Mini-review of RPA-CRISPR multiplex detection for foodborne pathogen screening

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Frontiers in Medicine Published May 7, 2026 Medically reviewed May 7, 2026 DOI ↗ By Dr. Amelia Tan, PhD · Internal Medicine & Chronic Disease

Key Takeaway

Consider RPA-CRISPR as a rapid, sensitive tool for foodborne pathogen detection, but note standardization and regulatory hurdles.

This mini-review summarizes the current state of recombinase polymerase amplification (RPA) combined with CRISPR-based multiplex detection for foodborne pathogen screening. The technology operates isothermally at 37-42°C, achieving attomolar sensitivity and detection times of 20-90 minutes. Multiplex strategies include two-tube, spatial separation one-tube, and homogeneous one-pot approaches.

The review highlights applications in complex food matrices such as poultry, milk, and lettuce, targeting pathogens like Salmonella and Listeria, as well as antimicrobial resistance profiling and on-site surveillance. Comparators include qPCR and next-generation sequencing (NGS).

Key challenges identified by the authors include standardization of protocols, matrix inhibition, and the need for regulatory approval. These limitations currently hinder widespread deployment in food safety and clinical settings.

Given the early stage of this technology, the review provides a useful overview but does not offer pooled effect sizes or quantitative comparisons. Practice relevance is potential, but real-world implementation awaits resolution of the noted challenges.

Study Details

Study typeSystematic review

EvidenceLevel 1

PublishedMay 2026

View Original Abstract ↓

The integration of recombinase polymerase amplification (RPA) with CRISPR-Cas systems has emerged as a powerful platform for rapid multiplex nucleic acid detection. Compared with quantitative polymerase chain reaction (qPCR) and Next-generation sequencing (NGS), RPA-CRISPR operates isothermally (37 °C–42 °C), requires minimal equipment, and achieves attomolar sensitivity in 20–90 min via collateral cleavage. Recent multiplex strategies, namely two-tube, spatial separation one-tube, and homogeneous one-pot, they have overcome crosstalk and enabled highly multiplexed detection in complex food matrices such as poultry, milk, and lettuce. These approaches are particularly suited for foodborne pathogen screening (e.g., Salmonella, Listeria), antimicrobial resistance profiling, and on-site surveillance, aligning with the scope of research at the frontier of food microbiology diagnostics. Despite advances, challenges persist in standardization, matrix inhibition, and regulatory approval. This mini-review summarizes recent advances (2020–2025) in RPA-CRISPR multiplex detection, outlines future directions for clinical implementation and food safety deployment, and provides guidance for subsequent research on its practical applications in these fields.