Abstract: A method of detecting a pathogen in a sample, comprising: mixing at least a portion of the sample with a plurality of capture particles functionalized with a molecular recognition element exhibiting specific binding to said pathogen to capture at least a portion of pathogen particles when present in the sample; exposing said captured pathogen particles to at least two fluorescent dyes, which emit fluorescent radiation at two different wavelengths in response to excitation, such that live pathogen particles among said captured pathogen particles are preferentially stained with one of the dyes and dead pathogen particles among said captured pathogen particles are preferentially stained with the other dye; irradiating the captured stained pathogen particles with excitation radiation to excite said fluorescent dyes; and detecting fluorescent radiation emitted by said excited fluorescent dyes; and distinguishing said live pathogen particles from said dead pathogen particles based on wavelengths of the detected flu