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Genomic evolution of antimicrobial resistance in Escherichia coli

Authors :: Leekitcharoenphon, Pimlapas
Johansson, Markus Hans Kristofer
Munk, Patrick
Malorny, Burkhard
Skarzynska, Magdalena
Wadepohl, Katharina
Moyano, Gabriel
Hesp, Ayla
Veldman, Kees T.
Bossers, Alex
Graveland, Haitske
van Essen, Alieda
Battisti, Antonio
Caprioli, Andrea
Blaha, Thomas
Hald, Tine
Daskalov, Hristo
Saatkamp, Helmut W.
Staerk, Katharina D. C.
Luiken, Roosmarijn E. C.
Van Gompel, Liese
Hansen, Rasmus Borup
Dewulf, Jeroen
Duarte, Ana Sofia Ribeiro
Zajac, Magdalena
Wasyl, Dariusz
Sanders, Pascal
Gonzalez-Zorn, Bruno
Brouwer, Michael S. M.
Wagenaar, Jaap A.
Heederik, Dick J. J.
Mevius, Dik
Aarestrup, Frank M.
EFFORT Consortium, for the
Technical University of Denmark [Lyngby] (DTU)
Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR)
Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM)
Wageningen BioVeterinary Research
Wageningen University and Research [Wageningen] (WUR)
Laboratoire de Fougères - ANSES
Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
European Project: 613754,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,EFFORT(2013)
Danmarks Tekniske Universitet = Technical University of Denmark (DTU)
IRAS OH Epidemiology Microbial Agents
Klinische infectiologie en microb. lab.
dI&I I&I-4
dIRAS RA-I&I RA
Faculteit Diergeneeskunde
Source :: Scientific Reports, Vol 11, Iss 1, Pp 1-12 (2021), Scientific Reports, Scientific Reports, Nature Publishing Group, 2021, 11 (1), pp.15108. ⟨10.1038/s41598-021-93970-7⟩, SCIENTIFIC REPORTS, Scientific Reports, 2021, 11 (1), pp.15108. ⟨10.1038/s41598-021-93970-7⟩, Scientific Reports 11 (2021), Scientific Reports, 11(1). NLM (Medline), Scientific Reports, 11, Leekitcharoenphon, P, Johansson, M H K, Munk, P, Malorny, B, Skarżyńska, M, Wadepohl, K, Moyano, G, Hesp, A, Veldman, K T, Bossers, A, Graveland, H, van Essen, A, Battisti, A, Caprioli, A, Blaha, T, Hald, T, Daskalov, H, Saatkamp, H W, Stärk, K D C, Luiken, R E C, Van Gompel, L, Hansen, R B, Dewulf, J, Duarte, A S R, Zając, M, Wasyl, D, Sanders, P, Gonzalez-Zorn, B, Brouwer, M S M, Wagenaar, J A, Heederik, D J J, Mevius, D, Aarestrup, F M & consortium, EFFORT 2021, ' Genomic evolution of antimicrobial resistance in Escherichia coli ', Scientific Reports, vol. 11, 15108 . https://doi.org/10.1038/s41598-021-93970-7
Publication Year :: 2021
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.