Mbanga Joshua, Amoako Daniel G, Abia Akebe L K, Allam Mushal, Ismail Arshad, Essack Sabiha Y
Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa.
Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe.
Front Microbiol. 2021 Jun 14;12:648454. doi: 10.3389/fmicb.2021.648454. eCollection 2021.
We investigated the antibiotic resistome, mobilome, virulome, and phylogenomic lineages of spp. obtained from a wastewater treatment plant and its associated waters using whole-genome sequencing (WGS) and bioinformatics tools. The whole genomes of isolates including ( = 4), ( = 5), ( = 2), and ( = 1) with similar resistance patterns from different sampling sites and time points were sequenced on an Illumina MiSeq machine. Multilocus sequence typing (MLST) analysis revealed two isolates that had a common sequence type ST179; the rest had unique sequence types ST841, and ST300. The genomes belonged to 3 sequence types, ST94 ( = 2), ST361 ( = 2), and ST1096 ( = 1). Detected resistance genes included those encoding tetracycline [(S), (M), and )], and macrolides [(C), , , and (A)] resistance. Antibiotic resistance genes were associated with insertion sequences (IS6, ISL3, and IS982), and transposons (Tn3 and Tn6000). The ) resistance gene was consistently found associated with a conjugative transposon protein (TcpC). A total of 20 different virulence genes were identified in and including those encoding for sex pheromones (, and ), adhesion (, and ), and cell invasion ( and ). Several virulence genes were associated with the insertion sequence IS256. No virulence genes were detected in and Phylogenetic analysis revealed that all spp. isolates were more closely related to animal and environmental isolates than clinical isolates. spp. with a diverse range of resistance and virulence genes as well as associated mobile genetic elements (MGEs) exist in the wastewater environment in South Africa.
我们使用全基因组测序（WGS）和生物信息学工具，对从一家污水处理厂及其相关水域分离得到的 spp. 的抗生素抗性组、可移动基因组、毒力组和系统发育谱系进行了研究。在Illumina MiSeq 测序仪上对来自不同采样地点和时间点、具有相似抗性模式的 株分离菌（包括 （ = 4）、 （ = 5）、 （ = 2）和 （ = 1））的全基因组进行了测序。多位点序列分型（MLST）分析显示，有两株 分离菌具有共同的序列类型 ST179；其余的具有独特的序列类型 ST841 和 ST300。 的基因组属于 3 种序列类型，ST94（ = 2）、ST361（ = 2）和 ST1096（ = 1）。检测到的抗性基因包括编码四环素 [（S）、（M）和 ]以及大环内酯类 [（C）、 、 和 （A）]抗性的基因。抗生素抗性基因与插入序列（IS6、ISL3 和 IS982）以及转座子（Tn3 和 Tn6000）相关。 抗性基因始终与一种接合转座子蛋白（TcpC）相关。在 和 中总共鉴定出 20 种不同的毒力基因，包括编码性信息素（ 、 和 ）、黏附（ 、 和 ）以及细胞侵袭（ 和 ）的基因。几种毒力基因与插入序列 IS256 相关。在 和 中未检测到毒力基因。系统发育分析表明，所有 spp. 分离菌与动物和环境分离菌的亲缘关系比与临床分离菌的更近。南非的废水环境中存在具有多种抗性和毒力基因以及相关可移动遗传元件（MGEs）的 spp. 。
