Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
PLoS One. 2011;6(9):e24737. doi: 10.1371/journal.pone.0024737. Epub 2011 Sep 13.
Mycobacterium tuberculosis has a global population structure consisting of six main phylogenetic lineages associated with specific geographic regions and human populations. One particular M. tuberculosis genotype known as "Beijing" has repeatedly been associated with drug resistance and has been emerging in some parts of the world. "Beijing" strains are traditionally defined based on a characteristic spoligotyping pattern. We used three alternative genotyping techniques to revisit the phylogenetic classification of M. tuberculosis complex (MTBC) strains exhibiting the typical "Beijing" spoligotyping pattern.
MTBC strains were obtained from an ongoing molecular epidemiological study in Switzerland and Nepal. MTBC genotyping was performed based on SNPs, genomic deletions, and 24-loci MIRU-VNTR. We identified three MTBC strains from patients originating from Tibet, Portugal and Nepal which exhibited a spoligotyping patterns identical to the classical Beijing signature. However, based on three alternative molecular markers, these strains were assigned to Lineage 3 (also known as Delhi/CAS) rather than to Lineage 2 (also known as East-Asian lineage). Sequencing of the RD207 in one of these strains showed that the deletion responsible for this "Pseudo-Beijing" spoligotype was about 1,000 base pairs smaller than the usual deletion of RD207 in classical "Beijing" strains, which is consistent with an evolutionarily independent deletion event in the direct repeat (DR) region of MTBC.
We provide an example of convergent evolution in the DR locus of MTBC, and highlight the limitation of using spoligotypes for strain classification. Our results indicate that a proportion of "Beijing" strains may have been misclassified in the past. Markers that are more phylogenetically robust should be used when exploring strain-specific differences in experimental or clinical phenotypes.
结核分枝杆菌具有全球种群结构，由六个主要的系统发育谱系组成，与特定的地理区域和人类群体相关。一种称为“北京”的特定结核分枝杆菌基因型与耐药性反复相关，并在世界上的一些地区出现。“北京”菌株传统上是根据特征性 spoligotyping 模式来定义的。我们使用三种替代的基因分型技术来重新审视表现出典型“北京” spoligotyping 模式的结核分枝杆菌复合群（MTBC）菌株的系统发育分类。
MTBC 菌株来自瑞士和尼泊尔正在进行的分子流行病学研究。根据单核苷酸多态性、基因组缺失和 24 个位点 MIRU-VNTR 对 MTBC 进行基因分型。我们从来自西藏、葡萄牙和尼泊尔的患者中鉴定出三株 MTBC 菌株，其 spoligotyping 模式与经典的北京特征相同。然而，基于三种替代的分子标记，这些菌株被分配到谱系 3（也称为德里/卡斯）而不是谱系 2（也称为东亚谱系）。对其中一株菌的 RD207 进行测序表明，导致这种“假北京” spoligotype 的缺失大约比经典“北京”菌株中 RD207 的常见缺失小 1000 个碱基对，这与 MTBC 直接重复（DR）区域中独立发生的缺失事件一致。
我们提供了 MTBC DR 基因座中趋同进化的一个例子，并强调了 spoligotypes 用于菌株分类的局限性。我们的结果表明，过去可能有一部分“北京”菌株被错误分类。在探索实验或临床表型中的菌株特异性差异时，应使用更具系统发育稳健性的标记。
