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: 31-Dec-2017
Date of Acceptance: 20-Dec-2016
ISSN: 2167-8359
Publisher: PeerJ
Journal / Book Title: PeerJ
Copyright Statement: This paper is embargoed until publication. Once published will be available fully open access.
Sponsor/Funder: Winnicott Foundation
National Institute for Health Research
Imperial College Healthcare NHS Trust - CLRN Funding
Funder's Grant Number: N/A
Publication Status: Accepted
Embargo Date: publication subject to indefinite embargo
Appears in Collections:Department of Medicine
Faculty of Medicine

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