A stochastic dose-response framework for environmentally persistent pathogens

Abstract

Infectious diseases caused by environmentally persistent pathogens can strongly affect host populations as transmission occurs not only through direct host-host contact but also via indirect exposure to contaminated environments. While in some systems environmental reservoirs help sustain exposure even when infected host numbers are low, reliance on environmental transmission pathway may also increase pathogen extinction risk. Infection risk may depend on both pathogen dose and timing of exposure. Thus, understanding how dose-response, stochasticity, and seasonal changes in host susceptibility or contact rates shape pathogen invasion and persistence remains an important challenge for environmentally transmitted disease systems. To address this, we develop a stochastic dose-response framework that integrates host infection dynamics with an explicit environmental pathogen reservoir. Transmission occurs through both direct contact with infectious hosts and indirect environmental exposure, with infection probability governed by dose-response functions. We focus on stochastic continuous-time Markov chain formulation and use branching process approximation to estimate disease extinction probabilities when infected hosts or environmental pathogen loads are low. We extend the framework to include seasonality in host susceptibility, environmental contact, and host-host contact. As a case study, we apply the model to snake fungal disease. Numerical simulations show that dose-response influences epidemic takeoff and infection levels, while seasonality creates windows of high and low extinction risk. These extinction risks depend strongly on the route and timing of introduction within the seasonal cycle. These results, coupled with global sensitivity analysis, illustrate how stochasticity, nonlinear dose-response, and seasonal timing shape outbreak dynamics for environmentally persistent pathogens.