Antibiotic resistance potential of the healthy preterm infant gut microbiome

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Title: Antibiotic resistance potential of the healthy preterm infant gut microbiome
Author(s): Rose, G
Shaw, AG
Sim, K
Wooldridge, DJ
Li, M-S
Gharbia, S
Misra, RV
Kroll, J
Item Type: Journal Article
Abstract: 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 13 genes per preterm infant, ranging across 8 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.
Publication Date: 25-Jan-2017
Date of Acceptance: 20-Dec-2016
URI: http://hdl.handle.net/10044/1/43565
DOI: https://dx.doi.org/10.7717/peerj.2928
ISSN: 2167-8359
Publisher: PeerJ
Journal / Book Title: PeerJ
Volume: 5
Copyright Statement: © 2017 Rose et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
Sponsor/Funder: Winnicott Foundation
National Institute for Health Research
Imperial College Healthcare NHS Trust - CLRN Funding
Funder's Grant Number: N/A
RDD02
RDD05
Keywords: Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
Preterm infants
Shotgun metagenomics
Antibiotic resistance
Gut microbiome
INTESTINAL MICROBIOTA
AMPICILLIN RESISTANCE
BACTERIAL DIVERSITY
GENE-TRANSFER
RESISTOME
STRAINS
GENOMES
LIFE
Antibiotic resistance
Gut microbiome
Preterm infants
Shotgun metagenomics
Publication Status: Published
Article Number: e2928
Appears in Collections:Department of Medicine
Faculty of Medicine



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