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, Haitske Graveland (Member of author collaboration), Alieda van Essen (Member of author collaboration), Antonio Battisti (Member of author collaboration), Andrea Caprioli (Member of author collaboration), Thomas Blaha (Member of author collaboration), Tine Hald (Member of author collaboration), Hristo Daskalov (Member of author collaboration), Helmut W. Saatkamp (Member of author collaboration), Katharina D.C. Stärk (Member of author collaboration), Roosmarijn E.C. Luiken (Member of author collaboration)Liese Van Gompel (Member of author collaboration), Rasmus Borup Hansen (Member of author collaboration), Jeroen Dewulf (Member of author collaboration), Ana Sofia Ribeiro Duarte (Member of author collaboration), 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, EFFORT consortium

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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
JournalScientific Reports
Volume11
Number of pages12
ISSN2045-2322
DOIs
Publication statusPublished - 2021

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