A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification

Abstract Metagenomic next-generation sequencing (mNGS) holds promise as a diagnostic tool for unbiased pathogen identification and precision medicine. However, its medical utility depends largely on assay simplicity reproducibility. In the current study, we aimed to develop streamlined Illumina Oxford Nanopore-based DNA/RNA library preparation protocol rapid data analysis pipeline. The sequencing-based mNGS method was first developed evaluated using set of samples with known aetiology. Its sensitivity RNA viruses (influenza A, H1N1) < 6.4 × 10 2 EID50/mL, good correlation between viral loads mapped reads observed. Then, turnaround time Nanopore tested by influenza A virus adenoviruses. Furthermore, 11 respiratory swabs or sputum pre-tested panel pathogens were analysed, identified showed 81.8% concordance qPCR results. Additional cerebrospinal fluid (CSF) from HIV-1-positive patients meningitis/encephalitis detected HIV-1 Toxoplasma gondii sequences. conclusion, have simplified that realizes efficient metagenomic variety clinical in clinically meaningful frame.