Although farmers will still have access to the antibiotics necessary for animal health, all antibiotics will soon be available only through a veterinarian or veterinary prescription.

One of the reasons for the new restriction, which is set to take effect in June 2023, is the growing issue of antibiotic resistance. At the same time microbes are developing resistance, fewer new antibiotics are being developed. Manure is one area that has clearly led to the proliferation of antibiotic resistance.

Antimicrobial resistance is a naturally occurring genetic mutation in a microbe. The use of antimicrobials selects for resistance, and the result is reduced antibiotic effectiveness for both humans and livestock.

During a recent webinar presented by the Livestock and Poultry Environmental Learning Community, Dr. Michelle Soupir, professor in the Department of Agricultural and Biological Systems Engineering at Iowa State University, said antibiotics move through an animal’s system and remain biologically active in waste treatment systems. Research goals include understanding what happens to antibiotics in manure applied to crops.

The process of resistance development is complex, with no single point at which antimicrobial resistance can be detected. “Cells develop different mechanisms to protect themselves from antibiotics they may be exposed to,” said Soupir. “There may be a surface site modification so the antibiotic is no longer able to penetrate the cell. There are many different genes responsible for behaviors within the cell, so looking for an indicator for antimicrobial resistance can be challenging.”

Soupir said the development of antimicrobial resistant organisms can occur at many different points along the environmental pathways. “In manure storage systems, we have concentrated antibiotics that have come through animals,” she said. “A lot of different bacteria are present in those systems which leads to conditions where antimicrobial resistance can develop. It may be present naturally, but the selective pressure from antibiotics may lead to additional proliferation of resistance.”

Antimicrobial resistance can be measured by phenotypic resistance, which involves culturing resistant bacteria on media to determine which organisms grow. Another method identifies genetic markers responsible for levels of resistance. The challenge with genotypic identification is the wide array of antibiotics used in animal and human medicine – many genes are specific to certain antibiotics. Soupir said scientists are in the early stages of learning which antibiotics can move through the environment and which are important for monitoring.

It’s also possible that once manure is applied to soil, the manure is in contact with the existing soil microbiome and the resistant genes can be transferred to the native microbe community. When precipitation occurs, water can move off the field through surface runoff, infiltrate through soil into groundwater or move through a tile drain outlet. This provides more opportunities for resistance to develop within the microbe community.

Manure management reduces antibiotic residue in the environment

It’s possible that once manure is applied to soil, the manure is in contact with the existing soil microbiome and the resistant genes can be transferred to the native microbe community in the soil. Photo by Sally Colby

Scientists can monitor different environmental aspects such as manure application and runoff. “We can also look at the soil,” said Soupir. “After manure has been applied, what kind of changes occur to bacteria that are naturally occurring in the soil? We also want to monitor water systems for exposure through recreational activities.”

Dr. Shannon Bartelt-Hunt, professor and head of the Department of Environmental and Civil Engineering at the University of Nebraska, said antibiotic use to treat humans and livestock has increased 65% between 2000 and 2015.

“Whether they’re used for humans or animals, antibiotics aren’t completely metabolized,” said Bartelt-Hunt. “Some fraction of the antibiotic is excreted from the human or animal in its biologically active form, released in urine or fecal material.” Antibiotics can be hydrophobic (won’t mix with water) and become concentrated in solids. Antibiotics enter the environment through either municipal wastewater treatment effluent or after land application of animal manure.

Once contaminant antibiotic compounds are in the environment, they can be transported through the aquifer down toward groundwater, and there are also processes that take place within the surface water body. Antibiotics can be attached to sediment, in the water column or taken up by aquatic organisms. Bartelt-Hunt said antibiotics are routinely found in waste, soil and dust. They’re also found in groundwater, surface water and wastewater.

The National Pork Board funded studies to determine the fate of antimicrobials after land application of swine manure. “We’re interested in mitigation strategies,” she said, “including buffer strips and timing of manure application relative to precipitation related to how antimicrobials are moving off cropland through runoff and potentially impact surface water.”

One study examined runoff following three manure application methods: broadcast, incorporation and injection. Researchers had good records on antibiotic use on the animals that produced the manure.

Regarding the presence of chlortetracycline in runoff, the concentration highest in manure was broadcast. “Concentration was reduced when manure was either injected or incorporated into the soil,” said Bartelt-Hunt. “In sequential rainfall events, the highest concentration of antibiotics in runoff occurred in the first runoff event.”

Another project determined the impact of manure application timing in either broadcast or injection. Following application was rainfall simulation with a gap between manure application and controlled rainfall. Simulated rainfall was conducted one day, one week, two weeks and three weeks following application. “The timing of manure application relative to rainfall is something that can control the corresponding concentration and transport of antibiotics and runoff with much lower concentrations observed in those longer time periods between manure application and the runoff event,” said Bartelt-Hunt. “That can’t always be timed, but can be used for guidance and apply when less likely rainfall to occur.”

Narrow grass hedges (unfarmed land between fields) clearly helped stop runoff. Swine manure was placed on one side of the grass hedge, rainfall occurred, then runoff was collected after it had passed through the grass hedge. Antibiotic concentrations were lower where grass hedges stopped runoff.

Bartelt-Hunt said there’s new focus on the antibiotic classes used in animal ag, as well as increased study of the more common human medicine classes to make a connection between human and animal antimicrobial resistance.

“We can find both antibiotics and resistant genes in various segments of the environment,” said Bartelt-Hunt, “and in soil, manure and water. Understanding movement and impact is important.”

by Sally Colby