Complex dynamic patterns of antimicrobial resistance of Escherichia coli isolated from poultry and swine over 10 years in Chongming Island, Shanghai

Abstract Background: Antimicrobial resistance (AMR) is one of the most serious threats to animal and public health. Here, we conducted a dynamic surveillance of E. coli on Chongming Island in Shanghai during 2009-2021 to reveal Chongming's specific epidemic AMR characteristics and trends. Methods: Rectal (cloaca) swabs from four poultry and nine swine farms were collected for strain culture and isolation. The routine micro-broth dilution method was used to test antimicrobial susceptibility of E. coli isolates against 9 antibiotic classes including 15 antimicrobials. Utilizing generalized linear mixed models (GLMMs) and co-occurrence analyses, we further explored the multidrug-resistant (MDR) combinations and dynamic patterns of E. coli over 10 years in two food animals.Results: 853 MDR isolates were found among 945 collected E. coli isolates, 337 from poultry and 608 from swine. Both animal isolates exhibited high resistance rates (>70%) to tetracyclines, phenicols, sulfonamides, β-lactams, and aminoglycosides (only in swine). The resistance to the four antibiotic classes listed above (excluding sulfonamides) was significantly greater in swine isolates than in poultry isolates, whereas fluoroquinolones resistance was reversed. Resistance to polymyxins decreased similarly in swine (42.4% in 2009 to 0% in 2021) and poultry isolates (16.5% to 0%). However, resistance to the other seven antibiotic classes (excluding carbapenems) declined dramatically only in swine isolates, particularly fluoroquinolones (from 80.5% to 14.4%). Surprisingly, except for fluoroquinolone resistance, which showed a modest decline in poultry isolates, the resistances to the other seven antibiotic classes showed markedly divergent patterns. Using Poisson GLMMs, despite the highly diverse MDR profiles, the most prevalent MDR combinations were aminoglycosides-tetracyclines-sulfonamides in poultry and aminoglycosides-phenicols-fluoroquinolones in swine. In addition, the beta-lactams-cephalosporins and aminoglycosides-polymyxins patterns in both animals exhibited strong coefficients, indicating an enhanced synergistic risk.Conclusion:Our study uncovered vastly distinct AMR patterns and dynamic tendencies of poultry and swine isolates from Chongming. Due to the ongoing implementation of national anti-AMR strategies, Chongming's AMR status has improved, as indicated by the decline in MDR prevalence (particularly in swine) and low resistance to carbapenems, cephalosporins, and polymyxins. Finally, Chongming Island can use these findings to execute the One Health plan to tackle AMR.