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Background  Leptospirosis is a neglected zoonosis affecting animals and humans caused by infection with  Leptospira . The bacteria can survive outside of hosts for long periods of time in soil and water. While identification of  Leptospira  species from human cases and animal reservoirs are increasingly reported, little is known about the diversity of pathogenic  Leptospira  species in the environment and how surveillance of the environment might be used for monitoring and controlling disease.    Methods and Findings  Water samples (n = 104) were collected from the peri-domestic environment of 422 households from farms, rural villages, and urban slums participating in a broader study on the eco-epidemiology of leptospirosis in the Los Rios Region, Chile, between October 2010 and April 2012. The  secY  region of samples, previously detected as pathogenic  Leptospira  by PCR, was amplified and sequenced. Sequences were aligned using ClustalW in MEGA, and a minimum spanning tree was created in PHYLOViZ using the goeBURST algorithm to assess sequence similarity. Sequences from four clinical isolates, 17 rodents, and 20 reference strains were also included in the analysis. Overall, water samples contained  L .  interrogans ,  L .  kirschneri , and  L .  weilii , with descending frequency. All species were found in each community type. The distribution of the species differed by the season in which the water samples were obtained. There was no evidence that community-level prevalence of  Leptospira  in dogs, rodents, or livestock influenced pathogen diversity in the water samples.    Conclusions  This study reports the presence of pathogenic  Leptospira  in the peri-domestic environment of households in three community types and the differences in  Leptospira  diversity at the community level. Systematic environmental surveillance of  Leptospira  can be used for detecting changes in pathogen diversity and to identify and monitor contaminated areas where an increased risk of human infection exists.

Distribution and Diversity of Pathogenic Leptospira Species in Peri-domestic Surface Waters from South Central Chile