QitanTech Nanopore Long-Read Sequencing Enables Rapid Resolution of Complete Genomes of Multi-Drug Resistant Pathogens.
QitanTech Nanopore Long-Read Sequencing Enables Rapid Resolution of Complete Genomes of Multi-Drug Resistant Pathogens.
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QitanTech 纳米孔长读长测序可快速解析多重耐药病原体的完整基因组
DOI：
10.3389/fmicb.2022.778659
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发表时间：
2022
影响因子：
5.2
通讯作者：
Li R
中科院分区：
文献类型：
--
作者：
Peng K;Yin Y;Li Y;Qin S;Liu Y;Yang X;Wang Z;Li R
新的测序技术的发展为现代生命科学和医学提供了前所未有的便利。利用长片段测序技术获得细菌全基因组序列对微生物基因组学研究具有重要意义。然而，第三代长读段测序技术的选择有限，这给科学研究带来了技术障碍。最近，一种新的QitanTech纳米孔长读测序技术在中国出现，但潜在的应用和性能尚未探索。在此，我们全面评估了新兴测序技术在组装MDR病原体完整基因组中的可行性。结果表明，采用标准文库制备方法，在一个流动池中可以在8 h内生成500 Mbp QitanTech纳米孔测序数据。QitanTech测序数据的平均读取长度、最长读取长度和平均读取水平准确度分别为6，041 bp、57，037 bp和81.50%（LAST）/81.40%（Minimap 2）。两种常规的组装策略，包括长读组装和杂交组装，使得能够实现完整的细菌基因组。通过使用精确的短读数据进行抛光，使用QitanTech长读数据组装的细菌基因组草图的准确性可以显著提高高达99.9%。此外，组装的细菌基因组覆盖了包含关键抗性基因如泰特（X）、tmexCD-toprJ和blaVIM-2的复杂抗性质粒的准确结构，甚至是由同源重组产生的复杂融合MDR质粒。总之，奇坦科技纳米孔测序作为中国推出的纳米孔长读测序技术，可能是复杂细菌基因组研究的一个很好的选择。基于这种新型平台的更多潜在应用值得研究。
Advancement of novel sequencing technologies facilitates modern life science and medicine unprecedentedly. Exploring complete genome sequences of bacteria by long-read sequencing technology is significant for microbial genomics research. However, third-generation long-read sequencing technologies are available with limited choices, which generate technological barrier to scientific research. Recently, a novel QitanTech nanopore long-read sequencing technology has emerged in China, but the potential application and performance were unexplored. Herein, we comprehensively evaluated the feasibility of the emerging sequencing technology in assembling complete genomes of MDR pathogens. The results showed that 500 Mbp QitanTech nanopore sequencing data could be generated within 8 h in one flow cell with the standard library preparation method. The mean read length, longest read length, and mean read-level accuracy of QitanTech sequencing data were 6,041 bp, 57,037 bp, and 81.50% (LAST)/81.40% (Minimap2), respectively. Two routine assembly strategies including long-read assembly and hybrid assembly enable the achievement of complete bacterial genomes. The accuracy of assembled draft bacterial genomes with QitanTech long-read data could be improved up to 99.9% dramatically by polishing using accurate short-read data. Furthermore, the assembled bacterial genomes cover accurate structures of complex resistance plasmids harboring critical resistance genes such as tet(X), tmexCD-toprJ, and blaVIM–2, even the complex fusion MDR plasmid generated from homologous recombination. In conclusion, QitanTech nanopore sequencing, as a nanopore long-read sequencing technology launched in China, could be a good option for investigation of complex bacterial genomes. More potential applications based on this novel platform warrant investigations.
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