Updates on the application of whole-genome sequencing for within-host heterogeneity of Mycobacterium tuberculosis

doi:10.19982/j.issn.1000-6621.20220250

Abstract

Abstract:

Tuberculosis (TB) is an infectious disease caused by the Mycobacterium tuberculosis (MTB). The genetic polymorphism of the MTB complex is relatively conservative. With the impressive progress in the field of next generation sequencing (NGS) and the whole-genome sequencing (WGS) analysis, vast genetic heterogeneity has been observed in MTB isolates from different hosts and even within the same host. The reasons for this phenomenon are complex, at least including multiple or mixed infections of different strains and microevolution of the same strain within the host. Still, its mechanism and role in drug resistance, transmission, diagnosis and treatment of TB are not fully understood. This article reviews the identification and current research progress of the within-host genetic heterogeneity of MTB.

Key words: Mycobacterium tuberculosis, Genetic heterogeneity, Whole-genome sequencing, Infection, Review

CLC Number:

Zhang Rui, Liu Yanping, Qian Jun, Fang Qianglin, Yang Chongguang. Updates on the application of whole-genome sequencing for within-host heterogeneity of Mycobacterium tuberculosis[J]. Chinese Journal of Antituberculosis, 2022, 44(11): 1199-1204. doi: 10.19982/j.issn.1000-6621.20220250

Figures/Tables 2

References 63

[1]	Eldholm V, Balloux F. Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out. Trends Microbiol, 2016, 24(8): 637-648. doi: 10.1016/j.tim.2016.03.007. doi: S0966-842X(16)00076-7 pmid: 27068531
[2]	Mogashoa T, Melamu P, Ley SD, et al. Genetic diversity of Mycobacterium tuberculosis strains circulating in Botswana. PLoS One, 2019, 14(5): e0216306. doi: 10.1371/journal.pone.0216306. doi: 10.1371/journal.pone.0216306
[3]	Byrne AS, Goudreau A, Bissonnette N, et al. Methods for Detecting Mycobacterial Mixed Strain Infections—A Systematic Review. Front Genet, 2020, 11: 600692. doi: 10.3389/fgene.2020.600692. doi: 10.3389/fgene.2020.600692 URL
[4]	Hu Y, Zheng X, Davies Forsman L, et al. Emergence of additional drug resistance during treatment of multidrug-resistant tuberculosis in China: a prospective cohort study. Clin Microbiol Infect, 2021, 27(12): 1805-1813. doi: 10.1016/j.cmi.2021.04.001. doi: 10.1016/j.cmi.2021.04.001 URL
[5]	Cohen T, Chindelevitch L, Misra R, et al. Within-Host Heterogeneity of Mycobacterium tuberculosis Infection Is Associated With Poor Early Treatment Response: A Prospective Cohort Study. J Infect Dis, 2016, 213(11): 1796-1799. doi: 10.1093/infdis/jiw014. doi: 10.1093/infdis/jiw014 pmid: 26768249
[6]	Bates JH, Stead WW, Rado TA. Phage type of tubercle bacilli isolated from patients with two or more sites of organ involvement. Am Rev Respir Dis, 1976, 114(2):353-358. doi: 10.1164/arrd.1976.114.2.353. doi: 10.1164/arrd.1976.114.2.353
[7]	Mankiewicz E, Liivak M. Phage types of mycobacterium tuberculosis in cultures isolated from Eskimo patients. Am Rev Respir Dis, 1975, 111(3):307-312. doi: 10.1164/arrd.1975.111.3.307. doi: 10.1164/arrd.1975.111.3.307
[8]	Hussien B, Zewude A, Wondale B, et al. Spoligotyping of Clinical Isolates of Mycobacterium tuberculosis Complex Species in the Oromia Region of Ethiopia. Front Public Health, 2022, 10:808626. doi: 10.3389/fpubh.2022.808626. doi: 10.3389/fpubh.2022.808626
[9]	Hadifar S, Kargarpour Kamakoli M, Eybpoosh S, et al. The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation. Front Microbiol, 2022, 13:978355. doi: 10.3389/fmicb.2022.978355. doi: 10.3389/fmicb.2022.978355
[10]	Desikan S, Narayanan S. Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis. Indian J Med Res, 2015, 141(6): 761-774. doi: 10.4103/0971-5916.160695. doi: 10.4103/0971-5916.160695 URL
[11]	Dookie N, Khan A, Padayatchi N, et al. Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front Microbiol, 2022, 13:775030. doi: 10.3389/fmicb.2022.775030. doi: 10.3389/fmicb.2022.775030
[12]	Niemann S, Supply P. Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches. Cold Spring Harb Perspect Med, 2014, 4(12):a021188. doi: 10.1101/cshperspect.a021188. doi: 10.1101/cshperspect.a021188
[13]	Anyansi C, Keo A, Walker BJ, et al. QuantTB-a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. BMC Genomics, 2020, 21(1):80. doi: 10.1186/s12864-020-6486-3. doi: 10.1186/s12864-020-6486-3 URL
[14]	Gabbassov E, Moreno-Molina M, Comas I, et al. SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data. Microb Genom, 2021, 7(6):000607. doi: 10.1099/mgen.0.000607. doi: 10.1099/mgen.0.000607
[15]	Gan M, Liu Q, Yang C, et al. Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis. PLoS One, 2016, 11(7): e0159029. doi: 10.1371/journal.pone.0159029. doi: 10.1371/journal.pone.0159029
[16]	Sobkowiak B, Glynn JR, Houben RMGJ, et al. Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC Genomics, 2018, 19(1):613. doi: 10.1186/s12864-018-4988-z. doi: 10.1186/s12864-018-4988-z pmid: 30107785
[17]	Wyllie D, Do T, Myers R, et al. M.tuberculosis microvariation is common and is associated with transmission: Analysis of three years prospective universal sequencing in England. J Infect, 2022, 85(1):31-39. doi: 10.1016/j.jinf.2022.05.011. doi: 10.1016/j.jinf.2022.05.011 URL
[18]	谢芳晖, 梁丽, 赵霞, 等. 肺结核患者痰标本采集的研究进展. 中国防痨杂志, 2022, 44(9): 978-982. doi: 10.19982/j.issn.1000-6621.20220188. doi: 10.19982/j.issn.1000-6621.20220188
[19]	Moreno-Molina M, Shubladze N, Khurtsilava I, et al. Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections. Nat Commun, 2021, 12(1): 2716. doi: 10.1038/s41467-021-22705-z. doi: 10.1038/s41467-021-22705-z pmid: 33976135
[20]	Hanekom M, Streicher EM, Van de Berg D, et al. Population structure of mixed Mycobacterium tuberculosis infection is strain genotype and culture medium dependent. PLoS One, 2013, 8(7): e70178. doi: 10.1371/journal.pone.0070178. doi: 10.1371/journal.pone.0070178
[21]	Ssengooba W, Cobelens FG, Nakiyingi L, et al. High Genotypic Discordance of Concurrent Mycobacterium tuberculosis Isolates from Sputum and Blood of HIV-Infected Individuals. PLoS One, 2015, 10(7): e0132581. doi: 10.1371/journal.pone.0132581. doi: 10.1371/journal.pone.0132581
[22]	Shin SS, Modongo C, Baik Y, et al. Mixed Mycobacterium tuberculosis-Strain Infections Are Associated With Poor Treatment Outcomes Among Patients With Newly Diagnosed Tuberculosis, Independent of Pretreatment Heteroresistance. J Infect Dis, 2018, 218(12): 1974-1982. doi: 10.1093/infdis/jiy480. doi: 10.1093/infdis/jiy480
[23]	Navarro Y, Pérez-Lago L, Sislema F, et al. Unmasking subtle differences in the infectivity of microevolved Mycobacterium tuberculosis variants coinfecting the same patient. Int J Med Microbiol, 2013, 303(8): 693-696. doi: 10.1016/j.ijmm.2013.10.002. doi: 10.1016/j.ijmm.2013.10.002 pmid: 24183098
[24]	Das S, Narayanan S, Hari L, et al. Simultaneous infection with multiple strains of Mycobacterium tuberculosis identified by restriction fragment length polymorphism analysis. Int J Tuberc Lung Dis, 2004, 8(2): 267-270. pmid: 15139459
[25]	Marx FM, Dunbar R, Enarson DA, et al. The temporal dynamics of relapse and reinfection tuberculosis after successful treatment: a retrospective cohort study. Clin Infect Dis, 2014, 58(12): 1676-1683. doi: 10.1093/cid/ciu186. doi: 10.1093/cid/ciu186 pmid: 24647020
[26]	Shamputa IC, Rigouts L, Eyongeta LA, et al. Genotypic and phenotypic heterogeneity among Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients. J Clin Microbiol, 2004, 42(12): 5528-5536. doi: 10.1128/jcm.42.12.5528-5536.2004. doi: 10.1128/jcm.42.12.5528-5536.2004 pmid: 15583277
[27]	Lazzarini LC, Rosenfeld J, Huard RC, et al. Mycobacterium tuberculosis spoligotypes that may derive from mixed strain infections are revealed by a novel computational approach. Infect Genet Evol, 2012, 12(4): 798-806. doi: 10.1016/j.meegid.2011.08.028. doi: 10.1016/j.meegid.2011.08.028 pmid: 21920466
[28]	吴小翠, 王晓樱, 魏剑浩, 等. 间隔区寡核苷酸分型技术用于结核分枝杆菌多重感染的初步研究. 中国人兽共患病学报, 2015, 31(1): 1-5. doi: 10.3969/cjz.j.issn.1002-2694.2015.01.001. doi: 10.3969/cjz.j.issn.1002-2694.2015.01.001
[29]	Abascal E, Herranz M, Acosta F, et al. Screening of inmates transferred to Spain reveals a Peruvian prison as a reservoir of persistent Mycobacterium tuberculosis MDR strains and mixed infections. Sci Rep, 2020, 10(1):2704. doi: 10.1038/s41598-020-59373-w. doi: 10.1038/s41598-020-59373-w URL
[30]	Baik Y, Modongo C, Moonan PK, et al. Possible Transmission Mechanisms of Mixed Mycobacterium tuberculosis Infection in High HIV Prevalence Country, Botswana. Emerg Infect Dis, 2020, 26(5): 953-960. doi: 10.3201/eid2605.191638. doi: 10.3201/eid2605.191638 URL
[31]	Pang Y, Zhou Y, Wang S, et al. Prevalence and risk factors of mixed Mycobacterium tuberculosis complex infections in China. J Infect, 2015, 71(2): 231-237. doi: 10.1016/j.jinf.2015.03.012. doi: 10.1016/j.jinf.2015.03.012 pmid: 25936744
[32]	Zheng C, Li S, Luo Z, et al. Mixed Infections and Rifampin Heteroresistance among Mycobacterium tuberculosis Clinical Isolates. J Clin Microbiol, 2015, 53(7): 2138-2147. doi: 10.1128/JCM.03507-14. doi: 10.1128/JCM.03507-14 pmid: 25903578
[33]	Bryant JM, Harris SR, Parkhill J, et al. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med, 2013, 1(10):786-792. doi: 10.1016/S2213-2600(13)70231-5. doi: 10.1016/S2213-2600(13)70231-5 URL
[34]	Guerra-Assunção JA, Houben RM, Crampin AC, et al. Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. J Infect Dis, 2015, 211(7): 1154-1163. doi: 10.1093/infdis/jiu574. doi: 10.1093/infdis/jiu574 pmid: 25336729
[35]	Dippenaar A, De Vos M, Marx FM, et al. Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS 6110 DNA fingerprinting. Infect Genet Evol, 2019, 75: 103948. doi: 10.1016/j.meegid.2019.103948. doi: 10.1016/j.meegid.2019.103948
[36]	Clark TG, Mallard K, Coll F, et al. Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One, 2013, 8(12): e83012. doi: 10.1371/journal.pone.0083012. doi: 10.1371/journal.pone.0083012
[37]	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. doi: 10.1016/S1473-3099(12)70277-3 URL
[38]	Blair JM, Webber MA, Baylay AJ, et al. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol, 2015, 13(1): 42-51. doi: 10.1038/nrmicro3380. doi: 10.1038/nrmicro3380 pmid: 25435309
[39]	Cohen KA, Manson AL, Desjardins CA, et al. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med, 2019, 11(1):45. doi: 10.1186/s13073-019-0660-8. doi: 10.1186/s13073-019-0660-8 URL
[40]	高旭, 李静, 柳清云, 等. 异质性耐药对结核分枝杆菌表型和基因型耐药检测结果的影响. 中华结核和呼吸杂志, 2014, 37(4): 260-265. doi: 10.3760/cma.j.issn.1001-0939.2014.04.007. doi: 10.3760/cma.j.issn.1001-0939.2014.04.007
[41]	Dheda K, Lenders L, Magombedze G, et al. Drug-Penetration Gradients Associated with Acquired Drug Resistance in Patients with Tuberculosis. Am J Respir Crit Care Med, 2018, 198(9): 1208-1219. doi: 10.1164/rccm.201711-2333OC. doi: 10.1164/rccm.201711-2333OC URL
[42]	Zhang X, Zhao B, Liu L, et al. Subpopulation analysis of heteroresistance to fluoroquinolone in Mycobacterium tuberculosis isolates from Beijing, China. J Clin Microbiol, 2012, 50(4): 1471-1474. doi: 10.1128/jcm.05793-11. doi: 10.1128/jcm.05793-11 URL
[43]	Sun G, Luo T, Yang C, et al. Dynamic population changes in Mycobacterium tuberculosis during acquisition and fixation of drug resistance in patients. J Infect Dis, 2012, 206(11): 1724-1733. doi: 10.1093/infdis/jis601. doi: 10.1093/infdis/jis601 URL
[44]	Kargarpour Kamakoli M, Sadegh HR, Farmanfarmaei G, et al. Evaluation of the impact of polyclonal infection and heteroresistance on treatment of tuberculosis patients. Sci Rep, 2017, 7:41410. doi: 10.1038/srep41410. doi: 10.1038/srep41410 URL
[45]	Chen Y, Jiang Q, Zou J, et al. Deep whole-genome sequencing reveals no evidence for heteroresistance influencing treatment outcomes among drug-susceptible tuberculosis patients. Tuberculosis (Edinb), 2021, 130: 102120. doi: 10.1016/j.tube.2021.102120. doi: 10.1016/j.tube.2021.102120
[46]	Chen Y, Ji L, Liu Q, et al. Lesion Heterogeneity and Long-Term Heteroresistance in Multidrug-Resistant Tuberculosis. J Infect Dis, 2021, 224(5): 889-893. doi: 10.1093/infdis/jiab011. doi: 10.1093/infdis/jiab011 pmid: 34467983
[47]	Nimmo C, Brien K, Millard J, et al. Dynamics of within-host Mycobacterium tuberculosis diversity and heteroresistance during treatment. EBioMedicine, 2020, 55: 102747. doi: 10.1016/j.ebiom.2020.102747. doi: 10.1016/j.ebiom.2020.102747
[48]	Abascal E, Herranz M, Ruiz Serrano MJ, et al. In-depth analysis of a mixed Mycobacterium tuberculosis infection involving a multidrug-resistant strain and a susceptible strain. Clin Microbiol Infect, 2021, 27(4): 641-643. doi: 10.1016/j.cmi.2020.09.032. doi: 10.1016/j.cmi.2020.09.032 URL
[49]	van Rie A, Victor TC, Richardson M, et al. Reinfection and mixed infection cause changing Mycobacterium tuberculosis drug-resistance patterns. Am J Respir Crit Care Med, 2005, 172(5): 636-642. doi: 10.1164/rccm.200503-449OC. doi: 10.1164/rccm.200503-449OC URL
[50]	Dreyer V, Utpatel C, Kohl TA, et al. Detection of low-frequency resistance-mediating SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains with binoSNP. Sci Rep, 2020, 10(1): 7874. doi: 10.1038/s41598-020-64708-8. doi: 10.1038/s41598-020-64708-8 pmid: 32398743
[51]	Jouet A, Gaudin C, Badalato N, et al. Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs. Eur Respir J, 2021, 57(3):2002338. doi: 10.1183/13993003.02338-2020. doi: 10.1183/13993003.02338-2020
[52]	Hjort K, Jurén P, Toro JC, et al. Dynamics of Extensive Drug Resistance Evolution of Mycobacterium tuberculosis in a Single Patient During 9 Years of Disease and Treatment. J Infect Dis, 2022, 225(6): 1011-1020. doi: 10.1093/infdis/jiaa625. doi: 10.1093/infdis/jiaa625 URL
[53]	Sonnenkalb L, Strohe G, Dreyer V, et al. Microevolution of Mycobacterium tuberculosis Subpopulations and Heteroresistance in a Patient Receiving 27 Years of Tuberculosis Treatment in Germany. Antimicrob Agents Chemother, 2021, 65(7):e0252020. doi: 10.1128/AAC.02520-20. doi: 10.1128/AAC.02520-20
[54]	Metcalfe JZ, Streicher E, Theron G, et al. Mycobacterium tuberculosis Subculture Results in Loss of Potentially Clinically Relevant Heteroresistance. Antimicrob Agents Chemother, 2017, 61(11):e00888-17. doi: 10.1128/AAC.00888-17. doi: 10.1128/AAC.00888-17
[55]	Liu Q, Via LE, Luo T, et al. Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment. Sci Rep, 2015, 5:17507. doi: 10.1038/srep17507. doi: 10.1038/srep17507 URL
[56]	O’Neill MB, Mortimer TD, Pepperell CS. Diversity of Mycobacterium tuberculosis across Evolutionary Scales. PLoS Pathog, 2015, 11(11): e1005257. doi: 10.1371/journal.ppat.1005257. doi: 10.1371/journal.ppat.1005257
[57]	García de Viedma D, Marín M, Ruiz MJ, et al. Analysis of clonal composition of Mycobacterium tuberculosis isolates in primary infections in children. J Clin Microbiol, 2004, 42(8): 3415-3418. doi: 10.1128/jcm.42.8.3415-3418.2004. doi: 10.1128/jcm.42.8.3415-3418.2004 pmid: 15297476
[58]	Yang C, Sobkowiak B, Naidu V, et al. Phylogeography and transmission of M.tuberculosis in Moldova: A prospective genomic analysis. PLoS Med, 2022, 19(2): e1003933. doi: 10.1371/journal.pmed.1003933. doi: 10.1371/journal.pmed.1003933
[59]	Nelson KN, Talarico S, Poonja S, et al. Mutation of Mycobacterium tuberculosis and Implications for Using Whole-Genome Sequencing for Investigating Recent Tuberculosis Transmission. Front Public Health, 2022, 9:790544. doi: 10.3389/fpubh.2021.790544. doi: 10.3389/fpubh.2021.790544
[60]	Pérez-Lago L, Comas I, Navarro Y, et al. Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission. J Infect Dis, 2014, 209(1): 98-108. doi: 10.1093/infdis/jit439. doi: 10.1093/infdis/jit439 pmid: 23945373
[61]	Séraphin MN, Norman A, Rasmussen EM, et al. Direct transmission of within-host Mycobacterium tuberculosis diversity to secondary cases can lead to variable between-host heterogeneity without de novo mutation: A genomic investigation. EBioMedicine, 2019, 47: 293-300. doi: 10.1016/j.ebiom.2019.08.010. doi: S2352-3964(19)30525-0 pmid: 31420303
[62]	Martin MA, Lee RS, Cowley LA, et al. Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microb Genom, 2018, 4(10):e000217. doi: 10.1099/mgen.0.000217. doi: 10.1099/mgen.0.000217
[63]	Didelot X, Fraser C, Gardy J, et al. Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks. Mol Biol Evol, 2017, 34(4):997-1007. doi: 10.1093/molbev/msw275. doi: 10.1093/molbev/msw275 pmid: 28100788

方法	分析对象	结果识别	微进化	多重/混合感染	参考文献
噬菌体分型	噬菌体菌落裂解	对特定结核分枝杆菌噬菌体的易感性	否	对多个不同的结核分枝杆菌噬菌体具有易感性	[6-7]
IS6110限制性片段长度多态性分型	特异性的插入序列	限制性内切酶带杂交指纹图谱	1~2个条带差异	> 2个条带	[24-25]
			1~3个条带差异	> 3个条带	[26]
间隔区寡核苷酸分型	直接重复区	直接重复区序列杂交指纹图谱	否	多个基因型认定为混合感染	[27-28]
结核分枝杆菌散在重复单元-可变数目串联重复序列	特异性重复序列	基于PCR的拷贝数的差异	<2个位点出现多个条带	≥2个位点出现多个条带	[5,22 29-32]
二代测序	全基因组多态性	异质性SNP	否	≥20个SNP或11~19个SNP且异质性SNP占比>1.5%	[16]
			≤80个SNP	>80个SNP	[33]
			≤140个SNP	>140个SNP	[34]
			0~5个SNP	757~833个SNP	[35]
			2~15个SNP	否	[36]
			每个基因组0.5个SNP/年	否	[37]
		生物信息软件/统计算法	否	不同进化路径等	[13⇓⇓⇓-17]