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Magnetic nanoparticles are composed of a core magnetic material (e.g., iron oxide) attached via a polymer spacer (e.g., polyethylene glycol) to ligands that are capable of binding specific pathogens. Ligands include zinc-coordinated bis(dipicolylamine) (bis-Zn-DPA), which selectively and rapidly (within five minutes) binds Gram-negative and Gram-positive bacteria in addition to endotoxins. The mixture is injected into a microfluidic system in which magnets along the flow path attract the nanoparticles that are bound to contaminants, thus restricting their flow to the outlet. The system achieves a near complete removal of bacteria from blood with a shorter incubation time and at a higher flow rate than existing methods.