Background Soil-transmitted helminths (STH) and schistosomiasis comprise the most wide-spread NTDs globally. Preventative chemotherapy is a cost-effective approach to controlling morbidity of both diseases, but relies on large scale surveys to determine and revise treatment frequency. Availability of detailed information on survey costs is limited despite recent methodological surveying innovations. We micro-costed a survey of STH and schistosomiasis in Kenya, and linked results to precision estimates of competing survey methods to compare cost-efficiency. Methods Costs from a 2017 Kenyan parasitological survey were retrospectively analyzed and extrapolated to explore marginal changes when altering survey size, defined by the number of schools sampled and the number of samples taken per school. Subsequent costs were applied to simulated precision estimates of model-based geostatistical (MBG) and traditional survey designs. Cost-precision was calculated for a range of survey sizes per method. Four traditional survey design scenarios, based around WHO guidelines, were selected to act as reference cases for calculating incremental cost-effectiveness ratios (ICERs) for MBG design. Findings MBG designed surveys showed improved cost-precision, particularly if optimizing number of schools against samples per school. MBG was found to be more cost-effective under 87 of 92 comparisons to reference cases. This comprised 14 situations where MBG was both cheaper and more precise, 42 which had cost saving with precision trade off (ICERs; $8,915-$344,932 per percentage precision lost); and 31 more precise with increased cost (ICERs; $426-$147,748 per percentage precision gained). The remaining 5 comparisons represented extremes of MBG simulated site selection, unlikely to be applied in practice. Interpretation Efficiency gains are possible for deworming surveys when considering cost alone, such as through minimizing sample or analysis costs. However further efficiency maximization is possible when designing surveys using MBG given its improved precision and ability to optimize the balance between number of schools and sample size per school.
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