Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

François Enault, Arnaud Briet, Léa Bouteille, Simon Roux, Matthew B. Sullivan, View ORCID ProfileMarie-Agnès Petit
doi: https://doi.org/10.1101/053025
François Enault
1Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes: Génome et Environnement,”, Clermont-Ferrand, France
2CNRS UMR 6023, LMGE, Aubière, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Arnaud Briet
3Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Léa Bouteille
3Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simon Roux
4Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Matthew B. Sullivan
4Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
5Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marie-Agnès Petit
3Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Marie-Agnès Petit
  • For correspondence: marie-agnes.petit@jouy.inra.fr
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Antibiotic resistance genes (ARG) are pervasive in gut microbiota, but it remains unclear how often ARG are transferred, particularly to pathogens. Traditionally, ARG spread is attributed to horizontal transfer mediated either by DNA transformation, bacterial conjugation or generalized transduction. However, recent viral metagenome (virome) analyses suggest that ARG are frequently carried by phages, which is inconsistent with the traditional view that phage genomes rarely encode ARG. Here we used exploratory and conservative bioinformatic strategies found in the literature to detect ARG in phage genomes, and experimentally assessed a subset of ARG predicted using exploratory thresholds. ARG abundances in 1,181 phage genomes were vastly over-estimated using exploratory thresholds (421 predicted vs 2 known), due to low similarities and matches to protein unrelated to antibiotic resistance. Consistent with this, 4 ARG predicted using exploratory thresholds were experimentally evaluated and failed to confer antibiotic resistance in Escherichia coli. Re-analysis of available human-or mouse-associated viromes for ARG and their genomic context suggested that bona fide ARG attributed to phages in viromes were previously over-estimated. These findings provide guidance for documentation of ARG in viromes, and re-assert that ARG are rarely encoded in phages.

Footnotes

  • Conflict of interest. The authors declare no conflict of interest.

  • Financial support: This work was supported in part by the French ANR grant Dynamophage to MAP and AB, the Gordon and Betty Moore Foundation grants (#2631, 3790) and the University of Arizona Technology and Research Initiative Fund through the Water, Environmental and Energy Solutions Initiative to MBS.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted May 12, 2016.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
François Enault, Arnaud Briet, Léa Bouteille, Simon Roux, Matthew B. Sullivan, Marie-Agnès Petit
bioRxiv 053025; doi: https://doi.org/10.1101/053025
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
François Enault, Arnaud Briet, Léa Bouteille, Simon Roux, Matthew B. Sullivan, Marie-Agnès Petit
bioRxiv 053025; doi: https://doi.org/10.1101/053025

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Ecology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3482)
  • Biochemistry (7329)
  • Bioengineering (5301)
  • Bioinformatics (20212)
  • Biophysics (9985)
  • Cancer Biology (7706)
  • Cell Biology (11273)
  • Clinical Trials (138)
  • Developmental Biology (6425)
  • Ecology (9923)
  • Epidemiology (2065)
  • Evolutionary Biology (13292)
  • Genetics (9353)
  • Genomics (12559)
  • Immunology (7681)
  • Microbiology (18964)
  • Molecular Biology (7421)
  • Neuroscience (40915)
  • Paleontology (298)
  • Pathology (1226)
  • Pharmacology and Toxicology (2130)
  • Physiology (3145)
  • Plant Biology (6842)
  • Scientific Communication and Education (1271)
  • Synthetic Biology (1893)
  • Systems Biology (5299)
  • Zoology (1086)