Using ESPEN data for evidence-based control of neglected tropical diseases in sub-Saharan Africa: A comprehensive model-based geostatistical analysis of soil-transmitted helminths

Background: The Expanded Special Project for the Elimination of Neglected Tropical Diseases (ESPEN) was launched in 2019 by the World Health Organization and African nations to combat Neglected Tropical Diseases (NTDs), including Soil-transmitted helminths (STH), which still affect over 1.5 billion people globally. In this study, we present a comprehensive geostatistical analysis of publicly available STH survey data from ESPEN to delineate inter-country disparities in STH prevalence and its environmental drivers while highlighting the strengths and limitations that arise from the use of the ESPEN data. To achieve this, we also propose the use of calibration validation methods to assess the suitability of geostatistical models for disease mapping at the national scale. Methods: We analysed the most recent survey data with at least 50 geo-referenced observations, and modelled each STH species data (hookworm, roundworm, whipworm) separately. Binomial geostatistical models were developed for each country, exploring associations between STH and environmental covariates, and were validated using the non-randomized probability integral transform. We produced pixel-, subnational-, and country-level prevalence maps for successfully calibrated countries. All the results were made publicly available through an R Shiny application. Results: Among 35 countries with STH data that met our inclusion criteria, the reported data years ranged from 2004 to 2018. Models from 25 countries were found to be well-calibrated. Spatial patterns exhibited significant variation in STH species distribution and heterogeneity in spatial correlation scale (1.14 km to 3,027.44 km) and residual spatial variation variance across countries. Conclusion: This study highlights the utility of ESPEN data in assessing spatial variations in STH prevalence across countries using model-based geostatistics. Despite the challenges posed by data sparsity which limit the application of geostatistical models, the insights gained remain crucial for directing focused interventions and shaping future STH assessment strategies within national control programs. Author summary: The Expanded Special Project for the Elimination of Neglected Tropical Diseases (NTDs, ESPEN) was established in 2019 to help monitor and control NTDs such as Soil-transmitted helminths (STH) in African countries. We carried out a geostatistical analysis of STH data for 35 countries from the ESPEN database. Separate geostatistical models were developed for each country to tailor the selection of spatial covariates and estimation of covariance parameters to the unique spatial patterns across countries. Moreover, it was observed that the geostatistical models exhibited inadequate calibration in some countries, and thus carrying out spatial predictions at unsampled locations was not possible. These findings urge caution in developing an Africa-wide model based solely on ESPEN data, given the observed heterogeneity in the model parameter estimates and the challenges encountered in model calibration across different species and countries. Despite challenges posed by data sparsity, the insights gained remain crucial for directing focused interventions and shaping future STH assessment strategies within national control programs.