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

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 and Till Strowig ()
Additional contact information
Marie Wende: Helmholtz Center for Infection Research
Lisa Osbelt: Helmholtz Center for Infection Research
Lea Eisenhard: Helmholtz Center for Infection Research
Till Robin Lesker: Helmholtz Center for Infection Research
Bamu F. Damaris: a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI)
Uthayakumar Mutukumarasamy: Helmholtz Center for Infection Research
Agata Bielecka: Helmholtz Center for Infection Research
Éva d. H. Almási: Helmholtz Center for Infection Research
Katrin Anja Winter: Helmholtz Center for Infection Research
Jennifer Schauer: Ruhr-University Bochum
Niels Pfennigwerth: Ruhr-University Bochum
Sören Gatermann: Ruhr-University Bochum
Katharina Schaufler: Department of Epidemiology and Ecology of Antimicrobial Resistance
Dirk Schlüter: Hannover Medical School
Marco Galardini: a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI)
Till Strowig: Helmholtz Center for Infection Research

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract 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.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-61327-7 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61327-7

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-61327-7

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().