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What is a resistance gene? Ranking risk in resistomes

Nature Reviews Microbiology volume 13, pages 116–123 (2015)Cite this article

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Abstract

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.

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Figure 1: Determination of epidemiological breakpoints of susceptibility to antibiotics.
Figure 2: Ranking the risks of detection of resistance genes in resistomes.

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Acknowledgements

Research in the author's laboratories is funded by the European Commission (EvoTAR-282004 for JLM, TMC and FB), the Ministry of Economy and Competitiveness (BIO2011-25255 for JLM, PI12-01581 for TMC, PI10-02588 for FB, and NEXTMICRO for FB and TMC), the Regional Government of Madrid in Spain (PROMPT-S2010/BMD2414 for JLM and FB), and by the Spanish Network for Research on Infectious Diseases (REIPI RD12/0015 for JLM) and the Spanish Network for the Study of Plasmids and Extrachromosomal Elements (REDEEX, BFU2011-14145-E for TMC).

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Authors and Affiliations

  1. Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Cantoblanco,Madrid 28049, Spain; and the Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,

    José L. Martínez

  2. and the Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,

    José L. Martínez

  3. Spain; and the Departamento de Microbiología, Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid 28034, Spain.,

    Teresa M. Coque & Fernando Baquero

  4. and the Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid 28034, Spain.,

    Teresa M. Coque & Fernando Baquero

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Correspondence to José L. Martínez.

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Martínez, J., Coque, T. & Baquero, F. What is a resistance gene? Ranking risk in resistomes. Nat Rev Microbiol 13, 116–123 (2015). https://doi.org/10.1038/nrmicro3399

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