Quantitative fluorescence in situ hybridization (FISH) of magnetically confined bacteria enables rapid determination of early-stage human bacteremia

The current diagnosis of bacteremia mainly uses blood culture, which is insufficient to offer rapid and quantitative determination of pathogens in blood. Here, we report a quantitative and sequential multiplexed fluorescence in situ hybridization in a microfluidic device (µFISH) that enables early and rapid (2-hour) diagnosis of bacteremia without prior blood culture. Mannose-binding lectin-coated magnetic nanoparticles enrich a broad range of pathogens, and µFISH enables identification and quantification of the magnetically confined bacteria. We detect Escherichia coli (E. coli) and measure their relative proportions to universal bacteria levels in the bacteremic blood of a porcine model and human whole blood collected from E. coli-infected patients, which was elusive with the conventional bacteremia diagnosis methods. Thus, µFISH can be used as a versatile tool to rapidly identify pathogens and further assess the number of both culturable and non-culturable bacteria in biological and environmental samples.