Cattle are the main reservoir of Shiga toxin-producing Escherichia coli (STEC), one of the world’s most important foodborne pathogens. The pathogen causes severe human diseases and outbreaks. This study aimed to identify and characterize non-O157 STEC isolated from cattle feces from central and southern Chile. We analyzed 446 cattle fecal samples and isolated non-O157 STEC from 12.6% (56/446); a total of 93 different isolates were recovered. Most isolates displayed β-glucuronidase activity (96.8%; 90/93) and fermented sorbitol (86.0%; 80/93), whereas only 39.8% (37/93) were resistant to tellurite. A subgroup of 30 representative non-O157 STEC isolates was selected for whole-genome sequencing and bioinformatics analysis. In silico analysis showed that they grouped into 16 different sequence types and 17 serotypes; the serotypes most frequently identified were O116:H21 and O168:H8 (13% each). A single isolate of serotype O26:H11 was recovered. One isolate was resistant to tetracycline and carried resistance genes tet(A) and tet(R); no other isolate displayed antimicrobial resistance or carried antimicrobial resistance genes. The intimin gene (eae) was identified in 13.3% (4/30) of the genomes and 90% (27/30) carried the stx2 gene. A phylogenetic reconstruction demonstrated that the isolates clustered based on serotypes, independent of geographical origin. These results indicate that cattle in Chile carry a wide diversity of STEC potentially pathogenic for humans based on the presence of critical virulence genes.

The global dissemination of multidrug-resistant (MDR) Salmonella through the international food trade poses a major One Health concern. We used whole-genome sequencing to characterize Salmonella isolates from poultry meat sold in Chile, including domestic and imported products from Brazil and Argentina. Sixty-one Salmonella isolates were recovered from poultry meat; S. Infantis predominated (59%), followed by S. Heidelberg. Among S. Heidelberg from imported-meat poultry, 92% carried the bla_CMY-2 gene, conferring resistance to β-lactams. Given the predominance of S. Infantis in poultry meat, we performed an additional in-depth genomic analysis of 73 S. Infantis isolates obtained from poultry meat (n = 32), surface water (n = 30), and human clinical cases (n = 11). Across sources, phenotypic resistance to ciprofloxacin and third-generation cephalosporins reached 93% and 70%, respectively, and MDR (≥3 antimicrobial classes) occurred in 71% of isolates, largely associated with bla_CTX-M-65 and gyrA mutations. The pESI (plasmid of emerging S. Infantis)-like plasmid, harboring antimicrobial resistance and virulence genes, appeared in 94% of isolates. Phylogenetic analyses showed close genetic relationships among food, environmental, and clinical isolates, suggesting potential transmission through contaminated poultry meat or water. These findings emphasize the emergence of MDR S. Infantis in Chile and underscore the need for integrated One Health surveillance and prudent antimicrobial use to mitigate foodborne AMR risks.