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Prioritizing risks of antibiotic resistance genes in all metagenomes

Nature Reviews Microbiology volume 13, page 396 (2015)Cite this article

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We have read with interest the Correspondence on our Opinion article (What is a resistance gene? Ranking risks in resistomes. Nature Rev. Microbiol. 13, 116–123 (2015))1 by Bengtsson-Palme and Larsson (Antibiotic resistance genes in the environment: prioritizing risks Nature Rev. Microbiol. http://dx.doi.org/10.1038/nrmicro3399-c1)2 and appreciate the observations raised by the authors. As they acknowledge, our article proposes the first framework (termed resistance readiness condition (RESCon)) for evaluating the risks associated with the presence of antibiotic resistance genes in bacterial metagenomes. Here, we wish to clarify and refine some of the arguments that this framework is based on.

The framework we propose relies on two fundamental principles: the likelihood of a known antibiotic resistance gene having a harmful effect on human health (during antibiotic therapy) and whether or not it is likely to transfer to human pathogens (the probability of which increases if it is located on a mobile genetic element). Following this scheme, we consider those resistance genes that are present on mobile elements and for which a role in resistance in human pathogens has been demonstrated to represent the highest risk (defined as RESCon 1). Novel resistance genes are ascribed a lower risk category in our framework if there is no evidence that they have a detrimental influence on the outcome of antibiotic therapy (RESCon 3), whereas the risk is scored higher (RESCon 2) if they are associated with mobile elements. In their Correspondence, Bengtsson-Palme and Larsson suggest that risk order should be reversed in our scheme, such that novel resistance genes present a higher risk because known resistance determinants are likely to be widespread and thus, their propensity to transfer to a pathogen would be minimal. Although this seems like a reasonable argument, in our view, current knowledge of the ecology of antibiotic resistance does not support a change in our risk-assessment scheme.

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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 Spain; and the Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al CSIC, Madrid, Spain.,

    José L. Martínez

  2. and the Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al 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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  1. José L. Martínez
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Correspondence to José L. Martínez.

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Martínez, J., Coque, T. & Baquero, F. Prioritizing risks of antibiotic resistance genes in all metagenomes. Nat Rev Microbiol 13, 396 (2015). https://doi.org/10.1038/nrmicro3399-c2

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