Article CC BY 4.0
refereed
published

Genomic evolution of antimicrobial resistance in Escherichia coli

Affiliation
National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, Kgs. Lyngby, Denmark
Leekitcharoenphon, Pimlapas;
Affiliation
National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, Kgs. Lyngby, Denmark
Johansson, Markus Hans Kristofer;
Affiliation
National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, Kgs. Lyngby, Denmark
Munk, Patrick;
Affiliation
German Federal Institute for Risk Assessment (BfR), Department 4 Biological Safety, Study Centre 4SZ - Genome Sequencing and Analysis, Germany
Malorny, Burkhard;
Affiliation
National Veterinary Research Institute, Puławy, Poland
Skarżyńska, Magdalena;
Affiliation
University of Veterinary Medicine Hannover, Bakum, Germany
Wadepohl, Katharina;
Affiliation
Department of Animal Health and Health Surveillance Center (VISAVET), Complutense University of Madrid, Madrid, Spain
Moyano, Gabriel;
Affiliation
Wageningen Bioveterinary Research, Lelystad, Netherlands
Hesp, Ayla;
Affiliation
Wageningen Bioveterinary Research, Lelystad, Netherlands
Veldman, Kees T.;
Affiliation
Wageningen Bioveterinary Research, Lelystad, Netherlands
Bossers, Alex;
Affiliation
Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
Graveland, Haitske;
Affiliation
Wageningen Bioveterinary Research, Lelystad, Netherlands
van Essen, Alieda;
Affiliation
Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio E Della Toscana, National Reference Laboratory for Antimicrobial Resistance, Rome, Italy
Battisti, Antonio;
Affiliation
Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio E Della Toscana, National Reference Laboratory for Antimicrobial Resistance, Rome, Italy
Caprioli, Andrea;
Affiliation
National Veterinary Research Institute, Puławy, Poland
Blaha, Thomas;
Affiliation
National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, Kgs. Lyngby, Denmark
Hald, Tine;
Affiliation
National Diagnostic Research Veterinary Institute, Sofia, Bulgaria
Daskalov, Hristo;
Affiliation
Wageningen Bioveterinary Research, Lelystad, Netherlands
Saatkamp, Helmut W.;
Affiliation
SAFOSO AG, Liebefeld, Switzerland
Stärk, Katharina D. C.;
Affiliation
Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
Luiken, Roosmarijn E. C.;
Affiliation
Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
Van Gompel, Liese;
Affiliation
Intomics A/S, Diplomvej 377, Kongens Lyngby, Denmark
Hansen, Rasmus Borup;
Affiliation
Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke, Belgium
Dewulf, Jeroen;
Affiliation
National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, Kgs. Lyngby, Denmark
Duarte, Ana Sofia Ribeiro;
Affiliation
National Veterinary Research Institute, Puławy, Poland
Zając, Magdalena;
Affiliation
National Veterinary Research Institute, Puławy, Poland
Wasyl, Dariusz;
Affiliation
Fougeres Laboratory, French Agency for Food, Environmental and Occupational Health and Safety, Fougères, France
Sanders, Pascal;
Affiliation
Department of Animal Health and Health Surveillance Center (VISAVET), Complutense University of Madrid, Madrid, Spain
Gonzalez-Zorn, Bruno;
Affiliation
Wageningen Bioveterinary Research, Lelystad, Netherlands
Brouwer, Michael S. M.;
Affiliation
Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
Wagenaar, Jaap A.;
Affiliation
Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
Heederik, Dick J. J.;
Affiliation
Wageningen Bioveterinary Research, Lelystad, Netherlands
Mevius, Dik;
Affiliation
National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, Kgs. Lyngby, Denmark
Aarestrup, Frank M.

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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