Frontiers in Microbiology (Mar 2022)
QitanTech Nanopore Long-Read Sequencing Enables Rapid Resolution of Complete Genomes of Multi-Drug Resistant Pathogens
Abstract
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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