Citation: González-López, I.; Medrano-Félix, J.A.; Castro-del Campo, N.; López-Cuevas, O.; González-Gómez, J.P.; Valdez-Torres, J.B.; Aguirre-Sánchez, J.R.; Martínez- Urtaza, J.; Gómez-Gil, B.; Lee, B.G.; et al. Prevalence and Genomic Diversity of Salmonella enterica Recovered from River Water in a Major Agricultural Region in Northwestern Mexico. Microorganisms 2022, 10, 1214. https://doi.org/10.3390/ microorganisms10061214 Academic Editors: Javier Garaizar and Lorena Laorden Received: 24 May 2022 Accepted: 12 June 2022 Published: 14 June 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). microorganisms Article Prevalence and Genomic Diversity of Salmonella enterica Recovered from River Water in a Major Agricultural Region in Northwestern Mexico Irvin González-López 1 , José Andrés Medrano-Félix 2 , Nohelia Castro-del Campo 1 , Osvaldo López-Cuevas 1 , Jean Pierre González-Gómez 1 , José Benigno Valdez-Torres 1 , José Roberto Aguirre-Sánchez 1 , Jaime Martínez-Urtaza 3 , Bruno Gómez-Gil 4 , Bertram G. Lee 5 , Beatriz Quiñones 5 and Cristóbal Chaidez 1, * 1 Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; irvin.gonzalez@estudiantes.ciad.mx (I.G.-L.); ncastro@ciad.mx (N.C.-d.C.); osvaldo.lopez@ciad.mx (O.L.-C.); jgonzalez.219@estudiantes.ciad.mx (J.P.G.-G.); jvaldez@ciad.mx (J.B.V.-T.); jose.aguirre.dc18@estudiantes.ciad.mx (J.R.A.-S.) 2 Investigadoras e Investigadores por México, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; jose.medrano@ciad.mx 3 Department of Genetics and Microbiology, Universitat Autờnoma de Barcelona, 08193 Bellaterra, Spain; jaime.martinez.urtaza@uab.cat 4 Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Mazatlán, Acuicultura y Manejo Ambiental, Mazatlán 82100, Sinaloa, Mexico; bruno@ciad.mx 5 U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, USA; bertram.lee@usda.gov (B.G.L.); beatriz.quinones@usda.gov (B.Q.) * Correspondence: chaqui@ciad.mx; Tel.: +52-(667)-480-6950 Abstract: Salmonella enterica is a leading cause of human gastrointestinal disease worldwide. Given that Salmonella is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of Salmonella 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 Salmonella isolation and quantitation. The recovered Salmonella isolates were examined by next-generation sequencing for genome characterization. Salmonella 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 (p = 0.00) on Salmonella levels. Molecular subtyping revealed Oranienburg, Anatum and Saintpaul were the most predominant Salmonella 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 stiA, sivH, and ratA, genes required for Salmonella fitness and survival, and these findings identified relevant markers to potentially develop improved methods for characterizing this pathogen. Keywords: environmental microbiology; food safety; foodborne pathogen; genomics; river water; Salmonella; serovars; single nucleotide polymorphisms; ultrafiltration method 1. Introduction Salmonella enterica is recognized as a significant causative agent of human gastrointesti- nal infections worldwide from foodborne and waterborne sources, and non-typhoid human salmonellosis is responsible for millions of human illnesses in a typical year [1–3]. Among the bacterial foodborne pathogens, S. enterica is one of most commonly reported in Mex- ico, according to the National Epidemiological Surveillance System (Sistema Nacional de Microorganisms 2022, 10, 1214. https://doi.org/10.3390/microorganisms10061214 https://www.mdpi.com/journal/microorganisms