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Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome

S Arredondo-Alonso, J Top, AC Schürch, A McNally, S Puranen, M Pesonen, J Pensar, P Marttinen, JC Braat, MRC Rogers, W van Schaik, S Kaski, J Corander, View ORCID ProfileRJL Willems
doi: https://doi.org/10.1101/530725
S Arredondo-Alonso
1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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J Top
1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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AC Schürch
1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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A McNally
2Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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S Puranen
3Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
4Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI- 00014 University of Helsinki, Finland
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M Pesonen
3Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
4Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI- 00014 University of Helsinki, Finland
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J Pensar
4Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI- 00014 University of Helsinki, Finland
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P Marttinen
3Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
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JC Braat
1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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MRC Rogers
1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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W van Schaik
2Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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S Kaski
3Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
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J Corander
4Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI- 00014 University of Helsinki, Finland
5Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
6Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
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RJL Willems
1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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  • ORCID record for RJL Willems
  • For correspondence: rwillems@umcutrecht.nl
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Abstract

Enterococcus faecium is a gut commensal of many mammals but is also recognized as a major nosocomial human pathogen, as it is listed on the WHO global priority list of multi-drug resistant organisms. Previous research has suggested that nosocomial strains have multiple zoonotic origins and are only distantly related to those involved in human commensal colonization. Here we present the first comprehensive population-wide joint genomic analysis of hospital, commensal and animal isolates using both short- and long-read sequencing techniques. This enabled us to investigate the population plasmidome, core genome variation and genome architecture in detail, using a combination of machine learning, population genomics and genome-wide co-evolution analysis. We observed a high level of genome plasticity with large-scale inversions and heterogeneous chromosome sizes, collectively painting a high-resolution picture of the adaptive landscape of E. faecium, and identified plasmids as the main indicator for host-specificity. Given the increasing availability of long-read sequencing technologies, our approach could be widely applied to other human and animal pathogen populations to unravel fine-scale mechanisms of their evolution.

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Posted January 28, 2019.
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Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome
S Arredondo-Alonso, J Top, AC Schürch, A McNally, S Puranen, M Pesonen, J Pensar, P Marttinen, JC Braat, MRC Rogers, W van Schaik, S Kaski, J Corander, RJL Willems
bioRxiv 530725; doi: https://doi.org/10.1101/530725
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Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome
S Arredondo-Alonso, J Top, AC Schürch, A McNally, S Puranen, M Pesonen, J Pensar, P Marttinen, JC Braat, MRC Rogers, W van Schaik, S Kaski, J Corander, RJL Willems
bioRxiv 530725; doi: https://doi.org/10.1101/530725

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