R scripts, input and output data for: Season of death, pathogen persistence and wildlife behaviour alter number of anthrax secondary infections from environmental reservoirs

An important part of infectious disease management is predicting factors
that influence disease outbreaks, such as R, the number of secondary
infections arising from an infected individual. Estimating R is
particularly challenging for environmentally transmitted pathogens given
time lags between cases and subsequent infections. Here, we calculated R
for Bacillus anthracis infections arising from anthrax carcass sites in
Etosha National Park, Namibia. Combining host behavioural data, pathogen
concentrations, and simulation models, we show that R is spatially and
temporally variable, driven by spore concentrations at death, host
visitation rates and early preference for foraging at infectious sites.
While spores were detected up to a decade after death, most secondary
infections occurred within two years. Transmission simulations under
scenarios combining site infectiousness and host exposure risk under
different environmental conditions led to dramatically different outbreak
dynamics, from pathogen extinction (R<1) to explosive outbreaks
(R>10). These transmission heterogeneities may explain variation in
anthrax outbreak dynamics observed globally, and more generally, the
critical importance of environmental variation underlying host-pathogens
interactions. Notably, our approach allowed us to estimate the lethal dose
of a highly virulent pathogen non-invasively from observational studies
and epidemiological data, useful when experiments on wildlife are
undesirable or impractical.