Antibiotic resistance potential of the healthy preterm infant gut microbiome

Graham Rose*, Alexander G. Shaw, Kathleen Sim, David J. Wooldridge, Ming Shi Li, Saheer Gharbia, Raju Misra, John Simon Kroll

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)


Background. Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results. Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions. We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.

Original languageEnglish
Article numbere2928
Issue number1
Publication statusPublished - 2017

Bibliographical note

Funding Information:
This study was supported by a programme grant (to J.Simon Kroll) from The Winnicott Foundation and generous additional funding from Micropathology Ltd., Meningitis Now and the National Institute for Health Research (NIHR) Biomedical Research Centre based at Imperial Healthcare NHS Trust and Imperial College London. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.The Winnicott Foundation. Micropathology Ltd. National Institute for Health Research (NIHR) Biomedical Research Centre. Imperial Healthcare NHS Trust and Imperial College London.

Publisher Copyright:
© 2017 Rose et al.


  • Antibiotic resistance
  • Gut microbiome
  • Preterm infants
  • Shotgun metagenomics


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