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Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat

BACKGROUND: As WGS comes of age, changes in EU legislation implemented in 2021 allow its usage for systematic monitoring of ESBL-producing Escherichia coli from livestock and meat, replacing phenotypic testing. Presently, phenotypic testing correlates well with antimicrobial resistance predicted fro...

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Autores principales: Brouwer, Michael S M, Zandbergen Van Essen, Alieda, Kant, Arie, Rapallini, Michel, Harders, Frank, Bossers, Alex, Wullings, Bart, Wit, Ben, Veldman, Kees T
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320162/
https://www.ncbi.nlm.nih.gov/pubmed/37248737
http://dx.doi.org/10.1093/jac/dkad158
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author Brouwer, Michael S M
Zandbergen Van Essen, Alieda
Kant, Arie
Rapallini, Michel
Harders, Frank
Bossers, Alex
Wullings, Bart
Wit, Ben
Veldman, Kees T
author_facet Brouwer, Michael S M
Zandbergen Van Essen, Alieda
Kant, Arie
Rapallini, Michel
Harders, Frank
Bossers, Alex
Wullings, Bart
Wit, Ben
Veldman, Kees T
author_sort Brouwer, Michael S M
collection PubMed
description BACKGROUND: As WGS comes of age, changes in EU legislation implemented in 2021 allow its usage for systematic monitoring of ESBL-producing Escherichia coli from livestock and meat, replacing phenotypic testing. Presently, phenotypic testing correlates well with antimicrobial resistance predicted from WGS data. WGS has added value in the wealth of additional information that is present in the data. OBJECTIVES: In this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli. METHODS: Susceptibility testing was performed with broth microdilution of selectively isolated E. coli. Short-read WGS was performed in parallel and phenotypes predicted based on the sequence data, which was also used to determine the phylogeny of the isolates. RESULTS: The phenotypically determined resistance and the predicted resistance correlated 90%–100% for the different antimicrobial classes. Furthermore, clonal relationships were detected amongst ESBL-producing E. coli within livestock sectors and the meat produced by this sector. CONCLUSIONS: Further implementation of WGS analysis of ESBL/AmpC-producing E. coli within the AMR monitoring programme of EU member states and global surveillance programmes will contribute to determining the attribution of livestock in the prevalence of ESBL/AmpC-encoding E. coli in humans.
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spelling pubmed-103201622023-07-06 Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat Brouwer, Michael S M Zandbergen Van Essen, Alieda Kant, Arie Rapallini, Michel Harders, Frank Bossers, Alex Wullings, Bart Wit, Ben Veldman, Kees T J Antimicrob Chemother Original Research BACKGROUND: As WGS comes of age, changes in EU legislation implemented in 2021 allow its usage for systematic monitoring of ESBL-producing Escherichia coli from livestock and meat, replacing phenotypic testing. Presently, phenotypic testing correlates well with antimicrobial resistance predicted from WGS data. WGS has added value in the wealth of additional information that is present in the data. OBJECTIVES: In this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli. METHODS: Susceptibility testing was performed with broth microdilution of selectively isolated E. coli. Short-read WGS was performed in parallel and phenotypes predicted based on the sequence data, which was also used to determine the phylogeny of the isolates. RESULTS: The phenotypically determined resistance and the predicted resistance correlated 90%–100% for the different antimicrobial classes. Furthermore, clonal relationships were detected amongst ESBL-producing E. coli within livestock sectors and the meat produced by this sector. CONCLUSIONS: Further implementation of WGS analysis of ESBL/AmpC-producing E. coli within the AMR monitoring programme of EU member states and global surveillance programmes will contribute to determining the attribution of livestock in the prevalence of ESBL/AmpC-encoding E. coli in humans. Oxford University Press 2023-05-30 /pmc/articles/PMC10320162/ /pubmed/37248737 http://dx.doi.org/10.1093/jac/dkad158 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Original Research
Brouwer, Michael S M
Zandbergen Van Essen, Alieda
Kant, Arie
Rapallini, Michel
Harders, Frank
Bossers, Alex
Wullings, Bart
Wit, Ben
Veldman, Kees T
Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat
title Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat
title_full Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat
title_fullStr Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat
title_full_unstemmed Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat
title_short Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat
title_sort implementation of wgs analysis of esbl-producing escherichia coli within eu amr monitoring in livestock and meat
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320162/
https://www.ncbi.nlm.nih.gov/pubmed/37248737
http://dx.doi.org/10.1093/jac/dkad158
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