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Clinical Therapeutics

High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

Fiona Fouhy, Caitriona M. Guinane, Seamus Hussey, Rebecca Wall, C. Anthony Ryan, Eugene M. Dempsey, Brendan Murphy, R. Paul Ross, Gerald F. Fitzgerald, Catherine Stanton, Paul D. Cotter
Fiona Fouhy
Teagasc Food Research Centre, Fermoy, Cork, IrelandMicrobiology Department, University College Cork, Cork, Ireland
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Caitriona M. Guinane
Teagasc Food Research Centre, Fermoy, Cork, IrelandAlimentary Pharmabiotic Centre, Cork, Ireland
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Seamus Hussey
Department of Paediatrics and Child Health, University College Cork, Cork, IrelandDivision of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada
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Rebecca Wall
Teagasc Food Research Centre, Fermoy, Cork, IrelandAlimentary Pharmabiotic Centre, Cork, Ireland
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C. Anthony Ryan
Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
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Eugene M. Dempsey
Department of Paediatrics and Child Health, University College Cork, Cork, IrelandDepartment of Neonatology, Cork University Maternity Hospital, Cork, Ireland
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Brendan Murphy
Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
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R. Paul Ross
Teagasc Food Research Centre, Fermoy, Cork, IrelandAlimentary Pharmabiotic Centre, Cork, Ireland
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Gerald F. Fitzgerald
Microbiology Department, University College Cork, Cork, IrelandAlimentary Pharmabiotic Centre, Cork, Ireland
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Catherine Stanton
Teagasc Food Research Centre, Fermoy, Cork, IrelandAlimentary Pharmabiotic Centre, Cork, Ireland
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Paul D. Cotter
Teagasc Food Research Centre, Fermoy, Cork, IrelandAlimentary Pharmabiotic Centre, Cork, Ireland
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DOI: 10.1128/AAC.00789-12
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ABSTRACT

The infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA and rpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions of Proteobacteria (P = 0.0049) and significantly lower proportions of Actinobacteria (P = 0.00001) (and the associated genus Bifidobacterium [P = 0.0132]) as well as the genus Lactobacillus (P = 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, the Proteobacteria levels remained significantly higher in the treated infants (P = 0.0049), but the Actinobacteria, Bifidobacterium, and Lactobacillus levels had recovered and were similar to those in the control samples. Despite this recovery of total Bifidobacterium numbers, rpoB-targeted pyrosequencing revealed that the number of different Bifidobacterium species present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.

FOOTNOTES

    • Received 16 April 2012.
    • Returned for modification 2 June 2012.
    • Accepted 20 July 2012.
    • Accepted manuscript posted online 4 September 2012.
  • Supplemental material for this article may be found at http://dx.doi.org/10.1128/AAC.00789-12.

  • Copyright © 2012, American Society for Microbiology. All Rights Reserved.
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High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin
Fiona Fouhy, Caitriona M. Guinane, Seamus Hussey, Rebecca Wall, C. Anthony Ryan, Eugene M. Dempsey, Brendan Murphy, R. Paul Ross, Gerald F. Fitzgerald, Catherine Stanton, Paul D. Cotter
Antimicrobial Agents and Chemotherapy Oct 2012, 56 (11) 5811-5820; DOI: 10.1128/AAC.00789-12

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High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin
Fiona Fouhy, Caitriona M. Guinane, Seamus Hussey, Rebecca Wall, C. Anthony Ryan, Eugene M. Dempsey, Brendan Murphy, R. Paul Ross, Gerald F. Fitzgerald, Catherine Stanton, Paul D. Cotter
Antimicrobial Agents and Chemotherapy Oct 2012, 56 (11) 5811-5820; DOI: 10.1128/AAC.00789-12
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