ARGs-OAP v3.0——抗生素抗性基因数据库的更新和分析流程升级

殷晓乐, 郑夏婉, 李丽观, 章安妮, 姜小涛, 张彤

工程（英文） ›› 2023, Vol. 27 ›› Issue (8) : 234-241.

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工程（英文） ›› 2023, Vol. 27 ›› Issue (8) : 234-241. DOI: 10.1016/j.eng.2022.10.011
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ARGs-OAP v3.0——抗生素抗性基因数据库的更新和分析流程升级

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ARGs-OAP v3.0: Antibiotic-Resistance Gene Database Curation and Analysis Pipeline Optimization

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摘要

由抗生素抗性基因（ARG）编码的抗生素抗性激增，对全球公共卫生构成日益严重的威胁。随着技术的进步，特别是在宏基因组测序的普及方面，科学家们已经获得了高速解读不同样本中ARG谱的能力。为了以高通量的方式分析数千个ARG，需要标准化和集成的流程。广泛使用的抗生素抗性基因在线分析流程（ARGs-OAP）的新版本（v3.0）对参考数据库——结构化抗生素抗性基因（SARG）数据库和综合分析流程都进行了重大改进。SARG通过序列管理得到加强，从而提高注释的可靠性，纳入新出现的抗性基因型，并确定严格的机制分类。该数据库以树状结构的形式在线组织和可视化。针对不同的应用程序场景将它划分为不同的子数据库。此外，ARGs-OAP已经通过调整量化方法、简化工具实施和用户自定义参考数据库的多种功能进行了改进。而且，该在线平台现在提供了一个多样化的生物统计分析工作流程和可视化软件包，用于有效解读ARG图谱。ARGs-OAP v3.0 具有改进的数据库和分析流程，将有利于学术界、政府管理部门和有关ARG环境流行率风险评估工作。

Abstract

Antibiotic resistance, which is encoded by antibiotic-resistance genes (ARGs), has proliferated to become a growing threat to public health around the world. With technical advances, especially in the popularization of metagenomic sequencing, scientists have gained the ability to decipher the profiles of ARGs in diverse samples with high accuracy at an accelerated speed. To analyze thousands of ARGs in a high-throughput way, standardized and integrated pipelines are needed. The new version (v3.0) of the widely used ARGs online analysis pipeline (ARGs-OAP) has made significant improvements to both the reference database—the structured ARG (SARG) database—and the integrated analysis pipeline. SARG has been enhanced with sequence curation to improve annotation reliability, incorporate emerging resistance genotypes, and determine rigorous mechanism classification. The database has been further organized and visualized online in the format of a tree-like structure with a dictionary. It has also been divided into sub-databases for different application scenarios. In addition, the ARGs-OAP has been improved with adjusted quantification methods, simplified tool implementation, and multiple functions with user-defined reference databases. Moreover, the online platform now provides a diverse biostatistical analysis workflow with visualization packages for the efficient interpretation of ARG profiles. The ARGs-OAP v3.0 with an improved database and analysis pipeline will benefit academia, governmental management, and consultation regarding risk assessment of the environmental prevalence of ARGs.

关键词

SARG数据库 / ARGs-OAP / 抗生素抗性基因 / 环境宏基因组 量化 /

Keywords

SARG database / ARGs-OAP / Antibiotic-resistance genes / Environmental metagenome / Quantification

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殷晓乐, 郑夏婉, 李丽观. ARGs-OAP v3.0——抗生素抗性基因数据库的更新和分析流程升级. Engineering. 2023, 27(8): 234-241 https://doi.org/10.1016/j.eng.2022.10.011

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