Emergence of multidrug resistant Escherichia coli coharboring fosA3 and ESBL genes from retail ducks along slaughter line

Abstract

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 extended-spectrum β-lactamases (ESBLs) genes in large-scale retail duck slaughterhouses in Sichuan Province, China. The antimicrobial susceptibility to 9 categories and 16 types of antimicrobial agents was assessed by using the broth microdilution method. Phylogenetic grouping and pulsed-field gel electrophoresis (PFGE) were used to investigate the phylogenetic groups and genetic characteristics of the isolates. Moreover, whole-genome sequencing (WGS) was performed on 35 representative E. coli isolates. Among 1, 059 samples collected, 895 E. coli were isolated by MacConkey (MAC) agar and eosin methylene blue (EMB) agar and PCR identification, and 150 strains of MDR E. coli co-carrying fosA3 and ESBL genes were finally screened for further analysis. The results indicated that 141 isolates were resistant to fosfomycin and exhibited high resistance to β-lactam antibiotics. All isolates demonstrated MDR patterns, with 148 isolates resistant to six or more classes of antimicrobial agents. 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 (14.29 %, 5/35) and ST155 (22.86 %, 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.