全基因组测序与生物信息学分析在细菌耐药性研究中的应用

Application of whole genome sequencing technology and bioinformatics analysis in antimicrobial resistance researches

摘要:

随着耐药细菌的大量出现及广泛传播，细菌耐药性成为全球备受关注的问题。耐药细菌的特征如耐药基因、毒力因子、质粒分型等以及不同菌株间亲缘关系对于细菌耐药性流行病学及分子生物学的研究有着十分重要的意义。但是传统的技术手段如聚合酶链式反应 (Polymerase chain reaction，PCR) 和脉冲场凝胶电泳 (Pulsed field gel electrophoresis，PFGE) 等得到的结果不够全面且精确度低，对于现有的研究存在很大的局限性。全基因组测序技术 (Whole genome sequencing，WGS) 和生物信息学分析 (Bioinformatics analysis) 由于能够快速详尽地得到耐药细菌的特征，也能更加精细地判断不同菌株间的进化关系，逐渐成为更加有效的技术手段，为耐药性研究提供了有效的帮助。因此，文中系统地介绍全基因组测序分析流程中的各个步骤，主要包括文库构建、平台测序以及后期数据分析三大方面的不同方法和其相应的特点，期望相关研究人员对此能够有更全面的了解，并得到一定的帮助。

Abstract:

The emergence and spread of antimicrobial resistance has become a serious global issue. Bacterial characteristics, such as antimicrobial resistance genes, virulence-associated genes, plasmid types, and phylogenetic relationship among different strains, are the keys to unravel the occurrence and dissemination of antimicrobial resistance. However, the accuracy and efficiency of the traditional techniques, such as polymerase chain reaction and pulsed field gel electrophoresis is insufficient to underlying the mystery of antimicrobial resistance. Recently, the whole genome sequencing and high-throughput bioinformatics analysis have been successfully used in antimicrobial resistance studies, helping scientists to obtain the nature of antimicrobial resistance bacteria quickly, and more precisely to paint the evolutionary relationship among different strains. Therefore, in this study, we aim to systematically introduce the recent development of whole genome sequencing analysis, including different methods and corresponding characteristics of library preparation, platform sequencing, data analysis, and the latest application of the technology in the antimicrobial resistance research. We hope that this review can provide more comprehensive knowledge about whole genome sequencing and bioinformatic analysis for antimicrobial resistance research.