Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia
文献类型：期刊论文
| 作者 | He,Yukun4; Fang,Kechi2,3 ; Shi,Xing4; Yang,Donghong4; Zhao,Lili4; Yu,Wenyi4; Zheng,Yali1,4; Xu,Yu4; Ma,Xinqian4; Chen,Li4
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| 刊名 | Journal of Translational Medicine
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| 出版日期 | 2022-05-04 |
| 卷号 | 20期号:1 |
| 关键词 | Pneumonia Metagenomic next-generation sequencing Early pathogen detection |
| DOI | 10.1186/s12967-022-03397-5 |
| 通讯作者 | Wang,Jing(wangjing@psych.ac.cn) ; Gao,Zhancheng(zcgao@bjmu.edu.cn) |
| 英文摘要 | AbstractBackgroundMetagenomic next-generation sequencing (mNGS) is an important supplement to conventional tests for pathogen detections of pneumonia. However, mNGS pipelines were limited by irregularities, high proportion of host nucleic acids, and lack of RNA virus detection. Thus, a regulated pipeline based on mNGS for DNA and RNA pathogen detection of pneumonia is essential.MethodsWe performed a retrospective study of 151 patients with pneumonia. Three conventional tests, culture, loop-mediated isothermal amplification (LAMP) and viral quantitative real-time polymerase chain reaction (qPCR) were conducted according to clinical needs, and all samples were detected using our optimized pipeline based on the mNGS (DNA and RNA) method. The performances of mNGS and three other tests were compared. Human DNA depletion was achieved respectively by MolYsis kit and pre-treatment using saponin and Turbo DNase. Three RNA library preparation methods were used to compare the detection performance of RNA viruses.ResultsAn optimized mNGS workflow was built, which had only 1-working-day turnaround time. The proportion of host DNA in the pre-treated samples decreased from 99 to 90% and microbiome reads achieved an approximately 20-fold enrichment compared with those without host removal. Meanwhile, saponin and Turbo DNase pre-treatment exhibited an advantage for DNA virus detection compared with MolYsis. Besides, our in-house RNA library preparation procedure showed a more robust RNA virus detection ability. Combining three conventional methods, 76 (76/151, 50.3%) cases had no clear causative pathogen, but 24 probable pathogens were successfully detected in 31 (31/76?=?40.8%) unclear cases using mNGS. The agreement of the mNGS with the culture, LAMP, and viral qPCR was 60%, 82%, and 80%, respectively. Compared with all conventional tests, mNGS had a sensitivity of 70.4%, a specificity of 72.7%, and an overall agreement of 71.5%.ConclusionsA complete and effective mNGS workflow was built to provide timely DNA and RNA pathogen detection for pneumonia, which could effectively remove the host sequence, had a higher microbial detection rate and a broader spectrum of pathogens (especially for viruses and some pathogens that are difficult to culture). Despite the advantages, there are many challenges in the clinical application of mNGS, and the mNGS report should be interpreted with caution. |
| 语种 | 英语 |
| 出版者 | BioMed Central |
| WOS记录号 | BMC:10.1186/S12967-022-03397-5 |
| 源URL | [http://ir.psych.ac.cn/handle/311026/42421]  |
| 专题 | 心理研究所_中国科学院心理健康重点实验室 |
| 通讯作者 | Wang,Jing; Gao,Zhancheng |
| 作者单位 | 1.Xiang’an Hospital of Xiamen University; Department of Respiratory, Critical Care, and Sleep Medicine 2.University of Chinese Academy of Sciences; Department of Psychology 3.Chinese Academy of Sciences; CAS Key Laboratory of Mental Health, Institute of Psychology 4.Peking University People’s Hospital; Department of Respiratory and Critical Care Medicine |
| 推荐引用方式 GB/T 7714 | He,Yukun,Fang,Kechi,Shi,Xing,et al. Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia[J]. Journal of Translational Medicine,2022,20(1). |
| APA | He,Yukun.,Fang,Kechi.,Shi,Xing.,Yang,Donghong.,Zhao,Lili.,...&Gao,Zhancheng.(2022).Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia.Journal of Translational Medicine,20(1). |
| MLA | He,Yukun,et al."Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia".Journal of Translational Medicine 20.1(2022). |
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来源：心理研究所
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