Antimicrobial resistance and virulence profiles of Escherichia coli isolated from poultry omphalitis following changes in antibiotic prevention strategies in Quebec, Canada

Omphalitis remains a major cause of mortality in poultry and is frequently associated with antimicrobial-resistant Escherichia coli. In Canada, antimicrobial stewardship programmes have progressively restricted the preventive use of antibiotics in poultry production, including the withdrawal of Category I and II antibiotics. The impact of these interventions on the prevalence and the antimicrobial resistance patterns in omphalitis-associated E. coli is not fully understood. In this study, omphalitis-associated E. coli isolates were collected across two sampling periods representing three different hatchery prevention strategies: ceftiofur administration (P1), lincomycin-spectinomycin administration (P2A), and no antibiotic (P2B). The prevalence of avian pathogenic E. coli (APEC) isolates remained stable across periods, independently of the treatment used. Overall, 86.3% (176/204), 82.9% (189/228), and 86.5% (205/237) of isolates from P1, P2A, and P2B, respectively, were classified as APEC, with no significant association between sampling period and APEC status (P > 0.05). In contrast, antimicrobial resistance varied significantly between sampling periods. P1 had a significantly higher prevalence of isolates resistant to β-lactam antibiotics, whereas P2A displayed a significantly higher prevalence of isolates resistant to several non-β-lactam classes but reduced resistance to β-lactams. Isolates from P2B exhibited reduced resistance to both β-lactam and non-β-lactam antibiotics. The prevalence of multidrug-resistant isolates differed significantly between periods (P < 0.005), with enrichment during P2A and depletion during P2B. Together, these findings highlight the strong association between antibiotic use and antimicrobial resistance patterns in poultry-associated E. coli, supporting the effectiveness of antimicrobial reduction strategies in decreasing resistance prevalence.RESEARCH HIGHLIGHTS No association between the sampling period and APEC status was observed.Antibiotic treatments did not affect the prevalence of APEC isolates observed.Antimicrobial resistance patterns in E. coli strongly correlated with antibiotic use.