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Antibiotic Resistance – Scientists look at feedlot bacteria to study resistance

by Wyoming Livestock Roundup

– “The big question my group tries to answer is whether or not antimicrobials in livestock cause or contribute to antimicrobial resistant infections in humans,” stated Noelle Noyes, a PhD student at Colorado State University (CSU) Veterinary Teaching Hospital.

Noyes and other scientists gathered at the University of Wyoming James C. Hageman Sustainable Agriculture Research and Extension Center (SAREC) in Lingle on Sept. 10 for the High Plains Nutrition and Management Roundtable to share their recent findings concerning livestock issues.

“This is a very contentious topic, and it gets sensationalized in the media,” noted Noyes.

Human resistance to antibiotics is often blamed on sectors of agricultural production, inspiring Noyes and her team to investigate how bacterial genetics change throughout a feedlot system.

Research methods

“Typically, when we do surveillance for resistance in livestock, we use a so-called indicator bacteria. This might be a non-type-specific E. coli or Salmonella, for example,” she explained.

The indicator bacteria are isolated and tested for resistance to a particular drug.

“This becomes a little bit suspect when we think about the ecology of where bacteria are actually living,” she stated.

To illustrate her point, Noyes shared a pie chart depicting the thousands of different bacteria present in the environment.

If scientists are only looking at one kind of bacteria instead of all of the different strains, Noyes mentioned, “We may get a really biased picture of what is going on.”

Thanks to new technology, scientists are now able to look at the bigger picture using equipment called Generation Sequencing Machines.

“This technology is becoming very widely available and widely used by different groups. I think it’s important to understand the technology and understand the types of results that we get from it so we can respond to results appropriately,” she continued.

Data collection

To use the technology, scientists collect samples from soil, water, feces, surfaces or rinsates. All DNA is then extracted from the samples, fragmented into small pieces and catalogued in a library.

“The sequencer reads through all of the little fragments and spits out a file that tells us the DNA sequences of all of the fragments,” she said.

Those sequences are then compared to a catalog of known resistance genes.

“It’s a little more complex than that, but basically, that’s what happens,” she noted.

Noyes and her team have conducted a number of studies using the sequencer, but she focused on two of them in her presentation at the Roundtable.

“In the first study, we went into four feedlots, gathering data from two pens per feedlot, and we followed the cattle from the time they were placed to the time they were shipped,” she explained.

Bacteria samples were collected at various time points from the pens and transport trucks. Samples were also collected from the surface of chuck and round conveyor belts after the cattle went through the slaughter and fabrication process.

Bacterial samples

“There were 88 samples total, representing 11 per pen across each of the time points,” she stated.

Once the samples were processed, 4 billion DNA fragments were produced, and 1.2 million matched an antibiotic resistant sequence.

“This is where we start worrying about people saying that we found millions of resistance genes in the samples,” Noyes commented.

Although there were millions of resistant genes throughout the samples, many of the DNA sequences were the same. Ninety-five percent of the resistance applied to only two drug types.

“We only identified 319 actual resistance genes,” she explained.

As a side note, she added that no bacteria with resistance genes were found in samples from the slaughter or fabrication process.

After analyzing and graphing the data, Noyes noted, “We are seeing that cattle arrive in the feedyard with a different resistance composition than when they leave the feedyard.”

Also, there appear to be more strains of resistant bacteria when the cattle arrive at the feedlot than there are when they leave.

“This is indicative of selective pressure,” Noyes said. “Only certain bacteria survive and flourish.”

Additional data

These findings are leading to further research as scientists are still unsure why certain bacteria survive and others don’t.

“There are a lot of other things going on during the feeding period. The cattle are being moved, their diet is being shifted, and they are all coming into one area. A lot of things could be affecting this change,” she commented.

In the second study that Noyes discussed, two pens of commercial cattle were studied over an 11-day period at a feedlot. One pen of cattle received the drug Draxxin, and the other did not.

“There was no difference between the treatments,” Noyes stated.

Results from the second study paralleled results from the first study, indicating that cattle arrived at the feedyard with a greater variety of antibiotic resistant bacteria than they had when they left.

“The take-away is that the transition into the feedlot does have a huge impact,” Noyes commented, adding that further research will be needed to learn more about how that information applies to animal and human health.

Further research

“Antimicrobial resistance is really complex,” she remarked. “There are a lot of places where antibiotics are used, and there are a lot of places where people can pick up resistant genes.”

Noyes is hopeful that the new technology will help scientists get a better idea of how bacteria interact and react to their surrounding environments.

“We are looking at these resistant genes as if they are all the same but different genes carry different risks to human health. We need to start coming up with a way to know, when we see these changes in a feedlot, if they are more or less risky. We don’t know yet,” she said.

Natasha Wheeler is editor of the Wyoming Livestock Roundup and can be contacted at

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