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What have we learned about antibiotic-resistant genes in groundwater?

Swine manure is a valuable resource for cropland, but understanding its potential impact on groundwater is an ongoing priority. This includes if and how antimicrobial-resistant organisms move through groundwater following manure application. Among the researchers looking for answers is Michelle Soupir, PhD, associate professor of agricultural and bioengineering at Iowa State University.  

“I’ve worked a lot with fecal-indicator bacteria E. coli and enterococcus — organisms that are important for protecting human health,” Soupir told Pig Health Today. “The next natural step was to look at some of these organisms to see if they’re also resistant to antibiotics, especially in areas influenced by animal manure.”  

This is particularly important across much of the upper Midwest, where tile drainage has lowered the water table and converted the soil to some of the world’s most productive cropland. “As a result, shallow drainage water hits a pipe and is quickly discharged to nearby surface waters,” she added.   

Soupir’s “laboratory” is comprised of 1-acre plots to create controlled environments to study the impact of manure application on the transport of antibiotics and antibiotic-resistant organisms to subsurface drainage waters.  Another bonus is that some of the plots had not received manure for 30 years, thereby providing a baseline measure for naturally occurring antibiotic-resistant organisms.    

“We know that many antibiotics are developed from soil microorganisms naturally,” she noted. “But this helps us see if there’s a bump up with the addition of manure from facilities that use antibiotics.”  

She has primarily studied the macrolide antibiotic tylosin but will investigate tetracycline next. “Before the expanded veterinary feed directive (VFD), we could always detect tylosin in the manure samples,” Soupir reported. “Hopefully that will be different following the VFD roll out and we see a change in antibiotic use.”  

Notably, different antibiotics perform differently in the environment. “Some are quite mobile; they don’t absorb into the soil profile as tightly,” Soupir noted.  “Others are highly hydrophobic so they won’t move offsite into the water system.”  

More research is underway to study the impact of manure applications done in the spring, early fall and late fall. Based on her research thus far, Soupir’s best advice to mitigate antibiotic transfer and possible resistance is to apply manure in the late fall.  

“If there’s not a big rain event, antibiotic-resistant organisms die off through the winter, and the concentrations are reduced,” Soupir added. “Also, the cropping rotation is important. With back-to-back years of corn, we see higher levels of resistant genes in the drainage water compared to when we have a corn/soybean rotation.”


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