Core-genome tree built from E. faecium isolates QF25-1 and WZ27-2 along with publicly available genomic data for 91 E. faecium. ClustalW was used to align the genome sequences under default parameters and the alignment was checked manually. Maximum-likelihood (ML) methods were performed for the genome-wide phylogenetic analyses using PhyML 3.0. Nucleotide substitution model selection was estimated with jModelTest 2.1.10 and Smart Model Selection in PhyML 3.0. The model GTR+G was selected for ML analyses with 1000 bootstrap replicates to calculate the bootstrap values of the topology. The results were treated with iTOL 3.4.3 and visualized by FigTree with a midpoint root. AUS, Australia; BEL, Belgium; CHN, China; DEU, Germany; DNK, Denmark; ESP, Spain; FRA, France; GBR, Great Britain; HUN, Hungary; IND, India; IRL, Ireland; ISR, Israel; ITA, Italy; KOR, South Korea; LVA, Latvia; NLD, Netherlands; NOR, Norway; PRT, Portugal; SWE, Sweden; TZA, Tanzania; USA, United States of America; ZAF, South Africa. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.