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

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.	任海濤, 房柯池, 范思遠, 等. 應用腦脊液宏基因組二代測序拷貝數變異分析技術診斷腦膜癌病 1 例. 中國臨床案例成果數據庫, 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.	《中華傳染病雜志》編輯委員會. 中國利什曼原蟲感染診斷和治療專家共識. 中華傳染病雜志, 2017, 35(9): 513-518.
23.	中國成人念珠菌病診斷與治療專家共識組. 中國成人念珠菌病診斷與治療專家共識. 中華傳染病雜志, 2020, 38(1): 29-43.
24.	中華醫學會結核病學分會結核性腦膜炎專業委員會. 2019 中國中樞神經系統結核病診療指南. 中華傳染病雜志, 2020, 38(7): 400-408.
25.	中華醫學會呼吸病學分會感染學組. 中國成人醫院獲得性肺炎與呼吸機相關性肺炎診斷和治療指南(2018 年版). 中華結核和呼吸雜志, 2018, 41(4): 255-280.
26.	謝正德, 鄧繼巋, 任麗麗, 等. 兒童呼吸道感染病原體核酸檢測專家共識. 中華實用兒科臨床雜志, 2022, 37(5): 321-332.
27.	宏基因組分析和診斷技術在急危重癥感染應用專家共識組. 宏基因組分析和診斷技術在急危重癥感染應用的專家共識. 中華急診醫學雜志, 2019, 28(2): 151-155.
28.	宏基因組學測序技術在中重癥感染中的臨床應用共識專家組, 中國研究型醫院學會膿毒癥與休克專業委員會, 中國微生物學會微生物毒素專業委員會, 等. 宏基因組學測序技術在中重癥感染中的臨床應用專家共識(第一版). 感染、炎癥、修復, 2020, 21(2): 75-81.
29.	中華醫學會器官移植學分會. 實體器官移植術后感染診療技術規范(2019 版)—總論與細菌性肺炎. 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.	中國醫師協會神經外科醫師分會神經重癥專家委員會, 北京醫學會神經外科學分會神經外科危重癥學組. 神經外科中樞神經系統感染診治中國專家共識(2021 版). 中華神經外科雜志, 2021, 37(1): 2-15.
32.	中華醫學會骨科學分會關節外科學組《中國 PJI 診斷和治療指南》編寫委員會. 中國人工關節感染診斷與治療指南. 中華外科雜志, 2021, 59(6): 430-442.
33.	《中華傳染病雜志》編輯委員會. 中國宏基因組學第二代測序技術檢測感染病原體的臨床應用專家共識. 中華傳染病雜志, 2020, 38(11): 681-689.
34.	中華醫學會檢驗醫學分會. 高通量宏基因組測序技術檢測病原微生物的臨床應用規范化專家共識. 中華檢驗醫學雜志, 2020, 43(12): 1181-1195.
35.	中華醫學會檢驗醫學分會臨床微生物學組, 中華醫學會微生物學與免疫學分會臨床微生物學組, 中國醫療保健國際交流促進會臨床微生物與感染分會. 宏基因組高通量測序技術應用于感染性疾病病原檢測中國專家共識. 中華檢驗醫學雜志, 2021, 44(2): 107-120.
36.	中華醫學會檢驗醫學分會. 宏基因組測序病原微生物檢測生物信息學分析規范化管理專家共識. 中華檢驗醫學雜志, 2021, 44(9): 799-807.
37.	中華醫學會神經病學分會感染性疾病與腦脊液細胞學學組. 中樞神經系統感染性疾病的腦脊液宏基因組學第二代測序應用專家共識. 中華神經科雜志, 2021, 54(12): 1234-1240.
38.	中華醫學會兒科學分會新生兒學組, 中華兒科雜志編輯委員會. 宏基因組二代測序技術在新生兒感染性疾病中的臨床應用專家共識. 中華兒科雜志, 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.	寧雅婷, 楊啟文, 陳新飛, 等. 臨床微生物快速檢測新技術發展現狀與前景. 協和醫學雜志, 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. 任海濤, 房柯池, 范思遠, 等. 應用腦脊液宏基因組二代測序拷貝數變異分析技術診斷腦膜癌病 1 例. 中國臨床案例成果數據庫, 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. 《中華傳染病雜志》編輯委員會. 中國利什曼原蟲感染診斷和治療專家共識. 中華傳染病雜志, 2017, 35(9): 513-518.
23. 中國成人念珠菌病診斷與治療專家共識組. 中國成人念珠菌病診斷與治療專家共識. 中華傳染病雜志, 2020, 38(1): 29-43.
24. 中華醫學會結核病學分會結核性腦膜炎專業委員會. 2019 中國中樞神經系統結核病診療指南. 中華傳染病雜志, 2020, 38(7): 400-408.
25. 中華醫學會呼吸病學分會感染學組. 中國成人醫院獲得性肺炎與呼吸機相關性肺炎診斷和治療指南(2018 年版). 中華結核和呼吸雜志, 2018, 41(4): 255-280.
26. 謝正德, 鄧繼巋, 任麗麗, 等. 兒童呼吸道感染病原體核酸檢測專家共識. 中華實用兒科臨床雜志, 2022, 37(5): 321-332.
27. 宏基因組分析和診斷技術在急危重癥感染應用專家共識組. 宏基因組分析和診斷技術在急危重癥感染應用的專家共識. 中華急診醫學雜志, 2019, 28(2): 151-155.
28. 宏基因組學測序技術在中重癥感染中的臨床應用共識專家組, 中國研究型醫院學會膿毒癥與休克專業委員會, 中國微生物學會微生物毒素專業委員會, 等. 宏基因組學測序技術在中重癥感染中的臨床應用專家共識(第一版). 感染、炎癥、修復, 2020, 21(2): 75-81.
29. 中華醫學會器官移植學分會. 實體器官移植術后感染診療技術規范(2019 版)—總論與細菌性肺炎. 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. 中國醫師協會神經外科醫師分會神經重癥專家委員會, 北京醫學會神經外科學分會神經外科危重癥學組. 神經外科中樞神經系統感染診治中國專家共識(2021 版). 中華神經外科雜志, 2021, 37(1): 2-15.
32. 中華醫學會骨科學分會關節外科學組《中國 PJI 診斷和治療指南》編寫委員會. 中國人工關節感染診斷與治療指南. 中華外科雜志, 2021, 59(6): 430-442.
33. 《中華傳染病雜志》編輯委員會. 中國宏基因組學第二代測序技術檢測感染病原體的臨床應用專家共識. 中華傳染病雜志, 2020, 38(11): 681-689.
34. 中華醫學會檢驗醫學分會. 高通量宏基因組測序技術檢測病原微生物的臨床應用規范化專家共識. 中華檢驗醫學雜志, 2020, 43(12): 1181-1195.
35. 中華醫學會檢驗醫學分會臨床微生物學組, 中華醫學會微生物學與免疫學分會臨床微生物學組, 中國醫療保健國際交流促進會臨床微生物與感染分會. 宏基因組高通量測序技術應用于感染性疾病病原檢測中國專家共識. 中華檢驗醫學雜志, 2021, 44(2): 107-120.
36. 中華醫學會檢驗醫學分會. 宏基因組測序病原微生物檢測生物信息學分析規范化管理專家共識. 中華檢驗醫學雜志, 2021, 44(9): 799-807.
37. 中華醫學會神經病學分會感染性疾病與腦脊液細胞學學組. 中樞神經系統感染性疾病的腦脊液宏基因組學第二代測序應用專家共識. 中華神經科雜志, 2021, 54(12): 1234-1240.
38. 中華醫學會兒科學分會新生兒學組, 中華兒科雜志編輯委員會. 宏基因組二代測序技術在新生兒感染性疾病中的臨床應用專家共識. 中華兒科雜志, 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. 寧雅婷, 楊啟文, 陳新飛, 等. 臨床微生物快速檢測新技術發展現狀與前景. 協和醫學雜志, 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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