Targeting RNA with Next‐ and Third‐Generation Sequencing Improves Pathogen Identification in Clinical Samples

Advanced Science

Binbin Xia¹  Wenhui Zhang¹  Jiabao Cao¹  Jiayue Xu¹  Jun Wang¹  Xuan Zhang¹  Na Zhao¹  Liang Chen¹  Yuqing Zhang¹  Kaifei Wang²  Kun Xiao²  Lixin Xie²  Zhimei Duan²  Fei Xie²  Bin Liu²  Hongwei Zhou³  Dingqiang Chen³  Beibei Liu⁴  Wei Yan⁴ 

[1] CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China;College of Pulmonary and Critical Care Medicine Chinese PLA General Hospital Beijing 100853 China;Microbiome Medicine Center Department of Laboratory Medicine Zhujiang Hospital Southern Medical University Guangzhou Guangdong 510282 China;Peking University Third Hospital Beijing 100191 China;

关键词: direct RNA sequencing;    metagenome;    metatranscriptome;    Oxford Nanopore Technology;   

DOI  :  10.1002/advs.202102593

来源: DOAJ

【 摘 要 】

Abstract Fast and accurate identification of microbial pathogens is critical for the proper treatment of infections. Traditional culture‐based diagnosis in clinics is increasingly supplemented by metagenomic next‐generation‐sequencing (mNGS). Here, RNA/cDNA‐targeted sequencing (meta‐transcriptomics using NGS (mtNGS)) is established to reduce the host nucleotide percentage in clinic samples and by combining with Oxford Nanopore Technology (ONT) platforms (meta‐transcriptomics using third‐generation sequencing, mtTGS) to improve the sequencing time. It shows that mtNGS improves the ratio of microbial reads, facilitates bacterial identification using multiple‐strategies, and discovers fungi, viruses, and antibiotic resistance genes, and displaying agreement with clinical findings. Furthermore, longer reads in mtTGS lead to additional improvement in pathogen identification and also accelerate the clinical diagnosis. Additionally, primary tests utilizing direct‐RNA sequencing and targeted sequencing of ONT show that ONT displays important potential but must be further developed. This study presents the potential of RNA‐targeted pathogen identification in clinical samples, especially when combined with the newest developments in ONT.

【 授权许可】

Unknown