Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus faecium

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1 Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
2 Microbiology Diagnostic Unit, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
3 Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia
4 School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
5 Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
6 Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
7 Department of infectious Diseases, Royal Perth hospital, Perth, WA, Australia
8 Department of Microbiology, PathWest Laboratory Medicine, Perth, WA, Australia
9 Victorian Life Sciences Computation Initiative, University of Melbourne, Carlton, Victoria, Australia
10 Department of Medicine, University of Melbourne, Heidelberg, Victoria, Australia
DOI
10.7287/peerj.preprints.2562v1
Published
Accepted
Subject Areas
Evolutionary Studies, Genomics, Microbiology, Epidemiology, Infectious Diseases
Keywords
Enterococcus faecium, vancomycin resistant, genome sequence, pacbio, evolution, hospital adapted, comparative genomics, recombination, accessory genome, antibiotic resistance
Copyright
© 2016 Buultjens et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Buultjens AH, Lam MMC, Ballard S, Monk IR, Mahony AA, Grabsch EA, Grayson ML, Pang S, Coombs GW, Robinson JO, Seemann T, Johnson PDR, Howden BP, Stinear TP. 2016. Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus faecium. PeerJ Preprints 4:e2562v1

Abstract

From early 2012, a novel clone of vancomycin resistant Enterococcus faecium (assigned the multi locus sequence type ST796) was simultaneously isolated from geographically separate hospitals in south eastern Australia and New Zealand. Here we describe the complete genome sequence of Ef_aus0233, a representative ST796 E. faecium isolate. We used PacBio single molecule real-time sequencing to establish a high quality, fully assembled genome comprising a circular chromosome of 2,888,087 bp and five plasmids. Comparison of Ef_aus0233 to other E. faecium genomes shows Ef_aus0233 is a member of the epidemic hospital-adapted lineage and has evolved from an ST555-like ancestral progenitor by the accumulation or modification of five mosaic plasmids and five putative prophage, acquisition of two cryptic genomic islands, accrued chromosomal single nucleotide polymorphisms and a 80kb region of recombination, also gaining Tn1549 and Tn916, transposons conferring resistance to vancomycin and tetracycline respectively. The genomic dissection of this new clone presented here underscores the propensity of the hospital E. faecium lineage to change, presumably in response to the specialized conditions of hospital and healthcare environments.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Strain table with associated metadata for E. faecium isolates described in this study

DOI: 10.7287/peerj.preprints.2562v1/supp-1

List of core-genome variable nucleotide and predicted consequences among ST555 and ST796 E. faecium isolates

DOI: 10.7287/peerj.preprints.2562v1/supp-2

Predicted chromosomal genomic island content among the ST555 and ST796 E. faecium isolates

DOI: 10.7287/peerj.preprints.2562v1/supp-3

Predicted chromosomal prophage content among the ST555 and ST796 E. faecium isolates

DOI: 10.7287/peerj.preprints.2562v1/supp-4

Predicted plasmid content among the ST555 and ST796 E. faecium isolates

DOI: 10.7287/peerj.preprints.2562v1/supp-5