Sequencing of multi-drug resistant Escherichia coli carrying fosA3 and ESBL genes

The excessive and indiscriminate use of antimicrobial agents in poultry production has increased antimicrobial resistance in E. coli, posing a significant threat to public health. This study investigated the prevalence of multidrug-resistant (MDR) E. coli co-harboring fosA3 and ESBL genes in large-scale retail duck slaughterhouses in Sichuan Province, China. Whole-genome sequencing (WGS) was performed on 35 representative E. coli isolates. The majority (70/150, 46.67%) belonged to phylogenetic group B1. Based on an 85% similarity threshold, all isolates were categorized into 40 distinct PFGE types. Genomic analysis revealed 27 different serotypes and 19 sequence types (STs), with O8 (22.86%, 5/35) and ST155 (22.85%, 8/35) being the most common. The IncFIB (AP001918) was the most prevalent plasmid replicon type, identified in 74.29% (26/35) of the isolates. In addition, 49 acquired antimicrobial resistance genes (ARGs) associated with resistance to 11 types of antimicrobial agents were identified and chromosomal mutation of p.S83L in gyrA gene (88.57%, 31/35) was the most common. Furthermore, 110 virulence factors (VFs) were identified, with those related to iron uptake and storage, adhesion, secretion and endotoxin production being the most prevalent. This study underscored the importance of rational use of antimicrobial agents in poultry farming and provided critical insights into the distribution of ARGs and VFs among retail duck-derived MDR E. coli.