Spatiotemporal recurrence and dissemination of Salmonella subpopulations in surface waters of central Chile

Agricultural waters have been identified as one of the primary sources of Salmonella contamination, which has resulted in numerous outbreaks associated with the consumption of contaminated produce. Consequently, an improved understanding of Salmonella contamination of agricultural waters could facilitate the development of control strategies to prevent food contamination. The objective of this study was to examine the diversity and spatiotemporal recurrence of Salmonella isolates in surface water related to agricultural activities. Water samples ( n = 2,690) were collected between 2019 and 2024 in central Chile using modified Moore swabs, and whole-genome sequencing was carried out for 1 to 10 Salmonella isolates per sample. Non-clonal genomes from each sample ( n = 1,034) were analyzed, showing that the most frequently identified serovars were Infantis (14.6%), Typhimurium (10.8%), Newport (8.5%), and Enteritidis (5.8%). The highest antimicrobial resistance burden was shown by Salmonella Infantis, which carried up to 11 antimicrobial resistance genes simultaneously. Importantly, phylogenomic analyses revealed a highly clonal population structure among the most prevalent serovars and identified recurrent subpopulations that were repeatedly detected across multiple watersheds and consecutive years, including lineages associated with human infections. These findings provide genomic evidence that agricultural surface waters may serve as reservoirs and dissemination routes for recurrent Salmonella subpopulations in central Chile, including multidrug-resistant strains. Our work underscores the critical importance of continuous environmental surveillance and the integration of environmental and clinical genomic surveillance data to improve our understanding of the Salmonella ecology and inform evidence-based mitigation strategies aiming to protect public health. IMPORTANCE Salmonella enterica is a leading cause of foodborne illness worldwide, and contaminated irrigation water is an important pathway by which this pathogen can reach fresh produce. By analyzing more than 1,000 Salmonella genomes collected from agricultural waters in central Chile over 5 years, we found that specific bacterial lineages persisted across multiple watersheds and years, including multidrug-resistant strains linked to human infections. These findings indicate that agricultural surface waters in Chile can serve as reservoirs and dissemination routes for recurrent Salmonella subpopulations. Our study highlights the value of continuous environmental surveillance and the need to integrate data from environmental and human sources to identify potential contamination sources and reduce the risk of foodborne disease.