To date, while various diagnostic approaches for pathogen detection have been proposed, most are too expensive, lengthy or limited in specificity for clinical use. Nanoparticle systems with unique material properties, however, circumvent these problems and offer improved accuracy over current methods. Herein, we present novel magneto-DNA probes capable of rapid and specific profiling of pathogens directly in clinical samples. A nanoparticle hybridisation assay, involving ubiquitous and specific probes that target bacterial 16S rRNAs, was designed to detect amplified target DNAs using a miniaturised nuclear magnetic resonance device. Ultimately, the magneto-DNA platform allowed both universal and specific detection of various clinically relevant bacterial species, with sensitivity down to single bacteria. Furthermore, the assay was robust and rapid, simultaneously diagnosing a panel of 13 bacterial species in clinical specimens within 2 hours. The generic platform described could be used to rapidly identify and phenotype pathogens for a variety of applications.