| Summary: | <i>Nocardia crassostreae</i> is a novel pathogen responsible for infections in oysters (<i>Crassostrea gigas</i>) and mussels (<i>Mytilus galloprovincialis</i>). <i>N. crassostreae</i> is also responsible for nocardiosis both in immunocompetent and immunocompromised patients. We investigated <i>N. crassostreae</i> DNA in mussels grown in marine sites of the Mediterranean Sea in the Campania Region. We examined 185 mussel pooled samples by droplet digital PCR (ddPCR) and real-time quantitative PCR (qPCR), each pool composed of 10 mussels and 149 individual mussels. ddPCR detected <i>N. crassostreae</i> DNA in 48 mussel pooled samples and in 23 individual mussel samples. qPCR detected <i>N. crassostreae</i> DNA in six pooled samples and six individual mussel samples. The two molecular assays for the detection of <i>N. crassostreae</i> DNA showed significant differences both in the pooled and in individual samples. Our study demonstrated that ddPCR outperformed real-time qPCR for <i>N. crassostreae</i> DNA detection, thus confirming that ddPCR technology can identify the pathogens in many infectious diseases with high sensitivity and specificity. Furthermore, in individual mussels showing histological lesions due to <i>N. crassostreae</i>, the lowest copy number/microliter detected by ddPCR of this pathogen was 0.3, which suggests that this dose could be enough to cause infections of <i>N. crassostreae</i> in mussels.
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