Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases
Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases
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DOI：
10.1099/jmm.0.05365-0
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发表时间：
2004-01-01
影响因子：
3
通讯作者：
Giffard, PM
中科院分区：
文献类型：
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作者：
Robertson, GA;Thiruvenkataswamy, V;Giffard, PM
一种统一的、生物信息学驱动的、基于单核苷酸多态性(SNP)的微生物基因分型方法已经开发出来。多位点序列分型(MLST)数据库包括。已知的标准化家务基因变种。通常，定义七个片段；序列类型(ST)由在特定分离物中发现的这些片段的变体组成。已经建立了一个计算机程序，可以在整个MLST数据库中识别高度信息量的SNPs集。SNP或者定义了特定用户指定的ST，或者为Simpson的多样性指数(D)提供了较高的值，因此可以普遍适用于该物种。鉴定了对脑膜炎奈瑟菌ST-11和ST-42有诊断作用的SNP集，以及对脑膜炎奈瑟菌和金黄色葡萄球菌有诊断作用的高密度SNP集，并建立了实时荧光定量聚合酶链式反应方法。在其他MLST数据库中也发现了高D SNP集合。这一广泛应用的方法允许对感染性病原体进行快速遗传指纹分析。
A unified, bioinformatics-driven, single nucleotide polymorphism (SNP)-based approach to microbial genotyping has been developed. Multilocus sequence typing (MLST) databases consist of. known variants of standardized housekeeping genes. Normally, seven fragments are defined; a sequence type (ST) consists of the variants of these fragments that are found in a particular isolate. A computer program that can identify highly informative sets of SNPs in entire MLST databases has been constructed. The SNPs either define a particular user-specified ST or provide a high value for Simpson's index of diversity (D), and may thus be generally applicable to that species. SNP sets that are diagnostic for Neisseria meningitidis ST-11 and ST-42, and high-D SNP sets for N. meningitidis and Staphylococcus aureus, were identified and real-time PCR methods to interrogate these SNPs were demonstrated. High-D SNP sets were also identified in other MLST databases. This widely applicable approach allows rapid genetic fingerprinting of infectious agents.