UCalgary researcher finds way to predict whirling disease with almost no data

A study led by a University of Calgary researcher has come up with an AI-based early detection system for river-borne pathogens — including whirling disease in trout and salmon.

The study, published in Methods in Ecology and Evolution, started in 2018 using data from Alberta Environment and Parks after several lakes and rivers were infected with whirling disease, which is named after the circular swimming pattern of infected fish. 

“Our work helps to predict the presence or absence of disease,” says lead author Dr. Pouria Ramazi, PhD, an assistant professor in the departments of Biological Sciences and Mathematics and Statistics, in the Faculty of Science. The study also involved researchers from the Indian Institute of Technology Kharagpur, Isfahan University of Technology in Iran, the University of Alberta and the University of Victoria.

Whirling disease is caused by Myxobolus cerebralis, a microscopic parasite of fish such as trout, salmon and whitefish. The research notes that effective management of waterborne diseases requires early prediction of the pathogens, but that test results on the presence/absence of the disease are notoriously rare in the beginning of disease outbreaks.

The study used an AI model — hidden Markov models — to work with detailed data on variables that are readily available in aquatic environments, such as air temperature. The model predicted pathogen distribution in the Oldman River in southern Alberta.

“What’s surprising is that, unlike most AI systems that need lots of confirmed examples, this model still performed well, even when it was trained on just one confirmed case of whirling disease,” explains Ramazi. “It pulled extra clues from environmental measurements in the other samples to map out where infestations were likely happening.”

Ramazi says the model also has the potential to provide early warning signals for other emerging diseases — such as cholera, salmonella and zebra mussels — in rivers at their early stages.

The paper notes that young fish are vulnerable to whirling disease, with mortality rates up to 90 per cent. It poses a threat to fish populations and fisheries due to economic loses because of its impact on recreational fishing and aquaculture.

Whirling disease was confirmed for the first time in Canada in Banff National Park and the Bow River in August 2016. It has since been detected in British Columbia.

Other research has shown that waterborne diseases, particularly in rivers, can lead to substantial costs to both the environment and health care.