A Novel Target Pathogen Identification and Tracking System Using Capillary Electrophoresis-Random Amplified Polymorphic DNA

Wei Ju Lin, Chien Yi Tung, Muh Yong Yen, Yu Jiun Chan, Chi Hung Lin*, Po Ren Hsueh

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

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.

Original languageEnglish
Article number15365
JournalScientific reports
Volume8
Issue number1
DOIs
StatePublished - 1 Dec 2018

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