MicrobeTrace: Retooling molecular epidemiology for rapid public health response

摘要

Outbreak investigations use data from interviews, healthcare providers, laboratories andsurveillance systems. However, integrated use of data from multiple sources requires apatchwork of software that present challenges in usability, interoperability, confidentiality,and cost. Rapid integration, visualization and analysis of data from multiple sources canguide effective public health interventions. We developed MicrobeTrace to facilitate rapidpublic health responses by overcoming barriers to data integration and exploration in molec ular epidemiology. MicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully operationalwithout an internet connection. Using publicly available data, we demonstrate the analysisof viral genetic distance networks and introduce a novel approach to minimum spanningtrees that simplifies results. We also illustrate the potential utility of MicrobeTrace in supportof contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 inSouth 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.