Genomic Surveillance of Foodborne Pathogens: Advances and Obstacles

Area of Science:

• Foodborne pathogen genomics
• Public health microbiology
• Genomic epidemiology

Background:

• Genomic surveillance of foodborne pathogens has rapidly advanced in the U.S. due to new technologies and data networks.
• This has improved the ability to link isolates and identify outbreak sources for timely public health interventions.

Purpose of the Study:

• To review advances in genomic epidemiology for food safety over the past decade.
• To identify obstacles in implementing these technologies within public health systems.

Main Methods:

• Analysis of national pathogen genome databases and data-sharing networks (e.g., GenomeTrakr, PulseNet).
• Evaluation of bioinformatics tools (e.g., GalaxyTrakr, NCBI Pathogen Detection) enabling broader lab participation.
• Examination of implementation challenges in State, Tribal, Local, and Territorial public health systems.

Main Results:

• Genomic surveillance demonstrates a clear return on investment for public health.
• Significant obstacles include workforce shortages, inadequate data sharing, and insufficient sustained funding.

Conclusions:

• Widespread adoption of genomic surveillance technologies in public health labs faces challenges.
• Integrating whole genome sequencing into existing workflows and information systems remains difficult.
• Centralized support, training, standardized protocols, and open-access software are crucial for progress.