{
  "abstract": "Background: Barcoding of isogenic strains is a powerful approach to assess pathogen population dynamics during infection. Here, we adapted WISH-barcoding to Salmonella Typhimurium ATCC14028s to evaluate its suitability for pooled infection experiments in streptomycin-pretreated mouse models. Results: WISH-barcoded wild-type pools showed pronounced population instability, characterized by reproducible strain loss and segregation into high- and low-fitness subpopulations. Whole-genome sequencing identified recurrent mutations in the methyltransferase gene rsmG and loss of the P3 plasmid carrying streptomycin resistance in low-fitness strains; neither was observed in ΔinvG or ΔssaV pools. We propose that rsmG mutations were enriched during strain construction carried out under streptomycin selection, following loss of the P3 plasmid. Control experiments demonstrated that rsmG mutations and P3 loss are counter-selected in vivo and attenuate gut-luminal colonization in streptomycin-pretreated mice. Conclusion: While population dynamics experiments with ATCC14028s are feasible in principle, wild-type strains are prone to acquiring fitness-altering mutations during in vitro construction when using the P3 plasmid and streptomycin, highlighting the need for careful pool validation prior to use and for minimizing antibiotic exposure during strain construction when the strain of interest has no natural resistance, to reduce the risk of selecting mutations.",
  "abstract_shown": true,
  "affiliations": [
    "Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland",
    "Department of Molecular Life Science and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Christopher Schubert"
    },
    {
      "affs": [
        1
      ],
      "name": "Jeongmin Kim"
    },
    {
      "name": "Nicolas Näpflin"
    },
    {
      "name": "Melanie Hoos"
    },
    {
      "name": "Jemina Huuskonen"
    },
    {
      "name": "Christian von Mering"
    },
    {
      "name": "Wolf-Dietrich Hardt"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bypfch3es9dvk.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0349327",
  "fulltext_url": null,
  "id": "bypfch3es9dvk",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0349327",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1106|Salmonella and Campylobacter epidemiology"
    ],
    [
      "plos",
      "/Biology and life sciences/Ecology/Ecological metrics/Species diversity/Shannon index"
    ],
    [
      "plos",
      "/Biology and life sciences/Evolutionary biology/Population genetics/Gene pool"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Animal genomics/Mammalian genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Population genetics/Gene pool"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Single nucleotide polymorphisms"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Salmonella/Salmonella typhimurium"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Microbial control/Antimicrobials/Antibiotics/Streptomycin"
    ],
    [
      "plos",
      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Enterobacteriaceae/Salmonella/Salmonella typhimurium"
    ],
    [
      "plos",
      "/Biology and life sciences/Population biology/Population genetics/Gene pool"
    ],
    [
      "plos",
      "/Ecology and environmental sciences/Ecology/Ecological metrics/Species diversity/Shannon index"
    ],
    [
      "plos",
      "/Medicine and health sciences/Medical conditions/Infectious diseases/Bacterial diseases/Salmonella/Salmonella typhimurium"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Salmonella/Salmonella typhimurium"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pharmacology/Drugs/Antimicrobials/Antibiotics/Streptomycin"
    ],
    [
      "plos",
      "/Research and analysis methods/Animal studies/Experimental organism systems/Animal models/Mouse models"
    ],
    [
      "plos",
      "/Research and analysis methods/Animal studies/Experimental organism systems/Model organisms/Mouse models"
    ],
    [
      "plos",
      "/Research and analysis methods/Model organisms/Mouse models"
    ],
    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
    ]
  ],
  "openalex": "W7221766137",
  "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0349327&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-14",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/bypfch3es9dvk.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:23Z",
      "native_id": "10.1371/journal.pone.0349327",
      "source": "plos",
      "url": "https://doi.org/10.1371/journal.pone.0349327"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "plos:ecology",
      "subfield": "ecology"
    },
    {
      "field": "biology",
      "origin": "plos:genomics",
      "subfield": "genetics-genomics"
    },
    {
      "field": "biology",
      "origin": "plos:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "WISH-barcoding of Salmonella Typhimurium ATCC14028s strains for population dynamics studies in vivo",
  "title_text": "WISH-barcoding of Salmonella Typhimurium ATCC14028s strains for population dynamics studies in vivo",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:23Z",
  "url": "https://research.draconitic.com/paper/bypfch3es9dvk",
  "venue": "PLOS One",
  "versions": []
}