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Background  In this report we have explored the genomic and microbiological basis for a sustained increase in bloodstream infections at a major Australian hospital caused by  Enterococcus faecium  multi-locus sequence type (ST) 203, an outbreak strain that has largely replaced a predecessor ST17 sequence type.    Results  To establish a ST203 reference sequence we fully assembled and annotated the genome of Aus0085, a 2009 vancomycin-resistant  Enterococcus faecium  (VREfm) bloodstream isolate, and the first example of a completed ST203 genome. Aus0085 has a 3.2 Mb genome, comprising a 2.9 Mb circular chromosome and six circular plasmids (2 kb–130 kb). Twelve percent of the 3222 coding sequences (CDS) in Aus0085 are not present in ST17  E. faecium  Aus0004 and ST18  E. faecium  TX16. Extending this comparison to an additional 12 ST17 and 14 ST203  E. faecium  hospital isolate genomes revealed only six genomic regions spanning 41 kb that were present in all ST203 and absent from all ST17 genomes. The 40 CDS have predicted functions that include ion transport, riboflavin metabolism and two phosphotransferase systems. Comparison of the vancomycin resistance-conferring Tn 1549  transposon between Aus0004 and Aus0085 revealed differences in transposon length and insertion site, and  van  locus sequence variation that correlated with a higher vancomycin MIC in Aus0085. Additional phenotype comparisons between ST17 and ST203 isolates showed that while there were no differences in biofilm-formation and killing of  Galleria mellonella , ST203 isolates grew significantly faster and out-competed ST17 isolates in growth assays.    Conclusions  Here we have fully assembled and annotated the first ST203 genome, and then characterized the genomic differences between ST17 and ST203  E. faecium . We also show that ST203  E. faecium  are faster growing and can out-compete ST17  E. faecium . While a causal genetic basis for these phenotype differences is not provided here, this study revealed conserved genetic differences between the two clones, differences that can now be tested to explain the molecular basis for the success and emergence of ST203  E. faecium .

Comparative analysis of the complete genome of an epidemic hospital sequence type 203 clone of vancomycin-resistant Enterococcus faecium