Collection and processing of Respiratory Tract Samples
Respiratory samples taken from CF patients including sputum and deep pharyngeal swab samples (DPS) collected with ESwab™ (Copan Diagnostics, Murrieta, CA) sent to the microbiology laboratory for processing and inoculation. An equal volume of Sputasol solution (Thermo Scientific™, USA) was added to the sputum samples and homogenized in a shaker incubator for 1 hour at 37 °C. The samples were vortexed in every 15 minutes and the resulting homogenates were inoculated whereas DPS samples were processed directly. Samples were inoculated into Mac Conkey agar, 5% sheep-blood agar, Haemophilus selective agar (chocolate agar including bacitracin), Burkholderia cepacia selective agar (BCSA), CHROMID®, S. aureus Elite agar (SAIDE) agar plates then incubated for 24-72 hours at 35.5 °C. All plates were purchased from bioMérieux. Culture media evaluated daily for significant bacterial growth and if colonies exist, identification of microorganisms done by Matrix-Assisted Laser Desorption/Ionization time-of-flight, Mass Spectrometry (MALDI-TOF MS, BioMerieux, France). Antimicrobial susceptibility testing has done by Kirby-Bauer disk diffusion method and Vitek 2 system (bioMérieux). Results were evaluated according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST).