We seek to develop a universal sample preparation method to support accurate, consistent, and sensitive pathogen quantification across a wide range of food matrices. We are open to approaches involving target concentration, DNA cleanup, or both, and are particularly interested in technologies capable of selectively separating target particles (typically <3–5 µm) from larger debris in samples where the targets are present in low abundance and minimizing loss is critical. The solution is intended for use in routine food safety testing and must ultimately deliver consistent recovery performance across diverse and complex matrices, supporting reliable and sensitive quantification via droplet digital PCR (ddPCR).

Solutions of interest include:

• Filtration technologies
• Magnetic bead-based on capture for ddPCR-grade purity
• Microfluidic cartridges for standardized sample processing
• Heat-stable, low-volume prep protocols for simple lab use
• Inhibitor-binding solutions like membranes or additives for complex sample cleanup
• Extraction kits optimized for meat, with relevance to other food types, such as dairy and plant-based matrices
• A combination of several approaches

Our must-have requirements are:

• Capable of purifying samples to yield DNA suitable for droplet digital PCR
• Able to concentrate large-volume eluates (>300 mL) to <100 µL for quantification of targets/microorganisms at low concentrations or capable of consistent recovery of microorganisms/DNA present at low concentrations
• Applicable to food matrices ranging from simple rinses to complex samples like ground beef
• Completed within a standard lab shift, without requiring overnight incubation
• Feasibility for parallel sample processing or potential for future scale-up

Our nice-to-have's are:

• Processing time is under three hours
• Adaptable to a wide range of food matrices without significant re-optimization
• Low hands-on time and minimal number of steps
• Shelf-stable reagents or kits requiring minimal cold chain logistics
• Minimal use of hazardous solvents or alignment with green chemistry principles