Fig. 2.

Phylogenetic tree of clade A1 isolates. This maximum-likelihood tree includes 95 of the 96 genome sequences generated in this study and 19 publicly available E. faecium genome sequences. The core genome alignment consisted of 1 637 117 nucleotides. The position of strain A_020709_82 is marked with an arrow. The genome of this isolate was sequenced and assembled to completion using a combination of short- and long-read sequencing for use as a reference genome in further analyses. The genome sequences are coded as follows: the letter represents the patient, the six-number code represents the date of isolation in a year–month–day format and the final number is the unique identifier for each genome sequence. The colours indicate the patient the isolate was taken from. Black and grey marks indicate the presence of the vanA or vanB vancomycin resistance operon in the genome, respectively.