Table 2 Comparison of the sensitivity of the different PCR formats for sputum dilutions extracted with easyMAG Generic 2.0.1 and proteinase K pretreatment PCR formata Cyclerc Primers Probes Annealing temperature (°C)d Last positive CP-690550 nmr dilution 1. PCR + AGEb 1 PAO1 S/PAO1 A None 55 6 2. PCR + FCE 1 PAO1 S/PAO1 A None 55 7 3. real-time PCR + SybrGreen 2 PAO1 S/PAO1 A None
55 7 4. real-time PCR + HybProbes 2 oprL F/oprL R oprL-LC-ROX/oprL-LC-FAM 57 8 5. real-time PCR + TaqMan probeb 2 PAO1 S/PAO1 A oprL TM 55 8 6. real-time PCR + TaqMan probe 3 Not specified Not specified 60 8 a AGE: Agarose gel electrophoresis + ethidium bromide staining; FCE: Fluorescent capillary electrophoresis on ABI310. b PCR formats that were used to compare the sensitivity of the different RG7112 DNA-extraction protocols (Table 1). c 1: Veriti 96-Well Thermal Cycler, Applied BioSystems, Foster City, Ca.; 2: LightCycler 1.5, Roche, Basel, Switzerland; 3: ABI Prism 7000 Sequence Detection System, Applied
BioSystems. d Annealing temperatures as specified by provider of primers and probes (PCR formats 1-5) or by provider of commercial kit (PCR format 6). Discussion Pseudomonas aeruginosa is the major pathogen in cystic fibrosis (CF) patients and is an indicator of poor prognosis in CF patients, especially from the onset of the chronic stage when colonies become mucoid and variant phenotypes emerge. Early detection is essential given the success of early aggressive eradication therapy [6, 7]. Therefore, the most prevalent detection and identification methods, i.e. culture and (real-time) PCR, should be optimized to achieve the highest
sensitivity. West et al.  reported that specific P. aeruginosa antibodies were detectable between 6 and 12 months prior to the first positive culture for P. aeruginosa from respiratory samples. These findings suggest that culture may miss P. aeruginosa in the early stages of colonization. Also at later stages, culture can miss the emerging P. aeruginosa phenotypic variants such as the pyoverdine negative mutants, the slowly growing variants, the small colony variants and the auxotrophs, which do not grow on standard media [9, 10]. Therefore, the development of improved culture methods and/or of molecular methods is warranted, not only for early detection but also for follow up of colonized patients. Mannose-binding protein-associated serine protease However, although several molecular Cytoskeletal Signaling assays for the detection of Pseudomonas species have been described (e.g., [11, 13–19, 22–26]), surprisingly few studies have compared selective and nonselective culture methods with the different molecular methods that have been described for the detection of P. aeruginosa directly from clinical samples. The studies comparing sensitivity of culture and species-specific PCR for the detection of P. aeruginosa from sputa of CF patients indicate comparable efficiency of both methods [8, 16], with slightly higher sensitivity for PCR in some studies [12, 18] or clearly higher sensitivity for PCR [13, 26].