A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification

Xiaofang Jia, Lvyin Hu, Min Wu, Yun Ling, Wei Wang, Hongzhou Lu, Zhenghong Yuan, Zhigang Yi, Xiaonan Zhang

Research output: Contribution to journalShort Survey/Scientific Reportpeer-review

14 Citations (Scopus)
57 Downloads (Pure)


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 and reproducibility. In the current study, we aimed to develop a streamlined Illumina and Oxford Nanopore-based DNA/RNA library preparation protocol and rapid data analysis pipeline. The Illumina sequencing-based mNGS method was first developed and evaluated using a set of samples with known aetiology. Its sensitivity for RNA viruses (influenza A, H1N1) was < 6.4 × 102 EID50/mL, and a good correlation between viral loads and mapped reads was observed. Then, the rapid turnaround time of Nanopore sequencing was tested by sequencing influenza A virus and adenoviruses. Furthermore, 11 respiratory swabs or sputum samples pre-tested for a panel of pathogens were analysed, and the pathogens identified by Illumina sequencing showed 81.8% concordance with qPCR results. Additional sequencing of cerebrospinal fluid (CSF) samples from HIV-1-positive patients with meningitis/encephalitis detected HIV-1 RNA and Toxoplasma gondii sequences. In conclusion, we have developed a simplified protocol that realizes efficient metagenomic sequencing of a variety of clinical samples and pathogen identification in a clinically meaningful time frame.

Original languageEnglish
Article number4405
Pages (from-to)4405
JournalScientific Reports
Issue number1
Publication statusPublished - Dec 2021
Externally publishedYes


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