Hunt for disease pathogens goes even smaller-scale

Researchers at the Agriculture and Agri-Food Canada (AAFC) research centre in Saskatoon are developing molecular diagnostic assays to detect significant pathogens associated with crops and livestock production.

Biological assays are methods for assessing the presence or biological activity of a substance in living cells and biological matter.

Tim Dumonceaux of AAFC said many pathogens are important for crop and animal production, and those are the ones they prioritize with assays.

Why it matters: Biological assays offer quick identification of pathogens.

We “develop and validate the assays and the model that we followed to make them available to producers is using a licensing approach, not so much a patent approach,” Dumonceaux said during the Ag in Motion farm show in July.

“This is so that companies can pick up the assays and offer them to the producers and package it in a way that will be relevant to them.”

Dumonceaux said systems that use these assays to test samples for specific pathogens can be simple to use with little training and can be conducted in the field or barn.

At Ag in Motion, AAFC displayed a few methods of using the assays to see if the DNA of a pathogen is present in a sample. Visitors to the booth could test samples for signs of sclerotinia in the air.

The samples were put in an assay and visitors could choose among three methods to find out if sclerotinia DNA was present.

A low technology method of DNA extraction involves samples placed in vial with the assay. If the solution changes colour, it indicates sclerotinia is present.

There were also more complicated solutions where a sample is placed in a machine that indicates whether the target pathogen is present. An even more advanced machine sequences all the DNA in a sample.

Dumonceaux said sampling strategies will vary depending on which pathogen is being investigated.

For instance, if a grower wanted to find out if fungi was present in stored grain, it’s possible to develop an assay and sampling technique that can detect the fungi before visual signs appear.

“You could do something like wash the outside of the seed with … a buffer with the light detergent in it to knock off whatever organisms are associated with seeds. We’ve done that in the past to get the bacteria and fungi that are associated with the seeds and you can detect pathogens in that way,” Dumonceaux said.

Plant tissue can also be tested, a strategy he used in his study on blueberry diseases in Quebec.

This study used the same molecular techniques to develop assays for blueberry stunt disease that’s caused by a phytoplasma, which is closely related to the bacterium that causes aster yellows in canola.

Dumonceaux said it’s possible to monitor the geographic distribution and spread of the pathogen in blueberry production fields, as well as the movement of the pathogen within and among plants.

“We use leaf samples from the actual plant itself. So, you clip the leaf off the plant and you can do the DNA extraction there in the field, and then you can do the actual detection assay and get the results back in just a few minutes,” Dumonceaux said. “We think it can work for other diseases as well.”

A separate display at the AAFC booth featured a project by Tara Funk that uses the same molecular techniques to detect bovine respiratory disease in cattle.

Funk is a PhD student at the Western College of Veterinary Medicine at the University of Saskatchewan, and she said BRD costs the beef industry in North America $800,000 to $900,000 every year.

“I am using a new type of diagnostic test called recombinase polymerase amplification (RPA), which uses specialized enzymes at a constant, low temperature to identify a DNA target of interest. Our team is developing new assays to identify bacteria responsible for causing BRD and will apply them to nasal swab samples that we took from beef calves on arrival at a feedlot,” Funk said.

The test provides results approximately 30 minutes after the DNA samples and RPA assay enzymes are combined.

“The machine is very straightforward,” Funk said. “Above all, what it does is provides us with information that we can get to producers and veterinarians on how to make an educated choice on the antibiotic that they might use to treat their cattle.”

A version of this article appeared in the Western Producer.