy","family":"Lynd","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel","family":"Gonahasa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah G.","family":"Staedke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ambrose","family":"Oruni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catherine","family":"Maiteki-Sebuguzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grant","family":"Dorsey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jimmy","family":"Opigo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adoke","family":"Yeka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agaba","family":"Katureebe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary","family":"Kyohere","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janet","family":"Hemingway","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Moses R.","family":"Kamya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin J.","family":"Donnelly","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,3,12]]},"reference":[{"key":"3353_CR1","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature15535","volume":"526","author":"S Bhatt","year":"2015","unstructured":"Bhatt S, Weiss DJ, Cameron E, Bisanzio D, Mappin B, Dalrymple U, et al. 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