中国防痨杂志 ›› 2018, Vol. 40 ›› Issue (2): 149-152.doi: 10.3969/j.issn.1000-6621.2018.02.007
收稿日期:
2018-01-14
出版日期:
2018-02-10
发布日期:
2018-03-14
Xin-chang CHEN,Wen-hong ZHANG()
Received:
2018-01-14
Online:
2018-02-10
Published:
2018-03-14
摘要:
随着技术的发展及成本的降低,全基因组测序已经广泛应用于结核分枝杆菌的各方面研究当中,包括微进化与传播、宏观进化与种系发生、耐药检测等。根据现有研究成果,全基因组测序已经解决了很多传统分子研究方法无法解决的问题,比如鉴定传播链、分辨复发与再感染、解析结核分枝杆菌的进化过程、快速诊断结核病耐药、诊断混合感染等。尽管如此,目前还存在很多问题亟需解决。笔者对全基因组测序技术的研究方向及成果进行回顾,提出其局限性,并展望其应用前景。
陈昕昶,张文宏. 全基因组测序在结核病研究中的应用进展[J]. 中国防痨杂志, 2018, 40(2): 149-152. doi: 10.3969/j.issn.1000-6621.2018.02.007
Xin-chang CHEN,Wen-hong ZHANG. Progress in the application of whole genome sequencing in tuberculosis research[J]. Chinese Journal of Antituberculosis, 2018, 40(2): 149-152. doi: 10.3969/j.issn.1000-6621.2018.02.007
[1] |
Roetzer A, Diel R, Kohl TA , et al. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med, 2013,10(2):e1001387.
doi: 10.1371/journal.pmed.1001387 URL |
[2] |
Gardy JL, Johnston JC, Ho Sui SJ , et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med, 2011,364(8):730-739.
doi: 10.1056/NEJMoa1003176 URL pmid: 21345102 |
[3] |
Walker TM, Ip CL, Harrell RH , et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis, 2013,13(2):137-146.
doi: 10.1016/S1473-3099(12)70277-3 URL |
[4] | Guerra-Assunção JA, Crampin AC, Houben RM , et al. Large-scale whole genome sequencing of M.tuberculosis provides insights into transmission in a high prevalence area. Elife, 2015,4. |
[5] |
Lee RS, Radomski N, Proulx JF , et al. Reemergence and amplification of tuberculosis in the Canadian arctic. J Infect Dis, 2015,211(12):1905-1914.
doi: 10.1093/infdis/jiv011 URL pmid: 25576599 |
[6] |
Walker TM, Lalor MK, Broda A , et al. Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study. Lancet Respir Med, 2014,2(4):285-292.
doi: 10.1016/S2213-2600(14)70027-X URL |
[7] |
Yang C, Luo T, Shen X , et al. Transmission of multidrug-resistant Mycobacterium tuberculosis in Shanghai, China: a retro-spective observational study using whole-genome sequencing and epidemiological investigation. Lancet Infect Dis, 2017,17(3):275-284.
doi: 10.1016/S1473-3099(16)30418-2 URL |
[8] |
Kato-Maeda M, Ho C, Passarelli B , et al. Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak. PLoS One, 2013,8(3):e58235.
doi: 10.1371/journal.pone.0058235 URL |
[9] |
Köser CU, Bryant JM, Becq J , et al. Whole-genome sequencing for rapid susceptibility testing of M.tuberculosis. N Engl J Med, 2013,369(3):290-292.
doi: 10.1056/NEJMc1215305 URL pmid: 23863072 |
[10] |
Brosch R, Gordon SV, Marmiesse M , et al. A new evolu-tionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A, 2002,99(6):3684-3689.
doi: 10.1073/pnas.052548299 URL pmid: 11891304 |
[11] |
Pfyffer GE, Auckenthaler R, van Embden JD , et al. Mycobacterium canettii, the smooth variant of M.tuberculosis, isolated from a Swiss patient exposed in Africa. Emerg Infect Dis, 1998,4(4):631-634.
URL pmid: 9661826 |
[12] |
Supply P, Marceau M, Mangenot S , et al. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet, 2013,45(2):172-179.
doi: 10.1038/ng.2517 URL |
[13] |
Comas I, Coscolla M, Luo T , et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet, 2013,45(10):1176-1182.
doi: 10.1038/ng.2744 URL |
[14] |
Brites D, Gagneux S . Co-evolution of Mycobacterium tuberculosis and Homo sapiens. Immunol Rev, 2015,264(1):6-24.
doi: 10.1111/imr.2015.264.issue-1 URL |
[15] |
Denkinger CM, Schumacher SG, Boehme CC , et al. Xpert MTB/RIF assay for the diagnosis of extrapulmonary tuberculosis: a systematic review and meta-analysis. Eur Respir J, 2014,44(2):435-446.
doi: 10.1183/09031936.00007814 URL |
[16] |
Schön T, Miotto P, Köser CU , et al. Mycobacterium tuberculosis drug-resistance testing: challenges, recent developments and perspectives. Clin Microbiol Infect, 2017,23(3):154-160.
doi: 10.1016/j.cmi.2016.10.022 URL |
[17] |
Farhat MR, Shapiro BJ, Kieser KJ , et al. Genomic analysis identifies targets of convergent positive selection in drug-resis-tant Mycobacterium tuberculosis. Nat Genet, 2013,45(10):1183-1189.
doi: 10.1038/ng.2747 URL |
[18] |
Zhang H, Li D, Zhao L , et al. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet, 2013,45(10):1255-1260.
doi: 10.1038/ng.2735 URL |
[19] |
Walker TM, Kohl TA, Omar SV , et al. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis, 2015,15(10):1193-1202.
doi: 10.1016/S1473-3099(15)00062-6 URL |
[20] | Shi W, Chen J, Feng J , et al. Aspartate decarboxylase (PanD) as a new target of pyrazinamide in Mycobacterium tuberculosis. Emerg Microbes Infect, 2014,3(8):e58. |
[21] |
Zhang S, Chen J, Shi W , et al. Mutations in panD encoding aspartate decarboxylase are associated with pyrazinamide resistance in Mycobacterium tuberculosis. Emerg Microbes Infect, 2013,2(6):e34.
doi: 10.1038/emi.2013.38 URL |
[22] |
Zhang S, Chen J, Cui P , et al. Identification of novel mutations associated with clofazimine resistance in Mycobacterium tuberculosis. J Antimicrob Chemother, 2015,70(9):2507-2510.
doi: 10.1093/jac/dkv150 URL |
[23] |
Zhang S, Chen J, Cui P , et al. Mycobacterium tuberculosis mutations associated with reduced susceptibility to linezolid. Antimicrob Agents Chemother, 2016,60(4):2542-2544.
doi: 10.1128/AAC.02941-15 URL pmid: 26810645 |
[24] |
Gu Y, Yu X, Jiang G , et al. Pyrazinamide resistance among multidrug-resistant tuberculosis clinical isolates in a national referral center of China and its correlations with pncA, rpsA, and panD gene mutations. Diagn Microbiol Infect Dis, 2016,84(3):207-211.
doi: 10.1016/j.diagmicrobio.2015.10.017 URL |
[25] |
Simons SO, Mulder A, van Ingen J , et al. Role of rpsA gene sequencing in diagnosis of pyrazinamide resistance. J Clin Microbiol, 2013,51(1):382.
doi: 10.1128/JCM.02739-12 URL pmid: 3536190 |
[26] |
Lee RS, Pai M . Real-time sequencing of Mycobacterium tuberculosis: are we there yet. J Clin Microbiol, 2017,55(5):1249-1254.
doi: 10.1128/JCM.00358-17 URL pmid: 28298449 |
[27] |
Votintseva AA, Pankhurst LJ, Anson LW , et al. Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures. J Clin Microbiol, 2015,53(4):1137-1143.
doi: 10.1128/JCM.03073-14 URL |
[28] |
Bradley P, Gordon NC, Walker TM , et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun, 2015,6:10063.
doi: 10.1038/ncomms10063 URL |
[29] |
Pankhurst LJ Del Ojo Elias C, Votintseva AA , et al. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. Lancet Respir Med, 2016,4(1):49-58.
doi: 10.1016/S2213-2600(15)00466-X URL |
[30] | Quan TP, Bawa Z, Foster D, et al. Evaluation of whole genome sequencing for Mycobacterial species identification and drug susceptibility testing in a clinical setting: a large-scale prospective assessment of performance against line-probe assays and phenotyping. J Clin Microbiol , 2017, pii: JCM. 01480-17. |
[31] | Hatherell H, Colijn C, Stagg HR , et al. Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review. BMC Med, 2016,14:21. |
[32] | Horne DJ, Pinto LM, Arentz M , et al. Diagnostic accuracy and reproducibility of WHO-endorsed phenotypic drug susceptibility testing methods for first-line and second-line antituberculosis drugs. J Clin Microbiol, 2013,51(2):393-401. |
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