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.

家禽养殖中抗菌药物的过度与无差别使用，导致大肠埃希菌（E. coli）耐药性攀升，对公共健康构成严重威胁。本研究针对中国四川省大型零售鸭屠宰场中，同时携带fosA3基因与超广谱β-内酰胺酶（ESBL）基因的多药耐药（MDR）大肠埃希菌的流行特征展开调查。研究对35株具有代表性的大肠埃希菌分离株实施了全基因组测序（WGS）。多数分离株（70/150，占比46.67%）隶属于系统发育群B1。基于85%的相似性阈值，所有分离株可被划分为40种不同的脉冲场凝胶电泳（PFGE）型别。基因组分析显示，本次研究共鉴定出27种不同的血清型与19种序列型（ST），其中最常见的为O8血清型（占比22.86%，5/35）与ST155序列型（占比22.85%，8/35）。IncFIB（AP001918）是检出率最高的质粒复制子型别，在74.29%（26/35）的分离株中均可被检测到。此外，本研究共鉴定出49种与11类抗菌药物耐药相关的获得性抗菌药物耐药基因（ARGs）；其中，gyrA基因的p.S83L染色体突变检出率最高，达88.57%（31/35）。除此之外，本研究还鉴定出110种毒力因子（VFs），其中与铁摄取储存、黏附、分泌及内毒素产生相关的毒力因子最为普遍。本研究强调了家禽养殖中合理使用抗菌药物的必要性，并为零售鸭源多药耐药大肠埃希菌中ARGs与VFs的分布规律提供了关键研究视角。