Genomic evolution of antimicrobial resistance in Escherichia coli

Abstract The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiot...

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Autores principales:	Pimlapas Leekitcharoenphon, Markus Hans Kristofer Johansson, Patrick Munk, Burkhard Malorny, Magdalena Skarżyńska, Katharina Wadepohl, Gabriel Moyano, Ayla Hesp, Kees T. Veldman, Alex Bossers, EFFORT Consortium, Magdalena Zając, Dariusz Wasyl, Pascal Sanders, Bruno Gonzalez-Zorn, Michael S. M. Brouwer, Jaap A. Wagenaar, Dick J. J. Heederik, Dik Mevius, Frank M. Aarestrup
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0b2d5832891146169401e3aaa32a2ff5
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spelling	oai:doaj.org-article:0b2d5832891146169401e3aaa32a2ff52021-12-02T17:56:56ZGenomic evolution of antimicrobial resistance in Escherichia coli10.1038/s41598-021-93970-72045-2322https://doaj.org/article/0b2d5832891146169401e3aaa32a2ff52021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93970-7https://doaj.org/toc/2045-2322Abstract The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.Pimlapas LeekitcharoenphonMarkus Hans Kristofer JohanssonPatrick MunkBurkhard MalornyMagdalena SkarżyńskaKatharina WadepohlGabriel MoyanoAyla HespKees T. VeldmanAlex BossersEFFORT ConsortiumMagdalena ZającDariusz WasylPascal SandersBruno Gonzalez-ZornMichael S. M. BrouwerJaap A. WagenaarDick J. J. HeederikDik MeviusFrank M. AarestrupNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pimlapas Leekitcharoenphon Markus Hans Kristofer Johansson Patrick Munk Burkhard Malorny Magdalena Skarżyńska Katharina Wadepohl Gabriel Moyano Ayla Hesp Kees T. Veldman Alex Bossers EFFORT Consortium Magdalena Zając Dariusz Wasyl Pascal Sanders Bruno Gonzalez-Zorn Michael S. M. Brouwer Jaap A. Wagenaar Dick J. J. Heederik Dik Mevius Frank M. Aarestrup Genomic evolution of antimicrobial resistance in Escherichia coli
description	Abstract The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.
format	article
author	Pimlapas Leekitcharoenphon Markus Hans Kristofer Johansson Patrick Munk Burkhard Malorny Magdalena Skarżyńska Katharina Wadepohl Gabriel Moyano Ayla Hesp Kees T. Veldman Alex Bossers EFFORT Consortium Magdalena Zając Dariusz Wasyl Pascal Sanders Bruno Gonzalez-Zorn Michael S. M. Brouwer Jaap A. Wagenaar Dick J. J. Heederik Dik Mevius Frank M. Aarestrup
author_facet	Pimlapas Leekitcharoenphon Markus Hans Kristofer Johansson Patrick Munk Burkhard Malorny Magdalena Skarżyńska Katharina Wadepohl Gabriel Moyano Ayla Hesp Kees T. Veldman Alex Bossers EFFORT Consortium Magdalena Zając Dariusz Wasyl Pascal Sanders Bruno Gonzalez-Zorn Michael S. M. Brouwer Jaap A. Wagenaar Dick J. J. Heederik Dik Mevius Frank M. Aarestrup
author_sort	Pimlapas Leekitcharoenphon
title	Genomic evolution of antimicrobial resistance in Escherichia coli
title_short	Genomic evolution of antimicrobial resistance in Escherichia coli
title_full	Genomic evolution of antimicrobial resistance in Escherichia coli
title_fullStr	Genomic evolution of antimicrobial resistance in Escherichia coli
title_full_unstemmed	Genomic evolution of antimicrobial resistance in Escherichia coli
title_sort	genomic evolution of antimicrobial resistance in escherichia coli
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/0b2d5832891146169401e3aaa32a2ff5
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Genomic evolution of antimicrobial resistance in Escherichia coli

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