A sensitive RAA-CRISPR/Cas13a-LFS assay for point-of-care detection of Salmonella.

Abstract

Salmonella is a major zoonotic pathogen that seriously endangers the poultry industry and threatens public health. Rapid and accurate monitoring is therefore essential for effective prevention and control. In this study, we developed a molecular detection method for Salmonella by integrating recombinase-assisted amplification (RAA) and the CRISPR/Cas13a system. We then adapted this method into a lateral flow strip (LFS) format that allows naked‑eye reading, enabling instrument‑free, rapid on‑site detection. The assay combines the efficient isothermal amplification ability of RAA with the high specificity recognition of CRISPR/Cas13a, targeting the conserved fimY gene of Salmonella. It achieves a detection sensitivity of 10° copies/μL. When further coupled with LFS for visual detection, the reaction can be finished within 40 min, with a detection limit of 102 copies/μL. In clinical sample validation, the method showed 100% agreement with qPCR results and significantly outperformed conventional PCR. This assay provides a sensitive and specific approach for Salmonella detection that is simple to operate and suitable for field deployment, offering a practical tool for rapid Salmonella screening in resource-limited settings.