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Grazing cows acquire antibiotic resistant microbes from soil, water

Feb. 21, 2019: An Emerging Pathogens Institute microbiologist has identified high concentrations of naturally-occurring antibiotic-resistant microbes within the guts of grazing cows and calves fed a diet free from antibiotics. The source? Soil, water and forage found in the cows’ environment.

Grazing cows acquire antibiotic resistant microbes from soil, water

An Emerging Pathogens Institute microbiologist has identified high concentrations of naturally-occurring antibiotic-resistant microbes within the guts of grazing cows and calves fed a diet free from antibiotics. The source? Soil, water and forage found in the cows’ environment. The discovery, published Feb. 7 in Frontiers in Microbiology, has implications for cattle farm management and the ability of doctors to treat serious infections caused by resistant microorganisms.

Cephalosporin antibiotics are used to treat a wide variety of human infections ranging from pneumonia to sepsis. But resistance to this medication is growing among a specific group of disease-causing bacteria and contributing to a major public health threat. These resistant microbes produce an enzyme known as extended-spectrum beta-lactamase, or ESBL, which breaks down commonly prescribed antibiotics. Originally first identified in people in hospital settings, ESBL-producing bacteria were thought to have emerged as a direct result of antibiotic overuse but have since been found in agricultural animals.    

“It was a puzzle, because the first cases of ESBL-producing bacterial infections were found in hospitals” said EPI investigator KC Jeong. “But when we started looking, we realized that ESBLs are already everywhere and probably did not originate in hospital environments. There is a high prevalence of these organism in nature, and even in farm animals who have not been fed or heavily dosed with antibiotics.”  EPI director Glenn Morris, and EPI digestive microbiome expert Volker Mai, contributed to the study.

Prior work by Jeong, who is also a professor of microbiology and food safety in IFAS’s animal sciences department, determined that on farms were cephalosporin antibiotics were not used to treat livestock, young calves routinely had much higher levels of cefotaxime-resistant bacteria, or CRB, present in their guts than did mature cows. This is likely because the young animals’ immune systems are still learning to identify and eliminate this specific type of ESBL-producing bacteria. But the question remained, how were cefotaxime-resistant bacteria colonizing the digestive tracts of grass-fed cows who were not fed or treated with antibiotics to begin with?

To investigate, Jeong’s team obtained a $2.2 million grant from the U.S. Department of Agriculture to examine sources of CRB acquisition in grass fed cows – meaning, the animals were not fed a diet laced with antibiotics, nor were they given antibiotics to promote growth. Jeong’s team obtained 1,098 soil, water, forage and cow fecal samples from 17 grass-fed cow-calf operations in north and central Florida and analyzed them for cefotaxime-resistant bacteria. They found that 98.7 percent of the soil samples contained the resistant bacteria, as did 95.7 percent of the forage, and 88.6 percent of the water samples. Cefotaxime-resistant bacteria in the cows’ feces ranged from a prevalence per farm of 21 percent to 87.5 percent.

Due to the wide range in occurrence of CRB from farm to farm, Jeong suspected that husbandry methods were influencing the presence of CRBs in these cattle. Further analysis revealed two major factors: first, when cows’ water troughs were cleaned regularly, they tended to have among the lowest CRB counts of any samples in the study; second, farms with fewer than 500 cows had a far lower prevalence of CRB than farms with greater numbers of cattle.

Because of the high prevalence of naturally-occurring resistant bacteria in the cows’ drinking water, Jeong recommends that farm operators can safeguard our food supply by simply cleaning their cows’ drinking troughs.  “Even though the source for the cefotaxime-resistant bacteria is in their environment, we may have a chance to reduce their occurrence in the farm animals,” Jeong said. Although cows will inevitably ingest some dirt while grazing, the greater and more constant source of CRB ingestion is likely from their drinking water.

“All cattle farms should implement a strategy of cleaning their drinking troughs with bleach at least once a week,” said Jeong. “It’s a simple and inexpensive step to mitigate the CRB levels quite effectively.”

Because ESBL-producing bacteria can enter the human food chain through meat contaminated with CRBs, reducing cows’ exposure to environmental CRBs minimizes the potential for contamination when the animals are slaughtered for food. Jeong said that farmers can also be directly infected with ESBL-producing bacteria due to their close contact with animals. Some reports indicate that farm workers have higher levels of ESBL in their digestive tracts than nonfarm workers.

“This tells us that farm animals who have acquired cefotaxime-resistant bacteria in their digestive tracts are an important reservoir to pay attention to and to better understand,” Jeong said.

EPI Explainer

How did antibiotic-resistant bacteria get into our soil?

Consider that bacteria are the most abundant microorganisms in soil, and that a single gram of backyard dirt may contain billions of bacteria. There are many different types of bacteria which have evolved over eons to survive against predators such as other bacteria or fungi. They produce all kinds of materials to kill the “other guys,” which is where our modern arsenal of antibiotics come from. One of the self-defense survival tools bacteria have evolved is production of the extended-spectrum beta-lactamase (ESBL) enzyme – it protects them from having their cell walls destroyed by naturally-occurring antibiotic substances produced by other bacteria. As a side effect, ESBL-producing bacteria just happen to be mucking up modern medicine for humans.  

Creator Credits

Written by DeLene Beeland; Top photo: beef cow and calf grazing in pasture, these animals were not a part of the reported study; credit: UF-IFAS; all other photos depict actual cows sampled in the study; credit: Shinyoung Lee, a PhD candidate in Dr. Jeong's lab.

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KC Jeong's EPI Profile

Glenn Morris's EPI Profile

Volker Mai's EPI Profile