title: Identification of aminoglycoside and β-lactam resistance genes from within an infant gut functional metagenomic library.
abstract: The 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-naïve 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 ∼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 β-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 β-lactam resistance reservoir even in the absence of selective pressure, confirming the infant resistome establishes early in life, perhaps even at birth.
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
authors.forename: Fiona
authors.initials: F
authors.lastname: Fouhy
authors.affiliation: School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, East Sussex, United Kingdom.
authors.forename: Lesley A
authors.initials: LA
authors.lastname: Ogilvie
authors.affiliation: School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, East Sussex, United Kingdom; Queen Victoria Hospital NHS Foundation Trust, East Grinstead, West Sussex, United Kingdom.
authors.forename: Brian V
authors.initials: BV
authors.lastname: Jones
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
authors.forename: R Paul
authors.initials: RP
authors.lastname: Ross
authors.affiliation: Department of Paediatrics and Child Health, University College Cork, Cork, Ireland.
authors.forename: Anthony C
authors.initials: AC
authors.lastname: Ryan
authors.affiliation: Department of Paediatrics and Child Health, University College Cork, Cork, Ireland; Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland.
authors.forename: Eugene M
authors.initials: EM
authors.lastname: Dempsey
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
authors.forename: Gerald F
authors.initials: GF
authors.lastname: Fitzgerald
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
authors.forename: Catherine
authors.initials: C
authors.lastname: Stanton
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Cotter
mesh_terms: D000617:Aminoglycosides / Q000494:pharmacology*; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D004352:Drug Resistance, Microbial / Q000235:genetics; D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000187:drug effects* / Q000382:microbiology; D006801:Humans; D007223:Infant; D056186:Metagenomics; D064307:Microbiota / Q000187:drug effects* / Q000235:genetics; D018440:beta-Lactam Resistance / Q000235:genetics*; D047090:beta-Lactams / Q000494:pharmacology*
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D047090:beta-Lactams