| Summary: | <i>Salmonella</i> isolated from dairy farms has a significant effect on animal health and productivity. Different serogroups of <i>Salmonella</i> affect both human and bovine cattle causing illness in both reservoirs. Dairy cows and calves can be silent <i>Salmonella</i> shedders, increasing the possibility of dispensing <i>Salmonella</i> within the farm. The aim of this study was to determine the genomic characteristics of <i>Salmonella</i> isolates from dairy farms and to detect the presence of virulence and antimicrobial resistance genes. A total of 377 samples were collected in a cross-sectional study from calves, periparturient cow feces, and maternity beds in 55 dairy farms from the states of Aguascalientes, Baja California, Chihuahua, Coahuila, Durango, Mexico, Guanajuato, Hidalgo, Jalisco, Queretaro, San Luis Potosi, Tlaxcala, and Zacatecas. Twenty <i>Salmonella</i> isolates were selected as representative strains for whole genome sequencing. The serological classification of the strains was able to assign groups to only 12 isolates, but with only 5 of those being consistent with the genomic serotyping. The most prevalent serovar was <i>Salmonella</i> Montevideo followed by <i>Salmonella</i> Meleagridis. All isolates presented the chromosomal <i>aac(6′)-Iaa</i> gene that confers resistance to aminoglycosides. The antibiotic resistance genes <i>qnr</i>B19, <i>qnr</i>A1, <i>sul</i>2, <i>aph</i>(6)-Id, <i>aph</i>(3)-ld, <i>dfr</i>A1, <i>tet</i>A, <i>tet</i>C, <i>flor</i>2, <i>sul</i>1_15, <i>mph</i>(A), <i>aad</i>A2, <i>bla</i>CARB, and <i>qac</i>E were identified. Ten pathogenicity islands were identified, and the most prevalent plasmid was Col(pHAD28). The main source of <i>Salmonella enterica</i> is the maternity areas, where periparturient shedders are contaminants and perpetuate the pathogen within the dairy in manure, sand, and concrete surfaces. This study demonstrated the necessity of implementing One Health control actions to diminish the prevalence of antimicrobial resistant and virulent pathogens including <i>Salmonella.</i>
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