Whole-Genome Analysis Revealed Antimicrobial Resistance and Virulence-Associated Genome Features in Environmental Salmonella enterica Isolates from Creek Sediments in the Mid-Atlantic United States

Whole-genome sequencing followed by comprehensive genomic analyses was used to characterize 16 Salmonella isolates from water-overlying sediments in Conococheague Creek (PA), an agricultural irrigation water source. Our goal was to characterize the genomic profiles and diversity of these Salmonella isolates. We identified eight distinct serotypes, including Newport, the most prevalent (43.8%), providing environmental context relevant to agricultural water systems. Genomic surveys showed various Salmonella Pathogenicity Island (SPI) profiles. Although widespread antimicrobial resistance (AMR) genes were not detected, the consistent presence of the aac(6’)-Iaa gene across all isolates and a parC (T57S) mutation in 14 isolates were identified as inherent genotypic markers. Six distinct plasmid replicon types were observed in over 60% of isolates. Replicons for IncF and IncI2 plasmids, frequently associated with β-lactamase genes, were found, documenting the presence of mobile genetic elements despite a lack of acquired AMR genes. Restriction-Modification (RM) systems and CRISPR/Cas loci were also detected, suggesting Salmonella genomic plasticity. Our study showed that sediment-associated Salmonella, notably serotype Newport, harbored diverse virulence-associated genomic features. These findings contributed to the genomic baseline for irrigation water quality and food safety.