结核分枝杆菌北京基因型菌株大片段的多态性研究

doi:10.3969/j.issn.1000-6621.2018.03.011

摘要/Abstract

摘要：

目的揭示结核分枝杆菌(Mycobacterium tuberculosis,MTB)北京基因型菌株的进化路径,在进化过程中产生的各个进化分支,以及每个分支的北京基因型菌株在人群中的流行情况。方法收集2014年1月至2016年4月天津地区临床分离的567株MTB菌株,首先采用多重PCR试验分析菌株基因组中差异片段207(RD207)的缺失情况,以鉴定收集的菌株是否为北京基因型;然后分析所有的北京基因型MTB菌株基因组中差异区域RD105、RD181、RD150和RD142的缺失情况,以及菌株基因组NTF(noise transfer function)区中插入序列6110(IS6110)的存在情况。结果 567株临床分离的MTB菌株中,517株(91.2%)为北京基因型菌株。所有北京基因型菌株中,447株(86.5%)为NTF区含有IS6110的北京基因型现代株;70株(13.5%)为NTF区不含IS6110的北京基因型古代株。基于大片段的多态性分析,北京基因型菌株被分为5个亚型,其中RD181(+)的北京基因型菌株为22株(4.3%),且全部为北京基因型古代株。RD181(-)/RD150(+)和RD181(-)/RD150(-)的北京基因型古代株分别为41株(7.9%)和7株(1.4%)。447株现代菌株中,RD181(-)/RD150(+)和RD181(-)/RD150(-)的分别为404株(78.1%)和43株(8.3%)。结论 MTB北京基因型中的现代株是天津地区的主要流行株;北京基因型MTB在人群传播流行中已经进化出5个分支,其中RD181(-)/RD150(+)的北京基因型现代株为主要的流行分支。

关键词: 分枝杆菌,结核, 基因型, 基因缺失, 扩增片段长度多态性分析, 生物进化

Abstract:

Objective To clarify the evolutionary pathway of Beijing genotype of Mycobacterium tuberculosis (MTB) and to elucidate the sublineages of Beijing strains.Methods The Beijing genotype isolates were identified from the 567 MTB isolates, which collected from the patients with pulmonary tuberculosis from Jan. 2014 to Apr. 2016 in Tianjin, China, by analyzing the deletion of regions of difference 207 (RD207). Large sequence polymorphism (LSP) of the Beijing strains were determined based on the presence or absence of RD105, RD181, RD150 and RD142. The insertion sequence 6110 (IS6110) insertion in noise transfer function (NTF) region was also analyzed.Results Of the 567 clinical isolates, 517 (91.2%) were identified as Beijing genotype. Among these Beijing strains, 447 (86.5%) belonged to modern Beijing strains that possessed IS6110 insertion in NTF region, whereas 70 (13.5%) belonged to ancient Beijing strains that had no IS6110 insertion in NTF region. Based on the LSP analy-sis, all 517 Beijing strains were further divided into five sublineages. 22 (4.3%) were RD181(+), and all these RD181(+) strains belonged to ancient Beijing genotype. 41 (7.9%) and 7 (1.4%) were RD181(-)/RD150(+) and RD181(-)/RD150(-) ancient Beijing strain, respectively. Of the 447 modern Beijing strains, there were 404 RD181(-)/RD150(+) and 43 RD181(-)/RD150(-) strains, accounting for 78.1% and 8.3% of the Beijing isolates, respectively.Conclusion Modern Beijing strains are the most predominant in Tianjin, China. Based on the LSP analysis, the Beijing genotype strains have evolved five sublineages and the majority of isolates is the RD181(-)/RD150(+) modern sublineage.

Key words: Mycobacterium tuberculosis, Genotype, Gene deletion, Amplified fragment length polymorphism analysis, Biological evolution

谢彤,孙蕊,巨韩芳,王春花,穆成,王志锐,赵慧. 结核分枝杆菌北京基因型菌株大片段的多态性研究[J]. 中国防痨杂志, 2018, 40(3): 269-273. doi: 10.3969/j.issn.1000-6621.2018.03.011

Tong XIE,Rui SUN,Han-fang JU,Chun-hua WANG,Cheng MU,Zhi-rui WANG,Hui ZHAO. Large sequence polymorphisms of the Mycobacterium tuberculosis Beijing genotype strains[J]. Chinese Journal of Antituberculosis, 2018, 40(3): 269-273. doi: 10.3969/j.issn.1000-6621.2018.03.011

图/表 2

参考文献 18

[1]	Ramazanzadeh R, Sayhemiri K . Prevalence of Beijing family in Mycobacterium tuberculosis in world population: systematic review and meta-analysis. Int J Mycobacteriol, 2014,3(1):41-45. doi: 10.1016/j.ijmyco.2014.01.001 URL
[2]	Garzelli C, Lari N, Rindi L . Genomic diversity of Mycobacterium tuberculosis Beijing strains isolated in Tuscany, Italy, based on large sequence deletions, SNPs in putative DNA repair genes and MIRU-VNTR polymorphisms. Tuberculosis, 2016,97:147-153. doi: 10.1016/j.tube.2015.10.008 URL
[3]	Hanekom M, Gey van Pittius NC, McEvoy C, et al. Mycobacterium tuberculosis Beijing genotype: a template for success. Tuberculosis (Edinb), 2011,91(6):510-523. doi: 10.1016/j.tube.2011.07.005 URL pmid: 21835699
[4]	Wan K, Liu J, Hauck Y , et al. Investigation on Mycobacterium tuberculosis diversity in China and the origin of the Beijing clade. PLoS One, 2011,6(12):e29190. doi: 10.1371/journal.pone.0029190 URL
[5]	Mokrousov I, Ly HM, Otten T , et al. Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: clues from human phylogeography. Genome Res, 2005,15(10):1357-1364. doi: 10.1101/gr.3840605 URL
[6]	Tsolaki AG, Gagneux S, Pym AS , et al. Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis. J Clin Microbiol, 2005,43(7):3185-3191. doi: 10.1128/JCM.43.7.3185-3191.2005 URL
[7]	赵德福, 谢彤, 巨韩芳 , 等. 利用多重PCR方法快速鉴定结核分枝杆菌北京基因型菌株. 中国防痨杂志, 2010,32(6):315-317.
[8]	Wada T, Iwamoto T, Maeda S . Genetic diversity of the Mycobacterium tuberculosis Beijing family in East Asia revealed through refined population structure analysis. FEMS Microbiol Lett, 2009,291(1):35-43. doi: 10.1111/fml.2009.291.issue-1 URL
[9]	Reed MB, Pichler VK, McIntosh F , et al. Major Mycobacterium tuberculosis lineages associate with patient country of origin. J Clin Microbiol, 2009,47(4):1119-1128. doi: 10.1128/JCM.02142-08 URL pmid: 2668307
[10]	Gagneux S, Small PM . Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis, 2007,7(5):328-337. doi: 10.1016/S1473-3099(07)70108-1 URL
[11]	Faksri K, Hanchaina R, Sangka A , et al. Development and application of single-tube multiplex real-time PCR for lineage classification of Mycobacterium tuberculosis based on large sequence polymorphism in Northeast Thailand. Tuberculosis (Edinb), 2015,95(4):404-410. doi: 10.1016/j.tube.2015.04.009 URL
[12]	Merker M, Blin C, Mona S , et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet, 2015,47(3):242-249. doi: 10.1038/ng.3195 URL pmid: 25599400
[13]	Rindi L, Lari N, Cuccu B , et al. Evolutionary pathway of the Beijing lineage of Mycobacterium tuberculosis based on genomic deletions and mutT genes polymorphisms. Infect Genet Evol, 2009,9(1):48-53. doi: 10.1016/j.meegid.2008.09.006 URL
[14]	Liu M, Jiang W, Liu Y , et al. Increased genetic diversity of the Mycobacterium tuberculosis W-beijing genotype that predomi-nates in eastern China. Infect Genet Evol, 2014,22:23-29. doi: 10.1016/j.meegid.2013.12.023 URL
[15]	Hu Y, Mathema B, Zhao Q , et al. Comparison of the socio-demographic and clinical features of pulmonary TB patients infected with sub-lineages within the W-Beijing and non-Beijing Mycobacterium tuberculosis. Tuberculosis (Edinb), 2016,97:18-25. doi: 10.1016/j.tube.2015.11.007 URL
[16]	Maeda S, Wada T, Iwamoto T , et al. Beijing family Mycobacterium tuberculosis isolated from throughout Japan: phylogeny and genetic features. Int J Tuberc Lung Dis, 2010,14(9):1201-1204.
[17]	Chen YY, Chang JR, Huang WF , et al. The pattern of cytokine production in vitro induced by ancient and modern Beijing Mycobacterium tuberculosis strains. PLoS One, 2014,9(4):e94296. doi: 10.1371/journal.pone.0094296 URL
[18]	Ribeiro SC, Gomes LL, Amaral EP , et al. Mycobacterium tuberculosis strains of the modern sublineage of the Beijing family are more likely to display increased virulence than strains of the ancient sublineage. J Clin Microbiol, 2014,52(7):2615-2624. doi: 10.1128/JCM.00498-14 URL

北京基因型进化分支	RD片段				NTF区IS6110	菌株[株 (构成比,%)]
北京基因型进化分支	RD105	RD181	RD150	RD142	NTF区IS6110	菌株[株 (构成比,%)]
1	-	+	+	+	-	22(4.3)
2	-	-	+	+	-	41(7.9)
3	-	-	-	+	-	7(1.4)
4	-	-	+	+	+	404(78.1)
5	-	-	-	+	+	43(8.3)