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Genomic evolution of antimicrobial resistance in Escherichia coli

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 be...

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Autores principales: Leekitcharoenphon, Pimlapas, Johansson, Markus Hans Kristofer, Munk, Patrick, Malorny, Burkhard, Skarżyńska, Magdalena, Wadepohl, Katharina, Moyano, Gabriel, Hesp, Ayla, Veldman, Kees T., Bossers, Alex, Zając, Magdalena, Wasyl, Dariusz, Sanders, Pascal, Gonzalez-Zorn, Bruno, Brouwer, Michael S. M., Wagenaar, Jaap A., Heederik, Dick J. J., Mevius, Dik, Aarestrup, Frank M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8302606/
https://www.ncbi.nlm.nih.gov/pubmed/34301966
http://dx.doi.org/10.1038/s41598-021-93970-7
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author Leekitcharoenphon, Pimlapas
Johansson, Markus Hans Kristofer
Munk, Patrick
Malorny, Burkhard
Skarżyńska, Magdalena
Wadepohl, Katharina
Moyano, Gabriel
Hesp, Ayla
Veldman, Kees T.
Bossers, Alex
Zając, Magdalena
Wasyl, Dariusz
Sanders, Pascal
Gonzalez-Zorn, Bruno
Brouwer, Michael S. M.
Wagenaar, Jaap A.
Heederik, Dick J. J.
Mevius, Dik
Aarestrup, Frank M.
author_facet Leekitcharoenphon, Pimlapas
Johansson, Markus Hans Kristofer
Munk, Patrick
Malorny, Burkhard
Skarżyńska, Magdalena
Wadepohl, Katharina
Moyano, Gabriel
Hesp, Ayla
Veldman, Kees T.
Bossers, Alex
Zając, Magdalena
Wasyl, Dariusz
Sanders, Pascal
Gonzalez-Zorn, Bruno
Brouwer, Michael S. M.
Wagenaar, Jaap A.
Heederik, Dick J. J.
Mevius, Dik
Aarestrup, Frank M.
author_sort Leekitcharoenphon, Pimlapas
collection PubMed
description 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.
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spelling pubmed-83026062021-07-27 Genomic evolution of antimicrobial resistance in Escherichia coli Leekitcharoenphon, Pimlapas Johansson, Markus Hans Kristofer Munk, Patrick Malorny, Burkhard Skarżyńska, Magdalena Wadepohl, Katharina Moyano, Gabriel Hesp, Ayla Veldman, Kees T. Bossers, Alex Zając, Magdalena Wasyl, Dariusz Sanders, Pascal Gonzalez-Zorn, Bruno Brouwer, Michael S. M. Wagenaar, Jaap A. Heederik, Dick J. J. Mevius, Dik Aarestrup, Frank M. Sci Rep Article 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. Nature Publishing Group UK 2021-07-23 /pmc/articles/PMC8302606/ /pubmed/34301966 http://dx.doi.org/10.1038/s41598-021-93970-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Leekitcharoenphon, Pimlapas
Johansson, Markus Hans Kristofer
Munk, Patrick
Malorny, Burkhard
Skarżyńska, Magdalena
Wadepohl, Katharina
Moyano, Gabriel
Hesp, Ayla
Veldman, Kees T.
Bossers, Alex
Zając, Magdalena
Wasyl, Dariusz
Sanders, Pascal
Gonzalez-Zorn, Bruno
Brouwer, Michael S. M.
Wagenaar, Jaap A.
Heederik, Dick J. J.
Mevius, Dik
Aarestrup, Frank M.
Genomic evolution of antimicrobial resistance in Escherichia coli
title 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_short Genomic evolution of antimicrobial resistance in Escherichia coli
title_sort genomic evolution of antimicrobial resistance in escherichia coli
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8302606/
https://www.ncbi.nlm.nih.gov/pubmed/34301966
http://dx.doi.org/10.1038/s41598-021-93970-7
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