MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
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DOI：
10.1038/nbt.3103
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发表时间：
2015-03-01
影响因子：
46.9
通讯作者：
O'Grady, Justin
中科院分区：
文献类型：
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作者：
Ashton, Philip M.;Nair, Satheesh;O'Grady, Justin
短读段、高通量测序技术不能鉴定重复插入序列的染色体位置，所述重复插入序列通常位于水平获得的基因（例如细菌毒力基因和抗生素抗性基因）的侧翼。MinION纳米孔测序仪可以在大小类似于USB记忆棒的设备上产生长测序读数。在这里，我们应用MinION测序仪来解析伤寒沙门氏菌单倍型58中复合抗生素耐药岛的结构和染色体插入位点。使用来自单次18小时运行的纳米孔测序数据来创建由短读段Illumina数据生成的组装体的支架。我们的研究结果证明了MinION设备在临床实验室中充分表征细菌病原体流行传播的潜力。
Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes. The MinION nanopore sequencer can produce long sequencing reads on a device similar in size to a USB memory stick. Here we apply a MinION sequencer to resolve the structure and chromosomal insertion site of a composite antibiotic resistance island in Salmonella Typhi Haplotype 58. Nanopore sequencing data from a single 18-h run was used to create a scaffold for an assembly generated from short-read Illumina data. Our results demonstrate the potential of the MinION device in clinical laboratories to fully characterize the epidemic spread of bacterial pathogens.