Fighting outbreaks with bacterial genomics: case review and workflow proposal

Area of Science:

• Microbiology
• Genomics
• Public Health

Background:

• Whole-genome sequencing (WGS) is increasingly used for bacterial pathogen analysis in public health.
• High-throughput sequencing technologies have made WGS more accessible for outbreak investigations.
• A gap exists in efficient and adequate systems for analyzing WGS data during bacterial outbreaks.

Purpose of the Study:

• To review current genomic investigation practices during bacterial outbreaks.
• To assess available bioinformatics tools for genomic analysis in this context.
• To propose a systematic analytical workflow for WGS data in outbreak investigations.

Main Methods:

• Literature review of recent bacterial outbreak genomic investigations.
• Review of existing bioinformatics tools for pathogen genome analysis.

Main Results:

• Genomic investigations provide timely insights into pathogen evolution, transmission, and virulence.
• WGS enables the development of strain-specific typing methods.
• A novel systematic genomic analytical workflow is proposed for efficient data extraction.

Conclusions:

• Decreasing sequencing costs and improving analytical tools will drive routine WGS application.
• The proposed workflow aims to facilitate timely genomic analysis in future bacterial outbreaks.
• WGS is expected to become a standard tool for rapid genomic analysis in public health surveillance.