The specimens were cultured on 5% horse blood agar and chocolate

The specimens were cultured on 5% horse blood agar and chocolate agar with semi-quantitative Selonsertib nmr determinations by dispersion of 1 and 10 μL on each half of the plate. The plates were incubated in 5% carbon dioxide at 35°C for 24-48 h. From 152 LRTI patients, blood samples were collected for culture with a Bactec blood-culturing system (BioMérieux, Marcy-Etoile, France) at the Department of Clinical Microbiology, Aarhus University Hospital. Non-frozen urine samples collected from 142 LRTI patients were sent to the Department of Bacteriology, Mycology and Parasitology, Statens Serum Institute, Copenhagen,

Denmark, and were analyzed for pneumococcal capsular polysaccharides by countercurrent immunoelectrophoresis [25]. CSF samples Repotrectinib cell line were submitted for routine bacterial culture and chemistry [26]. DNA extraction DNA

from 0.2-0.5 mL BAL was extracted by the automatic MagNa Pure LC DNA-Isolation system (Roche Diagnostics). Bacteria DNA used for determination of the analytical sensitivity of the Spn9802 and the P6 PCRs was purified from cultured isolates (S. pneumoniae CCUG 28588T and H. influenzae CCUG 23946 T) by phenol-chloroform extraction of bacteria harvested in exponential growth phase after culturing on chocolate agar at 37°C in 5% carbon dioxide and the concentration of DNA was determined by a Nanodrop instrument (NanoDrop Technologies, Inc. Wilmington, DE, USA). The genome copy number was determined according to conventional calculations based on molecular weight and one gene copy per genome. CSF samples (50 μL-1.5 mL) were centrifuged at 12 000 g for 20 min, after which DNA was extracted from the pellet with a bacterial DNA preparation kit (Roche Diagnostics, Indianapolis, USA), used according to the manufacturer’s instructions. qmPCR The quantitative Spn9802 PCR for the detection of S. pneumoniae [17] was combined with the P6 PCR for the detection of H. influenzae [21] and the ctrA PCR for the detection of Neisseria meningitidis [14]. All primers and probes are shown in Table

1 where positions with lower case letters indicate locked nucleic acid Farnesyltransferase [27]. Table 1 Oligonucleotide primers and probes for detection of S. pneumoniae, H. influenzae and N. meningitidis.   Sequence (5′ to 3′)a Positions in target gene S. pneumoniae     Spn9802 F 5′-A GTC GTT CCA AGG TAA CAA GTC T-3′ 3370-3392 Spn9802 R 5′-AC CAA CTC GAC CAC CTC TTT-3′ 3525-3506 Spn9802 FAM 5′-FAM-aTc AGa TTg CTg ATa AAa CgA-BHQ1-’3   H. influenzae     Hi P6 F 5′-CCA GCT GCT AAA GTA TTA GTA GAA G-3′ 302-326 Hi P6 R 5′-TTC ACC GTA AGA TAC TGT GCC-3′ 477-457 Hi P6 JOE 5′-JOE- CAg ATg CAg TTg AAg GTt Att tAG-BHQ1-’3   N. meningitidis     ctrA F 5′-GCTGCGGTAGGTGGTTCAA-3′ 617-635 ctrA R 5′-TTGTCGCGGATTTGCAACTA-3′ 727-708 ctrA ROX 5′-ROX-CATTGCCACGTGTCAGCTGCACAT- BHQ1-’3   a Positions with lower case letters indicate locked nucleic acid [27]. The PCR for detection of N. meningitidis was used as described previously, except that 3.

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