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采用宏基因组学指导策略进行β-内酰胺抗性基因的生物勘探。

Bioprospecting for β-lactam resistance genes using a metagenomics-guided strategy.

作者信息

Yang Chao, Yang Ying, Che You, Xia Yu, Li Liguan, Xiong Wenguang, Zhang Tong

机构信息

Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China.

Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China.

出版信息

Appl Microbiol Biotechnol. 2017 Aug;101(15):6253-6260. doi: 10.1007/s00253-017-8343-0. Epub 2017 Jun 5.

Abstract

Emergence of new antibiotic resistance bacteria poses a serious threat to human health, which is largely attributed to the evolution and spread of antibiotic resistance genes (ARGs). In this work, a metagenomics-guided strategy consisting of metagenomic analysis and function validation was proposed for rapidly identifying novel ARGs from hot spots of ARG dissemination, such as wastewater treatment plants (WWTPs) and animal feces. We used an antibiotic resistance gene database to annotate 76 putative β-lactam resistance genes from the metagenomes of sludge and chicken feces. Among these 76 candidate genes, 25 target genes that shared 40~70% amino acid identity to known β-lactamases were cloned by PCR from the metagenomes. Their resistances to four β-lactam antibiotics were further demonstrated. Furthermore, the validated ARGs were used as the reference sequences to identify novel ARGs in eight environmental samples, suggesting the necessity of re-examining the profiles of ARGs in environmental samples using the validated novel ARG sequences. This metagenomics-guided pipeline does not rely on the activity of ARGs during the initial screening process and may specifically select novel ARG sequences for function validation, which make it suitable for the high-throughput screening of novel ARGs from environmental metagenomes.

摘要

新型抗生素耐药菌的出现对人类健康构成了严重威胁,这在很大程度上归因于抗生素耐药基因(ARGs)的进化和传播。在这项工作中,我们提出了一种由宏基因组分析和功能验证组成的宏基因组学指导策略,用于从ARGs传播热点(如污水处理厂(WWTPs)和动物粪便)中快速鉴定新型ARGs。我们使用抗生素耐药基因数据库对来自污泥和鸡粪宏基因组的76个假定的β-内酰胺抗性基因进行注释。在这76个候选基因中,通过PCR从宏基因组中克隆出25个与已知β-内酰胺酶氨基酸同一性为40~70%的靶基因。进一步证明了它们对四种β-内酰胺抗生素的抗性。此外,将经过验证的ARGs用作参考序列,以鉴定八个环境样品中的新型ARGs,这表明有必要使用经过验证的新型ARG序列重新审视环境样品中ARGs的概况。这种宏基因组学指导的流程在初始筛选过程中不依赖于ARGs的活性,并且可以专门选择新型ARG序列进行功能验证,这使其适用于从环境宏基因组中高通量筛选新型ARGs。

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