Country-specific antibiotic use practices impact the human gut resistome
- Kristoffer Forslund1,
- Shinichi Sunagawa1,
- Jens Roat Kultima1,
- Daniel R. Mende1,
- Manimozhiyan Arumugam1,2,3,
- Athanasios Typas1 and
- Peer Bork1,4
- 1European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
- 2The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, DK 2100, Copenhagen, Denmark;
- 3BGI-Shenzhen, Shenzhen 518083, China
Abstract
Despite increasing concerns over inappropriate use of antibiotics in medicine and food production, population-level resistance transfer into the human gut microbiota has not been demonstrated beyond individual case studies. To determine the “antibiotic resistance potential” for entire microbial communities, we employ metagenomic data and quantify the totality of known resistance genes in each community (its resistome) for 68 classes and subclasses of antibiotics. In 252 fecal metagenomes from three countries, we show that the most abundant resistance determinants are those for antibiotics also used in animals and for antibiotics that have been available longer. Resistance genes are also more abundant in samples from Spain, Italy, and France than from Denmark, the United States, or Japan. Where comparable country-level data on antibiotic use in both humans and animals are available, differences in these statistics match the observed resistance potential differences. The results are robust over time as the antibiotic resistance determinants of individuals persist in the human gut flora for at least a year.
Footnotes
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↵4 Corresponding author
E-mail bork{at}embl.de
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.155465.113.
- Received January 28, 2013.
- Accepted April 3, 2013.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.