Abstract: The present invention is directed to methods and systems for rapidly identifying microorganisms such as bacteria, viruses, fungi and the like that may be present in an agricultural specimen. The methods of the present invention provide a process for rapidly and accurately identifying infectious or pathogenic microorganisms without the need for culturing. In addition, the methods of the present invention provide processes for assaying harvested agricultural crops for the presence of statistically significant quantities of microorganisms.

Abstract: An example embodiment of the invention includes a method of performing an assay comprising the steps of (1) providing a multimode waveguide; (2) fixing one or more fluidic cells to the multimode waveguide, wherein each of the one or more fluidic cells including a surface having a portion thereof sealed to the coated region, the surface including a depression therein defining a fluidic channel bounded at least in part by the optically exposed region, and a sample introduction port for the introduction of a fluid sample into the fluidic channel; (3) introducing a fluid sample into the fluidic channel via the sample introduction port so that the fluid sample physically contacts the optically exposed region; (4) launching light into the waveguide so as to produce a wave at the optically exposed region; and (5) detecting an optical signal generated at the optically exposed region in response to the wave, wherein the optical signal is correlated with the presence of a prion protein in the fluid sample.