Related Experiment Video
Updated: Jun 11, 2025
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
2.1K
Combined visualization of genomic and epidemiological data for outbreaks
Carl J E Suster1,2,3, Anne E Watt2,3,4, Qinning Wang1,4
1Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia.
Epidemiology and Infection
|September 30, 2024
Summary
Genomic epidemiology uses new visualizations to link pathogen evolution with disease spread. A novel
Area of Science:
- Epidemiology
- Genomics
- Bioinformatics
- Public Health
Background:
- Traditional epidemiology has limitations in integrating pathogen genomic data.
- Genomic epidemiology requires tools to synthesize molecular and epidemiological information.
- Existing visualization tools do not effectively link phylogenetic and epidemic timelines.
Purpose of the Study:
- To introduce a novel visualization, the 'phylepic' chart, for genomic epidemiology.
- To demonstrate the utility of the phylepic chart in outbreak investigations.
- To facilitate the integration of phylogenomic trees and epidemic curves.
Main Methods:
- Development of the 'phylepic' visualization combining phylogenomic trees and epidemic curves.
- Implementation of the visualization using an R package.
- Application of the chart to a foodborne bacterial outbreak case study.
Main Results:
- The phylepic chart successfully links molecular time from phylogenomic data to calendar time from epidemic data.
- Analysis of a foodborne outbreak revealed two distinct bacterial clades, challenging the point-source hypothesis.
- The visualization aids in understanding complex outbreak dynamics.
Conclusions:
- The phylepic visualization enhances the interpretation of genomic epidemiology data.
- Integrated genomic and epidemiological visualizations are crucial for effective outbreak investigations.
- This approach will advance public health surveillance of infectious diseases.
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