faecalis or other Gram-positive bacteria [59–61]. It is noteworthy that the genes encoding any of the established enterococcal virulence factors
were not among the CC2-enriched genes. Surface structures that promote adhesion of R788 pathogenic bacteria to human tissue are also promising targets for creation of effective vaccines. However, functional studies of the individual CC2-enriched genes are required in order to distinguish their implications in enterococcal virulence. Methods Bacterial strain and growth conditions Bacterial strains used in this study are listed in Table 1. E. faecalis strains were grown overnight (ON) in brain heart infusion broth (BHI; Oxoid) at 37° without shaking. All the strains have previously been sequence typed by the MLST scheme proposed by Ruiz-Garbajosa et al. . Comparative genomic hybridization Microarrays The microarray used in this
ABT 888 work has been described previously . The microarray design has been deposited in the ArrayExpress database with the accession number A-MEXP-1069 and A-MEXP-1765. DNA isolation Genomic DNA was isolated by using the FP120 FastPrep bead-beater (BIO101/Savent) and the QiaPrep MiniPrep kit (Qiagen) as previously described . Fluorescent labeling and hybridization Fifteen hospital-associated E. faecalis strains were selected for CGH based on their representation of MLST selleck screening library sequence types (STs) belonging to major CCs and potential HiRECCs, with a special focus on CC2, and their variety of geographical origins within Europe. Genomic DNA was labeled and purified with the BioPrime Array CGH Genomic labeling System (Invitrogen) and Cyanine Smart Pack dUTP (PerkinElmer Life Sciences), according to the manufacturer’s protocol. Purified samples were then dried, prior to resuspension in 140 μl hybridization solution (5 × SSC, 0.1% (w/v) SDS, 1.0% (w/v) bovine serum albumin, 50% (v/v) formamide and 0.01% (w/v) single-stranded salmon sperm DNA) and hybridized for 16 h at 42°C to the E. faecalis oligonucleotide array in a Tecan HS 400 pro hybridization station (Tecan). Arrays were washed twice at 42°C with 2 × SSC +
0.2% SDS, and twice at 23°C with 2 × SSC, followed by washes at 23°C with 1) 0.2 × SSC and 2) H2O. Two replicate hybridizations (dye-swap) were performed Cell press for each test strain. Hybridized arrays were scanned at wavelengths of 532 nm (Cy3) and 635 nm (Cy5) with a Tecan scanner LS (Tecan). Fluorescent intensities and spot morphologies were analyzed using GenePix Pro 6.0 (Molecular Devices), and spots were excluded based on slide or morphology abnormalities. All water used for the various steps of the hybridization and for preparation of solutions was filtered (0.2 μM) MilliQ dH20. Data analysis Standard methods in the LIMMA package  in R http://www.r-project.org/, available from the Bioconductor http://www.bioconductor.org were employed for preprocessing and normalization.