高灵敏度检测复杂微生物群落中 ARG-MGE 共定位的 TELCoMB 方案。

Jonathan E. Bravo, Ilya Slizovskiy, Nathalie Bonin, Marco Oliva, Noelle Noyes, Christina Boucher
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引用次数: 0

摘要

了解抗菌素耐药性的遗传基础对于制定有效的缓解策略至关重要。其中一个必要步骤是确定微生物种群中的抗菌药耐药性基因(ARGs)(称为耐药性组)以及携带 ARGs 的移动遗传因子(MGEs)。尽管霰弹枪元基因组学已成功检测出微生物群中的 ARGs 和 MGEs,但其灵敏度较低。使用 cRNA 生物素化探针进行富集可以解决这一局限性,从而提高对罕见 ARGs 和 MGEs 的检测能力,尤其是在与长线程测序相结合时。在这里,我们介绍一种Snakemake工作流程--TELCoMB协议,它能阐明抗性组和动员组的组成和多样性,并发现ARG-MGE共定位。该方案支持短线程和长线程测序,无需富集,因此适用于各种基因组数据类型。TELCoMB 可生成可供发表的图表和 CSV 文件,用于综合分析,从而提高我们对抗菌药耐药性机制和传播的认识。© 2024 作者。当前协议由 Wiley Periodicals LLC 出版。基本协议 1:在本地安装 TELCOMB 备选协议:基本协议 2:数据预处理 基本协议 3:抗性组分布和组成的计算 基本协议 4:ARG-MGE 共定位的识别。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

The TELCoMB Protocol for High-Sensitivity Detection of ARG-MGE Colocalizations in Complex Microbial Communities

The TELCoMB Protocol for High-Sensitivity Detection of ARG-MGE Colocalizations in Complex Microbial Communities

Understanding the genetic basis of antimicrobial resistance is crucial for developing effective mitigation strategies. One necessary step is to identify the antimicrobial resistance genes (ARGs) within a microbial population, referred to as the resistome, as well as the mobile genetic elements (MGEs) harboring ARGs. Although shotgun metagenomics has been successful in detecting ARGs and MGEs within a microbiome, it is limited by low sensitivity. Enrichment using cRNA biotinylated probes has been applied to address this limitation, enhancing the detection of rare ARGs and MGEs, especially when combined with long-read sequencing. Here, we present the TELCoMB protocol, a Snakemake workflow that elucidates resistome and mobilome composition and diversity and uncovers ARG-MGE colocalizations. The protocol supports both short- and long-read sequencing and does not require enrichment, making it versatile for various genomic data types. TELCoMB generates publication-ready figures and CSV files for comprehensive analysis, improving our understanding of antimicrobial resistance mechanisms and spread. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Installing TELCOMB Locally

Alternate Protocol: Installing TELCOMB on a SLURM Cluster

Basic Protocol 2: Data Preprocessing

Basic Protocol 3: Calculation of Resistome Distribution and Composition

Basic Protocol 4: Identification of ARG-MGE Colocalizations

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