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Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

View ORCID ProfileNicole Stoesser, View ORCID ProfileAnna E. Sheppard, View ORCID ProfileLouise Pankhurst, View ORCID ProfileNicola de Maio, View ORCID ProfileCatrin E. Moore, View ORCID ProfileRobert Sebra, View ORCID ProfilePaul Turner, View ORCID ProfileLuke W. Anson, View ORCID ProfileAndrew Kasarskis, View ORCID ProfileElizabeth M. Batty, View ORCID ProfileVeronica Kos, View ORCID ProfileDaniel J. Wilson, View ORCID ProfileRattanaphone Phetsouvanh, View ORCID ProfileDavid Wyllie, View ORCID ProfileEvgeni Sokurenko, View ORCID ProfileAmee R. Manges, View ORCID ProfileTimothy J. Johnson, View ORCID ProfileLance B. Price, View ORCID ProfileTimothy E. A. Peto, View ORCID ProfileJames R. Johnson, View ORCID ProfileXavier Didelot, View ORCID ProfileA. Sarah Walker, View ORCID ProfileDerrick W. Crook, Modernising Medical Microbiology Informatics Group (MMMIG)
doi: https://doi.org/10.1101/030668
Nicole Stoesser
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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  • For correspondence: nicole.stoesser@ndm.ox.ac.uk
Anna E. Sheppard
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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Louise Pankhurst
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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  • ORCID record for Louise Pankhurst
Nicola de Maio
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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Catrin E. Moore
2Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
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Robert Sebra
3Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, New York, USA
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Paul Turner
2Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
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  • ORCID record for Paul Turner
Luke W. Anson
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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Andrew Kasarskis
3Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, New York, USA
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Elizabeth M. Batty
5Infection Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
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Veronica Kos
5Infection Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
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Daniel J. Wilson
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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Rattanaphone Phetsouvanh
6Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic (Laos)
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David Wyllie
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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Evgeni Sokurenko
7Department of Microbiology, University of Washington, Seattle, USA
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Amee R. Manges
8University of British Columbia, School of Population and Public Health, Vancouver, British Columbia, Canada
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Timothy J. Johnson
9College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
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Lance B. Price
10Translational Genomics Research Institute (TGen) North, Flagstaff, Arizona, USA
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Timothy E. A. Peto
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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James R. Johnson
11Minneapolis Veterans Affairs Health Care System, Minneapolis, Minnesota, USA
12Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
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Xavier Didelot
13Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, UK
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A. Sarah Walker
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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Derrick W. Crook
1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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1Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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ABSTRACT

Background Escherichia coli sequence type 131 (ST131) has emerged globally as the most predominant lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined.

Results This study of the largest worldwide collection (n = 215) of sequenced ST131 E. coli isolates to date demonstrates that clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/H30Rx clade driven by the acquisition of a blaCTX-M-15-containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids, and chromosomal integration of blaCTX-M within sub-clusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed amongst ST131, the blaCTX-M-14/14-like group.

Conclusions The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages of E. coli. These data also highlight the global imperative to reduce specific antibiotic selection pressures, and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 06, 2015.
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Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131
Nicole Stoesser, Anna E. Sheppard, Louise Pankhurst, Nicola de Maio, Catrin E. Moore, Robert Sebra, Paul Turner, Luke W. Anson, Andrew Kasarskis, Elizabeth M. Batty, Veronica Kos, Daniel J. Wilson, Rattanaphone Phetsouvanh, David Wyllie, Evgeni Sokurenko, Amee R. Manges, Timothy J. Johnson, Lance B. Price, Timothy E. A. Peto, James R. Johnson, Xavier Didelot, A. Sarah Walker, Derrick W. Crook, Modernising Medical Microbiology Informatics Group (MMMIG)
bioRxiv 030668; doi: https://doi.org/10.1101/030668
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Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131
Nicole Stoesser, Anna E. Sheppard, Louise Pankhurst, Nicola de Maio, Catrin E. Moore, Robert Sebra, Paul Turner, Luke W. Anson, Andrew Kasarskis, Elizabeth M. Batty, Veronica Kos, Daniel J. Wilson, Rattanaphone Phetsouvanh, David Wyllie, Evgeni Sokurenko, Amee R. Manges, Timothy J. Johnson, Lance B. Price, Timothy E. A. Peto, James R. Johnson, Xavier Didelot, A. Sarah Walker, Derrick W. Crook, Modernising Medical Microbiology Informatics Group (MMMIG)
bioRxiv 030668; doi: https://doi.org/10.1101/030668

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