Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing
Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing
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利用纳米孔测序对耐药细菌进行基因组流行病学分析
DOI：
10.1007/978-1-0716-2996-3_16
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发表时间：
2023
影响因子：
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通讯作者：
Tomita Haruyoshi
中科院分区：
文献类型：
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作者：
Suzuki Masato;Hashimoto Yusuke;Hirabayashi Aki;Yahara Koji;Yoshida Mitsunori;Fukano Hanako;Hoshino Yoshihiko;Shibayama Keigo;Tomita Haruyoshi
由临床上重要的细菌引起的抗菌素耐药(AMR)细菌感染，包括ESKAPE病原菌(粪肠球菌、金黄色葡萄球菌、肺炎克雷伯菌、鲍曼不动杆菌、铜绿假单胞菌和肠杆菌)和分枝杆菌(结核分枝杆菌和非结核分枝杆菌)已成为全球公共卫生威胁。它们的流行和流行克隆通常在其基因组中积累有用的辅助基因，如AMR基因(ARGs)和毒力因子基因(VFGs)。这一过程是通过可移动遗传元件(MGE)在微生物群落之间水平转移基因来促进的，例如质粒和噬菌体。纳米孔长读测序使复杂的细菌基因组结构的分析变得容易和廉价，尽管测序数据计算和基因组分析方法的某些方面还没有系统地了解。在这里，我们描述了最新和最推荐的实验和生物信息学方法，可用于从纳米孔测序数据构建完整的细菌基因组，以及基于细菌染色体、ARGs、VFGs、质粒和其他MGE的基因组序列检测和分类，用于AMR细菌的基因组流行病学分析。
Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium,Staphylococcus aureus,Klebsiella pneumoniae,Acinetobacter baumannii,Pseudomonas aeruginosa, andEnterobacterspecies) and mycobacteria (Mycobacterium tuberculosisand nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.