Parasites in the genera Cryptocaryon and Neobenedenia , and subclass Scuticociliatia infect the skin, gills, and sometimes deeper tissues of marine fish, and they are among the most common pathogens in public aquaria and aquaculture. This ciliate Cryptocaryon irritans causes marine “white spot” disease, and has a complex life cycle that results in rapidly escalating infections and major subsequent mortality events. As part of the life cycle, there is a free-swimming stage which suggests that there should be a detectable amount of the organisms in the water column prior to major infection. The skin fluke Neobenedenia spp. is a monogenean capsalidae that attaches to and infests a broad range of aquarium fish. This parasite hatches from an egg stage and can remain in a free-swimming stage, for a few days before finding a suitable host. Members of the Scuticociliatia are free-living, opportunistic parasites that feed and reproduce once attached to a host causing visible ulcerations of the skin.
Currently, clinical diagnosis of these parasites is based on physical detection, and their presence is not often noticed until disease symptoms have developed. Cytologic detection methods such as microscopic examination of skin mucus, gill biopsies, sediment, substrate, or filtrate samples are crude, “needle-in-a-haystack” tools, having very low sensitivity. These organisms can be present in subclinical concentrations, where the presence of the organism is not recognized.
This study aimed at developing a TaqMan multiplex qPCR assay to not only detect the parasite, but also correlate abundance with disease, thus allowing use of the test to determine threshold levels of each parasite in the water column. This information can then be used to initiate treatment before major infection events take place. These methods also be adapted for other targets, such as bacterial or viral pathogens.