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Data from: Enumeration and genomic confirmation of viable Shiga-toxin-producing <i>Escherichia coli </i>from ground beef by integrating serial plating with long-read sequencing

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: August 01, 2026 at 04:50 AM | Dataset Last Updated: June 01, 2026
Consumption of food contaminated with Shiga toxin-producing Escherichia coli (STEC) causes millions of illnesses in the United States annually. Long-read sequencing could be used to reduce the time needed to test food for STEC, but sequencing is not quantitative and cannot differentiate between live and dead bacteria. Therefore, this study investigated combining serial plating with long-read sequencing to quantify only live STEC in a sample. Ground beef was inoculated with STEC and stomached. The liquid was filtered to remove eukaryotic cells and then centrifuged to pellet the bacteria. Serial dilutions of the pellet were plated on selective agar and then single colonies were selected for sequencing. During initial experiments where sample processing was conducted at room temperature, a 1 log increase in STEC concentration from the initial inoculated amount was observed. Subsequent experiments kept samples and reagents cold, and the amount of STEC recovered did not significantly differ from the amount inoculated. The DNA extracted from a single colony provided enough data to identify all virulence genes of interest multiple times. The amount of STEC in a sample could be quantified down to 1 cfu g-1. The ability of this method to quantify STEC in samples would improve risk assessment and guide mitigation in industry.

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Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
[
  "005:18"
]
contactPoint 
{
  "fn": "Counihan, Katrina, L.",
  "hasEmail": "mailto:katrina.counihan@usda.gov"
}
description <p dir="ltr">Consumption of food contaminated with Shiga toxin-producing <i>Escherichia coli</i> (STEC) causes millions of illnesses in the United States annually. Long-read sequencing could be used to reduce the time needed to test food for STEC, but sequencing is not quantitative and cannot differentiate between live and dead bacteria. Therefore, this study investigated combining serial plating with long-read sequencing to quantify only live STEC in a sample. Ground beef was inoculated with STEC and stomached. The liquid was filtered to remove eukaryotic cells and then centrifuged to pellet the bacteria. Serial dilutions of the pellet were plated on selective agar and then single colonies were selected for sequencing. During initial experiments where sample processing was conducted at room temperature, a 1 log increase in STEC concentration from the initial inoculated amount was observed. Subsequent experiments kept samples and reagents cold, and the amount of STEC recovered did not significantly differ from the amount inoculated. The DNA extracted from a single colony provided enough data to identify all virulence genes of interest multiple times. The amount of STEC in a sample could be quantified down to 1 cfu g<sup>-1</sup>. The ability of this method to quantify STEC in samples would improve risk assessment and guide mitigation in industry.</p>
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identifier 10.15482/USDA.ADC/31258642.v2
keyword 
[
  "Escherichia coli O157:H7",
  "Idenfication",
  "bioinformatics",
  "enumeration",
  "food safety",
  "long-read sequencing",
  "serial plating",
  "single colony"
]
license https://creativecommons.org/publicdomain/zero/1.0/
modified 2026-06-01
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2024-01-16/2025-01-07
title Data from: Enumeration and genomic confirmation of viable Shiga-toxin-producing <i>Escherichia coli </i>from ground beef by integrating serial plating with long-read sequencing

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