Prevalence and Genomic Diversity of Recovered from River Water in a Major Agricultural Region in Northwestern Mexico.

is a leading cause of human gastrointestinal disease worldwide. Given that is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of isolates recovered from major rivers in an important agricultural region in northwestern Mexico. During a 13-month period, a total of 143 river water samples were collected and subjected to size-exclusion ultrafiltration, followed by enrichment, and selective media for isolation and quantitation. The recovered isolates were examined by next-generation sequencing for genome characterization. prevalence in river water was lower in the winter months (0.65 MPN/100 mL) and significantly higher in the summer months (13.98 MPN/100 mL), and a Poisson regression model indicated a negative effect of pH and salinity and a positive effect of river water temperature ( = 0.00) on levels. Molecular subtyping revealed Oranienburg, Anatum and Saintpaul were the most predominant serovars. Single nucleotide polymorphism (SNP)-based phylogeny revealed that the detected 27 distinct serovars from river water clustered in two major clades. Multiple nonsynonymous SNPs were detected in , and , genes required for fitness and survival, and these findings identified relevant markers to potentially develop improved methods for characterizing this pathogen.