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Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants

Author

Listed:
  • Raymond Kiu

    (University of Birmingham
    University of Birmingham
    Norwich Research Park)

  • Elizabeth M. Darby

    (University of Birmingham
    University of Birmingham)

  • Cristina Alcon-Giner

    (Norwich Research Park)

  • Antia Acuna-Gonzalez

    (Norwich Research Park)

  • Anny Camargo

    (Norwich Research Park
    Universidad del Rosario
    Universidad de Boyacá)

  • Lisa E. Lamberte

    (University of Birmingham)

  • Sarah Phillips

    (Norwich Research Park)

  • Kathleen Sim

    (Imperial College London)

  • Alexander G. Shaw

    (Imperial College London)

  • Paul Clarke

    (Norfolk and Norwich University Hospital
    University of East Anglia)

  • Willem Schaik

    (University of Birmingham
    University of Birmingham)

  • J. Simon Kroll

    (Imperial College London)

  • Lindsay J. Hall

    (University of Birmingham
    University of Birmingham
    Norwich Research Park
    University of East Anglia)

Abstract

Preterm infants ( 300 metagenome-assembled genomes and obtained ~90 isolate genomes via targeted culturomics, allowing strain-level analysis. We also assessed ex vivo horizontal gene transfer (HGT) capacity of multidrug-resistant (MDR) Enterococcus using neonatal gut models. Here we show that probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and restored typical early-life microbiota profile. However, persistent MDR pathogens like Enterococcus, with high HGT potential, underscore the need for continued surveillance. Our findings underscore the complex interplay between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.

Suggested Citation

  • Raymond Kiu & Elizabeth M. Darby & Cristina Alcon-Giner & Antia Acuna-Gonzalez & Anny Camargo & Lisa E. Lamberte & Sarah Phillips & Kathleen Sim & Alexander G. Shaw & Paul Clarke & Willem Schaik & J. , 2025. "Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62584-2
    DOI: 10.1038/s41467-025-62584-2
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    References listed on IDEAS

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    1. Anna Samarra & Alejandro J. Alcañiz & Cecilia Martínez-Costa & Alberto Marina & Iñaki Comas & Nicola Segata & Narciso M. Quijada & Maria Carmen Collado, 2025. "Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    2. Charlotte J. Neumann & Alexander Mahnert & Christina Kumpitsch & Raymond Kiu & Matthew J. Dalby & Magdalena Kujawska & Tobias Madl & Stefan Kurath-Koller & Berndt Urlesberger & Bernhard Resch & Lindsa, 2023. "Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
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