The MSP profile showing the highest score was selected for each isolate and was included to construct the dendrogram using the statistical toolbox in MATLAB 7.1 integrated in the MALDI Biotyper 2.0 software (Bruker Daltonics). Based on the principle that identification score reflects the agreement of the spectra with the standard A. baumannii database entry, the MSP profile showing the highest score could mean that the specific spectra represents the most typical aspects of a certain strain from the database. This selection of the highest score marking spectra was necessary, especially when highly similar strains were studied, because several mass spectral features related to limited reproducibility of the method might eclipse mass spectral differences between the strains. Test strain clonality was determined with cut-off values at a distance of 250 [6 (link)].
For PFGE analysis of the 32 isolates, SmaI-digested genomic DNA was prepared according to the manufacturer's instructions (Bio-Rad, Hercules, CA, USA). Fragments were separated for 20 h at 6.0 V/cm at 11°C using a CHEF-DR II System (Bio-Rad) with initial and final pulse times of 0.5 s and 30 s, respectively [14 (link)]. The pattern was analyzed using the Fingerprinting II software (Bio-Rad). The cut-off value of 75 was applied for grouping as it was used previously [15 (link), 16 (link)].
For PFGE analysis of the 32 isolates, SmaI-digested genomic DNA was prepared according to the manufacturer's instructions (Bio-Rad, Hercules, CA, USA). Fragments were separated for 20 h at 6.0 V/cm at 11°C using a CHEF-DR II System (Bio-Rad) with initial and final pulse times of 0.5 s and 30 s, respectively [14 (link)]. The pattern was analyzed using the Fingerprinting II software (Bio-Rad). The cut-off value of 75 was applied for grouping as it was used previously [15 (link), 16 (link)].
Free full text: Click here
