| Summary: | <i>Alexandrium pacificum,</i> which produces the paralytic shellfish toxin (PST) saxitoxin (STX), is one of the causative species of paralytic shellfish poisoning outbreaks in coastal areas of Korea. In this study, we developed a chip-based digital PCR (dPCR) method for <i>A. pacificum</i> detection and tested it for monitoring in Jinhae-Masan Bay. Using the sequence of an <i>A. pacificum</i> strain isolated in 2017, species-specific primers targeting <i>sxtA4</i> (a STX biosynthesis-related gene) were designed and used in a dPCR, detecting 2.0 ± 0.24 gene copies per cell of <i>A. pacificum</i>. Cell abundance in field samples, estimated by a chip-based dPCR, was compared with the PST content, and measured using a mouse bioassay. A comparison with shellfish PST concentrations indicated that cell concentrations above 500 cells L<sup>−1</sup>, as measured using the dPCR assay, may cause shellfish PST concentrations to exceed the allowed limits for PSTs. Concordance rates between dPCR and PST results were 62.5% overall in 2018–2021, reaching a maximum of 91.7% in 2018–2019. The sensitivity of the dPCR assay was higher than that of microscopy and <i>sxtA4</i>-based qPCRs. Absolute quantification by chip-based dPCRs targeting <i>sxtA4</i> in <i>A</i>. <i>pacificum</i> exhibits potential as a complementary approach to mouse bioassay PST monitoring for the prevention of toxic blooms.
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