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Pathogen Detection in Water Samples A more recent approach for testing for aquatic pathogens such as bacteria and myxozoan parasites is water sampling. Water is collected either by hand or with an automatic sampler. Samples are filtered, the DNA is extracted and then molecular methods such as quantitative PCR are used to determine the identity and abundance of pathogens. Water sample data are usually obtained more quickly than sentinel fish exposure data, but have a higher detection threshold. We use a combined approach of water sampling and sentinel fish exposures to relate abundance of waterborne stages with fish health.