Country-specific antibiotic use practices impact the human gut resistome

Kristoffer Forslund; Shinichi Sunagawa; Jens Roat Kultima; Daniel R Mende; Manimozhiyan Arumugam; Athanasios Typas; Peer Bork

doi:10.1101/gr.155465.113

Country-specific antibiotic use practices impact the human gut resistome

Kristoffer Forslund, Shinichi Sunagawa, Jens Roat Kultima, Daniel R Mende, Manimozhiyan Arumugam, Athanasios Typas, Peer Bork

219 Citations (Scopus)

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.

Original language	English
Journal	Genome Research
Volume	23
Issue number	7
Pages (from-to)	1163-9
Number of pages	7
ISSN	1088-9051
DOIs	https://doi.org/10.1101/gr.155465.113
Publication status	Published - Jul 2013

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title = "Country-specific antibiotic use practices impact the human gut resistome",

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.",

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T1 - Country-specific antibiotic use practices impact the human gut resistome

AU - Forslund, Kristoffer

AU - Sunagawa, Shinichi

AU - Kultima, Jens Roat

AU - Mende, Daniel R

AU - Arumugam, Manimozhiyan

AU - Typas, Athanasios

AU - Bork, Peer

PY - 2013/7

Y1 - 2013/7

N2 - 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.

AB - 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.

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Country-specific antibiotic use practices impact the human gut resistome

Abstract

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