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Background Namibia is now ready to begin mass drug administration of praziquantel and albendazole against schistosomiasis and soil-transmitted helminths, respectively. Although historical data identifies areas of transmission of these neglected tropical diseases (NTDs), there is a need to update epidemiological data.

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For this reason, Namibia adopted a new protocol for mapping of schistosomiasis and geohelminths, formally integrating rapid diagnostic tests (RDTs) for infections and morbidity. In this article, we explain the protocol in detail, and introduce the concept of ‘mapping resolution’, as well as present results and treatment recommendations for northern Namibia. Methods/Findings/Interpretation This new protocol allowed a large sample to be surveyed (N = 17 896 children from 299 schools) at relatively low cost (7 USD per person mapped) and very quickly (28 working days).

All children were analysed by RDTs, but only a sub-sample was also diagnosed by light microscopy. Overall prevalence of schistosomiasis in the surveyed areas was 9.0%, highly associated with poorer access to potable water (OR = 1.5, P. Historical data indicates Namibia, particularly northern Namibia, as endemic for geohelminths and schistosomiasis, albeit to a lower extent than other areas in Sub-Saharan Africa. The National Ministry of Health and Social Services, with extensive backing from other governmental and non-governmental organizations, investigated the extent of the problem in preparation for deployment of a control programme.

Using a cost-effective strategy, a new generation protocol was developed for mapping these important neglected tropical diseases, bolstering field-standard microscopy results with those from commercially available rapid diagnostic tests. The protocol used increased the mapping coverage (one in every four schools mapped) with minimal added cost. Results from our surveys, which included 17 896 school-going children (3–19 years of age), identified hotspots of transmission for schistosomiasis and geohelminths, particularly hookworm infection, and allowed the recommendation of constituency- and region- specific treatment regimens, as well as improvements to water, sanitation and hygiene. Furthermore, we identified high levels of intestinal morbidity, believed to be associated with hookworm and Hymenolepis nana infections, and lower levels of urogenital pathology, associated with Schistosoma haematobium infection.

A cost-effectiveness analysis is also presented in addition to reporting the diagnostic accuracy of the rapid diagnostic tests employed. Introduction Namibia has recently established a national programme for the integrated control of neglected tropical diseases (NTDs) with support from The END Fund. The programme's first objective was to gather detailed information on the prevalence and distribution (mapping) of schistosomiasis (both intestinal and urogenital) and soil-transmitted helminths (STH). Although other NTDs are endemic in Namibia, of the five eligible for preventive chemotherapy (PCT), only schistosomiasis and STH infections are believed to be prevalent []. Lymphatic filariasis and onchocerciasis have never been identified at the community- or health facility-level [,], and for trachoma, although indicated by predictive mapping [,], no epidemiological confirmation has been reported []. According to WHO NTD maps, Namibia is indicated to have a prevalence of schistosomiasis below 10% [].