Open AccessTargeting RNA with Next‐ and Third‐Generation Sequencing Improves Pathogen Identification in Clinical Samples
Author(s) -
Zhao Na,
Cao Jiabao,
Xu Jiayue,
Liu Beibei,
Liu Bin,
Chen Dingqiang,
Xia Binbin,
Chen Liang,
Zhang Wenhui,
Zhang Yuqing,
Zhang Xuan,
Duan Zhimei,
Wang Kaifei,
Xie Fei,
Xiao Kun,
Yan Wei,
Xie Lixin,
Zhou Hongwei,
Wang Jun
Publication year - 2021
Publication title -
advanced science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.388
H-Index - 100
ISSN - 2198-3844
DOI - 10.1002/advs.202102593
Subject(s) - metagenomics , dna sequencing , computational biology , nanopore sequencing , identification (biology) , pathogen , biology , rna , transcriptome , gene , genetics , gene expression , botany
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.