Warren R M, Richardson M, Sampson S L, van der Spuy G D, Bourn W, Hauman J H, Heersma H, Hide W, Beyers N, van Helden P D
MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, University of Stellenbosch, PO Box 19063, Tygerberg, 7505, South Africa.
Tuberculosis (Edinb). 2001;81(4):291-302. doi: 10.1054/tube.2001.0300.
M. tuberculosis isolates were collected from patients attending health clinics in a high incidence urban community and in a low incidence rural setting in South Africa.
To reconstruct the evolutionary history of a group of closely related M. tuberculosis isolates using IS6110, DRr and MTB484(1) restriction fragment length polymorphism (RFLP) data.
Mycobacterium tuberculosis isolates containing an average of ten IS6110 elements, with a similarity index of > or = 65% were genotypically classified by DNA fingerprinting using the IS6110 derived probes IS-3' and IS-5', as well as the DRr and MTB484(1) probes, in combination with PvuII or Hinfl endonuclease digestion. These RFLP data were subjected to phylogenetic analysis using both genetic distance and parsimony algorithms.
Phylogenetic analysis predicted the existence of two independently evolving lineages, possibly evolving from a common ancestral strain. The topology of the phylogenetic tree was supported by comprehensive bootstrapping and the specific partitioning of DNA methylation phenotypes. The observed difference in the branch lengths of the two lineages may suggest differential evolutionary rates. Isolates collected from different geographical regions demonstrate independent evolution, suggesting that it is highly unlikely that strains have been recently transmitted between the two regions. The number of evolutionary events identified in this strain family differs significantly from that of previously characterized strain families, implying that evolutionary rate may be strain family dependent.
Based on this analysis we propose that the algorithm used to calculate recent epidemiological events should be revised to incorporate the evolutionary characteristics of individual strain families, thereby enhancing the accuracy of molecular epidemiological calculations.
结核分枝杆菌分离株取自南非一个城市高发病率社区和一个农村低发病率地区的卫生诊所就诊患者。
利用IS6110、DRr和MTB484(1)限制性片段长度多态性（RFLP）数据重建一组密切相关的结核分枝杆菌分离株的进化史。
对平均含有10个IS6110元件、相似性指数≥65%的结核分枝杆菌分离株，使用源自IS6110的探针IS-3'和IS-5'以及DRr和MTB484(1)探针，结合PvuII或Hinfl内切酶消化，通过DNA指纹图谱进行基因分型。这些RFLP数据使用遗传距离和简约算法进行系统发育分析。
系统发育分析预测存在两个独立进化的谱系，可能由一个共同的祖先菌株进化而来。系统发育树的拓扑结构得到了全面的自展检验和DNA甲基化表型的特定划分的支持。两个谱系分支长度的观察差异可能表明进化速率不同。从不同地理区域收集的分离株显示出独立进化，这表明菌株近期在两个区域之间传播的可能性极小。在这个菌株家族中鉴定出的进化事件数量与先前表征的菌株家族有显著差异，这意味着进化速率可能取决于菌株家族。
基于此分析，我们建议应修订用于计算近期流行病学事件的算法，以纳入各个菌株家族的进化特征，从而提高分子流行病学计算的准确性。
