Genomic epidemiology of antimicrobial-resistant non-typhoidal Salmonella isolated from beef at retail across Mexico

In this study, we conducted a nation-wide survey to determine the prevalence, serovar diversity, antimicrobial resistance (AMR) profile, and genomic epidemiology of non-typhoidal Salmonella (NTS) isolated from ground beef at retail (n=395) across of the 32 Mexican states. NTS prevalence varied across geographical regions (χ2 = 33.8, P = <0.001). The highest contamination rates were observed in the State of Mexico and Yucatán (14.7 and 9.2%, respectively), whereas it ranged from 0.5 to 6.5% in the remaining states, with 184 isolates collected overall. A total of 45 serovars and 47 sequence types (ST) were identified. Among these, serovars Anatum (ST64) and Newport (ST132, ST32, ST45 and ST118) represented nearly one third (58/184) of the study population, whereas serovar Typhimurium (ST19) was identified as the founding ST. Most isolates were either multidrug-resistant (MDR) or pansusceptible (42% each). The most frequent AMR phenotypes involved resistance to antibiotics tetracycline (n=84), streptomycin (n=80), chloramphenicol (n=74), and ampicillin (n=57). The most frequent AMR genes were those conferring resistance to tetracyclines (tetABC, 45%), folate pathway inhibitors (sul/dfrA alleles, 45%), penicillins (blaTEM/CARB alleles, 41%), phenicols (floR, 38%), and aminoglycosides (aac/aadA/aph alleles, 28%). Low-level quinolone resistance genes (qnr alleles) were the most widely distributed (51%), a phenomenon explained by the presence of the pHAD28 plasmid (χ2 = 22.26; p = <0.001). SNP-based phylogenetic analysis revealed well-defined clades with high resistance burden, especially in the Newport and Anatum serovars. In contrast, serovars such as Brandenburg, Give, and Goldcoast presented pan-susceptible profiles at both the genotypic and phenotypic levels.