Abstract
Apis mellifera honey bees are keystone species for agriculture and global biodiversity, yet their populations are increasingly affected by multiple stressors, including the microsporidian parasite Nosema ceranae. Early and accurate detection of this pathogen is critical to prevent colony losses and sustain pollination services. This study compares qPCR and ddPCR for detecting N. ceranae in bees and hive debris. qPCR is suitable for routine screening, whereas ddPCR offers higher sensitivity and precise quantification. The high diagnostic concordance between the two assays in bee samples, coupled with ddPCR's enhanced detection capability in debris, underscores their complementary value in apicultural monitoring. This study provides the first experimental comparison between qPCR and ddPCR applied to matched field samples of bees and hive debris, establishing a sensitive and practical diagnostic framework for Nosema ceranae surveillance. The findings support improved diagnostic accuracy and early detection in apicultural health programs.