Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome
Open accessAbstract
Development of the preterm infant gut microbiota is emerging as a critical research priority(1). Since preterm infants almost universally receive early and often extended antibiotic therapy(2), it is important to understand how these interventions alter gut microbiota development(3-6). Analysis of 401 stools from 84 longitudinally sampled preterm infants demonstrates that meropenem, cefotaxime and ticarcillin-clavulanate are associated with significantly reduced species richness. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness, but these can be predicted with 85% accuracy based on the relative abundance of only two bacterial species and two antibiotic resistance (AR) genes at treatment initiation. To investigate resistome development, we functionally selected resistance to 16 antibiotics from 21 faecal metagenomic expression libraries. Of the 794 AR genes identified, 79% had not previously been classified as AR genes. Combined with deep shotgun sequencing of all stools, we find that multidrug-resistant members of the genera Escherichia, Klebsiella and Enterobacter, genera commonly associated with nosocomial infections, dominate the preterm infant gut microbiota. AR genes that are enriched following specific antibiotic treatments are generally unique to the specific treatment and are highly correlated with the abundance of a single species. The most notable exceptions include ticarcillin-clavulanate and ampicillin, both of which enrich for a large number of overlapping AR genes, and are correlated with Klebsiella pneumoniae. We find that all antibiotic treatments are associated with widespread collateral microbiome impact by enrichment of AR genes that have no known activity against the specific antibiotic driver.
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Enterococcus, Escherichia, and Klebsiella are common nosocomial pathogens and are often implicated in late-onset infections in preterm infants.
“These findings align with reports from other NICU studies, where Enterococcus, Escherichia, and Klebsiella are common nosocomial pathogens and are often implicated in late-onset infections in preterm infants32,45,46.”
From Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. (2025) · cites this paper as [45]
The Abstract (page unavailable) describes Escherichia and Klebsiella as genera commonly associated with nosocomial infections and lists Enterococcus faecium in the ESKAPE pathogen family. It does not say that these three genera are often implicated in late-onset infections in preterm infants; the study examines their presence in the gut microbiota, not infection incidence. (LLM, conf=0.86)
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“These fi ndings align with reports from other NICU studies, where Enterococcus , Escherichia , and Klebsiella are common nosocomial pathogens and are often implicated in late-onset infections in preterm infants 32,45,46 .”
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- Authors
- Gibson, M. K., Wang, B., Ahmadi, S., Burnham, C.-A. D., Tarr, P. I., Warner, B. B., & Dantas, G.
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- Dantas, Gautam
- Venue
- Nature Microbiology
- Published
- 2016-03-07
- Volume
- 1
- Issue
- 4
- Pages
- 16024-16024
- ISSN
- 2058-5276 (ISSN-L)
- PMC
- PMC5031140
- OpenAlex
- W2331300001
- Cited by
- 457
- References
- 45
- Citations by year
- 2026: 33 · 2025: 44 · 2024: 47 · 2023: 46 · 2022: 59 · 2021: 48 · 2020: 49 · 2019: 50 · 2018: 37 · 2017: 33 · 2016: 11
- FWCI
- 22.56
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (UL1TR000448)
- National Institute of General Medical Sciences (R01GM099538)
- National Institute of Allergy and Infectious Diseases (UH3AI083265)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK052574)
- National Center for Advancing Translational Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- antibiotic resistome, antibiotic resistance genes, meropenem, cefotaxime, ticarcillin-clavulanic acid, vancomycin, gentamicin, multidrug resistance, Klebsiella pneumoniae, Escherichia, Enterobacter, nosocomial infections
- MeSH terms
- Gastrointestinal Microbiome, Anti-Bacterial Agents, Genes, Bacterial, Humans, Infant, Premature, Longitudinal Studies, Sequence Analysis, DNA, Drug Resistance, Bacterial, Gastrointestinal Tract
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