Converting from bioedit to mega1/3/2023 ![]() ![]() Implementation of these analytic tools can be complex and fraught with technical and administrative barriers. The burgeoning field of public health bioinformatics has given rise to a plethora of specialized software for analysis and visualization of pathogen genomic data to aid outbreak investigations. We provide real world examples of how MicrobeTrace has been used in public health, including COVID outbreak investigations. MicrobeTrace can be used offline, with analyses being performed locally in the field, ensuring secure and confidential use of personally identifiable information (PII). MicrobeTrace is an easy to use browser-based tool which can effectively merge contact tracing and/or microbial genomic data with demographic or behavioral information, resulting in elegant and informative networks as well as multiple customizable visualizations. We bridge this knowledge gap by development of an intuitive, standalone tool called MicrobeTrace to securely integrate, visualize and explore pathogen epidemiologic data. However, the need for specialized computer skills often impedes the use of many of these tools in the public heath domain. Rapid advances in the fields of data science and bioinformatics have significantly improved molecular epidemiology tools used in public health and have led to major changes in the way outbreak investigation and pathogen transmission studies are conducted. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. 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. 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. ![]() MicrobeTrace is a web-based, client-side, JavaScript application ( ) that runs in Chromium-based browsers and remains fully operational without an internet connection. We developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. ![]()
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