基于16S-23S rRNA基因内部转录间隔区序列对系统发育相关的缓慢生长分枝杆菌进行鉴别。
Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences.
作者信息
Roth A, Fischer M, Hamid M E, Michalke S, Ludwig W, Mauch H
机构信息
Institut für Mikrobiologie und Immunologie, Krankenhaus Zehlendorf, Berlin, Germany.
出版信息
J Clin Microbiol. 1998 Jan;36(1):139-47. doi: 10.1128/JCM.36.1.139-147.1998.
Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNA sequences, however, do not vary greatly within a species, and they are either indistinguishable in some species, for example, in Mycobacterium kansasii and M. gastri, or highly similar, for example, in M. malmoense and M. szulgai. We determined 16S-23S rDNA internal transcribed spacer (ITS) sequences of 60 strains in the genus Mycobacterium representing 13 species (M. avium, M. conspicuum, M. gastri, M. genavense, M. kansasii, M. malmoense, M. marinum, M. shimoidei, M. simiae, M. szulgai, M. triplex, M. ulcerans, and M. xenopi). An alignment of these sequences together with additional sequences available in the EMBL database (for M. intracellulare, M. phlei, M. smegmatis, and M. tuberculosis) was established according to primary- and secondary-structure similarities. Comparative sequence analysis applying different treeing methods grouped the strains into species-specific clusters with low sequence divergence between strains belonging to the same species (0 to 2%). The ITS-based tree topology only partially correlated to that based on 16S rDNA, but the main branching orders were preserved, notably, the division of fast-growing from slowly growing mycobacteria, separate branching for M. simiae, M. genavense, and M. triplex, and distinct branches for M. xenopi and M. shimoidei. Comparisons of M. gastri with M. kansasii and M. malmoense with M. szulgai revealed ITS sequence similarities of 93 and 88%, respectively. M. marinum and M. ulcerans possessed identical ITS sequences. Our results show that ITS sequencing represents a supplement to 16S rRNA gene sequences for the differentiation of closely related species. Slowly growing mycobacteria show a high sequence variation in the ITS; this variation has the potential to be used for the development of probes as a rapid approach to mycobacterial identification.
16S核糖体RNA基因（rDNA）的种间多态性被广泛用于分枝杆菌的菌种鉴定。然而，16S rDNA序列在一个物种内变化不大，在某些物种中无法区分，例如堪萨斯分枝杆菌和胃分枝杆菌，或者高度相似，例如马尔默分枝杆菌和苏尔加分枝杆菌。我们测定了分枝杆菌属中代表13个物种（鸟分枝杆菌、显著分枝杆菌、胃分枝杆菌、日内瓦分枝杆菌、堪萨斯分枝杆菌、马尔默分枝杆菌、海分枝杆菌、下田分枝杆菌、猿分枝杆菌、苏尔加分枝杆菌、三联分枝杆菌、溃疡分枝杆菌和非洲分枝杆菌）的60株菌株的16S - 23S rDNA内部转录间隔区（ITS）序列。根据一级和二级结构相似性，将这些序列与EMBL数据库中可用的其他序列（细胞内分枝杆菌、草分枝杆菌、耻垢分枝杆菌和结核分枝杆菌）进行比对。应用不同建树方法的比较序列分析将菌株分组为物种特异性簇，同一物种的菌株之间序列差异较小（0%至2%）。基于ITS的树形拓扑结构仅部分与基于16S rDNA的树形拓扑结构相关，但主要分支顺序得以保留，特别是快速生长分枝杆菌与缓慢生长分枝杆菌的区分、猿分枝杆菌、日内瓦分枝杆菌和三联分枝杆菌的单独分支，以及非洲分枝杆菌和下田分枝杆菌的不同分支。胃分枝杆菌与堪萨斯分枝杆菌以及马尔默分枝杆菌与苏尔加分枝杆菌的比较显示，ITS序列相似性分别为93%和88%。海分枝杆菌和溃疡分枝杆菌具有相同的ITS序列。我们的结果表明，ITS测序是对16S rRNA基因序列的补充，用于区分密切相关的物种。缓慢生长的分枝杆菌在ITS中表现出高度的序列变异；这种变异有可能用于开发探针，作为分枝杆菌鉴定的快速方法。
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