Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing
Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing
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DOI：
10.1099/mic.0.035188-0
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发表时间：
2010-04-01
期刊：
影响因子：
2.8
通讯作者：
Hu, Fen Z.
中科院分区：
文献类型：
--
作者：
Hall, Barry G.;Ehrlich, Garth D.;Hu, Fen Z.
目前应用最广泛的基于dna的细菌分型方法——多位点序列分型（MLST）缺乏足够的分辨率来区分一个物种内的许多细菌菌株。在这里，我们展示了基于分布基因存在与否的菌株分型能够解析六种细菌物种的所有完全测序基因组。这是通过开发一种聚类方法，邻居分组来实现的，该方法与低分辨率的MLST方法完全一致，但提供了更大的分辨率。由于分布式基因的存在/缺失可以通过低成本的微阵列分析来确定，因此它提供了一种实用的、高分辨率的MLST替代方案，可以为致病菌种类提供有价值的诊断和预后信息。
The most widely used DNA-based method for bacterial strain typing, multi-locus sequence typing (MLST), lacks sufficient resolution to distinguish among many bacterial strains within a species. Here, we show that strain typing based on the presence or absence of distributed genes is able to resolve all completely sequenced genomes of six bacterial species. This was accomplished by the development of a clustering method, neighbour grouping, which is completely consistent with the lower-resolution MLST method, but provides far greater resolving power. Because the presence/absence of distributed genes can be determined by low-cost microarray analyses, it offers a practical, high-resolution alternative to MLST that could provide valuable diagnostic and prognostic information for pathogenic bacterial species.