Genomic characterization of avian pathogenic Escherichia coli and its potential as a marker organism for antimicrobial resistance

(APEC) is a threat to poultry production and public health due to its ability to cause avian disease, economic losses, potential foodborne implications, and ability to carry antimicrobial resistance genes (ARGs) relevant to human health. In this study, we proposed APEC as a potential marker organism of antimicrobial resistance (AMR) due to its capacity to persist in diverse environments. Our findings show that APEC, across the vertically integrated poultry production chain, harbored clinically important ARGs and exhibited resistance to antimicrobials of human health importance. We also identified evidence of APEC transmission within the farm environment and into the processing plant, with the potential to reach consumers. By examining multiple stages of production and diverse environmental samples, our study provides a more comprehensive understanding of APEC ecology, its resistome, and dissemination. These insights highlight APEC's utility as a marker organism for AMR surveillance in poultry production.