Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat
BackgroundAs 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.ObjectivesIn this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli.MethodsSusceptibility 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.ResultsThe 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.ConclusionsFurther 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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dig-wur-nl-wurpubs-6164262024-10-02 Brouwer, M.S.M. van Essen-Zandbergen, A. Kant, A. Rapallini, M.L.B.A. Harders, F.L. Bossers, A. Wullings, B.A. Wit, Ben Veldman, K.T. Article/Letter to editor Journal of Antimicrobial Chemotherapy 78 (2023) ISSN: 0305-7453 Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat 2023 BackgroundAs 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.ObjectivesIn this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli.MethodsSusceptibility 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.ResultsThe 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.ConclusionsFurther 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. en application/pdf https://research.wur.nl/en/publications/implementation-of-wgs-analysis-of-esbl-producing-escherichia-coli 10.1093/jac/dkad158 https://edepot.wur.nl/633900 Life Science https://creativecommons.org/licenses/by-nc/4.0/ https://creativecommons.org/licenses/by-nc/4.0/ Wageningen University & Research |
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Life Science Life Science Brouwer, M.S.M. van Essen-Zandbergen, A. Kant, A. Rapallini, M.L.B.A. Harders, F.L. Bossers, A. Wullings, B.A. Wit, Ben Veldman, K.T. Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat |
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BackgroundAs 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.ObjectivesIn this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli.MethodsSusceptibility 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.ResultsThe 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.ConclusionsFurther 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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Article/Letter to editor |
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Life Science |
author |
Brouwer, M.S.M. van Essen-Zandbergen, A. Kant, A. Rapallini, M.L.B.A. Harders, F.L. Bossers, A. Wullings, B.A. Wit, Ben Veldman, K.T. |
author_facet |
Brouwer, M.S.M. van Essen-Zandbergen, A. Kant, A. Rapallini, M.L.B.A. Harders, F.L. Bossers, A. Wullings, B.A. Wit, Ben Veldman, K.T. |
author_sort |
Brouwer, M.S.M. |
title |
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_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_sort |
implementation of wgs analysis of esbl-producing escherichia coli within eu amr monitoring in livestock and meat |
url |
https://research.wur.nl/en/publications/implementation-of-wgs-analysis-of-esbl-producing-escherichia-coli |
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