宏基因组高通量测序技术能够引领呼吸感染性疾病迈进精准医学时代吗？_Chinese Journal of Respiratory and Critical Care Medicine

Authors：

周永召 ¹ , 陆思芬 ² , 刘丹 ¹ , 范红 ¹ , 王业 ¹ ,  李为民 ^1,2

1. ;
2. ;

Corresponding author：

李为民, Email: weimi003@scu.edu.cn

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DOI：

10.7507/1671-6205.202202029

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Citation： 周永召, 陆思芬, 刘丹, 范红, 王业, 李为民. 宏基因组高通量测序技术能够引领呼吸感染性疾病迈进精准医学时代吗？. Chinese Journal of Respiratory and Critical Care Medicine, 2022, 21(2): 137-141. doi: 10.7507/1671-6205.202202029 Copy

1.	Bassetti M, Poulakou G, Ruppe E, et al. Antimicrobial resistance in the next 30 years, humankind, bugs and drugs: a visionary approach. Intensive Care Med, 2017, 43(1): 1464-1475.
2.	Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet, 2022, 399(10325): 629-655.
3.	Zhang QQ, Ying GG, Pan CG, et al. Comprehensive evaluation of antibiotics emission and fate in the river basins of China: source analysis, multimedia modeling, and linkage to bacterial resistance. Environ Sci Technol, 2015, 49(11): 6772-6782.
4.	Jain S, Self WH, Wunderink RG, et al. Community-acquired pneumonia requiring hospitalization among US adults. N Engl J Med, 2015, 373(5): 415-427.
5.	Rogers GB, Wesselingh S. Precision respiratory medicine and the microbiome. Lancet Respir Med, 2016, 4(1): 73-82.
6.	Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet, 2019, 20(6): 341-355.
7.	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.
8.	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.
9.	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, 深圳市医学会重症医学专业委员会. 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). 中华危重病急救医学, 2020, 32(5): 531-536.
10.	《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.
11.	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.
12.	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.
13.	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.
14.	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.
15.	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.
16.	中华医学会呼吸病学分会. 中国成人社区获得性肺炎诊断和治疗指南(2016年版). 中华结核和呼吸杂志, 2016, 39(4): 253-279.
17.	Xie G, Zhao B, Wang X, et al. Exploring the Clinical utility of metagenomic next-generation sequencing in the diagnosis of pulmonary infection. Infect Dis Ther, 2021, 10(3): 1419-1435.
18.	Wu X, Li Y, Zhang M, Li 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.
19.	邹晓辉, 曹彬. 呼吸道感染病原学诊断年度进展2021. 中华结核和呼吸杂志, 2022, 45(1): 78-82.
20.	李冰, 缪青, 金文婷, 等. 宏基因二代测序技术对厌氧菌感染精准化诊断的临床价值. 中华医院感染学杂志, 2019, 29(13): 1927-1930, 1953.
21.	肖华, 周晨, 蔡峰, 等. NGS检出微小微单胞菌肺炎1例及文献复习. 中国实验诊断学, 2021, 25(2): 232-235.
22.	沈凌, 田贤江, 梁荣章, 等. 鹦鹉热衣原体肺炎48例临床特征分析. 中华结核和呼吸杂志, 2021, 44(10): 886-891.
23.	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.
24.	Li N, Li S, Tan W, Wang H, et al. Metagenomic next-generation sequencing in the family outbreak of psittacosis: first reported family outbreak of psittacosis in China under COVID-19. Emerg Microbes Infect, 2021, 10(1): 1-31.
25.	孙雯雯, 顾瑾, 范琳. 宏基因组二代测序对不同类型结核病的诊断价值. 中华结核和呼吸杂志, 2021, 44(2): 96-100.
26.	Clsa B, Peng HC, Pjta B, et al. Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J Infect, 2020, 81(4): 567-574.
27.	Liu X, Chen Y, Ouyang H, et al. Tuberculosis diagnosis by metagenomic next-generation sequencing on bronchoalveolar lavage fluid: a cross-sectional analysis. Int J Infect Dis, 2021, 104: 50-57.
28.	Sims D, Sudbery I, Ilott NE, et al. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet, 2014, 15(2): 121-132.
29.	Schlaberg, Robert, Chiu, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med, 2017, 141(6): 776-786.
30.	贾建超, 贾建敏, 刘姿, 等. 宏基因组学二代测序技术对重症肺炎真菌感染诊断价值. 中华实用诊断与治疗杂志, 2020, 34(10): 1023-1025.
31.	Jiang J, Bai L, Yang W, et al. Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii pneumonia in non-HIV-infected patients: a retrospective study. Infect Dis Ther, 2021, 10(3): 1733-1745.
32.	Zhan Y, Xu T, He F, et al. Clinical evaluation of a metagenomics-based assay for pneumonia management. Front Microbiol, 2021, 12: 751073.
33.	单玉璋, 苏逸, 姚雨濛, 等. 宏基因二代测序技术辅助诊断波氏假阿利什霉肺部感染1例报告. 中国临床医学, 2020, 27(4): 572-574.
34.	Ren LL, Wang YM, Wu ZQ, et al. Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study. Chin Med J, 2020, 133(9): 1015-1024.
35.	Ai JW, Zhang Y, Zhang HC, et al. Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned. Emerg Microbes Infect, 2020, 9(1): 597-600.
36.	Qian YY, Wang HY, Zhou Y, et al. Improving pulmonary infection diagnosis with metagenomic next generation sequencing. Front Cell Infect Microbiol, 2021, 10: 567615.
37.	卓惠长, 林建东, 尤彦菁. 基于宏基因组学的二代测序技术快速诊断肾移植术后单纯疱疹病毒性肺炎1例并文献复习. 福建医科大学学报, 2020, 54(1): 59-61.
38.	张甜, 陈名武, 张晓光, 等. 基于宏基因组二代测序技术的儿童重症腺病毒7型肺炎20例病例系列报告. 中国循证儿科杂志, 2020, 15(2): 130-134.
39.	Li ZJ, Zhang HY, Ren LL, et al. Etiological and epidemiological features of acute respiratory infections in China. Nat Commun, 2021, 12(1): 5026.
40.	Xie F, Duan Z, Zeng W, et al. Clinical metagenomics assessments improve diagnosis and outcomes in community-acquired pneumonia. BMC Infect Dis, 2021, 21(1): 352.
41.	Qu J, Zhang J, Chen Y, et al. Etiology of severe community acquired pneumonia in adults identified by combined detection methods: a multi-center prospective study in China. Emerg Microbes Infect, 2022, 11(1): 556-566.
42.	Han DS, Diao ZL, Lai HY, et al. Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection[J/OL]. J Adv Res, 2021. Available at: https://10.1016/j.jare.2021.09.011.
43.	Liu D, Zhou H, Xu T, et al. Multicenter assessment of shotgun metagenomics for pathogen detection. EBioMedicine, 2021, 74: 103649.
44.	刘东来, 张春涛, 王佑春, 等. 病原宏基因组高通量测序技术质量控制与评价的挑战和思考. 生物工程学报, 2020, 36(12): 2598-2609.
45.	周永召, 李亚伦, 范红, 等. 临床宏基因组学在呼吸感染性疾病精准诊疗中的疑问解析. 中国呼吸与危重监护杂志, 2018, 17(6): 539-543.
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1. Bassetti M, Poulakou G, Ruppe E, et al. Antimicrobial resistance in the next 30 years, humankind, bugs and drugs: a visionary approach. Intensive Care Med, 2017, 43(1): 1464-1475.
2. Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet, 2022, 399(10325): 629-655.
3. Zhang QQ, Ying GG, Pan CG, et al. Comprehensive evaluation of antibiotics emission and fate in the river basins of China: source analysis, multimedia modeling, and linkage to bacterial resistance. Environ Sci Technol, 2015, 49(11): 6772-6782.
4. Jain S, Self WH, Wunderink RG, et al. Community-acquired pneumonia requiring hospitalization among US adults. N Engl J Med, 2015, 373(5): 415-427.
5. Rogers GB, Wesselingh S. Precision respiratory medicine and the microbiome. Lancet Respir Med, 2016, 4(1): 73-82.
6. Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet, 2019, 20(6): 341-355.
7. 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.
8. 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.
9. 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, 深圳市医学会重症医学专业委员会. 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). 中华危重病急救医学, 2020, 32(5): 531-536.
10. 《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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 中华医学会呼吸病学分会. 中国成人社区获得性肺炎诊断和治疗指南(2016年版). 中华结核和呼吸杂志, 2016, 39(4): 253-279.
17. Xie G, Zhao B, Wang X, et al. Exploring the Clinical utility of metagenomic next-generation sequencing in the diagnosis of pulmonary infection. Infect Dis Ther, 2021, 10(3): 1419-1435.
18. Wu X, Li Y, Zhang M, Li 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.
19. 邹晓辉, 曹彬. 呼吸道感染病原学诊断年度进展2021. 中华结核和呼吸杂志, 2022, 45(1): 78-82.
20. 李冰, 缪青, 金文婷, 等. 宏基因二代测序技术对厌氧菌感染精准化诊断的临床价值. 中华医院感染学杂志, 2019, 29(13): 1927-1930, 1953.
21. 肖华, 周晨, 蔡峰, 等. NGS检出微小微单胞菌肺炎1例及文献复习. 中国实验诊断学, 2021, 25(2): 232-235.
22. 沈凌, 田贤江, 梁荣章, 等. 鹦鹉热衣原体肺炎48例临床特征分析. 中华结核和呼吸杂志, 2021, 44(10): 886-891.
23. 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.
24. Li N, Li S, Tan W, Wang H, et al. Metagenomic next-generation sequencing in the family outbreak of psittacosis: first reported family outbreak of psittacosis in China under COVID-19. Emerg Microbes Infect, 2021, 10(1): 1-31.
25. 孙雯雯, 顾瑾, 范琳. 宏基因组二代测序对不同类型结核病的诊断价值. 中华结核和呼吸杂志, 2021, 44(2): 96-100.
26. Clsa B, Peng HC, Pjta B, et al. Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J Infect, 2020, 81(4): 567-574.
27. Liu X, Chen Y, Ouyang H, et al. Tuberculosis diagnosis by metagenomic next-generation sequencing on bronchoalveolar lavage fluid: a cross-sectional analysis. Int J Infect Dis, 2021, 104: 50-57.
28. Sims D, Sudbery I, Ilott NE, et al. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet, 2014, 15(2): 121-132.
29. Schlaberg, Robert, Chiu, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med, 2017, 141(6): 776-786.
30. 贾建超, 贾建敏, 刘姿, 等. 宏基因组学二代测序技术对重症肺炎真菌感染诊断价值. 中华实用诊断与治疗杂志, 2020, 34(10): 1023-1025.
31. Jiang J, Bai L, Yang W, et al. Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii pneumonia in non-HIV-infected patients: a retrospective study. Infect Dis Ther, 2021, 10(3): 1733-1745.
32. Zhan Y, Xu T, He F, et al. Clinical evaluation of a metagenomics-based assay for pneumonia management. Front Microbiol, 2021, 12: 751073.
33. 单玉璋, 苏逸, 姚雨濛, 等. 宏基因二代测序技术辅助诊断波氏假阿利什霉肺部感染1例报告. 中国临床医学, 2020, 27(4): 572-574.
34. Ren LL, Wang YM, Wu ZQ, et al. Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study. Chin Med J, 2020, 133(9): 1015-1024.
35. Ai JW, Zhang Y, Zhang HC, et al. Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned. Emerg Microbes Infect, 2020, 9(1): 597-600.
36. Qian YY, Wang HY, Zhou Y, et al. Improving pulmonary infection diagnosis with metagenomic next generation sequencing. Front Cell Infect Microbiol, 2021, 10: 567615.
37. 卓惠长, 林建东, 尤彦菁. 基于宏基因组学的二代测序技术快速诊断肾移植术后单纯疱疹病毒性肺炎1例并文献复习. 福建医科大学学报, 2020, 54(1): 59-61.
38. 张甜, 陈名武, 张晓光, 等. 基于宏基因组二代测序技术的儿童重症腺病毒7型肺炎20例病例系列报告. 中国循证儿科杂志, 2020, 15(2): 130-134.
39. Li ZJ, Zhang HY, Ren LL, et al. Etiological and epidemiological features of acute respiratory infections in China. Nat Commun, 2021, 12(1): 5026.
40. Xie F, Duan Z, Zeng W, et al. Clinical metagenomics assessments improve diagnosis and outcomes in community-acquired pneumonia. BMC Infect Dis, 2021, 21(1): 352.
41. Qu J, Zhang J, Chen Y, et al. Etiology of severe community acquired pneumonia in adults identified by combined detection methods: a multi-center prospective study in China. Emerg Microbes Infect, 2022, 11(1): 556-566.
42. Han DS, Diao ZL, Lai HY, et al. Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection[J/OL]. J Adv Res, 2021. Available at: https://10.1016/j.jare.2021.09.011.
43. Liu D, Zhou H, Xu T, et al. Multicenter assessment of shotgun metagenomics for pathogen detection. EBioMedicine, 2021, 74: 103649.
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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

宏基因组高通量测序技术能够引领呼吸感染性疾病迈进精准医学时代吗？

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