On-site DNA Detection of Trypanosomatid Parasites and Nosema ceranae Through Alkaline Lysis Coupled to RPA/CRISPR/Cas12a System

Early on-site detection of microscopic pathogens is essential for the effective management and health of honeybee colonies. Currently, the gold standard for molecular detection of bee pathogens is qPCR or RT-qPCR. Here, we present a rapid, sensitive, and cost-effective alternative for field-deployable DNA pathogen detection. This method combines direct, amplification-ready cell lysis of worker bee abdomens with recombinase polymerase amplification (RPA), CRISPR/Cas12a-mediated trans-cleavage of reporter probes, and detection via lateral flow assays. We successfully validated this protocol in honeybees infected with Nosema ceranae and Lotmaria passim. The described protocol can be performed using a simple heat block or at room temperature and is potentially applicable to any DNA-based pathogen or gut microbiota of the honeybee. The entire process takes approximately 180 min and achieves a sensitivity comparable to qPCR, detecting as few as 96 parasite copies/µL. In conclusion, this approach offers a promising tool for reliable and rapid field diagnosis of honeybee infections without the need for complex laboratory equipment, making it ideal for on-site colony surveillance.