Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America

Zamudio, Roxana, Boerlin, Patrick, Beyrouthy, Racha, Madec, Jean-Yves, Schwarz, Stefan, Mulvey, Michael R., Zhanel, George G., Cormier, Ashley, Chalmers, Gabhan, Bonnet, Richard, Haenni, Marisa, Eichhorn, Inga, Kaspar, Heike, Garcia-Fierro, Raquel, Wood, James L. N. and Mather, Alison E. (2022) Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America. Nature Communications, 13. ISSN 2041-1723

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Extended-spectrum cephalosporins (ESCs) are critically important antimicrobial agents for human and veterinary medicine. ESC resistance (ESC-R) genes have spread worldwide through plasmids and clonal expansion, yet the distribution and dynamics of ESC-R genes in different ecological compartments are poorly understood. Here we use whole genome sequence data of Enterobacterales isolates of human and animal origin from Europe and North America and identify contrasting temporal dynamics. AmpC β-lactamases were initially more dominant in North America in humans and farm animals, only later emerging in Europe. In contrast, specific extended-spectrum β-lactamases (ESBLs) were initially common in animals from Europe and later emerged in North America. This study identifies differences in the relative importance of plasmids and clonal expansion across different compartments for the spread of different ESC-R genes. Understanding the mechanisms of transmission will be critical in the design of interventions to reduce the spread of antimicrobial resistance.

Item Type: Article
Additional Information: Data availability: Illumina sequence read data generated in this study have been deposited in the ENA under BioProject PRJEB38235, PRJEB42322, PRJNA523640, PRJNA556083, PRJNA740259 and PRJEB50837 and individual accession numbers are available in Source Data file. Long-read data for the subset of 20 genomes are deposited in the ENA under BioProject PRJEB54884; the accession numbers for each genome are placed in the Source Data file. Thus, the source data (Source Data file) provided with this paper lists accession numbers for each genome analysed in this study, alongside with the isolate collection metadata generated in this study. Source data are provided with this paper. Funding Information: This project was supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), through the Medical Research Council (MRC, MR/R000948/1) [R.Z., J.L.N.W., A.E.M.], the Canadian Institutes of Health Research (CFC-150770) [A.C., G.C., P.B.], and the Genomics Research and Development Initiative (Government of Canada) [M.R.M.], the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709 [I.E., H.K., S.S.], the French Agency for food environmental and occupational health & safety (Anses) [R.G.F., M.H., J.Y.M.], and the French National Reference Center (CNR) for antimicrobial resistance [R. Beyrouthy, R. Bonnet]. Support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain) [R.Z., A.E.M.]. We gratefully acknowledge use of the Quadram Institute Bioscience core facilities HPC cluster and the CLIMB-BIG-DATA-computing servers, an infrastructure supported by the UK Medical Research Council grant MR/T030062/1. We thank Dr. George M. Savva from the core science resources at Quadram Institute Bioscience for help and guidance with the logistic regression analysis.
Uncontrolled Keywords: chemistry(all),biochemistry, genetics and molecular biology(all),physics and astronomy(all),sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1600
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Depositing User: LivePure Connector
Date Deposited: 03 Aug 2023 15:33
Last Modified: 07 Aug 2023 00:49
URI: https://ueaeprints.uea.ac.uk/id/eprint/92771
DOI: 10.1038/s41467-022-34970-7


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