A sample preparation system includes a sample input, a first chamber fluidly coupled to the sample input and containing a sample preparation reagent, a second chamber containing a surface enhanced Raman spectroscopy (SERS) sensor structure and a third chamber containing a sensor preparation solution. The sample input, the first chamber and the second chamber are fluidly coupled to one another in a series and the third chamber is fluidly coupled to the third chamber outside of the series so as to sequentially direct a sample received by the sample input through the first chamber to the second chamber and out of the second chamber and so as to direct the sensor preparation solution into the second chamber following discharge of the sample out of the second chamber.