title: Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium.
abstract: Enterococcus faecium is a major nosocomial pathogen causing significant morbidity and mortality worldwide. Assessment of E. faecium using MLST to understand the spread of this organism is an important component of hospital infection control measures. Recent studies, however, suggest that MLST might be inadequate for E. faecium surveillance.
  
  
  
  To use WGS to characterize recently identified vancomycin-resistant E. faecium (VREfm) isolates non-typeable by MLST that appear to be causing a multi-jurisdictional outbreak in Australia.
  
  
  
  Illumina NextSeq and Pacific Biosciences SMRT sequencing platforms were used to determine the genome sequences of 66 non-typeable E. faecium (NTEfm) isolates. Phylogenetic and bioinformatics analyses were subsequently performed using a number of in silico tools.
  
  
  
  Sixty-six E. faecium isolates were identified by WGS from multiple health jurisdictions in Australia that could not be typed by MLST due to a missing pstS allele. SMRT sequencing and complete genome assembly revealed a large chromosomal rearrangement in representative strain DMG1500801, which likely facilitated the deletion of the pstS region. Phylogenomic analysis of this population suggests that deletion of pstS within E. faecium has arisen independently on at least three occasions. Importantly, the majority of these isolates displayed a vancomycin-resistant genotype.
  
  
  
  We have identified NTEfm isolates that appear to be causing a multi-jurisdictional outbreak in Australia. Identification of these isolates has important implications for MLST-based typing activities designed to monitor the spread of VREfm and provides further evidence supporting the use of WGS for hospital surveillance of E. faecium.
authors.affiliation: Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia glen.carter@unimelb.edu.au.|Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.
authors.forename: Glen P
authors.initials: GP
authors.lastname: Carter
authors.affiliation: Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.|Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Buultjens
authors.affiliation: The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.
authors.forename: Susan A
authors.initials: SA
authors.lastname: Ballard
authors.affiliation: Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.|Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Baines
authors.affiliation: The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.
authors.forename: Takehiro
authors.initials: T
authors.lastname: Tomita
authors.affiliation: The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.
authors.forename: Janet
authors.initials: J
authors.lastname: Strachan
authors.affiliation: Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia.
authors.forename: Paul D R
authors.initials: PD
authors.lastname: Johnson
authors.affiliation: Hunter New England Health, Pathology North and Universities of Newcastle and New England, John Hunter Hospital, Newcastle, New South Wales, Australia.
authors.forename: John K
authors.initials: JK
authors.lastname: Ferguson
authors.affiliation: Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.|Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.|Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia.
authors.forename: Torsten
authors.initials: T
authors.lastname: Seemann
authors.affiliation: Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.|Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.
authors.forename: Timothy P
authors.initials: TP
authors.lastname: Stinear
authors.affiliation: Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.|Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.|The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Howden
mesh_terms: D001315:Australia / Q000453:epidemiology; D015373:Bacterial Typing Techniques / Q000379:methods*; D021821:Communicable Diseases, Emerging / Q000453:epidemiology* / Q000382:microbiology; D019295:Computational Biology; D019353:Endemic Diseases; D016984:Enterococcus faecium / Q000145:classification / Q000302:isolation & purification*; D016680:Genome, Bacterial; D005838:Genotype; D016908:Gram-Positive Bacterial Infections / Q000453:epidemiology* / Q000382:microbiology; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods; D065507:Vancomycin-Resistant Enterococci / Q000145:classification / Q000302:isolation & purification*