宏基因组高通量测序在肺部感染诊疗中的应用研究进展_Chinese Journal of Respiratory and Critical Care Medicine

Authors：

倪月艳 , SHI Yi ,  SU Xin

南京医科大学附属金陵医院（东部战区总医院）呼吸与危重症医学科（江苏南京 210002）;

Corresponding author：

SU Xin, Email: suxinjs@163.com

Keywords：

DOI：

10.7507/1671-6205.202109046

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Citation： SHI Yi, SU Xin. 宏基因组高通量测序在肺部感染诊疗中的应用研究进展. Chinese Journal of Respiratory and Critical Care Medicine, 2022, 21(2): 142-147. doi: 10.7507/1671-6205.202109046 Copy

1.	Han DS, Li ZY, Li R, et al. mNGS in clinical microbiology laboratories: on the road to maturity. Crit Rev Microbiol, 2019, 45(5-6): 668-685.
2.	Rothberg JM, Leamon JH. The development and impact of 454 sequencing. Nat Biotechnol, 2008, 26(10): 1117-1124.
3.	Palacios G, Druce J, Du Lei, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med, 2008, 358(10): 991-998.
4.	Metsky HC, Siddle KJ, Gladden-Young A, et al. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol, 2019, 37(2): 160-168.
5.	Dekker JP. Metagenomics for clinical infectious disease diagnostics steps closer to reality. J Clin Microbiol, 2018, 56(9): e00850-18.
6.	Schmidt K, Mwaigwisya S, Crossman LC, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother, 2017, 72(1): 104-114.
7.	Charalampous T, Kay GL, Richardson H, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol, 2019, 37(7): 783-792.
8.	GBD 2019 Diseases and Injuries Collaborators. Global burden of 369 diseases and injuries in 204 countries and territories, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet, 2020, 396(10258): 1204-1222. Erratum in: Lancet, 2020, 396(10262): 1562.
9.	Chen X, Ding SZ, Lei C, et al. Blood and bronchoalveolar lavage fluid metagenomic next-generation sequencing in pneumonia. Clin Microbiol Infect, 2020, 2020: 6839103.
10.	Xie F, Duan ZM, Zeng WQ, et al. Clinical metagenomics assessments improve diagnosis and outcomes in community-acquired pneumonia. BMC Infect Dis, 2021, 21(1): 352.
11.	Pan TT, Tan RM, Qu HP, et al. Next-generation sequencing of the BALF in the diagnosis of community-acquired pneumonia in immunocompromised patients. J Infect, 2019, 79(1): 61-74.
12.	Zhou H, Larkin PMK, Zhao DD, et al. Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage in the diagnosis and management of pneumonia: a multicenter prospective observational study. J Mol Diagn, 2021, 23(10): 1259-1268.
13.	Chen YQ, Feng W, Ye K, et al. Application of metagenomic next-generation sequencing in the diagnosis of pulmonary infectious pathogens from bronchoalveolar lavage samples. Front Cell Infect Microbiol, 2021, 11: 541092.
14.	Long Y, Zhang YX, Gong YP, et al. Diagnosis of sepsis with cell-free DNA by next-generation sequencing technology in ICU patients. Arch Med Res, 2016, 47(5): 365-371.
15.	Blauwkamp TA, Thair S, Rosen M J, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol, 2019, 4(4): 663-674.
16.	Dickson RP, Erb-Downward JR, Freeman CM, et al. Bacterial topography of the healthy human lower respiratory tract. mBio, 2017, 8(1): e02287-16.
17.	Shi CL, Han P, Tang PJ, et al. Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J Infect, 2020, 81(4): 567-574.
18.	Kalantar KL, Moazed F, Christenson SC, et al. Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota. Am J Physiol Lung Cell Mol Physiol, 2019, 316(3): L578-L584.
19.	Miao Q, Ma YY, Wang QQ, et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis, 2018, 67(Suppl_2): S231-S240.
20.	Li H, Gao H, Meng H, et al. Detection of pulmonary infectious pathogens from lung biopsy tissues by metagenomic next-generation sequencing. Front Cell Infect Mi, 2018, 8: 205.
21.	Hong DK, Blauwkamp TA, Kertesz M, et al. Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease. Diagn Microbiol Infect Dis, 2018, 92(3): 210-213.
22.	Chen PX, Sun WW, He YY. Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB/RIF assay in the diagnosis of tuberculosis. J Thorac Dis, 2020, 12(8): 4014-4024.
23.	Zhu H, Zhu M, Lei JH, et al. Metagenomic next-generation sequencing can clinch diagnosis of non-tuberculous mycobacterial infections: a case report. Front Med (Lausanne), 2021, 8: 679755.
24.	Qian YY, Wang HY, Zhou Y, et al. Improving pulmonary infection diagnosis with metagenomic next generation sequencing. Front Cell Infect Microbiol, 2020, 10: 567615.
25.	Yan FG, Xiao Y, Li MK, et al. Metagenomic analysis identified human rhinovirus B91 infection in an adult suffering from severe pneumonia. Am J Resp Crit Care, 2017, 195(11): 1535-1536.
26.	Wang Y, Zhu N, Li Y, et al. Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China. Clin Microbiol Infect, 2016, 22(5): 451-458.
27.	van Rijn AL, van Boheemen S, Sidorov I, et al. The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. PLoS One, 2019, 14(10): e0223952.
28.	Xie D, Xian Y, You JY, et al. Co-infection pneumonia with Mycobacterium abscessus and Pneumocystis jiroveci in a patient without HIV infection diagnosed by metagenomic next-generation sequencing. Infect Drug Resist, 2021, 14: 879-888.
29.	沈轶, 潘雁, 尹成胜, 等. 二代测序诊断肺移植后耶氏肺孢子菌肺炎二例并文献复习. 中国呼吸与危重监护杂志, 2021, 20(7): 479-486.
30.	Xiao W, Han P, Xu ZJ, et al. Pulmonary scedosporiosis in a patient with acute hematopoietic failure: diagnosis aided by next-generation sequencing. Int J Infect Dis, 2019, 85: 114-116.
31.	He BC, Liu LL, Chen BL, et al. The application of next-generation sequencing in diagnosing invasive pulmonary aspergillosis: three case reports. Am J Transl Res, 2019, 11(4): 2532-2539.
32.	Zhao JN, Shi Y, Yuan DM, et al. A case report of fungal infection associated acute fibrinous and organizing pneumonitis. BMC Pulm Med, 2020, 20(1): 98.
33.	Gu L, Liu W, Ru M, et al. The application of metagenomic next-generation sequencing in diagnosing Chlamydia psittaci pneumonia: a report of five cases. BMC Pulm Med, 2020, 20(1): 65.
34.	王艳泓, 邱玉英, 唐健, 等. 结合宏基因组二代测序诊断的八例鹦鹉热患者临床分析. 中国呼吸与危重监护杂志, 2021, 20(7): 472-478.
35.	Wang YY, Dai YY, Lu HW, et al. Case Report: Metagenomic next-generation sequencing in diagnosis of Legionella pneumophila Pneumonia in a patient after umbilical cord blood stem cell transplantation. Front Med (Lausanne), 2021, 8: 643473.
36.	Sun T, Wu XJ, Cai Y, et al. Metagenomic next-generation sequencing for pathogenic diagnosis and antibiotic management of severe community-acquired pneumonia in immunocompromised adults. Front Cell Infect Microbiol, 2021, 11: 661589.
37.	Wang S, Ai JW, Cui P, et al. Diagnostic value and clinical application of next-generation sequencing for infections in immunosuppressed patients with corticosteroid therapy. Ann Transl Med, 2020, 8(5): 227.
38.	Wu X, Li Y, Zhang M, et al. Etiology of severe community-acquired pneumonia in adults based on metagenomic next-generation sequencing: a prospective multicenter study. Infect Dis Ther, 2020, 9(4): 1003-1015.
39.	Xie Y, Du J, Jin W, et al. Next generation sequencing for diagnosis of severe pneumonia: China, 2010-2018. J Infect, 2019, 78(2): 158-169.
40.	Zhang P, Chen Y, Li SY, et al. Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study. PeerJ, 2020, 8: e9623.
41.	Fang XW, Mei Q, Fan XQ, et al. Diagnostic value of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in ventilator-associated pneumonia patients. Front Microbiol, 2020, 11: 599756.
42.	《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.
43.	Quan J, Langelier C, Kuchta A, et al. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Nucleic Acids Res, 2019, 47(14): e83.
44.	Chen HB, Yin YY, 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.

1. Han DS, Li ZY, Li R, et al. mNGS in clinical microbiology laboratories: on the road to maturity. Crit Rev Microbiol, 2019, 45(5-6): 668-685.
2. Rothberg JM, Leamon JH. The development and impact of 454 sequencing. Nat Biotechnol, 2008, 26(10): 1117-1124.
3. Palacios G, Druce J, Du Lei, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med, 2008, 358(10): 991-998.
4. Metsky HC, Siddle KJ, Gladden-Young A, et al. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol, 2019, 37(2): 160-168.
5. Dekker JP. Metagenomics for clinical infectious disease diagnostics steps closer to reality. J Clin Microbiol, 2018, 56(9): e00850-18.
6. Schmidt K, Mwaigwisya S, Crossman LC, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother, 2017, 72(1): 104-114.
7. Charalampous T, Kay GL, Richardson H, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol, 2019, 37(7): 783-792.
8. GBD 2019 Diseases and Injuries Collaborators. Global burden of 369 diseases and injuries in 204 countries and territories, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet, 2020, 396(10258): 1204-1222. Erratum in: Lancet, 2020, 396(10262): 1562.
9. Chen X, Ding SZ, Lei C, et al. Blood and bronchoalveolar lavage fluid metagenomic next-generation sequencing in pneumonia. Clin Microbiol Infect, 2020, 2020: 6839103.
10. Xie F, Duan ZM, Zeng WQ, et al. Clinical metagenomics assessments improve diagnosis and outcomes in community-acquired pneumonia. BMC Infect Dis, 2021, 21(1): 352.
11. Pan TT, Tan RM, Qu HP, et al. Next-generation sequencing of the BALF in the diagnosis of community-acquired pneumonia in immunocompromised patients. J Infect, 2019, 79(1): 61-74.
12. Zhou H, Larkin PMK, Zhao DD, et al. Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage in the diagnosis and management of pneumonia: a multicenter prospective observational study. J Mol Diagn, 2021, 23(10): 1259-1268.
13. Chen YQ, Feng W, Ye K, et al. Application of metagenomic next-generation sequencing in the diagnosis of pulmonary infectious pathogens from bronchoalveolar lavage samples. Front Cell Infect Microbiol, 2021, 11: 541092.
14. Long Y, Zhang YX, Gong YP, et al. Diagnosis of sepsis with cell-free DNA by next-generation sequencing technology in ICU patients. Arch Med Res, 2016, 47(5): 365-371.
15. Blauwkamp TA, Thair S, Rosen M J, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol, 2019, 4(4): 663-674.
16. Dickson RP, Erb-Downward JR, Freeman CM, et al. Bacterial topography of the healthy human lower respiratory tract. mBio, 2017, 8(1): e02287-16.
17. Shi CL, Han P, Tang PJ, et al. Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J Infect, 2020, 81(4): 567-574.
18. Kalantar KL, Moazed F, Christenson SC, et al. Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota. Am J Physiol Lung Cell Mol Physiol, 2019, 316(3): L578-L584.
19. Miao Q, Ma YY, Wang QQ, et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis, 2018, 67(Suppl_2): S231-S240.
20. Li H, Gao H, Meng H, et al. Detection of pulmonary infectious pathogens from lung biopsy tissues by metagenomic next-generation sequencing. Front Cell Infect Mi, 2018, 8: 205.
21. Hong DK, Blauwkamp TA, Kertesz M, et al. Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease. Diagn Microbiol Infect Dis, 2018, 92(3): 210-213.
22. Chen PX, Sun WW, He YY. Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB/RIF assay in the diagnosis of tuberculosis. J Thorac Dis, 2020, 12(8): 4014-4024.
23. Zhu H, Zhu M, Lei JH, et al. Metagenomic next-generation sequencing can clinch diagnosis of non-tuberculous mycobacterial infections: a case report. Front Med (Lausanne), 2021, 8: 679755.
24. Qian YY, Wang HY, Zhou Y, et al. Improving pulmonary infection diagnosis with metagenomic next generation sequencing. Front Cell Infect Microbiol, 2020, 10: 567615.
25. Yan FG, Xiao Y, Li MK, et al. Metagenomic analysis identified human rhinovirus B91 infection in an adult suffering from severe pneumonia. Am J Resp Crit Care, 2017, 195(11): 1535-1536.
26. Wang Y, Zhu N, Li Y, et al. Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China. Clin Microbiol Infect, 2016, 22(5): 451-458.
27. van Rijn AL, van Boheemen S, Sidorov I, et al. The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. PLoS One, 2019, 14(10): e0223952.
28. Xie D, Xian Y, You JY, et al. Co-infection pneumonia with Mycobacterium abscessus and Pneumocystis jiroveci in a patient without HIV infection diagnosed by metagenomic next-generation sequencing. Infect Drug Resist, 2021, 14: 879-888.
29. 沈轶, 潘雁, 尹成胜, 等. 二代测序诊断肺移植后耶氏肺孢子菌肺炎二例并文献复习. 中国呼吸与危重监护杂志, 2021, 20(7): 479-486.
30. Xiao W, Han P, Xu ZJ, et al. Pulmonary scedosporiosis in a patient with acute hematopoietic failure: diagnosis aided by next-generation sequencing. Int J Infect Dis, 2019, 85: 114-116.
31. He BC, Liu LL, Chen BL, et al. The application of next-generation sequencing in diagnosing invasive pulmonary aspergillosis: three case reports. Am J Transl Res, 2019, 11(4): 2532-2539.
32. Zhao JN, Shi Y, Yuan DM, et al. A case report of fungal infection associated acute fibrinous and organizing pneumonitis. BMC Pulm Med, 2020, 20(1): 98.
33. Gu L, Liu W, Ru M, et al. The application of metagenomic next-generation sequencing in diagnosing Chlamydia psittaci pneumonia: a report of five cases. BMC Pulm Med, 2020, 20(1): 65.
34. 王艳泓, 邱玉英, 唐健, 等. 结合宏基因组二代测序诊断的八例鹦鹉热患者临床分析. 中国呼吸与危重监护杂志, 2021, 20(7): 472-478.
35. Wang YY, Dai YY, Lu HW, et al. Case Report: Metagenomic next-generation sequencing in diagnosis of Legionella pneumophila Pneumonia in a patient after umbilical cord blood stem cell transplantation. Front Med (Lausanne), 2021, 8: 643473.
36. Sun T, Wu XJ, Cai Y, et al. Metagenomic next-generation sequencing for pathogenic diagnosis and antibiotic management of severe community-acquired pneumonia in immunocompromised adults. Front Cell Infect Microbiol, 2021, 11: 661589.
37. Wang S, Ai JW, Cui P, et al. Diagnostic value and clinical application of next-generation sequencing for infections in immunosuppressed patients with corticosteroid therapy. Ann Transl Med, 2020, 8(5): 227.
38. Wu X, Li Y, Zhang M, et al. Etiology of severe community-acquired pneumonia in adults based on metagenomic next-generation sequencing: a prospective multicenter study. Infect Dis Ther, 2020, 9(4): 1003-1015.
39. Xie Y, Du J, Jin W, et al. Next generation sequencing for diagnosis of severe pneumonia: China, 2010-2018. J Infect, 2019, 78(2): 158-169.
40. Zhang P, Chen Y, Li SY, et al. Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study. PeerJ, 2020, 8: e9623.
41. Fang XW, Mei Q, Fan XQ, et al. Diagnostic value of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in ventilator-associated pneumonia patients. Front Microbiol, 2020, 11: 599756.
42. 《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.
43. Quan J, Langelier C, Kuchta A, et al. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Nucleic Acids Res, 2019, 47(14): e83.
44. Chen HB, Yin YY, 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.

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