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A Novel Target Pathogen Identification and Tracking System Using Capillary Electrophoresis-Random Amplified
Wei-Ju Lin1, Chien-Yi Tung2, Muh-Yong Yen3,4
1Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, 11221, Taiwan.
Scientific Reports
|October 20, 2018
Summary
This study introduces a novel Target Identification Score (TIS) system using capillary electrophoresis-random amplified polymorphic DNA (CE-RAPD) for rapid pathogen identification. The TIS system accurately identifies pathogens, aiding in outbreak prevention and data exchange.
Area of Science:
- Microbiology and Molecular Biology
- Infectious Disease Epidemiology
- Bioinformatics and Computational Biology
Background:
- Rapid and accurate pathogen identification is crucial for preventing infectious disease outbreaks and implementing effective quarantine strategies.
- Existing methods may face challenges with batch effects and require standardized analytical tools for reliable data comparison.
- Genomic variations between pathogen isolates can influence their characteristics, including antibiotic susceptibility.
Purpose of the Study:
- To develop and validate a novel Target Identification Score (TIS) system for highly discriminatory pathogen profiling.
- To reduce technical variability and batch effects in molecular typing data using capillary electrophoresis-random amplified polymorphic DNA (CE-RAPD).
- To establish a standardized tool for accurate pathogen identification, outbreak surveillance, and facilitate inter-laboratory data exchange.
Main Methods:
- Utilized capillary electrophoresis-random amplified polymorphic DNA (CE-RAPD) to generate highly discriminatory genetic profiles of pathogens.
- Implemented a novel normalization procedure and analysis of technical repeats to minimize batch effects between CE-RAPD profiles.
- Developed and optimized the Target Identification Score (TIS) system using training isolates and validated it with 200 clinical *Klebsiella pneumoniae* isolates.
Main Results:
- CE-RAPD profiles generated highly discriminatory pathogen signatures.
- Hierarchical clustering analysis of CE-RAPD profiles demonstrated clear differentiation based on species or sample source.
- The TIS system, with a signature of four patterns, accurately identified target pathogens among different isolates, showing potential correlation between similar profiles and antibiotic susceptibility.
Conclusions:
- The developed TIS system provides a standardized and accurate method for pathogen identification, crucial for outbreak prevention.
- CE-RAPD combined with the TIS system offers a robust approach to analyzing genomic variations and facilitating outbreak surveillance.
- This standardized tool enhances the ability to build 'outbreak firewalls' and promotes seamless data exchange in infectious disease control.
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