<i>Leptospira</i> prevalence and lineages vary across land-use types due to shifts in small mammal communities

Leptospirosis, a globally distributed, environmentally transmitted zoonosis, causes 2.9 million disability-adjusted life years annually, primarily among rural farmers in tropical regions. Infected animals' urine contaminates soils and water with <i>Leptospira</i> bacteria, where other individuals are then exposed. Understanding the impact of land use on the transmission of this disease is of considerable importance. In Madagascar, infection dynamics are impacted by the combined effects of converting forests to agricultural fields and colonization of these areas by non-native mammal species, which carry molecularly distinct lineages of <i>Leptospira</i>. We show that land use corresponds to the replacement of native species and endemic <i>Leptospira</i> lineages with non-native species and their cosmopolitan <i>L. interrogans</i> and <i>L. kirschneri</i>. Together, this contributes to higher infection prevalence in more disturbed habitats like flooded rice fields, where >50% of mice captured were infected, highlighting the important effects of land use on <i>Leptospira</i> prevalence and presence, which together impact zoonotic risk.