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Background: Success of mass drug administration (MDA) for control of neglected tropical diseases depends on treatment coverage and patterns across rounds. There has been limited opportunity to explore these features within programmes at scale. Here we use routinely-collected individual-level treatment records collated for the TUMIKIA trial, conducted in coastal Kenya from 2015-2017, to estimate the extent of -- and factors associated with -- systematic non-treatment in the targeted population. Methods: The trial baseline population (N=36327) was linked with treatment records from four rounds of biannual community-wide MDA for soil-transmitted helminthiasis. We fit logistic regression models to estimate the association of non-treatment with treatment status during the previous round, controlling for identified predictors of non-treatment, and used multinomial logistic regression to identify factors associated with partial or no treatment versus complete treatment. Findings: Children aged 2-14 years and individuals aged 15+ years were more likely to remain untreated if they were not treated during the previous MDA. For children, school attendance and rural residence were protective against receiving partial and no treatment. Women were more likely than men to receive partial and no treatment, unless periods of pregnancy and recent childbirth were excluded; then, women more likely received complete treatment. Adults aged 20-25 years were most likely to receive partial or no treatment. Interpretation: We identified eligible populations who received incomplete treatment across multiple MDA rounds and found that this non-treatment did not occur at random. This finding has important implications for MDA programme effectiveness and will be increasingly important as prevalence reaches low levels. Funding Statement: Funding for TUMIKIA was received from the Bill & Melinda Gates Foundation, the Joint Global Health Trials Scheme of the Medical Research Council, the UK Department for International Development, the Wellcome Trust, and the Children’s Investment Fund Foundation. This analysis was supported by the London Centre for Neglected Tropical Diseases. SK is supported by THRiVE-2, a DELTAS Africa grant # DEL-15-011 from Wellcome Trust grant # 107742/Z/15/Z and the UK government. Declaration of Interests: RMA was a non-executive director of GlaxoSmithKline during the TUMIKIA trial. GlaxoSmithKline had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. SJB is currently employed by the Bill & Melinda Gates Foundation (BMGF) but was employed by the London School of Hygiene & Tropical Medicine when TUMIKIA was designed and commenced. GlaxoSmithKline and BMGF played no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. All other authors declare no competing interests. Ethics Approval Statement: The TUMIKIA trial protocol, including measurement of treatment coverage and adherence using routine and household survey data, was approved by the Kenya Medical Research Institute and National Ethics Review Committee (SSC Number 2826) and the London School of Hygiene & Tropical Medicine (LSHTM) Ethics Committee (7177). Written informed consent was sought from the household head or adult answering the household-level questionnaire. All information and consent procedures were conducted in Kiswahili. |