The genome size of the E. LXH254 faecium strains vary substantially from 2.50 Mb (E1039) to 3.14 Mb (1,230,933), while the number of ORFs varies from 2,587 (E1039) to 3,118 (TX0133A). Ortholog analysis of TX16 compared to TX1330 and all

the available but unfinished E. faecium genomes using BLASTP of predicted protein find more sequences and orthoMCL resulted in 3,169 distributed genes shared among some strains (Figure 2), 2,543 unique genes (Figure 2), and 1,652 core gene families, of which 1,608 genes are present in a single copy in all strains and 44 gene families are present in multiple copies. The number of core genes (including those in single and multiple copies) converged to 1,726 at the 22nd genome, while the number of pan genes reached 6,262 genes at the 22nd genome (Figure 3A and B). The extrapolated number of core genes is very close to the number of core genes (1,772 genes) Leavis et al. reported in their microarray-based study

which used 97 isolates, yet the estimated number of pan genes is higher in the present analysis [31]. Furthermore, this study differs slightly from the analysis of van Schaik et al. which estimates the E. faecium core genome to SB273005 be 2172 ± 20 CDS [32]. Our data do, however, concur with the conclusion that a sizeable fraction of the E. faecium genome is accessory and that the pan genome is considered to open. Figure 2 Distribution of orthologs in 22 E. faecium strains. The orthologs were determined by orthoMCL as described in the Material and Methods. ORFs of the 3 plasmids in E. faecium TX16 were not included in the ortholog analysis. Figure 3 E. faecium core and pan genomes. A. E. faecium core genes. The number of shared genes is plotted as the function of number of strains Urease (n) added sequentially. An open circle represents the number of shared genes for each permutation at a give number of strains (n). 1,608 single copy genes are shared by all 22 genomes. The red line represents the least-squares fit to the

exponential decay function F c  = κ c exp[−n/τ c ] + Ω (κ c = 1871 ± 25, τ c  = 1.751 ± 0.027, Ω = 1726 ± 2). B. E. faecium pan-genes. The number of total genes is plotted as the function of strains (n). The open circle represents the number of total genes for each permutation at a give number of strains (n). The red line represents the least-squares fit to the power law function n = κ N γ (κ = 2876 ± 7, γ = 0.2517 ± 0.009). Phylogenetic, multi-locus sequence typing (MLST) and gene content similarity analysis Analysis of the 22 E. faecium genomes (Table 2) showed that the isolates separate into two clades, one branch consisting mostly of CA isolates, with most HA isolates found in the other, as was noted in our previous study [33] (Figure 4A and B).