The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes

Crit Rev Microbiol. 2021 Sep;47(5):543-561. doi: 10.1080/1040841X.2021.1907301. Epub 2021 Apr 24.


Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist in bacterial populations. Because bacteria, MGEs, and resistance genes can readily spread between different ecological compartments (e.g. soil, plants, animals, humans, wastewater), a "One Health" approach is needed to combat this problem. The equine hindgut is an understudied but potentially significant reservoir of ARGs and MGEs, since horses have close contact with humans, their manure is used in agriculture, they have a dense microbiome of both bacteria and fungi, and many antimicrobials used for equine treatment are also used in human medicine. Here, we collate information to date about resistance genes, plasmids, and class 1 integrons from equine-derived bacteria, we discuss why the equine hindgut deserves increased attention as a potential reservoir of ARGs, and we suggest ways to minimize the selection for ARGs in horses, in order to prevent their spread to the wider community.

Keywords: Integrons; antibiotic; antimicrobial; equine; resistance.

Publication types

  • Review

MeSH terms

  • Animal Feed
  • Animals
  • Anti-Bacterial Agents / pharmacology
  • Bacteria / drug effects
  • Bacteria / genetics
  • Dietary Supplements
  • Drug Resistance, Bacterial / genetics*
  • Gastrointestinal Microbiome*
  • Gene Transfer, Horizontal
  • Genes, Bacterial*
  • Horses / microbiology*
  • Interspersed Repetitive Sequences*
  • Intestine, Large / microbiology*
  • Plasmids
  • Soil


  • Anti-Bacterial Agents
  • Soil