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.