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New technologies may yield new insights on antibiotic use and resistance

Noelle Noyesa veterinarian and epidemiologist, University of Minnesota speaks to Pig Health Today.

by 5m Editor
18 March 2019, at 3:02pm

The pork industry has a reputation for using antibiotics responsibly, but when veterinarians and producers look at antimicrobial use and try to understand how products either mitigate or promote resistance, there aren’t always clear or easy answers.

That dilemma may be changing, Noelle Noyes, DVM, a veterinarian and epidemiologist, University of Minnesota, told Pig Health Today.

“I’m very excited about new technologies, because they will…provide better and more robust evidence for what we need to change, or maybe show what we’re already doing well,” she said.

She believes advanced tests will give a more comprehensive picture of how antibiotics are used and how they work in the fight against antimicrobial resistance.

More knowledge coming

Minimum inhibitory concentration (MIC) is the commonly used tool for measuring antibiotic resistance. Because it’s been used for some time, Noyes said it provides historical data that researchers and veterinarians can easily interpret.

“The MIC value comes from a culture-based approach to resistance,” she explained. “When we do a culture, we have to ‘pick’ our organisms, like salmonella or E. coli, or maybe an animal pathogen. We have to specifically grow that pathogen and determine whether it can fight off or will succumb to an antibiotic exposure.”

That’s important to know, but it also means a lot of other things could be going on in the host that aren’t being measured.

“We know our world and our bodies are inhabited by millions of different bacteria. We don’t even know what most of them are yet, but all of them can have resistance,” she said.

“When we’re looking at just one little [bacterium] among thousands of different types of bacteria [with the MIC test], we probably aren’t getting a very representative picture of the resistance dynamics across the whole population,” Noyes said. “In order to truly fight resistance, we need to understand what the entire microbial population is doing, not just the bugs that we’re interested in.”

That’s where the new technologies come into play, though there is a learning curve. Noyes said because the new tests are less familiar, it will take time to gain context about what a specific value means in terms of human health or animal health. However, on the plus-side, they’re broader-based and give a better overall picture of antibiotic resistance.

A snapshot of the animal

The new tests, which are basically a type of sequencing technology, are becoming more accessible. Noyes is excited about their potential.

“We can sequence all the bacteria in a sample now,” she said. “These machines are so powerful and can give us so much data. We can take a sample and instead of focusing on specific organisms, we sequence all of the DNA. Then, we can compare the DNA to sequences that we know exist already. If we find a match, we can say, ‘Okay, this is bacteria X, and this is resistance gene A.’ With this technology, we’re able to get a picture of the entire population.”

She said this “deep sequencing” provides a snapshot of the entire population within an animal. It can capture even rare bacteria, though she admits some of the information gathered in the samples isn’t yet fully understood. The new technology gives researchers an amplified look at what’s happening within an animal and a population of animals.

Resistance a natural phenomenon

With the new tests, researchers can look at what bacteria are present as well as what resistance genes are present.

“Instead of looking at salmonella and saying, ‘This specific salmonella has these three resistance genes,’ we’re finding hundreds or sometimes even thousands of different resistance genes in a single sample,” Noyes said.

“Bacteria are naturally resistant to different compounds,” she added. “It’s a way they’ve evolved to survive in the face of different challenges.”

She noted that even in pristine environments, like uninhabited islands or the Arctic, researchers are finding resistance genes in bacteria, despite the fact that they’ve never been exposed to modern-day antibiotics.

“This technology gives us a more comprehensive picture about resistance and the fact that it’s a natural phenomenon,” Noyes said. “The hard part is analysing and interpreting the data, and understanding our sensitivity for those measurements.”

A deeper understanding

The new technology gives researchers a more extensive look at how decisions made at the farm level impact animals and, hence, a deeper understanding of health interventions.

Whenever people manage populations, be it human, animal or environmental, those populations are impacted at a microbial level, Noyes explained.

“We don’t really think about it because they’re microscopic, but we’re shifting their ecology,” she said. “So, what we’re learning is not just about antimicrobial use; it’s about the whole system of livestock production.”

The swine-veterinary community has done an excellent job of stewardship related to antibiotic use, Noyes believes, but needs to continue creating evidence around that stewardship.

“We need to show that what we’re doing really is making a difference,” she said. How the industry uses antibiotics to combat disease as well as resistance is part of the evidence base proving those practices are having a positive effect.

No easy answers

Noyes said her opinions on antibiotic resistance have changed from her years as a student. She used to think antibiotic resistance was much more of a linear phenomenon: You administer a drug and you get resistance. One of her biggest surprises was to learn how complicated the antibiotic-resistance issue was and how challenging it is to predict when antimicrobial resistance is going to become a concern.

She also recognises antibiotic resistance isn’t a black-and-white issue. She wants the industry to continue to build evidence to help people understand that many of the practices employed by producers are pivotal to increasing animal health and welfare.

“The alternative may be harmful from an animal-welfare perspective as well as a resistance perspective,” Noyes said.

Providing information on the cost-benefit of preventive antibiotics will lay the foundation for an evidence-based discussion on antibiotic use, what it means for animal health and welfare, and what it means in terms of resistance implications, Noyes said.