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

Andrew H Buultjens; Margaret M C Lam; Susan Ballard; Ian R Monk; Andrew A Mahony; Elizabeth A Grabsch; M Lindsay Grayson; Stanley Pang; Geoffrey W Coombs; J Owen Robinson; Torsten Seemann; Paul D R Johnson; Benjamin P Howden; Timothy P Stinear

doi:10.7717/peerj.2916

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

PeerJ. 2017 Jan 24:5:e2916. doi: 10.7717/peerj.2916. eCollection 2017.

Affiliations

¹ Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Victoria , Australia.
² Microbiology Diagnostic Unit, Department of Microbiology and Immunology, 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; Department of Microbiology, Pathwest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia.
⁵ School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia; Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Western Australia, Australia.
⁶ Victorian Life Sciences Computation Initiative, University of Melbourne , Carlton , Victoria , Australia.
⁷ Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia; Department of Medicine, University of Melbourne, Heidelberg, Victoria, Australia.

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 80 kb 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 specific conditions of hospital and healthcare environments.

Keywords: Accessory genome; Antibiotic resistance; Comparative genomics; Enterococcus faecium; Evolution; Genome sequence; Hospital adapted; PacBio; Recombination; Vancomycin resistant.

Grants and funding

This research was supported by the National Health and Medical Research Council (NHMRC) of Australia (1027874, 1084015). BPH and TPS are recipients of NHMRC fellowships (1023526 and 1008549, respectively). SG and TS was supported in part by the VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and La Trobe Universities, and an initiative of the Victorian Government, Australia. AAM is a recipient of an Australian Postgraduate Award, University of Melbourne. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.