Fifty-six biochemically characterized clinical

isolates of E. cloacae were obtained from four different Selleck TSA HDAC sources, synlab (Dachau, Germany), Klinikum Bogenhausen (Munich, Germany), Labor Becker, Olgemöller & Kollegen (Munich, Germany) and the Bavarian Health and Food Safety Authority (LGL) routine diagnostic laboratory. All isolates were subjected to both MALDI-TOF MS and the newly developed real-time PCR. All reference strains and clinical isolates were subcultured at 37 °C on Columbia sheep blood agar. DNA was extracted from bacterial strains following either the instructions of the High Pure Template Preparation kit (Roche Applied Science, Mannheim, Germany) or via heat lysis. For heat lysis, bacteria grown on appropriate media (Endo-Agar or Columbia sheep blood agar; Oxoid, Wesel, Germany) were resuspended in 1.5 mL physiological BTK inhibitor saline solution (0.9%). Twenty microlitres of this solution were added to 400 μL sterile water and heated at 95 °C for 15 min. After centrifugation, the supernatant was used for amplification. Purity and concentration of the DNA were analysed with the Nanodrop 1000 Spectrophotometer (Peqlab Biotechnologie GmbH,

Erlangen, Germany). The sequences for the E. cloacae-specific oligonucleotide primers (dnaJ_f1 and dnaJ_r2) and the E. cloacae target probe (dnaJ_p3) were designed based on a multiple alignment of dnaJ sequences of species belonging to the Enterobacteriaceae family which were deposited in GenBank. Primer sets and probes for the internal amplification control (IAC) ntb2, a 125-bp sequence of Nicotiana tabacum, were adapted from the study by Anderson et al. (2011). Sequences of all primers and probes used in the multiplex PCR are listed in Table 3. Conventional PCR was performed in 25 μL reactions. The reaction mixtures contained 2.5 mM MgCl2, 0.2 mM dNTP, 0.4 pM primer (Table 3) and 0.06 U μL−1 HotStar-Taq-DNA-polymerase (Qiagen, Hilden, Germany). The PCR program consisted of an initial activation step for 5 min at 94 °C followed by 32 cycles

of denaturation for 60 s at 94 °C, annealing for 30 s at 56 °C and extension for 60 s at 72 °C. Real-time PCR Methane monooxygenase was performed in 20 μL reactions in a LightCycler® 480 multiwell plate 96 (Roche Applied Science). A quantity of 10× primer–probe mixes were prepared for each individual primer–probe set (Table 3). Each primer–probe mix contained the respective primers and probes at a final concentration of 2 μM. Each reaction mix contained 10 μL 2× QuantiTect Multiplex RT-PCR NoRox Mastermix (Qiagen); 2.0 μL primer–probe mix from each of the 10× primer–probe mix for detection of dnaJ and ntb2; 1 μL of 25 copies of IPC-ntb2 plasmid DNA (Anderson et al., 2011); and 4 μL template DNA. A quantity of 0.5 μL sterile PCR grade water was then added to bring the final volume to 20 μL.