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

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. Simon Kroll and Lindsay J. Hall ()
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Raymond Kiu: University of Birmingham
Elizabeth M. Darby: University of Birmingham
Cristina Alcon-Giner: Norwich Research Park
Antia Acuna-Gonzalez: Norwich Research Park
Anny Camargo: Norwich Research Park
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
Willem Schaik: University of Birmingham
J. Simon Kroll: Imperial College London
Lindsay J. Hall: University of Birmingham

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

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-62584-2

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