Methods and systems for Resonant Raman spectroscopy are provided. Methods according to certain embodiments include irradiating a sample with a monochromatic light source at a first irradiation intensity and a second irradiation intensity, determining the intensity of one or more of the Resonant Raman scattering and fluorescence scattering at the first irradiation intensity and second irradiation intensity, calculating a rate of change of one or more of the intensity of Resonant Raman scattering and fluorescence in response to the change in irradiation intensity from the first irradiation intensity to the second irradiation intensity and comparing one or more of the rate of change in the intensity of Resonant Raman scattering and the rate of change in the intensity of fluorescence scattering with the rate of change in the irradiation intensity by the monochromatic light source to determine the Resonant Raman response of the sample. Methods also include determining the presence or absence of a microorganism in a sample and correcting for variations associated with measurement instrumentation (e.g., monochromatic light source) and variations associated with the sample (e.g., fluorescence from non-target compounds). Also provided are methods for determining the antimicrobial susceptibility of a microorganism to an antimicrobial agent as well as methods for characterizing a phenotype of an unknown microorganism in a sample. Systems for practicing the subject methods are also provided.