AGRO SOLUTIONS
Researchers are testing new, compact equipment to see if it can quickly and accurately diagnose specific pathogens.
With cattle, most of our problems are not so simple. Point-of-care tests have been around for a long time but may not seem practical for a producer.
The Chief Scientific Officer at Prairie Diagnostic Services in Saskatoon, Canada, Dr. Anatoliy Trokhymchuk, said: “I think it might be practical for a veterinarian to keep rapid test tools, like the one we use for anthrax, around. But for more complex problems like bovine respiratory disease, the multifactorial and complex nature of the causation prevents us from being able to do something simple.”
The problem
Large-scale feedlots are here to stay to feed a growing and hungry world population. Antibiotics are a necessary tool for animal health, welfare and disease management at the feedlot.
“The trouble with antibiotics is the more you use them, the sooner they stop working,” Trokhymchuk says. “When it stops working, it not only stops working for animals but for humans too.”
The feedlot industry is getting a lot of flak from the World Health Organization over antibiotic uses, especially when it comes to bovine respiratory disease (BRD) prevention and treatment.
“We really need to up our diagnostics, because there is a real risk of losing antibiotics as a valuable tool for both animals and humans if we don’t.”
When deciding to treat an animal for BRD, producers and practitioners are relying on their experience and a gut sense. “This is where we are lacking diagnostic support. They are making decisions based on what they see in front of them, what they have experienced themselves, and what is the current standard of care. But it’s still a guess.”
Working for a diagnostic lab himself, Trokhymchuk and his colleagues realize what is being offered currently is not adequate.
“If people send us a diagnostic request, it takes us a week to get a report back. It’s way too slow to make a treatment decision.” Diagnostics need to align within the decision-making window for the veterinarian and the producer.
Testing new solutions
Fortunately, technological progress is here to help. There is a new tool that was out of reach to animal agriculture even five years ago. DNA sequencing technology is rapidly advancing in utility and accessibility. And thanks to COVID, we now know that PCR-based tests are not enough to tackle a fast- moving infectious disease. Global health care quickly advanced to genotyping, which is only possible when the entire genetic code of the pathogen is read.
“The good news, yes, the devices to read the entire genetic code are here. The biggest challenge though is how do we quickly analyze the mountains of data they produce?”
Computers are advancing and getting more powerful, wireless connection and streaming are everywhere, and there is a way to make large data analysis happen fast using machine learning — one of the examples of artificial intelligence applications.
“As humans, our intellect is not big enough to comprehend so much data.”
When it comes to sequencing DNA code, looking at one pathogen might be comparable to a thousand-page book, but when it comes to sequencing the DNA code of an entire cow that would be about two thousand times bigger. In a cow, not only do you have to sequence the animal’s DNA, but also that of the many “bugs” inside that cow.
“The amount of genetic information inside just one animal is humongous, which is why we need the computing and artificial intelligence to digest it.”
In 2018, a BRD mortality sample arrived at Prairie Diagnostic Services at 11am. At the lab, they were able to extract and prepare DNA from the sample, sequence and analyze it in just a few hours. By 5pm, they knew what kind of bacteria they were dealing with and what kind of drugs these bacteria might be resistant to.
“This kind of information is very valuable for making a precise treatment decision,” Trokhymchuk says. “Three days later, we confirmed the same information with traditional bacterial culture and susceptibility testing. The method worked.”
Prairie Diagnostic Services asked for and received help from prominent academics, industry and government to build expertise and capacity for genomics — a steep learning curve and an exciting journey they have been on since that early pilot work.
SOURCES: