b Real-time PCR with primers PAO1 S and PAO1 A and TaqMan probe oprL TM using the LightCycler 1.5. c The initial inoculum was Selleck LY2835219 calculated by averaging the number of cfu at dilution

8 on MC and CA, i.e. 2.5 cfu/50 μl, multiplying with 20 to obtain the cfu/ml, i.e. 50 cfu/ml, multiplying with AZD8186 mouse the dilution factor 1/3125000 to obtain the initial inoculum after dilution with Sputasol, i.e. 78 125 000 cfu/ml, and finally multiplying with factor 2 to obtain the original number of cfu/ml of sputum, i.e. 156 250 000 cfu/ml, or approx. 1.6 log8 cfu/ml. Based on these results, the number of culturable cells in the original sputum preparation was calculated to be 1.6 log8 cfu/ml. Comparison of DNA-extraction protocols For each sputum dilution, DNA was extracted by four protocols using the bioMérieux easyMAG Nuclisens semi-automated DNA-extractor and by the protocol for the manual High Pure PCR Template Preparation Kit (Roche). Results are listed in Table 1. In our hands, the BioMérieux easyMAG Nuclisens protocol Generic 2.0.1, combined with proteinase K pretreatment, was the DNA-extraction protocol that enabled the most sensitive detection of P. aeruginosa from sputum of CF patients, both with

conventional and with qualitative PCR, giving amplification of the P. aeruginosa oprL target GANT61 gene up to dilutions 6 and 8, respectively. This DNA-extraction protocol was used further to compare a total of two different conventional PCR and four different (quantitative) real-time PCR formats. Comparison of different PCR and real-time PCR formats Conventional PCR, using the Veriti 96-Well Thermal Cycler (Applied Biosystems), combined with visualisation of the PCR products by agarose gel electrophoresis and ethidium bromide staining respectively by capillary electrophoresis and fluorescence measurement, was compared with MycoClean Mycoplasma Removal Kit three different real-time PCR formats using the LightCycler

1.5 (Roche) and with a commercially available P. aeruginosa specific real-time PCR (TaqMan assay) using the ABI7000 (Applied Biosystems). One real-time PCR format used SybrGreen fluorescence as the detection method, whereas the other three real-time PCR formats relied on the fluorescence generated by probes for detection. Results are listed in Table 2. For the conventional PCR, combined with agarose gel electrophoresis, P. aeruginosa DNA could be detected up to dilution 6, while with capillary electrophoresis amplified P. aeruginosa DNA could be detected up to dilution 7. P. aeruginosa DNA could be detected up to dilution 7 with real-time PCR using SybrGreen, and up to dilution 8 with real-time PCR with the Hybprobes, with the TaqMan probe and with the commercial Pseudomonas aeruginosa TaqMan probe detection kit on the ABI7000.