CFIA Whole Genome Sequences for Foodborne Pathogens

Over 5 bacterial species, including Salmonella and E. coli, have their genome sequences cataloged by the Canadian Food Inspection Agency. This data originates from isolates collected from food, animal feed, fertilizer, and environmental samples. The dataset was last updated in April 2026.

Use Cases

• Identify outbreak clusters by comparing pathogen genome_sequence data across isolation sources.
• Predict bacterial species or serotype from genomic features using machine learning models.
• Analyze antimicrobial resistance gene presence in strains isolated from different food types.
• Track geographic and temporal trends in pathogen subtypes like Listeria monocytogenes lineages.

Strengths

• Includes genomic data for 5 major foodborne pathogen genera.
• Data is sourced from a national regulatory agency with standardized collection protocols.
• Last update was in April 2026, indicating recent maintenance.

Limitations

• The exact number of sequenced strains or rows is unknown.
• Sample metadata like collection date or geographic location may be incomplete or absent.
• Links to external sequence repositories may have inconsistent data formats or accessibility.

Provenance

Source

Canadian Food Inspection Agency (CFIA).

Collection Method

Isolated from food, animal feed, fertilizer, and environmental samples, followed by whole genome sequencing.

Freshness

Updated April 2026.

Geography

Canada.