Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

ISME J. 2015 Jun;9(6):1269-79. doi: 10.1038/ismej.2014.226. Epub 2014 Dec 12.


Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.

Publication types

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

MeSH terms

  • Anti-Bacterial Agents / chemistry
  • Bacteria / drug effects
  • Bacteria / genetics*
  • DNA Transposable Elements
  • Drug Resistance, Bacterial
  • Environmental Monitoring / methods*
  • Environmental Pollution*
  • Gene Transfer, Horizontal
  • Genetic Variation
  • Integrases / genetics*
  • Integrons / genetics*
  • Metals, Heavy / analysis*


  • Anti-Bacterial Agents
  • DNA Transposable Elements
  • Metals, Heavy
  • Integrases