Culturable Leptospira spp. exhibit no detectable spatial or matrix-associated structuring in Estero de Paco, Manila, Philippines

Leptospirosis is a globally important zoonotic disease that remains a major public health concern, particularly in tropical urban environments where flooding, inadequate sanitation, and high population density facilitate transmission. Despite its burden, the ecological and evolutionary processes governing the persistence and distribution of Leptospira in urban waterways remain poorly resolved. In particular, it is unclear whether environmental populations are structured by localized ecological conditions or maintained as system-wide reservoirs.

Using integrated culture-dependent, molecular, and phylogenetic approach, we characterized the Leptospira population in Estero de Paco, an urban waterway in Metro Manila, Philippines. Thirty-seven of the isolates were confirmed to be Leptospira and were recovered from both soil and water samples across different sampling sites. The number of Leptospira across the matrices and sampling sites indicates no significant differences potentially showing spatially uniform and matrix-independent distribution. No significant longitudinal trend was also observed along the distribution in the upstream-downstream gradient. Of the confirmed Leptospira, presence of pathogenic species were detected with isolates exhibiting 16S rRNA sequence highly similar to Leptospira yasudae. Phylogenetic reconstruction revealed and confirmed the placement of the pathogenic and saprophytic isolates. Furthermore, evolutionary relationship in reconstructed trees shows decoupling of these relationship from spatial location and environmental matrices.

These findings suggest that Leptospira populations in Estero de Paco may not be structured by localized environmental gradients but are possibly shaped by other factors which may include dispersal-driven processes and hydrological connectivity. While the lack of detected spatial or matrix-associated structuring is driven primarily by saprophytic lineages, the widespread presence of non-pathogenic Leptospira indicates that environmental conditions across the system are permissive to genus-level persistence, suggesting a latent capacity for broader dissemination of pathogenic strains. Together, these results challenge localized hotspot models and support a framework in which urban waterways function as continuous and dynamic reservoirs, with important implications for understanding and managing leptospirosis risk in tropical settings such as the Philippines.