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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Article info
Publication history
Published online: October 18, 2019
Accepted:
October 13,
2019
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© 2019 Published by Elsevier Ltd on behalf of The British Infection Association.
