MicrobeTrace: Retooling molecular epidemiology for rapid public health response

Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration,...

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Bibliographic Details
Published in:PLoS computational biology 2021-09, Vol.17 (9), p.e1009300-e1009300
Main Authors: Campbell, Ellsworth M, Boyles, Anthony, Shankar, Anupama, Kim, Jay, Knyazev, Sergey, Cintron, Roxana, Switzer, William M
Format: Article
Language:English
Subjects:
Bioinformatics
Biology and Life Sciences
Chromium
Computer and Information Sciences
Contact tracing
Cost analysis
Data analysis
Data integration
Disease control
Drug resistance
Electronic data processing
End users
Engineering and Technology
Epidemics
Epidemiology
Genetic analysis
Genetic distance
Graph theory
Health care
Integration
Interoperability
Java (programming language)
Medical research
Medicine and Health Sciences
Medicine, Experimental
Metadata
Methods
Outbreaks
Pathogens
Public health
Research and Analysis Methods
Seminars
Severe acute respiratory syndrome coronavirus 2
Software
Source code
Surveillance systems
Technology application
United States
Viral diseases
Web applications
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Summary:Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. We developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. MicrobeTrace is a web-based, client-side, JavaScript application ( https://microbetrace.cdc.gov ) that runs in Chromium-based browsers and remains fully operational without an internet connection. Using publicly available data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. Users can email microbetrace@cdc.gov for support. The source code is available at https://github.com/cdcgov/microbetrace .
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1009300