eBURST: Inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data
eBURST: Inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data
复制标题
DOI：
10.1128/jb.186.5.1518-1530.2004
复制
发表时间：
2004-03-01
影响因子：
3.2
通讯作者：
Spratt, BG
中科院分区：
文献类型：
--
作者：
Feil, EJ;Li, BC;Spratt, BG
用于精确表征细菌病原体分离株的多位点序列分型（MLST）的引入对常规流行病学监测和微生物种群生物学产生了显着影响。在这两个领域，利用这一资源的一个关键先决条件是能够辨别具有相似基因型的分离株之间的相关性和进化下降模式。传统的聚类技术（例如树状图）对最近的进化事件的表示非常差，因为它们试图在缺乏细菌克隆出现和多样化以形成克隆复合体的方式的现实模型的情况下重建关系。一种越来越流行的方法，称为 BURST，已被用作替代方案，但目前的实现无法应对非常大的数据集并提供粗略的图形输出。在这里，我们提出了该算法的新实现，eBURST，它将任意大小的 MLST 数据集划分为相关分离株和克隆复合体组，预测每个克隆复合体的创始（祖先）基因型，并计算分配的引导支持。然后显示来自预测创建者的每个克隆复合体中所有分离株的最简约的血统模式。 eBURST 在探索进化血统模式方面的优势通过许多例子得到了证明，包括肺炎链球菌的简单的 Spain(23F)-1 克隆复合体、整个肺炎链球菌和金黄色葡萄球菌 MLST 数据库的“群体快照”，以及观察到的空肠弯曲菌和金黄色葡萄球菌的更复杂的克隆复合体。 脑膜炎奈瑟菌。
The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain(23F)-1 clonal complex of Streptococcus pneumoniae, "population snapshots" of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.