Food-borne diseases can be caused by a long list of pathogens that number in the hundreds, or even thousands.

Current culture or DNA-based testing methods, while effective and accurate, can detect only one or a few organisms—like Listeria—at a time.

Plus, these methods can be resource- and time-intensive, requiring a different method for each organism to be cultured or amplified in a laboratory to detect which pathogen is present.

Over the past four years, Dr. Shu Chen and her team at the University of Guelph’s Agriculture and Food Laboratory (AFL) have been developing a new culture-independent diagnostic testing (CIDT) method for use on food-borne pathogens.

“For us, this new CIDT methodology represents a new level of efficiency and responsiveness in detecting and preventing pathogens,” says Chen. “Right now, we’re working closely with industry partners to see where CIDT could provide the most benefit.”

CIDT can simultaneously detect hundreds of organisms with a single test instead of having to test each organism separately. In place of individual testing, CIDT takes DNA extracted from the cells of all organisms and puts it through a PCR (polymerase chain reaction) process.

From there, specific segments of the DNA are amplified, allowing researchers to focus on targeted regions of the genome. Chen and her team then use high throughput DNA sequencing, which screens millions of DNA molecules to positively identify organisms.

From lab bench to beverage industry

Currently, Chen and her team are working closely with the beverage industry to use their CIDT method as a new, more efficient way to detect spoiler organisms. 

Organisms including Pediococcus bacteria, Brettanomyces yeasts and Aspergillus moulds cause a musty, sour taste in alcoholic and non-alcoholic drinks. Some pathogens, such as Listeria and Salmonella, create serious health risks, particularly in non-alcoholic drinks. 

And despite beverage makers’ best efforts to maintain vigilance and ensure clean facilities, there are umpteen ways contamination can creep in. Fluid lines, corners, valves, seals and even slight fluctuations in temperature can all create the ideal environment for spoilers and pathogens. 

According to Chen, non-alcoholic drinks like de-alcoholized beer and wine, fermented tea and mocktails are especially vulnerable to contamination.

“Each type of beverage can be spoiled by many different organisms. So we’re dealing with a significant challenge to the beverage industry in terms of both economic losses and safety concerns,” says Chen. “So far, we have had excellent results in using CIDT to detect spoiler organisms, and we’re confident that the methodology is ready to be implemented on a wider scale.” 

CIDT for plant disease diagnostics  

Chen and her team are also exploring how CIDT could soon be used for plant disease diagnostics in a wide range of Ontario crops from winter wheat, corn and soybeans to potatoes, apples and grapes. 

“We know that plants can be infected by hundreds of different pathogens,” says Chen. “But if you’re using targeted tests, you’re only detecting what you think the disease might be and you could be leaving out a wide spectrum of other possibilities.” 

She adds that targeted testing also requires specialized expertise, such as knowledge of the target pathogen, its growing conditions and the symptoms it causes. 

Using the CIDT methodology, researchers can drill down to the species level and quickly identify the most hard-to-pin-down pathogens, such as oomycetes (water mould) that have historically caused massive losses for Ontario growers and that routinely go misdiagnosed. 

“We’re very encouraged by the results we’ve been seeing in the field samples,” says Chen. “With disease diagnostics, timing is of the essence—and our goal is to provide a faster, less resource-intensive way of detecting as many important pathogens as possible at once.” 

The CIDT work was supported in part by the Ontario Agri-Food Research Initiative (OAFRI), funded by the Governments of Canada and Ontario through the Canadian Agricultural Partnership (the Partnership), a five-year (2018-2023), federal-provincial-territorial initiative.

The Agriculture and Food Laboratory receives funding from the Ontario Agri-Food Innovation Alliance, a collaboration between the Government of Ontario and the University of Guelph.