Data from: Distinguishing a live-attenuated Salmonella Typhimurium vaccine strain from native Salmonella Typhimurium strains using whole-cell MALDI-TOF mass spectrometry

Live-attenuated vaccines are an effective pre-harvest intervention to reduce Salmonella colonization in food animals, but vaccine strains can persist through production and be detected on food products. Accurate identification of vaccine strains is important to ensure poultry processing facilities are not penalized by regulatory agencies for using live-attenuated vaccines. Here, in a proof-of-concept study, we evaluated whole-cell matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry as a rapid, cost-effective alternative to whole genome sequencing for distinguishing native Salmonella enterica serovar Typhimurium strains from AviPro Megan Vac 1, a live-attenuated vaccine strain of Salmonella Typhimurium commonly used in poultry production. Despite their close phylogenetic relationship, MALDI-TOF spectral profiles of Megan Vac 1 isolates were distinct from those of native Salmonella Typhimurium strains. Temporal drift was identified as the main source of spectral variation in Megan Vac 1 isolates, exceeding the effects of sample preparation method. Random forest classifiers trained on a subset of peaks demonstrated a maximum balanced accuracy of 97.4% on a test set of spectra collected at later time points. A rule-based decision tree based on intensities from a single peak at 6046 m/z retained high predictive performance, achieving 97.0% balanced accuracy, 97.8% sensitivity, and 96.2% specificity. These findings indicate that MADLI-TOF mass spectrometry is a promising alternative to whole genome sequencing for identifying vaccine strains. This approach enhances the efficacy of regulatory performance assessments and supports the continued use of effective pre-harvest vaccination strategies, ultimately benefiting food safety and public health.

[
  "005:18"
]

{
  "fn": "Anderson, Christopher, L.",
  "hasEmail": "mailto:christopher.anderson2@usda.gov"
}

[
  {
    "@type": "dcat:Distribution",
    "title": "salmonella_typhimurium_spectra.zip",
    "format": "zip",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/67410990"
  }
]

[
  "MALDI-TOF MS analyses",
  "Salmonella Typhimurium"
]

[
  "005:040"
]

{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}