Abstract

Leptospira interrogans serovar Pomona has been circulating endemically in the California sea lion (Zalophus californianus) population since at least the mid-1980s, causing yearly, seasonal outbreaks of varying magnitude. Using serologic, molecular, demographic and ecological data and samples collected between 2010–19 we show that L. interrogans serovar Pomona disappeared from the California sea lion population in 2013 and re-emerged in 2017. We provide multiple lines of evidence that perturbations in both host demography and seasonal movement patterns caused pathogen fadeout in the system and facilitated re-emergence. In addition, we show that these perturbations were likely driven by climate related oceanographic anomalies through impacts on sea lion forage quality, density and distribution. This is the first recorded example of spontaneous fadeout of an endemically circulating pathogen from a large, robust, host population. In a future where greater fluctuations in global climatic variables are predicted, and the impacts of zoonoses on wildlife and human populations are increasingly of concern, our study provides novel insights into how climatic and intrinsic host factors may interact to influence pathogen transmission and persistence in a natural system.