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The effect of antibiotics on the composition of the intestinal microbiota - a systematic review

  • Petra Zimmermann
    Correspondence
    Corresponding author at: Faculty of Science and Medicine, University of Fribourg, Fribourg, Route des Arsenaux 41, 1700 Fribourg, Switzerland.
    Affiliations
    Department of Paediatrics, Fribourg Hospital HFR and Faculty of Science and Medicine, University of Fribourg, Switzerland

    Department of Paediatrics, The University of Melbourne, Parkville, Australia

    Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia

    Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
    Search for articles by this author
  • Nigel Curtis
    Affiliations
    Department of Paediatrics, The University of Melbourne, Parkville, Australia

    Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia

    Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
    Search for articles by this author
Published:October 18, 2019DOI:https://doi.org/10.1016/j.jinf.2019.10.008

      Highlights

      • Antibiotics cause profound changes in the intestinal microbiota. These changes including a decrease in bacterial diversity, changes in the abundances of certain bacteria and an increase in antibiotic resistance.
      • The longest duration of changes was observed after treatment with ciprofloxacin (one year), clindamycin (two years) and clarithromycin plus metronidazole (four years). However, these findings are limited by follow-up times.
      • Understanding the effects of antibiotics on the intestinal microbiota will help tailor antibiotic treatment to minimise this ‘collateral damage’.

      Abstract

      Objective

      Antibiotics change the composition of the intestinal microbiota. The magnitude of the effect of antibiotics on the microbiota and whether the effects are short-term or persist long-term remain uncertain. In this review, we summarise studies that have investigated the effect of antibiotics on the composition of the human intestinal microbiota.

      Methods

      A systematic search was done to identify original studies that have investigated the effect of systemic antibiotics on the intestinal microbiota in humans.

      Results

      We identified 129 studies investigating 2076 participants and 301 controls. Many studies reported a decrease in bacterial diversity with antibiotic treatment. Penicillin only had minor effects on the intestinal microbiota. Amoxicillin, amoxcillin/clavulanate, cephalosporins, lipopolyglycopeptides, macrolides, ketolides, clindamycin, tigecycline, quinolones and fosfomycin all increased abundance of Enterobacteriaea other than E. coli (mainly Citrobacter spp., Enterobacter spp. and Klebsiella spp.). Amoxcillin, cephalosporins, macrolides, clindamycin, quinolones and sulphonamides decreased abundance of E. coli, while amoxcillin/clavulante, in contrast to other penicillins, increased abundance of E. coli. Amoxicllin, piperacillin and ticarcillin, cephalosporins (except fifth generation cephalosporins), carbapenems and lipoglycopeptides were associated with increased abundance of Enterococcus spp., while macrolides and doxycycline decreased its abundance. Piperacillin and ticarcillin, carbapenems, macrolides, clindamycin and quinolones strongly decreased the abundance of anaerobic bacteria. In the studies that investigated persistence, the longest duration of changes was reported after treatment with ciprofloxacin (one year), clindamycin (two years) and clarithromycin plus metronidazole (four years). Many antibiotics were associated with a decrease in butyrate or butryrate-producing bacteria.

      Conclusion

      Antibiotics have profound and sometimes persisting effects on the intestinal microbiota, characterised by diminished abundance of beneficial commensals and increased abundance of potentially detrimental microorganisms. Understanding these effects will help tailor antibiotic treatment and the use of probiotics to minimise this ‘collateral damage’.

      Keywords

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