Characterizing the antibiotic resistance and virulence genes of diarrheagenic Escherichia coli from Brazilian beef cattle.

Diarrheagenic E. coli (DEC) can cause severe diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Because DEC is frequently found in ruminants, we investigated the genomic characteristics of different E. coli pathotypes collected from Brazilian beef abattoirs. Pathotypes included Shiga toxin-producing E. coli (STEC), enterohemorrhagic E. coli (EHEC) and enteropathogenic E. coli (EPEC). Bacterial isolates were collected from beef cattle carcasses (n = 3) and bovine feces (n = 28) in 2019. Antimicrobial resistance was documented by agar dilution method for six antibiotics (amoxicillin, ceftiofur, ciprofloxacin, chloramphenicol, sulfamethoxazole + trimethoprim and tetracycline) and later confirmed with genotypic data following whole genome sequencing. The majority of the isolates 29/31 (93%) were antibiotic susceptible although one multidrug-resistant isolate harbored several virulence factors. Among STEC and EHEC isolates (n = 24), stx2 was frequently encountered (21/24). All EPEC isolates were atypical (bfp negative), albeit with clinically important serotypes (O157:H7 and O26:H11). Several enterotoxigenic E. coli harbored genetic markers consistent with STEC and ETEC (n = 7), or EPEC and ETEC (n = 1). Fifteen serotypes were identified including O157:H7, O113:H21, and O26:H11, which have been previously associated with human infections. Phylogenetic analysis showed high similarity among human isolates from other countries, consistent with widespread dissemination. The integration of whole genome sequencing and epidemiological surveillance helped to identify the major pathotypes from Brazilian beef abattoirs, STEC and EHEC, naturally present in food producing animals harboring innumerous virulence factors.