Effects of short- and long-course antibiotics on the lower intestinal microbiome as they relate to traveller's diarrhea

J Travel Med. 2017 Apr 1;24(suppl_1):S35-S38. doi: 10.1093/jtm/taw084.


Background: Antibiotics have profound and lasting effects on the lower intestinal (gut) microbiome that can both promote resistance and increase susceptibility to colonization and infection; knowledge of these changes is important to the prevention and treatment of traveler's diarrhea.

Methods: Recent data from epidemiologic and modern metagenomics studies were reviewed in regard to how such findings could inform the prevention and treatment of traveler's diarrhea.

Results: Although it is well recognized that antibiotics increase the risk for Clostridium difficile infection, it is less recognized how they predispose patients to typically foodborne pathogens such as Salmonella or Camplyobacter spp. While these pathogens account for only a fraction of traveler's diarrhea, such predisposition reflects how antibiotic exposure that precedes or occurs during travel may increase the risk for infection with other more common pathogens, even possibly enterotoxigenic Eschericia coli, especially in the setting of acquired resistance. Even short antibiotic exposures disrupt the gut microbiome up to a year or more and repeated exposures appear to attenuate recovery from ever occurring. One bacterial phylum that commonly increases in the gut following antibiotics are the proteobacteria including Enterobacteriacea; these are pro-inflammatory and often carry antibiotic resistance genes, the number and diversity of these genes (i.e. the resistome) commonly expands following antibiotics. The gut resistome among healthy community-dwelling adults reflects geographic variability in antibiotic use practices in both humans and food-producing animals as well as possibly the transmission of antibiotic resistance genes through the food supply.

Conclusions: Because antibiotic use among travelers will influence the resistome and thereby promote geographic spread of resistance, it is important that antibiotic use recommendations for travelers be guided by resistance surveillance data as well as a careful assessment of the risks and benefits to both the individual and society.

Keywords: Traveller’s diarrhea; antibiotics; microbiome.

Publication types

  • Review

MeSH terms

  • Anti-Bacterial Agents / administration & dosage
  • Anti-Bacterial Agents / pharmacology*
  • Anti-Bacterial Agents / therapeutic use
  • Diarrhea / drug therapy*
  • Gastrointestinal Microbiome / drug effects*
  • Humans
  • Travel*


  • Anti-Bacterial Agents