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首页> 外文期刊>Journal of Clinical Microbiology >Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates
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Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates

机译：质粒的纳米孔快速测序和临床分离株的抗性基因检测

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Multidrug-resistant bacteria have been assessed as an urgent threat to global public health, and the sequencing of antimicrobial resistance (AMR) genes in these organisms is critical to understanding both the molecular mechanisms of resistance and the basis of their dissemination (1). As many resistance genes are located on plasmids, methods for plasmid sequencing are paramount to the success of these efforts. Sequencing of plasmids is also essential for accurate epidemiologic tracking in the settings of both hospital outbreaks and routine surveillance (2–4). However, the difficulty of achieving contiguous assemblies of plasmids using short-read sequencing technologies, such as those offered by the Illumina and Ion Torrent instruments, is well known (5). Sequence assemblies cannot unambiguously recover repeat-containing genomic regions if there are no reads that span the repeats. For short-read Illumina sequencing, fragment length is typically not longer than ～400 to 500 bp, substantially shorter than the lengths of most mobile genetic elements. As a consequence, assemblies of plasmids that are enriched for these repeats are often extensively fragmented and frequently incomplete. Long-read sequencing with Pacific Biosystems (PacBio) instruments allows full assembly of plasmids to closure in many cases (3), but these instruments are expensive and large and remain inaccessible to most research and clinical labs.
机译：对多种药物具有耐药性的细菌已被评估为对全球公共健康的紧急威胁，在这些生物中对抗菌素耐药性（AMR）基因进行测序对于了解耐药性的分子机制及其传播基础至关重要（1）。由于许多抗性基因位于质粒上，因此质粒测序方法对于这些努力的成功至关重要。在医院暴发和常规监测中，质粒的测序对于准确的流行病学追踪也是必不可少的（2-4）。但是，众所周知，使用短读测序技术（例如Illumina和Ion Torrent仪器提供的技术）很难实现质粒的连续组装（5）。如果没有跨越重复序列的读数，则序列装配不能明确地恢复包含重复序列的基因组区域。对于短读Illumina测序，片段长度通常不超过〜400至500 bp，大大短于大多数可移动遗传元件的长度。结果，针对这些重复而富集的质粒的组装常常被广泛地片段化并且经常是不完整的。使用Pacific Biosystems（PacBio）仪器进行的长时间阅读测序可以在许多情况下完全组装质粒以封闭（3），但这些仪器价格昂贵且体积庞大，大多数研究和临床实验室仍无法使用。

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