Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade
Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade
复制标题
DOI：
10.1371/journal.pone.0052841
复制
发表时间：
2012-12-27
期刊：
影响因子：
3.7
通讯作者：
Vergnaud, Gilles
中科院分区：
文献类型：
--
作者：
Blouin, Yann;Hauck, Yolande;Vergnaud, Gilles
分子生物学和地理学的研究已经导致结核分枝杆菌复合群（MTBC）内的一些地理型和生态型的定义，显示出优先的地理位置或宿主偏好。MTBC被认为出现在非洲，最有可能是非洲之角，并随着人类迁徙而传播到世界各地。在这种假设下，有一种可能性，未知的深分支谱系存在于该地区。我们通过spoligotyping和多位点可变数目串联重复序列（VNTR）分析（MLVA）对435例从患者中回收的MTBC分离株进行基因分型。在吉布提共和国收集了411个分离株超过12年的时间，与其他24个分离株来自邻国。都是M少校结核谱系，只有两个M。africanum和M.牛分离物。与世界各地的分型数据进行比较后，我们观察到，几个菌株表现出聚类特征与新的深分支兼容。七个分离株的全基因组测序（WGS）和与来自分布在不同谱系中的38个基因组的可用WGS数据的比较证实了几个进化枝的祖先节点的鉴定，最重要的是一个新的谱系，这里称为谱系7。特定缺失的调查证实了这一谱系的新奇，其精确的系统发育位置的分析表明，构成MTBC的其他三个超谱系独立出现，但在相对较短的时间内从非洲之角。与主要谱系相比，这些菌株的可用性和共享非常古老的祖先将为确定现代谱系成功的一些遗传因素开辟新的途径。通过对撒哈拉以南非洲国家的分离株进行大规模MLVA筛选，然后对一些选定的分离株进行WGS分析，可以容易且有效地鉴定其他深分支谱系。
Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.