Genomic evolution of antimicrobial resistance in Escherichia coli

Pimlapas Leekitcharoenphon, Markus Hans Kristofer Johansson, Patrick Munk, Burkhard Malorny, Magdalena Skarżyńska, Katharina Wadepohl, Gabriel Moyano, Ayla Hesp, Kees T Veldman, Alex Bossers, Magdalena Zając, Dariusz Wasyl, Bruno Gonzalez-Zorn, Pascal Sanders, Michael S M Brouwer, Jaap A Wagenaar, Dick J J Heederik, Dik Mevius, EFFORT consortium , Frank M Aarestrup

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
Article number15108
Number of pages12
JournalScientific Reports
Volume11
Issue number1
DOIs
Publication statusPublished - Dec 2021

Bibliographical note

Funding Information:
This work was supported by the European Union-funded EFFORT project (www.effort-against-amr.eu) (FP7-KBBE-2013-7, Grant Agreement 613754). By the EJP-one health project Full-force (Grant Agreement No. 773830) and by The Novo Nordisk Foundation (NNF16OC0021856: Global Surveillance of Antimicrobial Resistance). In addition, whole-genome sequencing done at National Veterinary Research Institute was possible due to support of Department of Omics Analyses from the Ministry of Science and Higher Education (Grant No. 4477/E-180/SPUB/2018).

Publisher Copyright:
© 2021, The Author(s).

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