Automated Sample Treatment System for Enhanced Molecular Pathogen Detection in Blood

Abstract Clinical samples contain various biological substances, such as proteins and lipids, which can inhibit molecular detection of pathogens, often present at concentrations below the limit of detection (LOD). While existing sample preparation techniques can remove inhibitors and enrich pathogens, they are generally labor-intensive, manual processes that increase the risk of exposure. We present a fully automated sample treatment system that integrates immunomagnetic separation (IMS) and DNA extraction within a microfluidic film device, specifically designed to streamline pathogen detection from clinical samples. The system can process up to 1 mL of whole blood and concentrate the final eluent to 20 µL, obtaining purified DNA in less than 1 h. When combined with PCR or quantitative PCR (qPCR), the system detects Escherichia coli O157 at concentrations as low as 1 CFU/mL in spiked whole blood—achieving a sensitivity 100 times greater than PCR or qPCR alone. This enhanced sensitivity is due to the effective integration of bacterial pre-concentration and DNA purification steps, which remove PCR inhibitors and improve detection in complex sample matrices, such as blood. These results demonstrate that our automated system is highly suitable for rapid, sensitive pathogen diagnostics in clinical settings, with potential for further adaptation to a wide range of pathogens and sample types, advancing molecular diagnostics for healthcare applications.