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

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. Targeting ribonucleic acid (RNA), the authors develop meta‐transcriptomic‐based pathogen detection using next‐generation sequencing (mtNGS) with Illumina and third generation sequencing (mtTGS) using Oxford Nanopore Technology (ONT), and show they outperform the current DNA‐based approaches in efficiency and accuracy, covering wider range of pathogens including bacteria, viruses and fungi. Further, direct RNA sequencing with ONT shows promising advantages and warrants further investigation.