Genomic evolution of antimicrobial resistance in Escherichia coli

Pimlapas Leekitcharoenphon; M.H.K. Johansson; P. Munk; B. Malorny; Magdalena Skarzyńska; Katharina Wadepohl; Gabriel Moyano; A. Hesp; K.T. Veldman; A. Bossers; Magdalena Zajac; Dariusz Wasyl; P. Sanders; B. Gonzales-Zorn; M.S.M. Brouwer; J.A. Wagenaar; D.J.J. Heederik; D.J. Mevius; F.M. Aarestrup

doi:10.1038/s41598-021-93970-7

Genomic evolution of antimicrobial resistance in Escherichia coli

Pimlapas Leekitcharoenphon^*, M.H.K. Johansson, P. Munk, B. Malorny, Magdalena Skarzyńska, Katharina Wadepohl, Gabriel Moyano, A. Hesp, K.T. Veldman, A. Bossers, Magdalena Zajac, Dariusz Wasyl, P. Sanders, B. Gonzales-Zorn, M.S.M. Brouwer, J.A. Wagenaar, D.J.J. Heederik, D.J. Mevius, F.M. Aarestrup

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

45 Citations (Scopus)

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 language	English
Article number	15108
Journal	Scientific Reports
Volume	11
DOIs	https://doi.org/10.1038/s41598-021-93970-7
Publication status	Published - 23 Jul 2021

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One Health EJP: Promoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards.
1/01/18 → 30/09/23
Project: EU research project
EFFORT: Ecology from Farm to Fork Of microbial drug Resistance and Transmission
1/12/13 → 30/11/18
Project: EU research project

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Leekitcharoenphon, P., Johansson, M. H. K., Munk, P., Malorny, B., Skarzyńska, M., Wadepohl, K., Moyano, G., Hesp, A., Veldman, K. T., Bossers, A., Zajac, M., Wasyl, D., Sanders, P., Gonzales-Zorn, B., Brouwer, M. S. M., Wagenaar, J. A., Heederik, D. J. J., Mevius, D. J., & Aarestrup, F. M. (2021). Genomic evolution of antimicrobial resistance in Escherichia coli. Scientific Reports, 11, Article 15108 . https://doi.org/10.1038/s41598-021-93970-7

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title = "Genomic evolution of antimicrobial resistance in Escherichia coli",

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",

author = "Pimlapas Leekitcharoenphon and M.H.K. Johansson and P. Munk and B. Malorny and Magdalena Skarzy{\'n}ska and Katharina Wadepohl and Gabriel Moyano and A. Hesp and K.T. Veldman and A. Bossers and Magdalena Zajac and Dariusz Wasyl and P. Sanders and B. Gonzales-Zorn and M.S.M. Brouwer and J.A. Wagenaar and D.J.J. Heederik and D.J. Mevius and F.M. Aarestrup",

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Leekitcharoenphon, P, Johansson, MHK, Munk, P, Malorny, B, Skarzyńska, M, Wadepohl, K, Moyano, G, Hesp, A, Veldman, KT , Bossers, A, Zajac, M, Wasyl, D, Sanders, P, Gonzales-Zorn, B, Brouwer, MSM, Wagenaar, JA, Heederik, DJJ, Mevius, DJ & Aarestrup, FM 2021, 'Genomic evolution of antimicrobial resistance in Escherichia coli', Scientific Reports, vol. 11, 15108 . https://doi.org/10.1038/s41598-021-93970-7

TY - JOUR

T1 - Genomic evolution of antimicrobial resistance in Escherichia coli

AU - Leekitcharoenphon, Pimlapas

AU - Johansson, M.H.K.

AU - Munk, P.

AU - Malorny, B.

AU - Skarzyńska, Magdalena

AU - Wadepohl, Katharina

AU - Moyano, Gabriel

AU - Hesp, A.

AU - Veldman, K.T.

AU - Bossers, A.

AU - Zajac, Magdalena

AU - Wasyl, Dariusz

AU - Sanders, P.

AU - Gonzales-Zorn, B.

AU - Brouwer, M.S.M.

AU - Wagenaar, J.A.

AU - Heederik, D.J.J.

AU - Mevius, D.J.

AU - Aarestrup, F.M.

PY - 2021/7/23

Y1 - 2021/7/23

N2 - 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

AB - 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

U2 - 10.1038/s41598-021-93970-7

DO - 10.1038/s41598-021-93970-7

M3 - Article

SN - 2045-2322

VL - 11

JO - Scientific Reports

JF - Scientific Reports

M1 - 15108

ER -

Genomic evolution of antimicrobial resistance in Escherichia coli

Abstract

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Projects

One Health EJP: Promoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards.

EFFORT: Ecology from Farm to Fork Of microbial drug Resistance and Transmission

Cite this