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Genomic evolution of antimicrobial resistance in Escherichia coli

Scientific reports publish this investigation article

July 23rd, 2021

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




Leekitcharoenphon P., Hans Kristofer Johansson M., Munk P., Malorny B., Skarzynska M., Wadepohl K., Moyano G., Hesp A., Veldman KT., Bossers A., EFFORT Consortium., Zajac M., Wasyl D., Sanders P., Gonzalez-Zorn B., Brouwer A., Wagenaar J., Heederik D., Mevius D. and Aarestrup FM.




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Genomic evolution of antimicrobial resistance in Escherichia coli

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Genomic evolution of antimicrobial resistance in Escherichia coli



Participants:

Technical University of DenmarkNational Food Institute (DTU Food). Technical University of Denmark (DTU).

Department Biological Safety. German Federal Institute for Risk Assessment.

National Veterinary Research Institute (PIWET).

University of Veterinary Medicine Hannover (TiHo).

Universidad ComplutenseServicio de Zoonosis de Transmisión Alimentaria y Resistencia a Antimicrobianos (ZTA). Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Universidad Complutense (UCM).

Universidad ComplutenseDepartamento de Sanidad Animal. Facultad de Veterinaria. Universidad Complutense (UCM).

Wageningen Bioveterinary Research.

Utrecht UniversityInstitute for Risk Assessment Sciences. Utrecht University (UU).

French Agency for Food. Environmental and Occupational Safety. National Agency for Veterinary Medicinal Products.

Utrecht UniversityDepartment of Infectious Diseases and Immunology. Faculty of Veterinary Medicine. Utrecht University (UU).







Scientific reports
FACTOR YEAR Q
4.379 2020

NLMID: 101563288

PMID: 34301966

ISSN: 2045-2322



TITLE: Genomic evolution of antimicrobial resistance in Escherichia coli


JOURNAL: Sci Rep


NUMERACIÓN: 11(1):15108


AÑO: 2021


PUBLISHER: Nature Publishing Group


AUTHORS: Leekitcharoenphon P., Hans Kristofer Johansson M., Munk P., Malorny B., Skarzynska M., Wadepohl K., Moyano G., Hesp A., Veldman KT., Bossers A., EFFORT Consortium., Zajac M., Wasyl D., Sanders P., Gonzalez-Zorn B., Brouwer A., Wagenaar J., Heederik D., Mevius D. and Aarestrup FM.


VISAVET PARTICIPANTS


Bruno González Zorn

DOI: https://doi.org/10.1038/s41598-021-93970-7


CITE THIS PUBLICATION:

Leekitcharoenphon P., Hans Kristofer Johansson M., Munk P., Malorny B., Skarzynska M., Wadepohl K., Moyano G., Hesp A., Veldman KT., Bossers A., EFFORT Consortium., Zajac M., Wasyl D., Sanders P., Gonzalez-Zorn B., Brouwer A., Wagenaar J., Heederik D., Mevius D. and Aarestrup FM. Genomic evolution of antimicrobial resistance in Escherichia coli. Scientific reports. 11(1):15108. 2021. (A). ISSN: 2045-2322. DOI: 10.1038/s41598-021-93970-7


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