BACKGROUND Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Enterococcus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. RESULTS VRE isolates, including E. faecalis (n = 24), E. faecium (n = 11), E. casseliflavus (n = 2) and E. gallinarum (n = 2) were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium (p < 0.001) and E. faecalis (p < 0.001) and with the number of AMR genes in E. faecium (p = 0.005). Genes conferring vancomycin resistance, including vanA and vanM (E. faecium), vanG (E. faecalis), and vanC (E. casseliflavus/E. gallinarum), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium, E. faecalis, E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium, than E. casseliflavus and E. gallinarum. A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium. Phylogenetic analysis demonstrated differential clustering of isolates based on original source but not WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. CONCLUSIONS There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp.

中文翻译：

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多重耐药肠球菌属的比较基因组学。从废水处理厂中分离出来。


背景技术废水处理厂(WWTP)被认为是抗菌素耐药性(AMR)决定因素环境传播的热点。耐万古霉素肠球菌 (VRE) 是测量废水中 AMR 细菌程度的候选细菌。粪肠球菌和屎肠球菌是公认的水中粪便污染的指标。对从传统活性污泥 (CAS) 和曝气生物滤池 (BAF) 污水处理厂分离的肠球菌进行了比较基因组学研究。结果 根据污水处理厂来源、物种，选择 VRE 分离株进行测序，包括粪肠球菌 (n = 24)、粪肠球菌 (n = 11)、卡氏肠球菌 (n = 2) 和鸡肠球菌 (n = 2)和 AMR 表型。屎肠球菌和粪肠球菌的全基因组都是开放的。与移动组相关的基因组分数与屎肠球菌 (p < 0.001) 和粪肠球菌 (p < 0.001) 的基因组大小以及屎肠球菌中 AMR 基因的数量呈正相关 (p = 0.005)。在 20 个基因组中检测到了赋予万古霉素耐药性的基因，包括 vanA 和 vanM（屎肠球菌）、vanG（粪肠球菌）和 vanC（卡塞利弗拉菌/鸡肠球菌）。最突出的功能性 AMR 基因是外排泵和转运蛋白。在屎肠球菌、粪肠球菌、卡氏肠球菌和鸡肠球菌中分别检测到至少 16、6、5 和 3 个毒力基因。毒力基因在粪肠球菌和屎肠球菌中比卡氏肠球菌和鸡肠球菌更常见。许多可移动的遗传元件在物种之间是共享的。在 13 个粪肠球菌基因组中检测到功能性 CRISPR/Cas 阵列，除了一个之外，所有基因组都含有原噬菌体。缺乏功能性 CRISPR/Cas 阵列与屎肠球菌的多重耐药性有关。 系统发育分析表明，分离株的差异聚类基于原始来源，而不是污水处理厂。与噬菌体和 CRISPR/Cas 阵列相关的基因有可能作为环境生物标志物。结论 CAS 和 BAF 污水处理厂的肠球菌基因组之间没有明显差异。与其他肠球菌属相比，粪肠球菌和屎肠球菌的基因组更小，具有更强的毒力、AMR 和移动遗传元件。