Gen-FS coordinated proficiency test data for genomic foodborne pathogen surveillance, 2017 and 2018 exercises

Area of Science:

• Food safety
• Genomics
• Microbiology

Background:

• The US PulseNet and GenomeTrakr networks are key players in foodborne pathogen surveillance.
• Genomics for Food Safety (Gen-FS) consortium facilitates collaboration between these networks.
• Harmonization of genomic data collection and analysis is crucial for effective surveillance.

Purpose of the Study:

• To release reference genomes and raw data from harmonized proficiency testing exercises.
• To support the collaborative efforts of PulseNet and GenomeTrakr within the Gen-FS consortium.
• To enhance the accuracy and comparability of genomic data for foodborne pathogen surveillance.

Main Methods:

• Harmonization of proficiency test exercises between PulseNet and GenomeTrakr starting in 2017.
• Agreement on a single strain-set for proficiency testing.
• Adoption of a standardized operating procedure (SOP) for genomic data collection.

Main Results:

• Successful joint coordination of annual proficiency test exercises in 2017 and 2018.
• Publication of reference genomes from these exercises.
• Availability of raw data submissions for the 2017 and 2018 proficiency tests.

Conclusions:

• The harmonization of proficiency tests strengthens collaborative foodborne pathogen surveillance.
• The released genomic data provides valuable resources for research and public health.
• Standardized methods improve the reliability of genomic surveillance data.