2.5 FTIR-S spectra acquisition and processing
FTIR-S was performed only on the strains which had combined PFGE plus WGS information in the initial study by Acosta et al. (n=20) (Acosta et al., 2020). FTIR-S spectra acquisition was performed using IR Biotyper (Bruker Daltonics) following the manufacturers’ instructions. Briefly, a 1 µl loopful of biomass was resuspended in 50 µl of 70% ethanol and homogenized with metal rods (Bruker Daltonics). Then, 50 µl of sterile water were added and 15 µl of the suspension were spotted on a silicon plate. Samples were analyzed in triplicates in three independent experiments along with two standards (Bruker Infrared Test Standard 1 and 2, Bruker Daltonics). Spectra with valid target quality controls were further analysed using Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA). Moreover, FTIR-S spectra were visualized and processed using Clover MS Data Analysis Software. The processing consisted on standard normal variation followed by Savitzky-Golay filter with 9 smoothing points, polynomial order=2 and second derivative.