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<p>Human gut colonization by multi-drug resistant Enterobacterales (MDR-E) poses a risk for subsequent infections. Because of the collateral damage antibiotics cause to the microbiota, microbiome-based interventions aimed at promoting decolonization have garnered interest. In this study, we evaluate the strain-specific potential of 430 commensal <i>Escherichia coli</i> isolates to inhibit the growth of an MDR <i>E. coli</i> strain. Comparative analyses using in vitro, ex vivo, and mouse models reveal that only a subset of commensal strains can facilitate gut decolonization. Bioinformatic and experimental analyses of the antagonism among representative strains demonstrate that both direct and indirect carbohydrate competition contribute to niche exclusion between <i>E. coli</i> strains. Finally, the combination of a protective <i>E. coli</i> strain with a <i>Klebsiella oxytoca</i> strain enhances the inhibitory potential against metabolically diverse MDR <i>E. coli</i> strains and additional MDR-E species, highlighting that rationally designed metabolically complementary approaches can contribute to developing next-generation probiotics with broad-spectrum activity.</p>

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Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年7月1日

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  • Marie Wende,
  • Lisa Osbelt,
  • Lea Eisenhard,
  • Till Robin Lesker,
  • Bamu F. Damaris,
  • Uthayakumar Mutukumarasamy,
  • Agata Bielecka,
  • Éva d. H. Almási,
  • Katrin Anja Winter,
  • Jennifer Schauer,
  • Niels Pfennigwerth,
  • Sören Gatermann,
  • Katharina Schaufler,
  • Dirk Schlüter,
  • Marco Galardini,
  • Till Strowig

摘要

Human gut colonization by multi-drug resistant Enterobacterales (MDR-E) poses a risk for subsequent infections. Because of the collateral damage antibiotics cause to the microbiota, microbiome-based interventions aimed at promoting decolonization have garnered interest. In this study, we evaluate the strain-specific potential of 430 commensal Escherichia coli isolates to inhibit the growth of an MDR E. coli strain. Comparative analyses using in vitro, ex vivo, and mouse models reveal that only a subset of commensal strains can facilitate gut decolonization. Bioinformatic and experimental analyses of the antagonism among representative strains demonstrate that both direct and indirect carbohydrate competition contribute to niche exclusion between E. coli strains. Finally, the combination of a protective E. coli strain with a Klebsiella oxytoca strain enhances the inhibitory potential against metabolically diverse MDR E. coli strains and additional MDR-E species, highlighting that rationally designed metabolically complementary approaches can contribute to developing next-generation probiotics with broad-spectrum activity.