MicrobeTrace 2.0: the enhanced visualization multitool for molecular epidemiology and bioinformatics

Area of Science:

• Bioinformatics
• Genomic Epidemiology
• Public Health

Background:

• MicrobeTrace is a widely used, free, secure bioinformatics tool for integrating and visualizing outbreak investigation data.
• Over 14,000 users across 127 countries rely on MicrobeTrace.
• User feedback and testing identified needs for architectural and functional improvements.

Purpose of the Study:

• To present the major upgrades in MicrobeTrace 2.0, focusing on architectural and functional enhancements.
• To improve scalability, performance, and usability for outbreak investigations.
• To enhance integration capabilities with external phylogenetic analysis tools.

Main Methods:

• Refactored the codebase using Angular for improved performance and scalability.
• Replaced the D3.js visualization engine with Cytoscape.js for efficient rendering of large networks.
• Integrated support for external phylogenetic platforms like Nextstrain and UShER.

Main Results:

• MicrobeTrace 2.0 features enhanced visualizations and new analytical tools.
• The tool now supports seamless import and visualization of phylogenetic trees.
• Users can enrich imported phylogenetic data with epidemiological and demographic metadata.

Conclusions:

• MicrobeTrace 2.0 is a significantly improved, next-generation tool for genomic epidemiology.
• The enhancements position MicrobeTrace as a key interoperable platform for data-driven public health response.
• The tool facilitates a more comprehensive analysis of infectious disease outbreaks.