HT-ARGfinder: A Comprehensive Pipeline for Identifying Horizontally Transferred Antibiotic Resistance Genes and Directionality in Metagenomic Sequencing Data
HT-ARGfinder: A Comprehensive Pipeline for Identifying Horizontally Transferred Antibiotic Resistance Genes and Directionality in Metagenomic Sequencing Data
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DOI：
10.3389/fenvs.2022.901917
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发表时间：
2022-06-03
影响因子：
4.6
通讯作者：
Zhang, Liqing
中科院分区：
文献类型：
--
作者：
Das, Badhan;Emon, Muhit Islam;Zhang, Liqing
抗生素耐药性是对全球健康的一个不断上升的威胁。耐药病原体新菌株进化的主要驱动力是抗生素耐药基因（ARG）的水平基因转移（HGT）。然而，识别和量化受HGT影响的ARG仍然是一个重大挑战。在这里，我们介绍了HT-ARGfinder（水平转移ARG finder），这是一个检测和枚举宏基因组数据中水平转移的ARG的管道，同时还估计转移的方向性。为了展示管道，我们将其应用于一系列公开的废水宏基因组，包括医院污水。我们比较了在不同样本类型中检测到的水平转移的ARG，并估计了它们在供体和受体之间转移的方向性。这项研究介绍了一个全面的工具来跟踪移动的ARGs在废水和其他水生环境。
Antibiotic resistance is a continually rising threat to global health. A primary driver of the evolution of new strains of resistant pathogens is the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). However, identifying and quantifying ARGs subject to HGT remains a significant challenge. Here, we introduce HT-ARGfinder (horizontally transferred ARG finder), a pipeline that detects and enumerates horizontally transferred ARGs in metagenomic data while also estimating the directionality of transfer. To demonstrate the pipeline, we applied it to an array of publicly-available wastewater metagenomes, including hospital sewage. We compare the horizontally transferred ARGs detected across various sample types and estimate their directionality of transfer among donors and recipients. This study introduces a comprehensive tool to track mobile ARGs in wastewater and other aquatic environments.