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Journal Articles Scientific Reports Year : 2021

Genomic evolution of antimicrobial resistance in Escherichia coli

Patrick Munk
Magdalena Skarżyńska
  • Function : Author
Katharina Wadepohl
  • Function : Author
Haitske Graveland
  • Function : Contributor
Alieda van Essen
  • Function : Contributor
Antonio Battisti
  • Function : Contributor
Andrea Caprioli
  • Function : Contributor
Thomas Blaha
  • Function : Contributor
Tine Hald
  • Function : Contributor
Hristo Daskalov
  • Function : Contributor
Helmut W Saatkamp
  • Function : Contributor
Katharina D C Stärk
  • Function : Contributor
Roosmarijn E C Luiken
  • Function : Contributor
Liese van Gompel
Rasmus Borup Hansen
  • Function : Contributor
Jeroen Dewulf
Ana Sofia Ribeiro Duarte
  • Function : Contributor
Magdalena Zając
Dariusz Wasyl
  • Function : Author
Bruno Gonzalez-Zorn
  • Function : Author
Michael S M Brouwer
  • Function : Author
Jaap A Wagenaar
  • Function : Author
Dick J J Heederik
  • Function : Author
Dik Mevius
  • Function : Author
Frank M Aarestrup


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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Dates and versions

anses-03444491 , version 1 (23-11-2021)





Pimlapas Leekitcharoenphon, Markus Hans Kristofer Johansson, Patrick Munk, Burkhard Malorny, Magdalena Skarżyńska, et al.. Genomic evolution of antimicrobial resistance in Escherichia coli. Scientific Reports, 2021, 11 (1), pp.15108. ⟨10.1038/s41598-021-93970-7⟩. ⟨anses-03444491⟩


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