WISH-barcoding of Salmonella Typhimurium ATCC14028s strains for population dynamics studies in vivo
- 1Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- 2Department of Molecular Life Science and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
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.
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BibTeX
@article{schubert2026wishbarcoding,
title = {{WISH-barcoding of Salmonella Typhimurium ATCC14028s strains for population dynamics studies in vivo}},
author = {Christopher Schubert and Jeongmin Kim and Nicolas Näpflin and Melanie Hoos and Jemina Huuskonen and Christian von Mering and Wolf-Dietrich Hardt},
journal = {PLOS One},
year = {2026},
month = oct,
doi = {10.1371/journal.pone.0349327},
url = {https://doi.org/10.1371/journal.pone.0349327},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - WISH-barcoding of Salmonella Typhimurium ATCC14028s strains for population dynamics studies in vivo
AU - Christopher Schubert
AU - Jeongmin Kim
AU - Nicolas Näpflin
AU - Melanie Hoos
AU - Jemina Huuskonen
AU - Christian von Mering
AU - Wolf-Dietrich Hardt
PY - 2026
DA - 2026/10/14
JO - PLOS One
DO - 10.1371/journal.pone.0349327
UR - https://doi.org/10.1371/journal.pone.0349327
AB - 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.
SN - 1932-6203
ER -