Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases
Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases
复制标题
DOI：
10.1016/j.annepidem.2005.04.010
复制
发表时间：
2006-03-01
影响因子：
5.6
通讯作者：
Barlow, M
中科院分区：
文献类型：
--
作者：
Hall, BG;Barlow, M
系统发生学是微生物流行病学的有力工具，但它是一种经常被该领域误用和误解的工具。微生物流行病学家警告说，为了对共同祖先的血统顺序进行任何推断，有必要正确地建立系统发育树。微生物种群的流行病学样本通常包括祖先及其后代。为了说明这些分离株之间的关系，所使用的系统发育方法必须能够检测到零长度分支。UPGMA法是微生物流行病学中应用最广泛的系统发育分析方法。因为UPGMA不能检测零长度分支，并且因为它基于通常错误的假设放置树根，所以UPGMA是可用的几种系统发育方法中最差的选择。由于微生物流行病学研究的是一个物种内菌株之间的关系，而不是物种之间的关系，这些物种内的重组可能使系统发育树毫无意义，并产生积极的误导。当有证据表明在感兴趣的物种内发生了重大重组时，根本不应该使用系统发育树。相反，应使用替代工具（如eBURST）来了解分离株之间的关系。
Phylogenetics is a powerful tool for microbial epidemiology, but it is a tool that is often misused and misinterpreted by the field. Microbial epidemiologists are cautioned that in order to draw any inferences about the order of descent from a common ancestor it is necessary to correctly root a phylogenetic tree. Epidemiological samples of microbial populations typically include both ancestors and their descendants. In order to illustrate the relationships of those isolates, the phylogenetic method used must be able to detect zero-length branches. Unweighted Pair-Group Method (UPGMA) is the phylogenetic method that is most widely used in microbial epidemiology. Because UPGMA cannot detect zero length branches, and because it places the root of the tree based on a usually-false assumption, UPGMA is the worst possible choice among the several phylogenetic methods available. Because microbial epidemiology deals with relationships among strains within a species, rather than with relationships among species, recombination within those species can render phylogenetic trees meaningless and positively misleading. When there is evidence of significant recombination within the species of interest phylogenetic trees should not be used at all. Instead, alternative tools such as eBURST should be used to understand relationships among isolates.