Progress in the application of whole genome sequencing in tuberculosis research

doi:10.3969/j.issn.1000-6621.2018.02.007

Abstract

Abstract:

With the development of technology and the reduction of cost, whole genome sequencing has been widely used in the research of Mycobacterium tuberculosis (M.tuberculosis) in various respects, including micro-evolution and transmission, macro-evolution and phylogeny, and drug resistance detection. According to the existing research results, genome-wide sequencing has solved many problems that can not be solved by traditional molecular research methods, such as identification of transmission chain, differentiation of recurrent and re-infection, analysis of the evolution of M.tuberculosis, rapid diagnosis of tuberculosis resistance, and diagnosis of mixed infection. Nonetheless, there are still many problems that need to be solved urgently. In this paper, the current research directions and achievements of whole genome sequencing are reviewed, the limitations are proposed, and the future applications are prospected.

Key words: Mycobacterium tuberculosis, Genome, bacterial, Genetic testing, Evolution, molecular, Phylogeny

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

References 32

[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.