Modeling the spatial distribution of anthrax in southern Kenya

Abstract

Background: Anthrax is an important zoonotic disease in Kenya associated with high animal and public health burden and widespread socio-economic impacts. The disease occurs in sporadic outbreaks that involve livestock, wildlife, and humans, but knowledge on factors that affect the geographic distribution of these outbreaks is limited, challenging public health intervention planning.

Methods: Anthrax surveillance data reported in southern Kenya from 2011 to 2017 were modeled using a boosted regression trees (BRT) framework. An ensemble of 100 BRT experiments was developed using a variable set of 18 environmental covariates and 69 unique anthrax locations. Model performance was evaluated using AUC (area under the curve) ROC (receiver operating characteristics) curves.

Results: Cattle density, rainfall of wettest month, soil clay content, soil pH, soil organic carbon, length of longest dry season, vegetation index, temperature seasonality, in order, were identified as key variables for predicting environmental suitability for anthrax in the region. BRTs performed well with a mean AUC of 0.8. Areas highly suitable for anthrax were predicted predominantly in the southwestern region around the shared Kenya-Tanzania border and a belt through the regions and highlands in central Kenya. These suitable regions extend westwards to cover large areas in western highlands and the western regions around Lake Victoria and bordering Uganda. The entire eastern and lower-eastern regions towards the coastal region were predicted to have lower suitability for anthrax.

Conclusion: These modeling efforts identified areas of anthrax suitability across southern Kenya, including high and medium agricultural potential regions and wildlife parks, important for tourism and foreign exchange. These predictions are useful for policy makers in designing targeted surveillance and/or control interventions in Kenya. We thank the staff of Directorate of Veterinary Services under the Ministry of Agriculture, Livestock and Fisheries, for collecting and providing the anthrax historical occurrence data.

Fig 1. Map of Kenya showing the study area and the spatial distribution of anthrax occurence data (red circles) recorded between 2011 and 2017.

Areas 1–4 arbitrarily represent important regions for describing the predicted distribution of anthrax: 1) western highlands; 2) Lake Victoria basin; 3) southwestern region; 4) central highlands.

Fig 2. Panel A: Predicted geographic distribution of anthrax in southern Kenya based on the mean prediction of an ensemble of 100 boosted regression tree experiments.

Panel B shows the upper 97.5% and C the lower 2.5% confidence intervals. Regions 1–4 are used as reference areas for the discussion: 1) western highlands; 2) Lake Victoria basin; 3) southwestern region; 4) central highlands.

Fig 3. Location of National Parks and Game Reserves overlaid on the predicted distribution of anthrax in southern Kenya based on boosted regression tree experiments.

Fig 4. Variable relative influence for final variable set used to model the distribution of anthrax in southern Kenya using boosted regression tree experiments.

Error bars represent variability across an ensemble of 100 BRT experiments.

Fig 5. Partial dependency plots (PDP) showing marginal effects on the mean prediction probability of potential anthrax distribution by each variable across the 100 BRT experiments.