GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data...

Area of Science:

• Microbiology
• Genomics
• Food Safety Science

Background:

• Whole genome sequence (WGS) data integration with epidemiological data can improve food safety risk assessments.
• Significant growth in WGS data collections (e.g., NCBI Pathogen Detection) highlights the need for effective data integration.
• Current limitations include the lack of coupling high-quality genomic data with robust epidemiological or food chain metadata.

Purpose of the Study:

• To develop and present a set of tools (GenomeGraphR) for cleaning, curation, integration, analysis, and visualization of microbial genome sequencing data.
• To enable querying of foodborne pathogen WGS data and associated metadata for research questions on transmission, dynamics, and persistence.
• To provide a user-friendly interface for exploring complex microbial genomic and epidemiological relationships.

Main Methods:

• Development of a suite of tools for data processing and analysis.
• Testing the tools using Salmonella enterica and Listeria monocytogenes datasets from NCBI Pathogen Detection (160,000 isolates).
• Implementation of a user-friendly interface for data visualization and querying.

Main Results:

• GenomeGraphR successfully integrates and analyzes microbial WGS data with curated metadata.
• The application allows users to explore transmission sources, dynamics, global reach, and genotype persistence.
• Demonstrated utility with large datasets of foodborne pathogens.

Conclusions:

• Effective integration of WGS data and metadata is crucial for advancing food safety.
• GenomeGraphR provides a valuable, accessible platform for analyzing foodborne pathogen genomic and epidemiological data.
• This tool supports research into contamination sources and foodborne illness dynamics, enhancing public health protection.