Age-structured next generation matrix and R0 calculation for Mycobacterium avium subsp. paratuberculosis (MAP)

Paratuberculosis (Johne's disease), caused by <i>Mycobacterium avium</i> subspecies <i>paratuberculosis</i> (MAP), is known for its age-specific susceptibility, lifelong infection, varied shedding patterns, low diagnostic sensitivity, long latent period, and prolonged environmental persistence, all of which make eradication challenging. Here, we present an age-structured next-generation matrix (NGM) for a closed, year-round calving, free stall dairy herd to quantify MAP transmission and evaluate the potential of five animal traits that could be targeted by genetic selection and three herd management interventions to reduce the basic reproduction number (R₀). The NGM is based on a compartmental model, that captures dam-to-calf and environmental transmission. Hosts are represented in discrete, one-week age groups, each with its age-dependent susceptibility and location (calving pen for newborns, calf pen for calves, and adult pen for heifer/adults), to reflect both host demography and age-specific exposure. Our baseline NGM yields R₀ = 2.90, with 91.1 % of new infections occurring in calves (1-52 weeks), 5.01 % in newborns (0-1 week), and 3.91 % in heifers/adults (>52 weeks). Univariate analysis identifies two traits that (when successfully selected for) could drive R₀ below one: reducing the initial susceptibility level from 1 to 0.303 (or lower) or increasing the age-specific susceptibility decrease rate from 0.0629 to 0.214 wk^-1 (or higher). We further derive a linear approximation for ΔR₀ that enables rapid scenario testing without reconstructing the full matrix. This study provides methods for quantifying farm-level MAP transmission dynamics and identifying key traits and measures for targeted interventions.