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Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites
Open accessAbstract
The intestine is the primary colonisation site for carbapenem-resistant Enterobacteriaceae (CRE) and serves as a reservoir of CRE that cause invasive infections (e.g. bloodstream infections). Antibiotics disrupt colonisation resistance mediated by the gut microbiota, promoting the expansion of CRE within the intestine. We used ex vivo faecal cultures to measure the impact of antibiotics (that promote CRE intestinal colonisation) on the faecal microbiota from healthy human donors. We demonstrated that antibiotics decreased the abundance of gut commensals (including Bifidobacteriaceae and Bacteroidales ) in human faecal microbiota, resulting in an enrichment of nutrients and a depletion of microbial metabolites. We measured the nutrient utilisation abilities, nutrient preferences, and metabolite inhibition susceptibilities of several carbapenem-resistant Enterobacteriaceae strains, including Escherichia coli , Klebsiella pneumoniae , and Enterobacter hormaechei . Nutrients (which were elevated with antibiotics) acted as carbon and nitrogen sources to support CRE growth, where CRE strains showed an ordered preference for specific nutrients. These nutrients were also increased in faeces from antibiotic-treated mice but decreased following intestinal colonisation with carbapenem-resistant E. coli . Microbial metabolites (which decreased with antibiotics) were inhibitory towards CRE growth in vitro . Carbapenem-resistant E. coli growth was decreased in faecal samples from mice treated with a mixture of inhibitory metabolites compared with PBS-treated mice. These findings demonstrated that killing gut commensals with antibiotics disrupts colonisation resistance by enriching nutrients that support CRE growth and depleting metabolites that inhibit CRE growth. These results support the development of new microbiome therapeutics to prevent CRE intestinal colonisation, which would also prevent the subsequent development of invasive CRE infections.
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Different species of Enterobacteriaceae have different nutrient utilization profiles in aerobic and anaerobic environments.
“Different species of Enterobacteriaceae have different nutrient utilization profiles in aerobic and anaerobic environments and also have a different order of nutrient preference [79, 128].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [79]
Different species of Enterobacteriaceae have a different order of nutrient preference.
“Different species of Enterobacteriaceae have different nutrient utilization profiles in aerobic and anaerobic environments and also have a different order of nutrient preference [79, 128].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [79]
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- Raja Makendran Nandan Raja Rajendran. Enzymatic conversion of rna from yeast extract to guanosine monophosphate (a flavoring agent). Master’s thesis, Chalmers University of Technology https://odr.chalmers.se/handle/20.500.12380/166692 (2012).
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Horrocks, V., King, O. G., Yip, A. Y. G., Marques, I. M., & McDonald, J. A. K. (2023) · Microbiology · doi:10.1099/mic.0.001377 · Cited by 104
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Metadata
- Authors
- Yip, A. Y. G., King, O. G., Omelchenko, O., Kurkimat, S., Horrocks, V., Mostyn, P., Danckert, N., Ghani, R., Satta, G., Jauneikaite, E., Davies, F. J., Clarke, T. B., Mullish, B. H., Marchesi, J. R., & McDonald, J. A. K.
- Affiliations
- Imperial College London (GB)
- St Mary's Hospital (GB)
- Imperial College Healthcare NHS Trust (GB)
- University College London (GB)
- National Institute for Health and Care Research (GB)
- Corresponding author
- McDonald, Julie A. K.
- ORCID
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2023-03-25
- Volume
- 14
- Issue
- 1
- Pages
- 5094-5094
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10444851
- OpenAlex
- W4386070166
- Cited by
- 91
- References
- 82
- Citations by year
- 2026: 24 · 2025: 32 · 2024: 33 · 2023: 2
- FWCI
- 8.11
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- journal article
- Language
- en
- Open access
- gold
- doi.org
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- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Spiral (Imperial College London) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (107660/Z/15/Z)
- UK Research and Innovation (MR/X502959/1)
- National Institute for Health Research Health Protection Research Unit
- National Institute for Health and Care Research (CL‐2019‐21‐002)
- University of Warwick
- Imperial College London
- Imperial College Healthcare NHS Trust
- University of Oxford
- Rosetrees Trust
- Medical Research Council (MR/W025655/1, 2288243, MR/X502959/1, MR/T005254/1, MR/X020258/1)
- NIHR Imperial Biomedical Research Centre
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Microbiology (medical) › Antibiotic Resistance in Bacteria
- Health Sciences › Medicine › Infectious Diseases › Antibiotic Use and Resistance
- Keywords
- carbapenem-resistant Enterobacteriaceae, carbapenem-resistant Escherichia coli, broad-spectrum antibiotics, gut microbiota, antibiotic-induced dysbiosis, intestinal colonization, nutrient enrichment, microbial metabolites, inhibitory metabolites, Bifidobacteriaceae, Bacteroidales, gut commensals
- MeSH terms
- Carbapenem-Resistant Enterobacteriaceae, Nutrients, Animals, Anti-Bacterial Agents, Escherichia coli, Humans, Intestinal Neoplasms, Actinobacteria, Bacteroidetes, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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