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oa Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance
- Authors: Sebastiaan J. van Hal1 ,2 , Camilla L. C. Ip3 , M. Azim Ansari4 , Daniel J. Wilson5 , Bjorn A. Espedido2 ,6 , Slade O. Jensen2 ,6 , Rory Bowden3
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- VIEW AFFILIATIONS
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1 1 Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia 2 2 Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia 3 3 Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK 4 4 Oxford Martin School, University of Oxford, 34 Broad Street, Oxford, UK 5 5 Nuffield Department of Medicine, University of Oxford, Oxford, UK 6 6 Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
- Correspondence Sebastiaan J. van Hal ([email protected])
- First Published Online: 19 January 2016, Microbial Genomics , 2016 2, doi: 10.1099/mgen.0.000048
- Subject: Microbial evolution and epidemiology: Population Genomics
- Received:
- Accepted:
- Cover date:
- This is an open access article published by the Microbiology Society under the Creative Commons Attribution License




Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance, Page 1 of 1
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Enterococcus faecium, a major cause of hospital-acquired infections, remains problematic because of its propensity to acquire resistance to vancomycin, which currently is considered first-line therapy. Here, we assess the evolution and resistance acquisition dynamics of E. faecium in a clinical context using a series of 132 bloodstream infection isolates from a single hospital. All isolates, of which 49 (37 %) were vancomycin-resistant, underwent whole-genome sequencing. E. faecium was found to be subject to high rates of recombination with little evidence of sequence importation from outside the local E. faecium population. Apart from disrupting phylogenetic reconstruction, recombination was frequent enough to invalidate MLST typing in the identification of clonal expansion and transmission events, suggesting that, where available, whole-genome sequencing should be used in tracing the epidemiology of E. faecium nosocomial infections and establishing routes of transmission. Several forms of the Tn1549-like element–vanB gene cluster, which was exclusively responsible for vancomycin resistance, appeared and spread within the hospital during the study period. Several transposon gains and losses and instances of in situ evolution were inferred and, although usually chromosomal, the resistance element was also observed on a plasmid background. There was qualitative evidence for clonal expansions of both vancomycin-resistant and vancomycin-susceptible E. faecium with evidence of hospital-specific subclonal expansion. Our data are consistent with continuing evolution of this established hospital pathogen and confirm hospital vancomycin-susceptible and vancomycin-resistant E. faecium patient transmission events, underlining the need for careful consideration before modifying current E. faecium infection control strategies.
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Three supplementary tables and three supplementary figures are available with the online Supplementary Material. We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
- Keyword(s): multi-locus sequence typing, transposon, recombination, vancomycin resistance, Enterococcus faecium, infection control
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Abbreviations: CC clonal complex SNV single nucleotide variant ST sequence type VRE vancomycin-resistant Enterococcus faecium VSE vancomycin-susceptible Enterococcus faecium WGS whole-genome sequencing
© 2016 The Authors | Published by the Microbiology Society
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