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Researchers to trace 'superbug' genes

Study to determine where infectious organisms originate and degree to which antibiotic use in food animals contributes to resistance.

Researchers at Colorado State University are investigating the weighty topic of antibiotic resistance — an issue with ramifications for global food safety and public health — by tracking the genetic footprints of drug-resistant bacteria.

They want to determine where infectious organisms originate and how they move through the food system and environment to people. The study, funded with $2.25 million from the U.S. Department of Agriculture, is one of the largest of its kind and is enabled by recent advances in DNA sequencing technology.

The project is expected to provide insights about the factious topic of antibiotic use in food animals, chiefly beef and dairy cattle, and the degree to which the longstanding agricultural practice contributes to development of "superbugs" that infect people whose illnesses are difficult and expensive to treat.

"Antimicrobial resistance is one of the most significant grand challenges to human animal and food safety," said Alan Rudolph, Colorado State vice president for research.

Food-animal production has been blamed for contributing to antimicrobial-resistant illness, but these suspicions are not well-founded in science, said Keith Belk, professor in Colorado State's Center for Meat Safety & Quality, and Dr. Paul Morley, a Colorado State veterinarian and infectious-disease expert.

With multiple collaborators, Belk and Morley are leading the research project, "Paradigm Shift: Revolutionizing Our Understanding of Antimicrobial Resistance Ecology through Whole Genome Analysis of Microbial Communities."

The scientists hope to gain a much better understanding of the role of production agriculture in antimicrobial resistance. It often is assumed that providing antibiotics in feed rations for livestock contributes to drug-resistant germs, but the practice also has a protective effect, Belk said.

"Most people believe they are consuming antimicrobial-resistant bacteria in their food because of intensive food production systems. In fact, those modern food-production systems are effectively controlling bacteria in food," Belk explained.

Antibiotics — used in agriculture and by countless people around the world — kill dangerous bacteria and other germs. Yet surviving infectious agents replicate, producing greater antimicrobial resistance.

"Use over time promotes increasingly resistant populations that may threaten public health because bacteria susceptible to the antibiotics die, while those that are not survive," Morley explained.

In order to successfully solve the problem of antibiotic resistance, scientists must better understand where resistance originates and how drug-resistant germs move through the food system and environment to people, the researchers said.

"There's not a farmer in the world who doesn't take pride in their product," Morley said, adding that it is in agriculture's best interest to understand if and how livestock production contributes to drug-resistant germs in people. "We are looking at production methods to see if they have an impact on (antimicrobial resistance) promotion, and if they do, we'll need to change those production methods — within reason — as an industry."

Using DNA sequencing technology, the two professors will trace genes that cause resistance in bacteria. This will allow them to determine sources and paths, including whether and how antimicrobial-resistant bugs move from livestock to people.

The cost of advanced genetic-sequencing technology has dropped dramatically in the past decade, allowing researchers to conduct more thorough examinations of the hundreds of millions of bacteria that can be found in a single sample of cow feces, for instance.

Belk and Morley will compare antimicrobial resistance in traditional and organic processes, and in different environments, to identify what resistant genes are present and how they are transferred. They also want to learn whether different production methods affect abundance of antimicrobial resistance.

Partners on the three-year project include the Colorado State departments of computer science, environmental and radiological health sciences, education and food science and human nutrition. Others include the Colorado School of Public Health, University of Colorado Health Sciences Center, Public Health Agency of Canada, USDA's Animal & Plant Health Inspection Service, and industry collaborators providing access to their animals.

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