After centrifugation (at 3000 rpm, for 3 minutes), the supernatant was discarded and the pellet was suspended in 100 μl of TE. Two heating steps of 95°C for five PF299804 datasheet minutes were performed sequentially with a 2 minutes cooling step between them. Finally, the solution was centrifuged (at 13 000 rpm, for 10 minutes) and the supernatant containing DNA was collected. In the case of the blood culture samples, 100 μl of the samples were collected for DNA extraction. The DNA was extracted using an automated nucleic acid extraction instrument Nuclisens®easyMAG™ (bioMérieux, France) according to the manufacturer’s protocol (Generic 1.0.6). The eluation volume was 55 μl. A negative control, i.e., sterile water was included

in each test series. Dna Amplification and Labelling The broad-range PCR primers gBF (5′-CGICCIGGKATGTAYATHGG-3′)

and gBR (5′-RMICCWACICCRTGYAGICCICC-3′) were modified from primers introduced Ruxolitinib by Roth and colleagues (2004) [4]. We reduced the number of degenerated regions in primers by using inosines. The primers amplified a ~300 bp region of the bacterial gyrB and parE genes. In addition, specific primers for mecA gene, mecAR (5′-TTACTCATGCCATACATAAATGGATAGACG-3′) and mecAF (5′-AATACAATCGCACATACATTAATA-3′), were designed. To enhance S. aureus amplification SaurF (5′-AGACCTGGTATGTATATTGG-3′) and SaurR (5′-CCAACACCATGTAAACCACC-3′) primers were further designed. All the reverse primers were biotinylated at their respective 5′-end. The PCR reaction mixture SB203580 contained 1 μM of gBF primer mixture (Metabion, Germany), 1 μM of biotin-labeled gBR primer mixture (Metabion, Germany), 0.165 μM of SaurF primer (Metabion, Germany), 0.165 μM of biotin-labeled SaurR primer (Metabion,

Germany), 0.25 μM of mecAF primer (Metabion, Germany), 0.25 μM biotin-labeled mecAR primer (Metabion, Germany), 1× Hot Start Taq® PCR buffer (Qiagen, Germany), in which the final concentration MgCl2was 2.0 mM, 300 μM of each of dNTP (Finnzymes, Finland), 1.5 g/l BSA (EuroClone, Italy), 0.125 U/μl Hot Start Taq® DNA polymerase (Qiagen, Germany), Reverse transcriptase 1.5 μl of isolated DNA, and water to bring the total volume to 15 μl. In the blood culture dataset, 1.5 μl of PCR control template was added in the reaction and the equivalent amount of water was reduced. A negative control, i.e., sterile water was included in each test series. The PCR was performed using a Mastercycler® epgradient S thermal cycler (Eppendorf, Germany). The following PCR program was used: a denaturation step at 95°C for 15 minutes, 36 cycles of 10 seconds at 96°C, 35 seconds at 52°C, 10 seconds at 72°C, 5 cycles of 5 seconds at 96°C, 30 seconds at 65°C, 5 cycles of 5 seconds at 96°C and finally 30 seconds at 68°C. After the PCR, the success of the amplification of double-stranded DNA and single-stranded DNA was ascertained by gel electrophoresis using a 2% agarose gel containing SYBR® Green II (Invitrogen, USA) or using Agilent BioAnalyzer (Agilent Technologies, USA).