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.