Molecular detection of parasites based on water sampling offers an early warning system for fish farmers

Giana Bastos Gomes

By Bianca Nogrady

Detecting disease in aquaculture is challenging. Fish cannot tell you when they are starting to feel unwell, even when they are seriously ill.

As a result, an outbreak of disease such as saltwater ich (also known as white spot disease) – caused by the ciliate protozoan parasite Cryptocaryon irritans – is often not detected until it is too late and infection has run rampant through a whole fish population. This is the challenge that veterinarian and PhD candidate Giana Bastos Gomes is hoping to meet. Her research recently won both the 2016 Minister and FRDC Science and Innovation Award for Young People in Agriculture, Fisheries and Forestry, presented by Deputy Prime Minister Barnaby Joyce.

Her PhD is focused on developing new molecular tools to detect ciliate protozoan parasites affecting Barramundi (Lates calcarifer). Her project includes the development of new genetic technologies that will help in early diagnosis of fish parasites. She is working to develop a DNA-based point-of-care device to be used by fish farmers for the early detection of waterborne parasites and prevent disease outbreaks.This device will help fill the existing knowledge gap on rapid and effective pathogen detection methods in aquaculture systems.

Originally trained in Brazil, Giana Bastos Gomes had always wanted to work in farming, but when she saw an advertisement for a job in a prawn hatchery, it captured her attention. “I realised there were not many vets working in this area, so it was the chance to do something different,” says Giana Bastos Gomes, now with James Cook University. She also sees the opportunity to help tackle a global issue – food security – as aquaculture has the potential to become a major source of food. “I come from Brazil. We have some poverty and we have people without much access to food, but we also have so much water, so there is a chance to use that resource.”

Molecular tools

About 40 per cent of global aquaculture production is lost each year to disease. Giana Bastos Gomes is interested in how to improve early detection of disease in aquaculture by using molecular tools that can pick up low levels of pathogens in the water before any infection begins to manifest in farmed fish. The initial focus of her research is white spot, an insidious saltwater fish disease that affects Barramundi. It presents as white dots on the fish’s skin and gills. In its early stages animals demonstrate skin irritation and difficulty breathing but without any white dots visible. When the infection progresses, the white dots grow in size and spread across the fish’s body. The animals stop eating and eventually they die.

“One of the problems when working in aquaculture is that we can’t really see much sign of a problem until infections are in advanced stages; animals come to the surface, they stop eating and they show signs of sickness,” Giana Bastos Gomes says. “But usually when this happens it is too late to save them, particularly when farms are located in remote areas, far from diagnostic laboratories.”

Preventive action

“Instead of waiting until animals get sick, we can collect water from the farm and extract genetic material from that water,” Giana Bastos Gomes says. She then uses molecular markers that help to tag and amplify DNA from the ciliate parasite in water samples. The amount of this parasite’s genetic material present indicates the risk level for the farm. It can also be combined with other information about the conditions at the time of sampling, such as oxygen levels and water temperature, to provide clues about other factors influencing the risk of infection.

With early detection, aquaculture farms can implement interventions such as exchanging water, new diet protocols, or chemical or ultraviolet treatments to get rid of the parasite before it spreads through the entire fish farm. Giana Bastos Gomes is also keen to expand the approach to other aquaculture species, both freshwater and saltwater, and to other diseases caused by bacteria and viruses.

Executive officer of the Australian Barramundi Farmers Association Chris Calogeras says the possibilities that might arise from Giana Bastos Gomes’s work would be a significant gain for farm management.

“Any tools that will allow fish farmers to better manage their stock, improve productivity and allow quicker responses to any problems is a great step forward for industry. We eagerly look forward to the commercialisation of her work and the benefits it will provide to industry,” he says. 

FRDC Research Code: 2008-339

More information

Giana Bastos Gomes, gianabg@hotmail.com