Multidrug-Resistant Escherichia coli in the Swine Production Chain: Genomic Evidence of Abattoir-Associated Dissemination

Antimicrobial resistance (AMR) is a rising public health issue that compromises human, animal, and environmental health. This study assessed AMR in the swine production chain in Costa Rica using commensal E. coli as an indicator microorganism. Sampling of feces, carcass, and lymphoid tissue at exporting swine abattoirs yielded 269 presumed E. coli isolates identified by lactose-positive growth on MacConkey agar and indole production. A subset of isolates (n = 40) was confirmed as E. coli by VITEK® 2 GN testing. Antimicrobial susceptibility testing against 18 antibiotics was performed using the antibiotic disk agar diffusion method in 242 recovered isolates, and resistance to all antimicrobial classes evaluated was detected. The highest resistance levels were observed for ampicillin, cefazolin, and chloramphenicol, and notable resistance to quinolones, trimethoprim-sulfamethoxazole, and β-lactam combination agents. Resistance to clinically important drugs including ceftazidime, cefepime, aztreonam, and imipenem was observed, as well as selected β-lactamase genes. Overall, 50 distinct AMR profiles were identified, and more than half of the isolates displayed multidrug resistance. A subset of isolates (n = 30) underwent uidA PCR and ERIC-PCR analysis, revealing evidence of fecal and cross-contamination as plausible routes for dissemination of resistant bacteria during slaughter. Antimicrobial susceptibility testing by the VITEK® 2 automated system and whole-genome sequencing (WGS) of 27 isolates further characterized phenotype-genotype concordance, AMR determinants, virulence factors, serotypes, and sequence types of public health relevance. These findings provide insight into current AMR trends in the Costa Rican swine production system and highlight the role of abattoir-level contamination in AMR transmission, supporting targeted interventions to mitigate the emergence and dissemination of AMR along the pork production chain.