It's in the genes

by Steve Dittmer
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DNA strands
Scientists have been taking a thorough look into antibiotics and animals.

DENVER – Near the top of the list of concerns for animal agriculture is the use, availability and public perception of antibiotics for livestock.

Many of the restrictions placed on antibiotic use in livestock in recent decades have been due to pressures from outside the agricultural world. Animal agriculture has been accused by some, and assumed by others, to be a major contributor to the development of antibiotic resistance in humans.

A new, scientific study examining the issue, using the latest DNA sequencing technology, explores whether some form of antimicrobial resistance material can be passed from food animals to humans through the food supply. In addition, the study examined and tested possible environmental influences.

The study involved 16 researchers from Colorado State Univ.; Agriculture and Agri-Food Canada Research Centre, Canada; Univ. of Saskatoon, Canada and the Univ. of Colorado, Denver School of Medicine. The project tracked antimicrobial resistance genes, genes that some thought could be transmitted from livestock systems through meat products or environmental effluents. While public health officials have made some assumptions about the risk to humans through these two routes, little has been documented.

The study pooled samples from eight different pens of cattle totaling 1,741 head, in four different feedlots in two different states, collecting soil, water and manure samples in multiple stages, from feeder cattle incoming through post-slaughter. The researchers identified over 300 unique antimicrobial resistance genes. But during the feeding period, the array of antimicrobial resistance genes narrowed, indicating some sort of selective pressures. All cattle received macrolides (tylosin) in the feed but administration of antimicrobial drugs to individual animals was infrequent but documented. At least one animal within each group received doses of tetracyclines.

But it is post slaughter, after all the precautions and interventions packers now use during slaughter to drastically reduce the incidence of pathogens, where the researchers hit pay dirt. Testing the beef trimmings during processing—perhaps the most likely place for contamination to occur — the researchers found no antimicrobial resistance genes. That suggests that the interventions packers use today for pathogens appear to remove the antimicrobial resistance genes that could be transmitted to humans and suggested beef products are not a likely source of antimicrobial resistance. The study did suggest that environment pathways might carry more risk than the food supply.

Noelle R. Noyes, with the department of clinical sciences at CSU, and the team of researchers used next-generation sequencing to describe the antibiotic resistance potential (known as the “resistome”) found in a sample, whether taken from feedyards, trucks or packing plants. This allowed the team to follow the resistome population, discovering that some groups of resistance genes present at the beginning of the feeding period disappeared by the end of the feeding period. The resistance groups that hung around for the entire period correlated with whatever antibiotics were used in the group of cattle. But when the resulting beef products were sampled, no resistance groups could be found.

This Noyes study is the first to “have specifically tracked antimicrobial use in cattle while investigating antimicrobial resistance in market-ready products or consumers.”

At the packing plant, typical antimicrobial interventions were used during carcass processing, including hot water pasteurization, lactic and peroxyacetic acid spray, as well as knife trimming and spot steam vacuuming.

Researchers found some notable environmental discoveries. A small number of soil and water samples, involving a feedyard pen, a plant holding pen and trucks, showed the presence of antimicrobial resistance genes that were not used on the study cattle, are not cleared for cattle but confer resistance to antimicrobials important in human health. It is unclear whether these antimicrobial resistance genes were triggered by the use of other drugs or migrated there via feedlot workers, working dogs or horses.

“While our results suggest that slaughter-based intervention systems minimize the likelihood of intact antimicrobial resistance genes being passed through the food chain, they also highlight the potential risk posed by indirect environmental exposures to the feedlot resistome,” the study concluded. 

This study was conducted through the support of JBS USA packing plants, Fiver Rivers Cattle Feeding, and the Univ. of Colorado Denver High Throughput Sequencing Core, which is supported in part by the Genomics and Microarray Shared Resource of Colorado’s NIH/NCI Cancer Center Support Grant. It was funded by the National Beef Checkoff.

Whether this study will put the brakes on the public perception that antibiotic resistance is significantly related to livestock antibiotic use is an open question. The White House is planning an antibiotic resistance conference later this month.

The full text of this study was published in the peer reviewed scientific journal “eLife” at http://elifesciences.org/content/5/e13195v1, March 8, 2016, under the title, "Resistome diversity in cattle and the environment decreases during beef production."

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