There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the bla_TEM1B gene and a single isolate the bla_CTX−M−14 and bla_CTX−M−55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.

关于抗生素耐药性的比较基因组多样性的信息有限大肠杆菌来自废水。我们试图描绘环境特征大肠杆菌使用全基因组测序 (WGS) 和一系列生物信息学工具，从污水处理厂 (WWTP) 及其受纳水中获得属于各种致病型的分离株，以阐明抗性组、病毒组、移动组、克隆性和系统发育。十二种多重耐药 (MDR) 腹泻性药物大肠杆菌从污水处理厂的最终流出物中获得分离株，并在 Illumina MiSeq 机器上对污水处理厂上游和下游的接收河流进行测序。多位点序列分型（MLST）分析揭示了多种序列类型（ST），其中最常见的是 ST69（n= 4) 和 ST10 (n= 2)，然后是属于 ST372、ST101、ST569、ST218 和 ST200 的单例。一个分离株被分配给一个新的 ST ST11351。总共 66.7% 的分离株β-内酰胺酶基因呈阳性，其中 58.3% 含有布拉_TEM1B基因和单个分离的 bla _CTX−M−14和 bla _CTX−M−55超广谱 β-内酰胺酶 (ESBL) 基因。1 株分离株呈阳性MCR-9 动员粘菌素抗性基因。大多数抗生素抗性基因 (ARG) 与移动遗传支持相关：1 类整合子（In22、In54、In191 和 In369）、插入序列 (IS) 和/或转座子（Tn402 或 Tn21）。在研究分离株中总共鉴定出 31 个毒力基因，包括那些负责粘附的基因（LPFA, 伊哈， 和聚合R）、免疫力（空气、嘎德， 和国际空间站）和毒素（senB、增值税、astA， 和坐）。毒力基因主要与 IS（IS1、IS3、IS91、IS66、IS630 和 IS481）或前噬菌体相关。一些分离株对重金属/杀菌剂、抗生素具有明显的共抗性。与南非的系统发育分析大肠杆菌来自不同来源（动物、鸟类和人类）的分离株显示，本研究中的分离株大多与临床分离株聚集在一起。与元数据相关的系统发育表明，分离株不是根据来源聚类，而是根据 ST 聚类。污水处理厂废水和相关河流中致病菌和多重耐药菌的出现是一个公共卫生问题。