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. 2019 Feb 26;10:212. doi: 10.3389/fmicb.2019.00212

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Copyright © 2019 Allemann, Kraemer, Korten, Ramsey, Casaulta, Wüthrich, Ramette, Endimiani, Latzin and Hilty.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Antimicrobial resistance genes (ARG) and the related phyla. We related all identified ARG (n = 171) to the closest bacterial phyla using RAIphy on the contigs sequences obtained. Protein sequences were grouped according the main following families: β-lactamases (with Ambler classification), dihydrofolate reductases, thymidylate synthase, ribosomal protection protein, acetyltransferase, transporters/efflux pumps (ABC, MSF or others) and non-described proteins. We reveal the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, while other phyla are grouped into the “others.” (A) The majority of ARG came from Proteobacteria and Firmicutes. (B) Classes A and B β-lactamases were related to Proteobacteria, Firmicutes or Bacteroidetes while class C and D were exclusively related to Proteobacteria.