Viable Shiga-Toxin-Producing E. Coli Genomic Data from Ground Beef Experiments

A 28.6 GB dataset from a 2026 study investigating a method to quantify live Shiga-toxin-producing Escherichia coli (STEC) in ground beef. The research, authored by Katrina Counihan, combined serial plating with long-read sequencing to identify virulence genes and quantify STEC down to 1 colony-forming unit per gram. Data files are in POD5 and GZ formats, representing raw sequencing outputs from single bacterial colonies.

Use Cases

• Benchmarking genomic confirmation methods for foodborne pathogens based on the described long-read sequencing protocol.
• Developing models for STEC quantification in food matrices based on the described serial plating and colony sequencing approach.
• Studying the genomic features and virulence gene presence in STEC isolates recovered from inoculated ground beef samples.

Strengths

• Dataset size is 28.6 GB, indicating substantial raw sequencing data.
• Method described achieved quantification sensitivity down to 1 colony-forming unit per gram of ground beef.
• Data is released under a permissive CC0-1.0 license, allowing for broad reuse.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• The experimental data is derived from controlled inoculations, which may not fully represent natural contamination scenarios.

Provenance

Source

figshare, authored by Katrina Counihan.

Collection Method

Generated by inoculating ground beef with STEC, processing via filtration and centrifugation, performing serial dilutions and plating on selective agar, and sequencing DNA from single colonies.

Freshness

Last updated 2026-06-01 19:11:17; freshness should be verified.