Phylogenomic analysis of E. faecium. Panel (A): Unrooted maximum likelihood tree of E. faecium based on the concatenated alignments of 649 orthologous proteins (containing 11639 residues). Bootstrap values are based on 1000 permutations. Panel (B): Unrooted neighbour-joining tree depicting differences in gene content in E. faecium. The distance matrix used to generate this phylogenomic tree is provided as Additional file 7.