This again suggests that these isolates are more distantly related to the other strains within the HA-clade. Table 3 Antibiotic resistance gene profiles of the 21 E. faecium strains Gene cat ermA ermB aad6 aad9 aadE aacA- aphD tetL tetM vanA gyrA b parC c pbp5-R d Resistance CHL ERY ERY SPC/ STR SPC/ STR SPC/ STR GEN TET TET VAN CIP CIP AMP Strains                           1,141,733                           Com12                           Com15             Dactolisib               E980                           Y-27632 TX1330                           1,230,933     X X   X X   X X X X X 1,231,408     X X   X X       X X X 1,231,410     X X   X       X X   X 1,231,501                           1,231,502     X X   X X     X X X X C68

    X X   X X   X   X X X D344SRFa     X X   X   X X         TX16 X   X X   X   X X       X E1039                         X E1071 X   X X X X   X   X     X E1162               X X       X E1636                 X       X E1679   X X X X   X     X X X X TX82     X X   X     X X X X X TX0133A X   X X   X X   X   X X X U0317     X X   X X       X X X a A rifampin- and fusidic acid-resistant derivative of clinical PHA-848125 supplier strain E. faecium D344S in which the spontaneous loss of pbp5 and its surrounding region resulted in an ampicillin-susceptible phenotype. b Amino acid change (E to K/G) in residue 87 or (S to R/Y/I) in residue 83 of GyrA. c Amino acid change (E to K) in residue 86 or (S

to R/I) in residue 82 of ParC. dConsensus sequence of the pbp5-R allele encoding the low affinity Pbp5-R. eTC6 was not included in this analysis as it is a transconjugant of C68 and D344SRF, so therefore is not a unique genome. Two groups have previously analyzed CRISPR-associated genes within E. faecalis and E. faecium genomes [32, 61]. Partial CRISPR-like loci were previously described in E1071, E1679, and U0317; however, these loci were within a gene and were considered non-functional [32]. In addition, Palmer stiripentol et al. identified CRISPR-cas predicted proteins in the Broad Institute strains Com12; 1,141,733; and 1,231,408 [61]. Similarly, we only found a CRISPR-cas locus in strain TX1330 (Additional file 9: Table S6) out of the

6 strains not previously studied (TX1330; TX16; TX0082; TX0133A; D344SRF; and C68). In summary, out of the 22 available genomes, only one of the HA-clade isolates contained CRISP-loci, namely the hybrid strain 1,231,408. The three other strains containing CRISPR-loci of the CA-clade (Com12; 1,141,733; and TX1330) all lacked antibiotic resistance determinants. Therefore, our data coincide with the previous observation that members of the recently emerged high-risk enterococcal lineages lack CRISPR-loci and the inverse relationship between the presence of a CRISPR-cas locus and acquired antibiotic resistance [61]. Metabolic pathway Metabolic pathways of E. faecium might have contributed to the recently increased incidence of E. faecium colonization and infection. To help understand E.