Identification of aminoglycoside and beta-lactam resistance genes from within an infant gut functional metagenomic library

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dc.contributor.authorFouhy, Fiona
dc.contributor.authorOgilvie, Lesley A.
dc.contributor.authorJones, Brian V.
dc.contributor.authorRoss, R. Paul
dc.contributor.authorRyan, C. Anthony
dc.contributor.authorDempsey, Eugene M.
dc.contributor.authorFitzgerald, Gerald F.
dc.contributor.authorStanton, Catherine
dc.contributor.authorCotter, Paul D.
dc.contributor.funderIrish Research Council
dc.contributor.funderTeagasc
dc.contributor.funderScience Foundation Ireland
dc.contributor.funderIrish Government
dc.contributor.funderAPC Microbiome Institute, College of Medicine and Health, University College Cork
dc.contributor.funderMedical Research Council, United Kingdom
dc.contributor.funderSociety for Applied Microbiology, United Kingdom
dc.contributor.funderUniversity of Brighton, United Kingdom
dc.contributor.funderHealthcare Infection Society, United Kingdom
dc.date.accessioned2016-02-17T11:43:39Z
dc.date.available2016-02-17T11:43:39Z
dc.date.issued2014
dc.description.abstractThe infant gut microbiota develops rapidly during the first 2 years of life, acquiring microorganisms from diverse sources. During this time, significant opportunities exist for the infant to acquire antibiotic resistant bacteria, which can become established and constitute the infant gut resistome. With increased antibiotic resistance limiting our ability to treat bacterial infections, investigations into resistance reservoirs are highly pertinent. This study aimed to explore the nascent resistome in antibiotically-naive infant gut microbiomes, using a combination of metagenomic approaches. Faecal samples from 22 six-month-old infants without previous antibiotic exposure were used to construct a pooled metagenomic library, which was functionally screened for ampicillin and gentamicin resistance. Our library of similar to 220Mb contained 0.45 ampicillin resistant hits/Mb and 0.059 gentamicin resistant hits/Mb. PCR-based analysis of fosmid clones and uncloned metagenomic DNA, revealed a diverse and abundant aminoglycoside and beta-lactam resistance reservoir within the infant gut, with resistance determinants exhibiting homology to those found in common gut inhabitants, including Escherichia coli, Enterococcus sp., and Clostridium difficile, as well as to genes from cryptic environmental bacteria. Notably, the genes identified differed from those revealed when a sequence-driven PCR-based screen of metagenomic DNA was employed. Carriage of these antibiotic resistance determinants conferred substantial, but varied (2-512x), increases in antibiotic resistance to their bacterial host. These data provide insights into the infant gut resistome, revealing the presence of a varied aminoglycoside and beta-lactam resistance reservoir even in the absence of selective pressure, confirming the infant resistome establishes early in life, perhaps even at birth.en
dc.description.sponsorshipIrish Research Council (EMBARK scholarship); Science Foundation Ireland (Investigator Award 11/PI/1137); Medical Research Council, United Kingdom (Grant No. G0901553)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleide108016
dc.identifier.citationFouhy F, Ogilvie LA, Jones BV, Ross RP, Ryan AC, Dempsey EM, et al. (2014) Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library. PLoS ONE 9(9): e108016. doi:10.1371/journal.pone.0108016
dc.identifier.doi10.1371/journal.pone.0108016
dc.identifier.issn1932-6203
dc.identifier.issued9en
dc.identifier.journaltitlePLOS ONEen
dc.identifier.urihttps://hdl.handle.net/10468/2326
dc.identifier.volume9en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
dc.rights© 2015 Fouhy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are crediteden
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectAntibiotic resistanceen
dc.subjectIntestinal microbiotaen
dc.subjectStaphylococcus aureusen
dc.subjectEscherichia colien
dc.subjectCTX-Men
dc.subjectRevealsen
dc.subjectPCRen
dc.subjectEnterococcien
dc.subjectAmpicillinen
dc.subjectEnzymesen
dc.titleIdentification of aminoglycoside and beta-lactam resistance genes from within an infant gut functional metagenomic libraryen
dc.typeArticle (peer-reviewed)en
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