Based on molecular-specific surface-enhanced Raman scattering (SERS) spectroscopy we were able to discriminate between rough and smooth strains of Escherichia coli and Proteus mirabilis bacteria. For this purpose, bacteria have been immobilized through electrostatic forces by inducing a positive charge on the glass slide. This way, SERS spectra on bacterial biomass and also on single bacteria could be recorded in less than 2 h, by using concentrated silver nanoparticles as SERS-active substrate. Single-bacterium SERS spectral fingerprints showed to be sensitive to the presence of the O-antigen at strain level and to the microorganisms growth phase. By using principal component analysis (PCA) on the SERS spectra recorded from E. coli and P. mirabilis, these two uropathogens could be fairly discriminated.