Comparative assessment of genotyping methods for epidemiologic study of Burkholderia cepacia genomovar III
Comparative assessment of genotyping methods for epidemiologic study of Burkholderia cepacia genomovar III
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DOI：
10.1128/jcm.40.9.3300-3307.2002
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发表时间：
2002-09-01
影响因子：
9.4
通讯作者：
LiPuma, JJ
中科院分区：
文献类型：
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作者：
Coenye, T;Spilker, T;LiPuma, JJ
我们分析了收集的97个良好的特点洋葱伯克霍尔德菌基因型III菌株，以评估多个基因组分型系统，包括脉冲场凝胶电泳（PFGE），BOX-PCR指纹图谱和随机扩增多态性DNA（RAPD）分型。对这些技术的可分型性、再现性和辨别力进行了评价，并将结果相互比较，并与使用多位点限制性分型（MLRT）在以前的研究中获得的数据进行比较。所有方法均表现出良好的可分型性。与RAPD和BOX-PCR指纹相比，SpeI的PFGE具有更高的重复性。方法的区分能力是可变的，PFGE和RAPD分型具有较高的区分指数比BOX-PCR指纹。总体而言，PFGE、BOX-PCR指纹图谱和MLRT获得的结果一致。我们的数据表明，不同的基因组为基础的方法，可用于A型洋葱genomovar III分离株取决于情况和流行病学问题正在解决。PFGE和RAPD指纹图谱最适合于解决小规模研究（即，本地流行病学），而BOX-PCR指纹分析更适合于大规模研究（即，全球流行病学）。在这方面，BOX-PCR指纹图谱可以被认为是MLRT的快速和简单的替代方法。
We analyzed a collection of 97 well-characterized Burkholderia cepacia genomovar III isolates to evaluate multiple genomic typing systems, including pulsed-field gel electrophoresis (PFGE), BOX-PCR fingerprinting and random amplified polymorphic DNA (RAPD) typing. The typeability, reproducibility, and discriminatory power of these techniques were evaluated, and the results were compared to each other and to data obtained in previous studies by using multilocus restriction typing (MLRT). All methods showed excellent typeability. PFGE with SpeI was more reproducible than RAPD and BOX-PCR fingerprinting. The discriminatory power of the methods was variable, with PFGE and RAPD typing having a higher index of discrimination than BOX-PCR fingerprinting. In general, the results obtained by PFGE, BOX-PCR fingerprinting, and MLRT were in good agreement. Our data indicate that different genomic-based methods can be used to type A cepacia genomovar III isolates depending on the situation and the epidemiologic question being addressed. PFGE and RAPD fingerprinting are best suited to addressing small-scale studies (i.e., local epidemiology), whereas BOX-PCR fingerprinting is more appropriate for large-scale studies (i.e., global epidemiology). In this regard, BOX-PCR fingerprinting can be considered a rapid and easy alternative to MLRT.