Diverse Antibiotic Resistance Genes in Dairy Cow Manure

ABSTRACT Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limite...

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Autores principales:	Fabienne Wichmann, Nikolina Udikovic-Kolic, Sheila Andrew, Jo Handelsman
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/8ac6f10ad22a4363b23a7da0a0d3942f
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spelling	oai:doaj.org-article:8ac6f10ad22a4363b23a7da0a0d3942f2021-11-15T15:45:13ZDiverse Antibiotic Resistance Genes in Dairy Cow Manure10.1128/mBio.01017-132150-7511https://doaj.org/article/8ac6f10ad22a4363b23a7da0a0d3942f2014-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01017-13https://doaj.org/toc/2150-7511ABSTRACT Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings. IMPORTANCE The increasing prevalence of antibiotic resistance among bacteria is one of the most intractable challenges in 21st-century public health. The origins of resistance are complex, and a better understanding of the impacts of antibiotics used on farms would produce a more robust platform for public policy. Microbiomes of farm animals are reservoirs of antibiotic resistance genes, which may affect distribution of antibiotic resistance genes in human pathogens. Previous studies have focused on antibiotic resistance genes in manures of animals subjected to intensive antibiotic use, such as pigs and chickens. Cow manure has received less attention, although it is commonly used in crop production. Here, we report the discovery of novel and diverse antibiotic resistance genes in the cow microbiome, demonstrating that it is a significant reservoir of antibiotic resistance genes. The genomic resource presented here lays the groundwork for understanding the dispersal of antibiotic resistance from the agroecosystem to other settings.Fabienne WichmannNikolina Udikovic-KolicSheila AndrewJo HandelsmanAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 2 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Fabienne Wichmann Nikolina Udikovic-Kolic Sheila Andrew Jo Handelsman Diverse Antibiotic Resistance Genes in Dairy Cow Manure
description	ABSTRACT Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings. IMPORTANCE The increasing prevalence of antibiotic resistance among bacteria is one of the most intractable challenges in 21st-century public health. The origins of resistance are complex, and a better understanding of the impacts of antibiotics used on farms would produce a more robust platform for public policy. Microbiomes of farm animals are reservoirs of antibiotic resistance genes, which may affect distribution of antibiotic resistance genes in human pathogens. Previous studies have focused on antibiotic resistance genes in manures of animals subjected to intensive antibiotic use, such as pigs and chickens. Cow manure has received less attention, although it is commonly used in crop production. Here, we report the discovery of novel and diverse antibiotic resistance genes in the cow microbiome, demonstrating that it is a significant reservoir of antibiotic resistance genes. The genomic resource presented here lays the groundwork for understanding the dispersal of antibiotic resistance from the agroecosystem to other settings.
format	article
author	Fabienne Wichmann Nikolina Udikovic-Kolic Sheila Andrew Jo Handelsman
author_facet	Fabienne Wichmann Nikolina Udikovic-Kolic Sheila Andrew Jo Handelsman
author_sort	Fabienne Wichmann
title	Diverse Antibiotic Resistance Genes in Dairy Cow Manure
title_short	Diverse Antibiotic Resistance Genes in Dairy Cow Manure
title_full	Diverse Antibiotic Resistance Genes in Dairy Cow Manure
title_fullStr	Diverse Antibiotic Resistance Genes in Dairy Cow Manure
title_full_unstemmed	Diverse Antibiotic Resistance Genes in Dairy Cow Manure
title_sort	diverse antibiotic resistance genes in dairy cow manure
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/8ac6f10ad22a4363b23a7da0a0d3942f
work_keys_str_mv	AT fabiennewichmann diverseantibioticresistancegenesindairycowmanure AT nikolinaudikovickolic diverseantibioticresistancegenesindairycowmanure AT sheilaandrew diverseantibioticresistancegenesindairycowmanure AT johandelsman diverseantibioticresistancegenesindairycowmanure
_version_	1718427597388382208

Diverse Antibiotic Resistance Genes in Dairy Cow Manure

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