This is where SERS and the nano particles come in. When struck with light of certain frequencies, nanoparticles can induce a plasmon resonance. This resonance can give rise to a strong magnification (1000–100 000x) of parts of the Raman spectrum.
Several academic papers describe how they used Surface Enhanced Raman Spectroscopy to distinguish bacterial species from colonies grown on a Petri dish. The nature of SERS enhancement depends however on the characteristics of the nano particles than are being used.