Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis:: Insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set
Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis:: Insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set
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DOI：
10.1128/jb.188.2.759-772.2006
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发表时间：
2006-01-01
影响因子：
3.2
通讯作者：
Alland, D
中科院分区：
文献类型：
--
作者：
Filliol, I;Motiwala, AS;Alland, D
我们使用212个单核苷酸多态性（SNP）标记分析了全球结核分枝杆菌菌株。SNP核苷酸多样性高（所有SNP的平均值为0.19），96%的SNP位点对处于完全连锁不平衡。聚类分析确定了六个深分支，遗传学上不同的SNP簇组（SCG）和五个亚组。SCG与M的地理来源密切相关。结核病样本和人类宿主的出生地。来自印度次大陆的患者中最古老的簇（SCG-1）占主导地位，而来自东亚的患者中SCG-1和另一个祖先簇（SCG-2）占主导地位，这表明M.结核病首先出现在印度次大陆，并通过东亚传播到全世界。在乌干达和墨西哥的土著人群中，SCG多样性有限，祖先较少的SCG普遍存在，这表明M.肺结核进入这些地区。东非印度和北京的spoligotypes与SCG-1和SCG-2，分别一致; X和中亚spoligotypes也与一个SCG或亚组组合。其他分支与SCG的关联不太一致。分枝杆菌散在重复单位（MIRU）分析提供了不太强大的系统发育信息，只有6的12个MIRU微卫星位点之间的SCG（ST）测量高度分化。最后，设计了一种算法，以确定两个最小集的45或6个SNPs，可用于未来的调查，使全球合作的进化，菌株分化和生物学差异的研究M。结核
We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of the M. tuberculosis samples and the birthplace of the human hosts. The most ancestral cluster (SCG-1) predominated in patients from the Indian subcontinent, while SCG-1 and another ancestral cluster (SCG-2) predominated in patients from East Asia, suggesting that M. tuberculosis first arose in the Indian subcontinent and spread worldwide through East Asia. Restricted SCG diversity and the prevalence of less ancestral SCGs in indigenous populations in Uganda and Mexico suggested a more recent introduction of M. tuberculosis into these regions. The East African Indian and Beijing spoligotypes were concordant with SCG-1 and SCG-2, respectively; X and Central Asian spoligotypes were also associated with one SCG or subgroup combination. Other clades had less consistent associations with SCGs. Mycobacterial interspersed repetitive unit (MIRU) analysis provided less robust phylogenetic information, and only 6 of the 12 MIRU microsatellite loci were highly differentiated between SCGs as measured by G(ST). Finally, an algorithm was devised to identify two minimal sets of either 45 or 6 SNPs that could be used in future investigations to enable global collaborations for studies on evolution, strain differentiation, and biological differences of M. tuberculosis.