High bacterial community diversity and complexity greatly challenge the cost-efficient monitoring of clinically prevalent antibiotic-resistant bacteria, which are usually present as rare and important populations involved in the environmental dissemination of clinical resistance. Here, we introduce culture-enriched phenotypic metagenomics that integrates culture enrichment, phenotypic screening, and metagenomic analyses as an emerging standardized methodology for targeted resistome monitoring and apply it to decipher the extended-spectrum β-lactam resistome in a municipal wastewater treatment plant (WWTP) and its receiving river. The results showed that clinically prevalent carbapenemase genes (e.g., the NDM and KPC families) and extended-spectrum β-lactamase genes (e.g., the CTX-M, TEM, and OXA families) were prevalent in the WWTP and showed prominent potential in horizontal dissemination. Strikingly, carbapenem and polymyxin resistance genes co-occurred in the highly virulent nosocomial pathogens Enterobacter kobei and Citrobacter freundii. Overall, this study exemplifies phenotypic metagenomics for high-throughput surveillance of a targeted clinically important fraction of antibiotic resistomes and substantially expands current knowledge on extended-spectrum β-lactam resistance in WWTPs.

中文翻译：

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使用富含培养的表型宏基因组学对 β-内酰胺电阻体的临床重要部分进行靶向高通量监测

高细菌群落多样性和复杂性极大地挑战了临床流行的抗生素耐药细菌的成本效益监测，这些细菌通常作为稀有和重要的群体存在，参与临床耐药性的环境传播。在这里，我们介绍了富含培养物的表型宏基因组学，它整合了培养物富集、表型筛选和宏基因组分析，作为一种新兴的靶向耐药监测标准化方法，并将其应用于破译城市污水处理厂 (WWTP) 中的广谱 β-内酰胺耐药组。 ) 及其接收河流。结果表明，临床上普遍存在的碳青霉烯酶基因（例如，NDM 和 KPC 家族）和超广谱 β-内酰胺酶基因（例如，CTX-M、TEM、和 OXA 家族）在污水处理厂中普遍存在，并在横向传播中表现出显着的潜力。引人注目的是，碳青霉烯类和多粘菌素抗性基因同时存在于高毒力的医院病原体中科贝肠杆菌和弗氏柠檬酸杆菌。总体而言，本研究举例说明了表型宏基因组学可用于对抗生素抗性组的靶向临床重要部分进行高通量监测，并大大扩展了当前关于 WWTP 中广谱 β-内酰胺抗性的知识。