Grissa Ibtissem, Bouchon Patrick, Pourcel Christine, Vergnaud Gilles
Univ Paris-Sud, Institut de Génétique et Microbiologie, Orsay F-91405, France.
Biochimie. 2008 Apr;90(4):660-8. doi: 10.1016/j.biochi.2007.07.014. Epub 2007 Jul 28.
The control of bacterial pathogens requires the development of tools allowing the precise identification of strains at the subspecies level. It is now widely accepted that these tools will need to be DNA-based assays (in contrast to identification at the species level, where biochemical based assays are still widely used, even though very powerful 16S DNA sequence databases exist). Typing assays need to be cheap and amenable to the designing of international databases. The success of such subspecies typing tools will eventually be measured by the size of the associated reference databases accessible over the internet. Three methods have shown some potential in this direction, the so-called spoligotyping assay (Mycobacterium tuberculosis, 40,000 entries database), Multiple Loci Sequence Typing (MLST; up to a few thousands entries for the more than 20 bacterial species), and more recently Multiple Loci VNTR Analysis (MLVA; up to a few hundred entries, assays available for more than 20 pathogens). In the present report we will review the current status of the tools and resources we have developed along the past seven years to help in the setting-up or the use of MLVA assays or lately for analysing Clustered Regularly Interspaced Short Palindromic Repeats called CRISPRs which are the basis for spoligotyping assays.
对细菌病原体的控制需要开发能在亚种水平精确鉴定菌株的工具。现在人们普遍认为，这些工具将需要基于DNA的检测方法（与物种水平的鉴定不同，在物种水平，即使存在非常强大的16S DNA序列数据库，基于生化的检测方法仍被广泛使用）。分型检测方法需要成本低廉且便于设计国际数据库。此类亚种分型工具的成功最终将通过可通过互联网访问的相关参考数据库的规模来衡量。有三种方法在这个方向上显示出了一些潜力，即所谓的间隔寡核苷酸分型检测（结核分枝杆菌，40000条记录的数据库）、多位点序列分型（MLST；20多种细菌物种有多达数千条记录），以及最近的多位点可变数目串联重复序列分析（MLVA；多达数百条记录，有超过20种病原体的检测方法）。在本报告中，我们将回顾过去七年我们开发的工具和资源的现状，以帮助建立或使用MLVA检测方法，或者最近用于分析成簇规律间隔短回文重复序列（CRISPRs），这是间隔寡核苷酸分型检测的基础。
