Using bacterial whole genome sequencing to design targeted toxin assays in black tiger shrimp (Penaeus monodon)

To investigate mortalities of Penaeus monodon post-larvae in a prawn hatchery, water samples from a hatchery tank treated with erythromycin were plated out on two agar plates, one containing additional erythromycin. DNA from a sample from each plate was sequenced on a MiSeq. Reads were assembled using Shovill, CDS determined using Prokka, and annotated using blastx. From the annotated sequences, four toxin genes were selected and qPCR primers were designed. To further evaluate the presence of the toxins, one metagenomic sample of a prawn post-larval sample was sequenced and reads were mapped back to the four toxin sequences. The qPCR and high-throughput sequencing results showed that the four toxin genes were associated with moribund larvae, while not being present in larvae without symptoms.