What is a resistance gene? Ranking risk in resistomes

Nat Rev Microbiol. 2015 Feb;13(2):116-23. doi: 10.1038/nrmicro3399. Epub 2014 Dec 15.


Metagenomic studies have shown that antibiotic resistance genes are ubiquitous in the environment, which has led to the suggestion that there is a high risk that these genes will spread to bacteria that cause human infections. If this is true, estimating the real risk of dissemination of resistance genes from environmental reservoirs to human pathogens is therefore very difficult. In this Opinion article, we analyse the current definitions of antibiotic resistance and antibiotic resistance genes, and we describe the bottlenecks that affect the transfer of antibiotic resistance genes to human pathogens. We propose rules for estimating the risks associated with genes that are present in environmental resistomes by evaluating the likelihood of their introduction into human pathogens, and the consequences of such events for the treatment of infections.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Anti-Bacterial Agents / pharmacology*
  • Bacteria / drug effects
  • Bacteria / genetics*
  • Bacteria / metabolism*
  • Bacterial Infections / epidemiology
  • Bacterial Infections / microbiology
  • Drug Resistance, Bacterial / genetics*
  • Environmental Microbiology
  • Gene Expression Regulation, Bacterial
  • Gene Transfer, Horizontal
  • Humans


  • Anti-Bacterial Agents