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Salmonella enterica is a pathogen with a wide host-range that presents great concern in developed and developing countries. To determine and characterize Salmonella strains found in Chile's waterfowl, we sampled 758 birds along 2000 km of the Chilean coast. In this sample, 46 isolates from 10 serotypes were detected, several with multidrug resistance phenotypes and different combinations of virulence-associated genes (virulotypes). These results suggest that Salmonella infection in waterfowl in Chile could have impacts on public and animal health.