宏基因组学二代测序在结核病诊断中的应用现状及发展前景_Chinese Journal of Respiratory and Critical Care Medicine

Authors：

赵聪琳 ¹ , ZHOU Yongzhao ² , YANG Yang ¹ , MENG Chunli ¹ ,  LIU Kai ¹

1. ;
2. ;

Corresponding author：

LIU Kai, Email: liubusiness@163.com

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DOI：

10.7507/1671-6205.202207067

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Citation： ZHOU Yongzhao, YANG Yang, MENG Chunli, LIU Kai. 宏基因组学二代测序在结核病诊断中的应用现状及发展前景. Chinese Journal of Respiratory and Critical Care Medicine, 2022, 21(9): 674-677. doi: 10.7507/1671-6205.202207067 Copy

1.	Chakaya J, Khan M, Ntoumi F, et al. Global Tuberculosis Report 2020 - Reflections on the global TB burden, treatment and prevention efforts. IntJ Infect Dis, 2021, 113(Suppl 1): S7-S12.
2.	Wu SS, Zhang YL, Sun F, et al. Adverse events associated with the treatment of multidrug-resistant tuberculosis: a systematic review and meta-analysis. Am J Ther, 2016, 23(2): e521-e530.
3.	尤媛媛, 张国龙, 陈裕. 120例初治耐多药肺结核患者治疗依从性的影响因素分析. 中国防痨杂志, 2020, 42(3): 249-254.
4.	Crawford E, Kamm J, Miller S, et al. Investigating transfusion-related sepsis using culture-independent metagenomic sequencing. Clin Infect Dis, 2020, 71(5): 1179-1185.
5.	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.
6.	Votintseva AA, Bradley P, Pankhurst L, et al. Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples. J Clin Microbiol, 2017, 55(5): 1285-1298.
7.	Zhou X, Wu HL, Ruan QL, et al. Clinical evaluation of diagnosis efficacy of active Mycobacterium tuberculosis complex infection via metagenomic next-generation sequencing of direct clinical samples. Front Cell Infect Microbiol, 2019, 9: 351.
8.	Shi CL, Han P, Tang PJ, et al. Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J Infect, 2020, 81(4): 567-574.
9.	Luo W, Lin YH, Li ZB, et al. Comparison of sputum induction and bronchoscopy in diagnosis of sputum smear-negative pulmonary tuberculosis: a systemic review and meta-analysis. BMC Pulm Med, 2020, 20(1): 146.
10.	Ai JW, Zhang HC, Cui P, et al. Dynamic and direct pathogen load surveillance to monitor disease progression and therapeutic efficacy in central nervous system infection using a novel semi-quantitive sequencing platform. J Infect, 2018, 76(3): 307-310.
11.	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.
12.	Doyle RM, Burgess C, Williams R, et al. Direct whole-genome sequencing of sputum accurately identifies drug-resistant Mycobacterium tuberculosis faster than MGIT culture sequencing. J Clin Microbiol, 2018, 56(8): e00666-18.
13.	Takeuchi S, Kawada JI, Horiba K, et al. Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure. Sci Rep, 2019, 9(1): 12909.
14.	Li Y, Sun B, Tang X, et al. Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients. Eur J Clin Microbiol Infect Dis, 2020, 39(2): 369-374.
15.	Zhu N, Zhou DB, Li SQ. Diagnostic accuracy of metagenomic next-generation sequencing in sputum-scarce or smear-negative cases with suspected pulmonary tuberculosis. Biomed Res Int, 2021, 2021: 9970817.
16.	Hogan JI, Hurtado RM, Nelson SB. Mycobacterial musculoskeletal infections. Thorac Surg Clin, 2019, 29(1): 85-94.
17.	Khan FY, Aladab AH. Role of fiberoptic bronchoscopy in the rapid diagnosis of sputum smear-negative disseminated tuberculosis with pulmonary miliary infiltrates. Oman Med J, 2020, 35(1): e87.
18.	Liu X, Chen YL, 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.
19.	Nongrum S, Singh VA, Paul R, et al. A study about co-infection of fungal pathogens in active tuberculosis patients. Mymensingh Med J, 2019, 28(4): 920-924.
20.	Ding L, Liu YM, Wu XR, et al. Pathogen metagenomics reveals distinct lung microbiota signatures between bacteriologically confirmed and negative tuberculosis patients. Front Cell Infect Microbiol, 2021, 11: 708827.
21.	Langelier C, Zinter MS, Kalantar K, et al. Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients. Am J Respir Crit Care Med, 2018, 197(4): 524-528.
22.	Li N, Cai QQ, Miao Q, et al. High-throughput metagenomics for identification of pathogens in the clinical settings. Small Methods, 2021, 5(1): 2000792.
23.	Solovic I, Jonsson J, Korzeniewska-Koseła M, et al. Challenges in diagnosing extrapulmonary tuberculosis in the European Union, 2011. Euro Surveill, 2013, 18(12): 20432.
24.	Pang Y, An J, Shu W, et al. Epidemiology of Extrapulmonary Tuberculosis among Inpatients, China, 2008-2017. Emerg Infect Dis, 2019, 25(3): 457-464.
25.	Seddon JA, Wilkinson R, Van Crevel R, et al. Knowledge gaps and research priorities in tuberculous meningitis. Wellcome Open Res, 2019, 4: 188.
26.	Leonard JM. Central nervous system tuberculosis. Microbiol Spectr, 2017, 5(2): TNMI7-0044-2017.
27.	Yan LP, Sun WW, Lu ZH, et al. Metagenomic next-generation sequencing (mNGS) in cerebrospinal fluid for rapid diagnosis of tuberculosis meningitis in HIV-negative population. Int J Infect Dis, 2020, 96: 270-275.
28.	Wang SN, Chen YL, Wang DM, et al. The feasibility of metagenomic next-generation sequencing to identify pathogens causing tuberculous meningitis in cerebrospinal fluid. Front Microbiol, 2019, 10: 1993.
29.	Zhang Y, Cui P, Zhang HC, et al. Clinical application and evaluation of metagenomic next-generation sequencing in suspected adult central nervous system infection. J Transl Med, 2020, 18(1): 199.
30.	Brown JR, Bharucha T, Breuer J, et al. Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases. J Infect, 2018, 76(3): 225-240.
31.	Chen YX, Wang YQ, Liu XJ, et al. Comparative diagnostic utility of metagenomic next-generation sequencing, GeneXpert, modified Ziehl-Neelsen staining, and culture using cerebrospinal fluid for tuberculous meningitis: A multi-center, retrospective study in China. J Clin Lab Anal, 2022, 36(4): e24307.
32.	Yu GC, Wang XD, Zhu PF, et al. Comparison of the efficacy of metagenomic next-generation sequencing and Xpert MTB/RIF in the diagnosis of tuberculous meningitis. J Microbiol Methods, 2021, 180: 106124.
33.	Chakravorty S, Simmons AM, Rowneki M, et al. The new Xpert MTB/RIF Ultra: improving detection of Mycobacterium tuberculosis and resistance to rifampin in an assay suitable for point-of-care testing. mBio, 2017, 8(4): e00812-17.
34.	Huang ZD, Zhang CJ, Hu DQ, et al. Diagnosis of osteoarticular tuberculosis via metagenomic next-generation sequencing: a case report. Exp Ther Med, 2019, 18(2): 1184-1188.
35.	Steingart KR, Ng V, Henry M, et al. Sputum processing methods to improve the sensitivity of smear microscopy for tuberculosis: a systematic review. Lancet Infect Dis, 2006, 6(10): 664-674.
36.	Boehme CC, Nicol MP, Nabeta P, et al. Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study. Lancet, 2011, 377(9776): 1495-1505.
37.	Hogan CA, Yang S, Garner OB, et al. Clinical impact of metagenomic next-generation sequencing of plasma cell-free DNA for the diagnosis of infectious diseases: a multicenter retrospective cohort study. Clin Infect Dis, 2021, 72(2): 239-245.
38.	Park J, Shin SY, Kim K, et al. Determining genotypic drug resistance by ion semiconductor sequencing with the Ion AmpliSeq^TM TB Panel in multidrug-resistant Mycobacterium tuberculosis isolates. Ann Lab Med, 2018, 38(4): 316-323.
39.	Park J, Jang W, Kim M, et al. Molecular drug resistance profiles of Mycobacterium tuberculosis from sputum specimens using ion semiconductor sequencing. J Microbiol Methods, 2018, 145: 1-6.
40.	Tagliani E, Cirillo DM, Kodmon C, et al. EUSeqMyTB to set standards and build capacity for whole genome sequencing for tuberculosis in the EU. Lancet Infect Dis, 2018, 18(4): 377-377.
41.	Laxminarayan R, Dune A, Wattal C. Antibiotic resistance-the need for global solutions. Lancet Infect Dis, 2013, 13(12): 1057-1098.
42.	Kadura S, King N, Nakhoul M, et al. Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid. J Antimicrob Chemother, 2020, 75(8): 2031-2043.
43.	Petrella S, Cambau E, Chauffour A, et al. Genetic basis for natural and acquired resistance to the diarylquinoline R207910 in mycobacteria. Antimicrob Agents Chemother, 2006, 50(8): 2853-2856.
44.	Zhu YM, Ai JW, Xu B, et al. Rapid and precise diagnosis of disseminated T. marneffei infection assisted by high-throughput sequencing of multifarious specimens in a HIV-negative patient: a case report. BMC Infect Dis, 2018, 18(1): 379.
45.	Chiang AD, Dekker JP. From the pipeline to the bedside: advances and challenges in clinical metagenomics. J Infect Dis, 2020, 221(Suppl 3): S331-S340.
46.	Gutierrez M C, Brisse S, Brosch R, et al. Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog, 2005, 1(1): e5.
47.	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. Peer J, 2020, 8: e9623.

1. Chakaya J, Khan M, Ntoumi F, et al. Global Tuberculosis Report 2020 - Reflections on the global TB burden, treatment and prevention efforts. IntJ Infect Dis, 2021, 113(Suppl 1): S7-S12.
2. Wu SS, Zhang YL, Sun F, et al. Adverse events associated with the treatment of multidrug-resistant tuberculosis: a systematic review and meta-analysis. Am J Ther, 2016, 23(2): e521-e530.
3. 尤媛媛, 张国龙, 陈裕. 120例初治耐多药肺结核患者治疗依从性的影响因素分析. 中国防痨杂志, 2020, 42(3): 249-254.
4. Crawford E, Kamm J, Miller S, et al. Investigating transfusion-related sepsis using culture-independent metagenomic sequencing. Clin Infect Dis, 2020, 71(5): 1179-1185.
5. 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.
6. Votintseva AA, Bradley P, Pankhurst L, et al. Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples. J Clin Microbiol, 2017, 55(5): 1285-1298.
7. Zhou X, Wu HL, Ruan QL, et al. Clinical evaluation of diagnosis efficacy of active Mycobacterium tuberculosis complex infection via metagenomic next-generation sequencing of direct clinical samples. Front Cell Infect Microbiol, 2019, 9: 351.
8. Shi CL, Han P, Tang PJ, et al. Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J Infect, 2020, 81(4): 567-574.
9. Luo W, Lin YH, Li ZB, et al. Comparison of sputum induction and bronchoscopy in diagnosis of sputum smear-negative pulmonary tuberculosis: a systemic review and meta-analysis. BMC Pulm Med, 2020, 20(1): 146.
10. Ai JW, Zhang HC, Cui P, et al. Dynamic and direct pathogen load surveillance to monitor disease progression and therapeutic efficacy in central nervous system infection using a novel semi-quantitive sequencing platform. J Infect, 2018, 76(3): 307-310.
11. 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.
12. Doyle RM, Burgess C, Williams R, et al. Direct whole-genome sequencing of sputum accurately identifies drug-resistant Mycobacterium tuberculosis faster than MGIT culture sequencing. J Clin Microbiol, 2018, 56(8): e00666-18.
13. Takeuchi S, Kawada JI, Horiba K, et al. Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure. Sci Rep, 2019, 9(1): 12909.
14. Li Y, Sun B, Tang X, et al. Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients. Eur J Clin Microbiol Infect Dis, 2020, 39(2): 369-374.
15. Zhu N, Zhou DB, Li SQ. Diagnostic accuracy of metagenomic next-generation sequencing in sputum-scarce or smear-negative cases with suspected pulmonary tuberculosis. Biomed Res Int, 2021, 2021: 9970817.
16. Hogan JI, Hurtado RM, Nelson SB. Mycobacterial musculoskeletal infections. Thorac Surg Clin, 2019, 29(1): 85-94.
17. Khan FY, Aladab AH. Role of fiberoptic bronchoscopy in the rapid diagnosis of sputum smear-negative disseminated tuberculosis with pulmonary miliary infiltrates. Oman Med J, 2020, 35(1): e87.
18. Liu X, Chen YL, 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.
19. Nongrum S, Singh VA, Paul R, et al. A study about co-infection of fungal pathogens in active tuberculosis patients. Mymensingh Med J, 2019, 28(4): 920-924.
20. Ding L, Liu YM, Wu XR, et al. Pathogen metagenomics reveals distinct lung microbiota signatures between bacteriologically confirmed and negative tuberculosis patients. Front Cell Infect Microbiol, 2021, 11: 708827.
21. Langelier C, Zinter MS, Kalantar K, et al. Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients. Am J Respir Crit Care Med, 2018, 197(4): 524-528.
22. Li N, Cai QQ, Miao Q, et al. High-throughput metagenomics for identification of pathogens in the clinical settings. Small Methods, 2021, 5(1): 2000792.
23. Solovic I, Jonsson J, Korzeniewska-Koseła M, et al. Challenges in diagnosing extrapulmonary tuberculosis in the European Union, 2011. Euro Surveill, 2013, 18(12): 20432.
24. Pang Y, An J, Shu W, et al. Epidemiology of Extrapulmonary Tuberculosis among Inpatients, China, 2008-2017. Emerg Infect Dis, 2019, 25(3): 457-464.
25. Seddon JA, Wilkinson R, Van Crevel R, et al. Knowledge gaps and research priorities in tuberculous meningitis. Wellcome Open Res, 2019, 4: 188.
26. Leonard JM. Central nervous system tuberculosis. Microbiol Spectr, 2017, 5(2): TNMI7-0044-2017.
27. Yan LP, Sun WW, Lu ZH, et al. Metagenomic next-generation sequencing (mNGS) in cerebrospinal fluid for rapid diagnosis of tuberculosis meningitis in HIV-negative population. Int J Infect Dis, 2020, 96: 270-275.
28. Wang SN, Chen YL, Wang DM, et al. The feasibility of metagenomic next-generation sequencing to identify pathogens causing tuberculous meningitis in cerebrospinal fluid. Front Microbiol, 2019, 10: 1993.
29. Zhang Y, Cui P, Zhang HC, et al. Clinical application and evaluation of metagenomic next-generation sequencing in suspected adult central nervous system infection. J Transl Med, 2020, 18(1): 199.
30. Brown JR, Bharucha T, Breuer J, et al. Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases. J Infect, 2018, 76(3): 225-240.
31. Chen YX, Wang YQ, Liu XJ, et al. Comparative diagnostic utility of metagenomic next-generation sequencing, GeneXpert, modified Ziehl-Neelsen staining, and culture using cerebrospinal fluid for tuberculous meningitis: A multi-center, retrospective study in China. J Clin Lab Anal, 2022, 36(4): e24307.
32. Yu GC, Wang XD, Zhu PF, et al. Comparison of the efficacy of metagenomic next-generation sequencing and Xpert MTB/RIF in the diagnosis of tuberculous meningitis. J Microbiol Methods, 2021, 180: 106124.
33. Chakravorty S, Simmons AM, Rowneki M, et al. The new Xpert MTB/RIF Ultra: improving detection of Mycobacterium tuberculosis and resistance to rifampin in an assay suitable for point-of-care testing. mBio, 2017, 8(4): e00812-17.
34. Huang ZD, Zhang CJ, Hu DQ, et al. Diagnosis of osteoarticular tuberculosis via metagenomic next-generation sequencing: a case report. Exp Ther Med, 2019, 18(2): 1184-1188.
35. Steingart KR, Ng V, Henry M, et al. Sputum processing methods to improve the sensitivity of smear microscopy for tuberculosis: a systematic review. Lancet Infect Dis, 2006, 6(10): 664-674.
36. Boehme CC, Nicol MP, Nabeta P, et al. Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study. Lancet, 2011, 377(9776): 1495-1505.
37. Hogan CA, Yang S, Garner OB, et al. Clinical impact of metagenomic next-generation sequencing of plasma cell-free DNA for the diagnosis of infectious diseases: a multicenter retrospective cohort study. Clin Infect Dis, 2021, 72(2): 239-245.
38. Park J, Shin SY, Kim K, et al. Determining genotypic drug resistance by ion semiconductor sequencing with the Ion AmpliSeq^TM TB Panel in multidrug-resistant Mycobacterium tuberculosis isolates. Ann Lab Med, 2018, 38(4): 316-323.
39. Park J, Jang W, Kim M, et al. Molecular drug resistance profiles of Mycobacterium tuberculosis from sputum specimens using ion semiconductor sequencing. J Microbiol Methods, 2018, 145: 1-6.
40. Tagliani E, Cirillo DM, Kodmon C, et al. EUSeqMyTB to set standards and build capacity for whole genome sequencing for tuberculosis in the EU. Lancet Infect Dis, 2018, 18(4): 377-377.
41. Laxminarayan R, Dune A, Wattal C. Antibiotic resistance-the need for global solutions. Lancet Infect Dis, 2013, 13(12): 1057-1098.
42. Kadura S, King N, Nakhoul M, et al. Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid. J Antimicrob Chemother, 2020, 75(8): 2031-2043.
43. Petrella S, Cambau E, Chauffour A, et al. Genetic basis for natural and acquired resistance to the diarylquinoline R207910 in mycobacteria. Antimicrob Agents Chemother, 2006, 50(8): 2853-2856.
44. Zhu YM, Ai JW, Xu B, et al. Rapid and precise diagnosis of disseminated T. marneffei infection assisted by high-throughput sequencing of multifarious specimens in a HIV-negative patient: a case report. BMC Infect Dis, 2018, 18(1): 379.
45. Chiang AD, Dekker JP. From the pipeline to the bedside: advances and challenges in clinical metagenomics. J Infect Dis, 2020, 221(Suppl 3): S331-S340.
46. Gutierrez M C, Brisse S, Brosch R, et al. Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog, 2005, 1(1): e5.
47. 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. Peer J, 2020, 8: e9623.

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宏基因组学二代测序在结核病诊断中的应用现状及发展前景

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