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Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance
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Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

Published on: May 2, 2018

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Genomic evolution of antimicrobial resistance in Escherichia coli

Pimlapas Leekitcharoenphon1, Markus Hans Kristofer Johansson2, Patrick Munk2

  • 1National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800, Kgs. Lyngby, Denmark. pile@food.dtu.dk.

Scientific Reports
|July 24, 2021
PubMed

Insights

Antimicrobial resistance (AMR) in Escherichia coli is a global threat. Mobile genetic elements facilitate AMR gene spread, and metagenomics shows promise for AMR surveillance in poultry.

Area of Science:

  • Microbiology
  • Genomics
  • Public Health

Background:

  • Antimicrobial resistance (AMR) is a significant global health challenge.
  • The intestinal microbiota and mobile genetic elements (MGEs) play key roles in AMR emergence and spread.
  • Escherichia coli is a relevant model organism for studying AMR in food-producing animals.

Purpose of the Study:

  • To investigate the phylogeny of Escherichia coli (E. coli) across different European countries, animal hosts, and farms.
  • To examine the evolution of AMR in E. coli, including associations with virulence genes, plasmids, and MGEs.
  • To compare metagenomic sequencing with whole-genome sequencing for AMR surveillance.

Main Methods:

  • Isolation of E. coli from fecal samples of poultry, swine, and veal calves across six European countries.
  • Whole-genome sequencing of E. coli isolates.
  • Metagenomic sequencing of fecal samples.
  • Phylogenetic analysis and comparative genomics to identify AMR, virulence genes, and MGEs.

Main Results:

  • E. coli isolates showed no clear clonality or clustering based on country, host, or genetic markers.
  • Mobile genetic elements were found to be associated with the acquisition of AMR and virulence genes.
  • Metagenomic and whole-genome sequencing showed agreement in AMR abundance for several classes in poultry, suggesting metagenomics as a potential surveillance tool.

Conclusions:

  • Phylogenetic analysis did not reveal distinct E. coli clusters based on origin or genetic markers.
  • MGEs are crucial facilitators of AMR and virulence gene acquisition in E. coli.
  • Metagenomic sequencing offers a viable approach for monitoring AMR in E. coli, particularly in poultry farming contexts.

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