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    • Long-read sequencing data from pure cultures of <i>Escherichia coli</i> O157:H7 and ground beef inoculated with <i>E. coli</i> O157:H7

    Metadata Updated: April 21, 2025

    Foodborne pathogens are a significant cause of illness and infection with Shiga toxin-producing Escherichia coli (STEC) has the potential to produce life-threatening complications. The current methods to identify STEC in meat involve culture-based, molecular, and proteomic assays and take at least four days to complete. This time could be reduced by using long-read whole genome sequencing to identify foodborne pathogens. Therefore, the goal of this project was to evaluate using long-read sequencing to detect STEC in ground beef. The objectives of the project included: establishing optimal sequencing parameters, determining the limit of detection of all STEC virulence genes of interest in pure cultures and spiked ground beef, and evaluating selective sequencing to enhance STEC detection in ground beef. Sequencing libraries were run on Oxford Nanopore Technologies’ MinION sequencer. Optimal sequencing output was obtained using the default parameters in MinKNOW, except for setting the minimum read length to 1 kb. All genes of interest (eae, stx1, stx2, fliC, wzx, wzy, rrsC) were detected in DNA extracted from STEC pure cultures within 1 hour of sequencing, and 30X coverage was obtained within 2 hours. All virulence genes were confidently detected in STEC DNA quantities as low as 12.5 ng. In STEC inoculated ground beef, software-controlled selective sequencing improved virulence gene detection; however, several virulence genes were not detected due to high bovine DNA concentrations in the samples. Growth enrichment of inoculated meat samples in mTSB resulted in a 100-fold increase in virulence gene detection as compared to the unenriched samples. The results of this project suggest that further development of long-read sequencing protocols may result in a faster, less labor-intensive method to detect STEC in ground beef. The sequencing data from this project has been uploaded.

    Access & Use Information

    Public: This dataset is intended for public access and use. License: us-pd

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    Dates

    Metadata Created Date March 30, 2024
    Metadata Updated Date April 21, 2025

    Metadata Source

    Harvested from USDA JSON

    Other Data Resources

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date March 30, 2024
    Metadata Updated Date April 21, 2025
    Publisher Agricultural Research Service
    Maintainer
    Identifier 10.15482/USDA.ADC/25164449.v1
    Data Last Modified 2024-03-21
    Public Access Level public
    Bureau Code 005:18
    Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
    Schema Version https://project-open-data.cio.gov/v1.1/schema
    Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
    Harvest Object Id 510b492a-bab5-4307-96d9-abb83a805971
    Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
    Harvest Source Title USDA JSON
    License https://www.usa.gov/publicdomain/label/1.0/
    Program Code 005:040
    Source Datajson Identifier True
    Source Hash 912ee19c84139c6bc36e6fa20ce4cae7d035b6f5ea3061c488e119401f4a5d0c
    Source Schema Version 1.1
    Temporal 2022-05-03/2023-12-15

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