Genome-based assessment of antimicrobial resistance of <i>Escherichia coli</i> recovered from diseased swine in eastern China for a 12-year period

The global rise of antimicrobial resistance (AMR), driven by antibiotic use in healthcare and agriculture, poses a major public health threat. While AMR in clinical settings is well studied, there is a gap in understanding the resistance profiles of <i>Escherichia coli</i> from diseased livestock, particularly regarding zoonotic transmission. This study analyzes 114 <i>E. coli</i> isolates from diseased swine over 12 years, revealing that 99.12% were multidrug-resistant. Resistance was highest for ampicillin and amoxicillin/clavulanic acid (100%), followed by ciprofloxacin (96.49%) and tetracycline (94.74%). Furthermore, 21.05% of isolates were resistant to colistin, and 1.75% to tigecycline. A total of 76 antimicrobial resistance genes (ARGs) were identified, with <i>mcr-1</i> found in 18.42%, <i>mcr-3</i> in 4.39%, and <i>tet</i>(X4) in 1.75%. Significant co-occurrence of ARGs and plasmids suggests potential for co-selective dissemination. This study is the first to report enterotoxigenic <i>E. coli</i> (ETEC) strains carrying both <i>mcr-1</i> and <i>mcr-3</i> genes. After the 2017 colistin ban in China, <i>mcr-1</i> detection rates significantly decreased, while florfenicol resistance rates increased in 2018-2021 (94.29%) compared to 2010-2017 (79.55%). This work provides valuable insights into the AMR profiles of <i>E. coli</i> from diseased swine and highlights trends that can inform strategies for monitoring and controlling public health risks associated with zoonotic <i>E. coli</i> transmission.IMPORTANCEThis study highlights the critical role of diseased and deceased swine in the spread of antimicrobial resistance (AMR), providing new insights into the transmission of resistance genes in zoonotic contexts. By analyzing <i>E. coli</i> from diseased swine, we identify key resistance genes such as <i>mcr-1</i>, <i>mcr-3</i>, and <i>tet</i>(X4), which pose significant public health risks, especially regarding last-resort antibiotics like colistin. Moreover, the study identifies novel transmission patterns of <i>mcr</i> genes, including ETEC strains carrying the <i>mcr-3</i> gene and strains harboring both <i>mcr-1</i> and <i>mcr-3</i> genes. The role of plasmids in horizontal gene transfer is also revealed, facilitating rapid AMR spread across species. The long-term persistence of resistant strains highlights the challenges in controlling AMR in livestock. These findings underscore the need for enhanced surveillance and a One Health approach to mitigate AMR risks across animal, human, and environmental health.