A suite of ddPCR assays targeting microbial pathogens for improved management of shellfish aquaculture

Climate change is drastically altering the environment and changing the abundance and geographical distribution of marine pathogens. These microbial species put additional pressure on the aquaculture industry by acting as sources of disease for animals important to the food industry as well as for humans upon consumption of contaminated food. To address growing concerns, high-resolution monitoring of pathogens can offer insights for effective management in a critical industry. Validated in the field, the suite of molecular droplet digital PCR assays presented here improves upon current methods, enabling the simultaneous quantification of several targets. This technology makes it possible to track pathogens as they move through the environment and reveals changes in abundance that may inform adjustments to farming practices aimed at mitigating negative outcomes. Additionally, this work presents a unique approach to molecular assay design that unveils potential drivers of ecological shifts and emerging etiologies of disease more efficiently.