Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-41346, Gothenburg, Sweden.
Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden.
J Antimicrob Chemother. 2017 Oct 1;72(10):2690-2703. doi: 10.1093/jac/dkx199.
Antibiotic resistance is a global health concern declared by the WHO as one of the largest threats to modern healthcare. In recent years, metagenomic DNA sequencing has started to be applied as a tool to study antibiotic resistance in different environments, including the human microbiota. However, a multitude of methods exist for metagenomic data analysis, and not all methods are suitable for the investigation of resistance genes, particularly if the desired outcome is an assessment of risks to human health. In this review, we outline the current state of methods for sequence handling, mapping to databases of resistance genes, statistical analysis and metagenomic assembly. In addition, we provide an overview of important considerations related to the analysis of resistance genes, and recommend some of the currently used tools and methods that are best equipped to inform research and clinical practice related to antibiotic resistance.
抗生素耐药性是一个全球性的健康问题，世界卫生组织（WHO）已将其列为对现代医疗保健的最大威胁之一。近年来，宏基因组 DNA 测序已开始被用作研究不同环境（包括人类微生物群）中抗生素耐药性的工具。然而，存在多种宏基因组数据分析方法，并非所有方法都适用于耐药基因的研究，特别是如果期望的结果是评估对人类健康的风险。在这篇综述中，我们概述了当前用于序列处理、耐药基因数据库映射、统计分析和宏基因组组装的方法。此外，我们还概述了与耐药基因分析相关的重要注意事项，并推荐了一些目前用于告知与抗生素耐药性相关的研究和临床实践的最适合的工具和方法。
