MIDAS: rapid, multiplexed molecular profiling for integrated host-pathogen analysis.

Addressing the need for integrated molecular analysis in complex infectious conditions requires technologies that rapidly quantify both pathogens and host responses. This is particularly relevant in sepsis research, where existing tools typically measure either microbial or host biomarkers. Here, we present MIDAS (Multiplexed Intelligent Diffraction Analysis System), a proof-of-concept platform that integrates shape-encoded hydrogel particles with lens-free diffraction imaging and deep learning-based analysis to enable simultaneous quantification of bacterial RNA and inflammatory proteins in a single system optimized for potential point-of-care use. The assay completes multiplexed measurements in under 4 h, significantly faster than standard culture workflows ( ~ 20-40 h). Beyond spiked studies, MIDAS is evaluated using specimens from a clinically relevant porcine sepsis model, showing high concordance with culture, qPCR and ELISA. Although further clinical validation is required, this flexible platform may support the development of accessible host-pathogen profiling tools with broad applications in healthcare, agriculture, food safety, and beyond.