Stepwise approach of the data analysis method. Dot blots illustrate MFI values for 43 genetic markers targeted in 88 clinical isolates and laboratory strains  obtained from (A) the MAGPIX csv file, (B) after normalization and (C) after normalization and correction. (A) Raw MFI values obtained for every targeted marker per strain. The dashed line indicates the threshold of MFI 150 which was initially chosen for the classification of targeted makers. Red dots show the MFI values obtained which are located in the intermediate range after normalization and correction in panel C. (B) MFI values after intra-strain normalization of raw MFI values. (C) MFI signals after normalization and inter-strain correction using marker-specific correction factors. The grey area defines the intermediate range calculated as the area between one and two standard deviations from the average MFINORM = 860.