Pathogenic metagenomic sequencing technology and its application in clinical infection diagnosis_West China Medical Journal

Authors：

ZHANG Jiangfeng ¹ , MA Bing ¹ , CHU Yafei ¹ , XU Junhong ¹ , XU Wenbo ¹ , WANG Shanmei ¹ , CAO Xuefang ² , CHEN Xiaoxi ² ,  LI Yi ¹

1. Department of Clinical Laboratory, Henan Provincial People’s Hospital, Zhengzhou, Henan 450003, P. R. China;
2. Hangzhou Matridx Biotechnology Company, Hangzhou, Zhejiang 311113, P. R. China;

Corresponding author：

LI Yi, Email: liyilabmed@henu.edu.cn

Keywords：

Metagenomic; pathogen; high-throughput sequencing technology

DOI：

10.7507/1002-0179.202206107

Video：

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Abstract Full text Figures/Tables Video References Cited by

In recent years, pathogenic metagenomic next-generation sequencing (mNGS) technology has become more and more widely used in the field of clinical infection. Driven by clinical needs, mNGS technology is constantly being optimized and developed. From manual operation to automated process, from simple qualitative detection to quantitative monitoring, from infection identification to multi-dimensional diagnosis of “infection+tumor”, certain research results have been achieved. Of course, there are still some limitations in clinical application of this technology. For example, there are many mNGS detection related reagents in China, but a systematic and complete quality management control and evaluation system has not been established. Further research is needed. This article summarizes the development and application of pathogen metagenomic sequencing technology in recent years, as well as the standardization and normalized process of mNGS detection, in order to provide a reference for pathogen mNGS sequencing to better assist clinical infection diagnosis.

Citation： ZHANG Jiangfeng, MA Bing, CHU Yafei, XU Junhong, XU Wenbo, WANG Shanmei, CAO Xuefang, CHEN Xiaoxi, LI Yi. Pathogenic metagenomic sequencing technology and its application in clinical infection diagnosis. West China Medical Journal, 2022, 37(8): 1134-1139. doi: 10.7507/1002-0179.202206107 Copy

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7.	Zhang R, Zhuang Y, Xiao ZH, et al. Diagnosis and surveillance of neonatal infections by metagenomic next-generation sequencing. Front Microbiol, 2022, 13: 855988.
8.	Gu W, Deng X, Lee M, et al. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med, 2021, 27(1): 115-124.
9.	Zhang D, Zhang J, Du J, et al. Optimized sequencing adaptors enable rapid and real-time metagenomic identification of pathogens during runtime of sequencing. Clin Chem, 2022, 68(6): 826-836.
10.	Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell, 2011, 144(5): 646-674.
11.	Guo Y, Li H, Chen H, et al. Metagenomic next-generation sequencing to identify pathogens and cancer in lung biopsy tissue. EBioMedicine, 2021, 73: 103639.
12.	Guan Y, Wang X, Guan K, et al. Copy number variation of urine exfoliated cells by low-coverage whole genome sequencing for diagnosis of prostate adenocarcinoma: a prospective cohort study. BMC Med Genomics, 2022, 15(Suppl 2): 104.
13.	Gu W, Talevich E, Hsu E, et al. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. Genome Med, 2021, 13(1): 98.
14.	Gu W, Rauschecker AM, Hsu E, et al. Detection of neoplasms by metagenomic next-generation sequencing of cerebrospinal fluid. JAMA Neurol, 2021, 78(11): 1355-1366.
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16.	Wei P, Gao Y, Zhang J, et al. Diagnosis of lung squamous cell carcinoma based on metagenomic next-generation sequencing. BMC Pulm Med, 2022, 22(1): 108.
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20.	Dai T, Hu Q, Xie Z, et al. Case report: infective endocarditis caused by Aspergillus flavus in a hemodialysis patient. Front Med (Lausanne), 2021, 8: 655640.
21.	Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med, 2014, 370(25): 2408-2417.
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25.	中华医学会呼吸病学分会感染学组. 中国成人医院获得性肺炎与呼吸机相关性肺炎诊断和治疗指南(2018 年版). 中华结核和呼吸杂志, 2018, 41(4): 255-280.
26.	谢正德, 邓继岿, 任丽丽, 等. 儿童呼吸道感染病原体核酸检测专家共识. 中华实用儿科临床杂志, 2022, 37(5): 321-332.
27.	宏基因组分析和诊断技术在急危重症感染应用专家共识组. 宏基因组分析和诊断技术在急危重症感染应用的专家共识. 中华急诊医学杂志, 2019, 28(2): 151-155.
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31.	中国医师协会神经外科医师分会神经重症专家委员会, 北京医学会神经外科学分会神经外科危重症学组. 神经外科中枢神经系统感染诊治中国专家共识(2021 版). 中华神经外科杂志, 2021, 37(1): 2-15.
32.	中华医学会骨科学分会关节外科学组《中国 PJI 诊断和治疗指南》编写委员会. 中国人工关节感染诊断与治疗指南. 中华外科杂志, 2021, 59(6): 430-442.
33.	《中华传染病杂志》编辑委员会. 中国宏基因组学第二代测序技术检测感染病原体的临床应用专家共识. 中华传染病杂志, 2020, 38(11): 681-689.
34.	中华医学会检验医学分会. 高通量宏基因组测序技术检测病原微生物的临床应用规范化专家共识. 中华检验医学杂志, 2020, 43(12): 1181-1195.
35.	中华医学会检验医学分会临床微生物学组, 中华医学会微生物学与免疫学分会临床微生物学组, 中国医疗保健国际交流促进会临床微生物与感染分会. 宏基因组高通量测序技术应用于感染性疾病病原检测中国专家共识. 中华检验医学杂志, 2021, 44(2): 107-120.
36.	中华医学会检验医学分会. 宏基因组测序病原微生物检测生物信息学分析规范化管理专家共识. 中华检验医学杂志, 2021, 44(9): 799-807.
37.	中华医学会神经病学分会感染性疾病与脑脊液细胞学学组. 中枢神经系统感染性疾病的脑脊液宏基因组学第二代测序应用专家共识. 中华神经科杂志, 2021, 54(12): 1234-1240.
38.	中华医学会儿科学分会新生儿学组, 中华儿科杂志编辑委员会. 宏基因组二代测序技术在新生儿感染性疾病中的临床应用专家共识. 中华儿科杂志, 2022, 60(6): 516-521.
39.	Miller S, Naccache SN, Samayoa E, et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res, 2019, 29(5): 831-842.
40.	Blauwkamp TA, Thair S, Rosen MJ, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol, 2019, 4(4): 663-674.
41.	Jing C, Chen H, Liang Y, et al. Clinical evaluation of an improved metagenomic next-generation sequencing test for the diagnosis of bloodstream infections. Clin Chem, 2021, 67(8): 1133-1143.
42.	Langelier C, Kalantar KL, Moazed F, et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A, 2018, 115(52): E12353-E12362.
43.	Chen H, Yin Y, Gao H, et al. Clinical utility of in-house metagenomic next-generation sequencing for the diagnosis of lower respiratory tract infections and analysis of the host immune response. Clin Infect Dis, 2020, 71(Suppl 4): S416-S426.
44.	Liu D, Zhou H, Xu T, et al. Multicenter assessment of shotgun metagenomics for pathogen detection. EBioMedicine, 2021, 74: 103649.
45.	宁雅婷, 杨启文, 陈新飞, 等. 临床微生物快速检测新技术发展现状与前景. 协和医学杂志, 2021, 12(4): 427-432.
46.	Gargis AS, Kalman L, Berry MW, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol, 2012, 30(11): 1033-1036.

1. Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet, 2019, 20(6): 341-355.
2. Li N, Cai Q, Miao Q, et al. High-throughput metagenomics for identification of pathogens in the clinical settings. Small Methods, 2021, 5(1): 2000792.
3. Miao Q, Ma Y, Wang Q, et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis, 2018, 67(suppl 2): S231-S240.
4. Luan Y, Hu H, Liu C, et al. A proof-of-concept study of an automated solution for clinical metagenomic next-generation sequencing. J Appl Microbiol, 2021, 131(2): 1007-1016.
5. Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol, 2019, 14: 319-338.
6. Zhou H, Ouyang C, Han X, et al. Metagenomic sequencing with spiked-in internal control to monitor cellularity and diagnosis of pneumonia. J Infect, 2022, 84(1): e13-e17.
7. Zhang R, Zhuang Y, Xiao ZH, et al. Diagnosis and surveillance of neonatal infections by metagenomic next-generation sequencing. Front Microbiol, 2022, 13: 855988.
8. Gu W, Deng X, Lee M, et al. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med, 2021, 27(1): 115-124.
9. Zhang D, Zhang J, Du J, et al. Optimized sequencing adaptors enable rapid and real-time metagenomic identification of pathogens during runtime of sequencing. Clin Chem, 2022, 68(6): 826-836.
10. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell, 2011, 144(5): 646-674.
11. Guo Y, Li H, Chen H, et al. Metagenomic next-generation sequencing to identify pathogens and cancer in lung biopsy tissue. EBioMedicine, 2021, 73: 103639.
12. Guan Y, Wang X, Guan K, et al. Copy number variation of urine exfoliated cells by low-coverage whole genome sequencing for diagnosis of prostate adenocarcinoma: a prospective cohort study. BMC Med Genomics, 2022, 15(Suppl 2): 104.
13. Gu W, Talevich E, Hsu E, et al. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. Genome Med, 2021, 13(1): 98.
14. Gu W, Rauschecker AM, Hsu E, et al. Detection of neoplasms by metagenomic next-generation sequencing of cerebrospinal fluid. JAMA Neurol, 2021, 78(11): 1355-1366.
15. Liu K, Gao Y, Han J, et al. Diffuse large B-cell lymphoma of the mandible diagnosed by metagenomic sequencing: a case report. Front Med (Lausanne), 2021, 8: 752523.
16. Wei P, Gao Y, Zhang J, et al. Diagnosis of lung squamous cell carcinoma based on metagenomic next-generation sequencing. BMC Pulm Med, 2022, 22(1): 108.
17. 任海涛, 房柯池, 范思远, 等. 应用脑脊液宏基因组二代测序拷贝数变异分析技术诊断脑膜癌病 1 例. 中国临床案例成果数据库, 2022, 4(1): E01291-E01291.
18. Su J, Han X, Xu X, et al. Simultaneous detection of pathogens and tumors in patients with suspected infections by next-generation sequencing. Front Cell Infect Microbiol, 2022, 12: 892087.
19. Fan H, Gai W, Zhang L, et al. Parasite circulating cell-free DNA in the blood of alveolar echinococcosis patients as a diagnostic and treatment-status indicator. Clin Infect Dis, 2021, 73(1): e246-e251.
20. Dai T, Hu Q, Xie Z, et al. Case report: infective endocarditis caused by Aspergillus flavus in a hemodialysis patient. Front Med (Lausanne), 2021, 8: 655640.
21. Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med, 2014, 370(25): 2408-2417.
22. 《中华传染病杂志》编辑委员会. 中国利什曼原虫感染诊断和治疗专家共识. 中华传染病杂志, 2017, 35(9): 513-518.
23. 中国成人念珠菌病诊断与治疗专家共识组. 中国成人念珠菌病诊断与治疗专家共识. 中华传染病杂志, 2020, 38(1): 29-43.
24. 中华医学会结核病学分会结核性脑膜炎专业委员会. 2019 中国中枢神经系统结核病诊疗指南. 中华传染病杂志, 2020, 38(7): 400-408.
25. 中华医学会呼吸病学分会感染学组. 中国成人医院获得性肺炎与呼吸机相关性肺炎诊断和治疗指南(2018 年版). 中华结核和呼吸杂志, 2018, 41(4): 255-280.
26. 谢正德, 邓继岿, 任丽丽, 等. 儿童呼吸道感染病原体核酸检测专家共识. 中华实用儿科临床杂志, 2022, 37(5): 321-332.
27. 宏基因组分析和诊断技术在急危重症感染应用专家共识组. 宏基因组分析和诊断技术在急危重症感染应用的专家共识. 中华急诊医学杂志, 2019, 28(2): 151-155.
28. 宏基因组学测序技术在中重症感染中的临床应用共识专家组, 中国研究型医院学会脓毒症与休克专业委员会, 中国微生物学会微生物毒素专业委员会, 等. 宏基因组学测序技术在中重症感染中的临床应用专家共识(第一版). 感染、炎症、修复, 2020, 21(2): 75-81.
29. 中华医学会器官移植学分会. 实体器官移植术后感染诊疗技术规范(2019 版)—总论与细菌性肺炎. 器官移植, 2019, 10(4): 343-351.
30. Timsit JF, Ruppé E, Barbier F, et al. Bloodstream infections in critically ill patients: an expert statement. Intensive Care Med, 2020, 46(2): 266-284.
31. 中国医师协会神经外科医师分会神经重症专家委员会, 北京医学会神经外科学分会神经外科危重症学组. 神经外科中枢神经系统感染诊治中国专家共识(2021 版). 中华神经外科杂志, 2021, 37(1): 2-15.
32. 中华医学会骨科学分会关节外科学组《中国 PJI 诊断和治疗指南》编写委员会. 中国人工关节感染诊断与治疗指南. 中华外科杂志, 2021, 59(6): 430-442.
33. 《中华传染病杂志》编辑委员会. 中国宏基因组学第二代测序技术检测感染病原体的临床应用专家共识. 中华传染病杂志, 2020, 38(11): 681-689.
34. 中华医学会检验医学分会. 高通量宏基因组测序技术检测病原微生物的临床应用规范化专家共识. 中华检验医学杂志, 2020, 43(12): 1181-1195.
35. 中华医学会检验医学分会临床微生物学组, 中华医学会微生物学与免疫学分会临床微生物学组, 中国医疗保健国际交流促进会临床微生物与感染分会. 宏基因组高通量测序技术应用于感染性疾病病原检测中国专家共识. 中华检验医学杂志, 2021, 44(2): 107-120.
36. 中华医学会检验医学分会. 宏基因组测序病原微生物检测生物信息学分析规范化管理专家共识. 中华检验医学杂志, 2021, 44(9): 799-807.
37. 中华医学会神经病学分会感染性疾病与脑脊液细胞学学组. 中枢神经系统感染性疾病的脑脊液宏基因组学第二代测序应用专家共识. 中华神经科杂志, 2021, 54(12): 1234-1240.
38. 中华医学会儿科学分会新生儿学组, 中华儿科杂志编辑委员会. 宏基因组二代测序技术在新生儿感染性疾病中的临床应用专家共识. 中华儿科杂志, 2022, 60(6): 516-521.
39. Miller S, Naccache SN, Samayoa E, et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res, 2019, 29(5): 831-842.
40. Blauwkamp TA, Thair S, Rosen MJ, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol, 2019, 4(4): 663-674.
41. Jing C, Chen H, Liang Y, et al. Clinical evaluation of an improved metagenomic next-generation sequencing test for the diagnosis of bloodstream infections. Clin Chem, 2021, 67(8): 1133-1143.
42. Langelier C, Kalantar KL, Moazed F, et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A, 2018, 115(52): E12353-E12362.
43. Chen H, Yin Y, Gao H, et al. Clinical utility of in-house metagenomic next-generation sequencing for the diagnosis of lower respiratory tract infections and analysis of the host immune response. Clin Infect Dis, 2020, 71(Suppl 4): S416-S426.
44. Liu D, Zhou H, Xu T, et al. Multicenter assessment of shotgun metagenomics for pathogen detection. EBioMedicine, 2021, 74: 103649.
45. 宁雅婷, 杨启文, 陈新飞, 等. 临床微生物快速检测新技术发展现状与前景. 协和医学杂志, 2021, 12(4): 427-432.
46. Gargis AS, Kalman L, Berry MW, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol, 2012, 30(11): 1033-1036.

West China Medical Journal

Pathogenic metagenomic sequencing technology and its application in clinical infection diagnosis

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