Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, 11221, Taiwan.
VYM Genome Research Center, National Yang-Ming University, Taipei, 11221, Taiwan.
Sci Rep. 2018 Oct 18;8(1):15365. doi: 10.1038/s41598-018-33702-6.
Rapid and accurate identification of pathogen is a major quarantine strategy for outbreak prevention. We used capillary electrophoresis-random amplified polymorphic DNA (CE-RAPD) to generate highly discriminatory pathogen profiles, reduced batch effects between profiles by novel normalization procedure and pattern of technical repeats, followed by target similarity evaluation using target identification score (TIS). A full target signature contains several patterns. TIS system was optimized by training set isolates that included three species, and validated using two hundred clinical Klebsiella pneumoniae isolates. Hierarchical clustering analysis showed CE-RAPD profiles arrange clusters according to the species or the source. Moreover, samples with similar profile may display similar antibiotic susceptibility. By using a signature of four patterns, the TIS system could accurately identify target among different isolates. The variation between isolates may be caused by small change in genome. TIS system provides a standardized tool for building of outbreak firewall and facilitate data exchange.
快速准确地鉴定病原体是暴发预防的主要检疫策略。我们使用毛细管电泳随机扩增多态性 DNA（CE-RAPD）生成高度区分病原体的图谱，通过新颖的标准化程序和技术重复模式来减少图谱之间的批次效应，然后使用目标识别评分（TIS）评估目标相似性。完整的目标特征包含多个模式。TIS 系统通过包括三个物种的训练集分离株进行优化，并使用两百株临床肺炎克雷伯菌分离株进行验证。层次聚类分析表明，CE-RAPD 图谱根据物种或来源排列聚类。此外，具有相似图谱的样本可能表现出相似的抗生素敏感性。通过使用四个模式的特征，TIS 系统可以准确识别不同分离株中的目标。分离株之间的变异可能是由于基因组的微小变化引起的。TIS 系统为建立暴发防火墙提供了标准化工具，并促进了数据交换。
