Comparative Assessment of Genotyping Methods for Epidemiologic Study of Burkholderia cepacia Genomovar III

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 B. 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.

本研究对97株经过充分表征的洋葱伯克霍尔德氏菌（Burkholderia cepacia）基因组群III分离株进行分析，以评估多种基因组分型技术，包括脉冲场凝胶电泳（pulsed-field gel electrophoresis, PFGE）、BOX-PCR指纹图谱技术以及随机扩增多态性DNA（random amplified polymorphic DNA, RAPD）分型。本研究对上述技术的可分型率、重复性与区分能力进行了评估，并将所得结果相互比较，同时与此前研究中采用多位点限制性片段分型（multilocus restriction typing, MLRT）获得的数据进行对比。所有检测方法均展现出优异的可分型率。采用SpeI酶切的PFGE技术，其重复性优于RAPD分型与BOX-PCR指纹图谱技术。各技术的区分能力存在差异：PFGE与RAPD分型的区分指数高于BOX-PCR指纹图谱技术。总体而言，PFGE、BOX-PCR指纹图谱与MLRT所获得的结果一致性良好。本研究数据表明，针对洋葱伯克霍尔德氏菌基因组群III分离株的基因组分型，可根据实际场景与待解决的流行病学问题选择不同的技术方案。PFGE与RAPD分型技术最适用于小规模研究（如局部流行病学调查），而BOX-PCR指纹图谱技术则更适合大规模研究（如全球流行病学调研）。就此而言，BOX-PCR指纹图谱技术可被视为MLRT的一种快速便捷的替代方案。