Jordan Wirfs-Brock: Manure Happens

Manure happens: Agriculture's role in antibiotic resistance
Note: This was my enterprise story for Science Writing.

December 17, 2008

Standing at the edge of a lagoon - filled with feces, not fish - Heather Storteboom pulled on a rope. On the other end, Chad McKinney tried in vain to keep liquid manure from splashing into his raft. McKinney scraped a metal bucket across the bottom of the lagoon, collecting sludge as Storteboom reeled him ashore.

Even on a day where temperatures hovering around zero slow the ferment of manure, livestock waste releases noxious gasses - like ammonia, hydrogen sulfide and methane - that sit thick in the air over northern Colorado's feedlots.

But Storteboom and McKinney, graduate students who worked together at Colorado State University, looked for something invisible and odorless: strands of DNA that render bacteria immune to antibiotics.

According to Storteboom, a PhD candidate at CSU, livestock manure is packed with antibiotics and antibiotic resistant genes that can run off into surface water and contribute to the growing public health threat of antibiotic resistance.

Every year, only half of the 50 million pounds of antibiotics made in the U.S. are destined for humans. The rest is laced into the feed of cows, pigs and chickens. Most aren't even sick: antibiotics make them grow faster, though the reasons for this aren't understood. As much as 80 percent of antibiotics are excreted completely un-metabolized, appearing as chemically pure in human or animal waste as when they were manufactured.

As a result, we're flooding the environment with antibiotics, and bacteria are developing defenses against them. Harmful bacteria immune to antibiotics, like vancomycin-resistant Enterococci and methicillin-resistant Staphylococcus aureus - VRE and MSRA - are spreading in hospitals, nursing homes, and childcare centers. Often, this type of drug resistance can be traced back to agriculture. Storteboom and McKinney, a PhD candidate at Virginia Tech with a master's from CSU, are searching for ways to slow the transfer of antibiotic resistance from the guts of animals into soil and streams. They've found promising solutions in the unlikeliest of places: piles of manure.

"The problem of antimicrobial resistance is getting worse every day," said Stuart Levy, professor of microbiology and medicine at Tufts University and director of the Center for Adaptation Genetics and Drug Resistance. A big reason is that "antibiotics are being misused in animals," according to Levy, who's been studying antibiotic resistance for more than 30 years.

Most antibiotics were originally combed from the soil, where a turf war between bacteria and fungi has waged for millennia. Fungi and bacteria evolved ways to keep other bacteria from encroaching. Penicillin, for example, a mold extract, prevents bacteria from growing cell walls.

Bacteria didn't succumb: for every antibiotic we've pulled from the earth, some bacterium, somewhere, has developed a counterattack. Because natural antibiotics existed in low levels, bacteria that were immune coexisted with bacteria that weren't.

Then we started producing mass quantities of antimicrobial drugs.

When the amount of antibiotic in any system - a Petri dish, a human, a cow - reaches critical mass, it eliminates bacteria that can't fight back. Some antibiotics, like tetracyclines, attack a bacteriumâ€™s ability to build proteins. Others, like sulfa drugs, attack a bacterium's ability to convert sugar into energy. Either way, antibiotics wipe out bacteria.

Except, that is, for bacteria with proper defenses.

Defenses like genes that allow bacteria to block antibiotics from entering, or pump invading antibiotics back out of the cell. Bacteria with defenses like these survive, and thus are left to multiply, repopulating the environment with antibiotic resistance.

Antibiotic resistance is "a natural phenomenon," Levy said. "What we have done is increase the amount of selective pressure."

Storteboom looks for resistant genes in places like the Cache La Poudre River and steaming piles of manure. She uses a device that looks like an oversized electric bread maker with fewer controls to fastidiously replicate genes - particularly genes for antibiotic resistance - from her river and manure samples and determine how much of each is present.

"The genes themselves are the potential for antibiotic resistance," Storteboom said. "If the genes are there, they can easily be acquired by pathogenic bacteria."

Bacteria transfer genes amongst themselves by exchanging small fragments of DNA. This helps bacteria acquire new traits, such as antibiotic resistance, when they absorb those fragments of DNA into their genome.

While humans transfer genes at only one stage of life - to children during fertilization - "bacteria transfer genes really frequently," Storteboom said.

To share genes, bacteria don't have to be related. Or even alive. If you transferred genetic material with the speed and abandon of bacteria, it would be like taking a trip to the zoo and swapping genes with the lion, the antelope the lion had for lunch, and the microbes swimming in the antelope's stomach.

Some bacteria release their genes into the environment when they die. DNA can exist free-floating in water or manure. The problem is that sewage treatment plants are designed to remove bacteria, not individual pieces of DNA.

"Depending on the conditions," said McKinney, "DNA can last for months, even years" outside a cell.That's why Storteboom and McKinney look for individual genes, not whole bacteria.

Storteboom collected water samples and sediments from the Poudre as it flowed from its headwaters in the Rockies through Fort Collins and Greeley. She found resistant genes everywhere. Downstream of urban centers and farmland, their numbers increased by an order of magnitude.

"Some people view it as a medical problem. Some people view it as an animal problem. Really, it's both," Storteboom said.

The Poudre flows into the South Platte in Weld County. Here, cows outnumber people two to one. Of the more than half a million cows, 86 percent live on farms with more than 500 cattle, according to the USDA Census of Agriculture. The EPA calls farms like these Confined Animal Feeding Operations. They are the likely source of most of the agricultural antibiotics in the environment.

Cattle are counted by the head, but perhaps they should be counted by the intestine. In a single year, 15 tons of manure passes through the gut of an average-sized cow - 100 times the amount a human produces. In Weld County, where feedlots can house tens of thousands of head of cattle, waste is stored in lagoons and stockpiles.

While at CSU, McKinney sampled organic and conventional dairy farm lagoons in northern Colorado to see how well they eliminated antibiotic resistant genes. He found that lagoons are largely ineffective for treating conventional and antibiotic-related pollutants.

"It was pretty disgusting," McKinney said. "I'd be sitting in manure most of the time."

In lagoons, rectangular pits with sloping walls, sludge settles to the bottom. Wastewater floats on top.

"It's brown-black water," McKinney said. When he was working, he would paddle a raft directly into the middle of it.

McKinney found that the ratio of antibiotic resistant to nonresistant genes was higher in wastewater from conventional dairy farms than from organic farms that don't use antibiotics. In the sludge, however, organic and conventional farms had similar levels of resistant genes.

Lagoon sludge is dredged roughly once every decade. Wastewater, however, is frequently drained and sprayed on fields as fertilizer. McKinney thinks sludge with resistant genes remains from several years ago, before the dairy farms became organic and stopped using antibiotics.

The use of manure as fertilizer can proliferate antibiotic contamination in the environment. Holly Dolliver and Satish Gupta of the University of Minnesota showed through their research that certain plants take up antibiotics from manure fertilizer. A bite of corn, lettuce or potato could come with a dose of sulfamethazine, an antibiotic used in livestock.

Manure is spread over 2 percent of Weld County's land area. Not all farms using manure are large or commercial. Shirley Mason, a former nurse living in Fort Collins, uses manure from a local sheep farm on her garden.

On a sunny afternoon in November, Mason knelt down to fold faded blankets back from her raised beds, uncovering cabbages the size of microwaves. The ground looked barren and dry. Then she plunged her hand into the soil - rich and moist under the surface - and pulled out a golden beet. Next, she harvested a carrot, thick as a rolling pin.

"You can see some egg shells," said Mason, examining the soil in her palm. "That's a peach pit. I've got lots of those." She pointed to an empty peach tree 20 feet away, once so full of fruit its branches broke under the weight. These items come from the food waste and leaves that Mason composts. She mixes the compost with manure before spreading it.

Are these well-intentioned techniques causing unseen harm, or reducing the amount of antibiotic resistant genes entering the environment? To find out, Storteboom experimented with similar composting methods on 50 tons of cow manure. Her goal was to see if they would reduce the amount of antibiotic resistance entering the environment. She had 30 truckloads of manure delivered to a plot on the fringe of CSU's campus at the foothills of the Rocky Mountains.

"And I don't just mean your friend's pick up, I mean semi-trucks," Storteboom said. "It was messy."

For six months, Storteboom let some of the manure sit. She actively managed the rest: mixing it with leaves and twigs, aerating and turning it like a compost heap. Her research showed that in the actively managed manure, heat and decomposition sped up degradation of resistant genes and antibiotics twofold.

However, you can't ever assume that "just because you are using manure or compost it's antibiotic-free," Storteboom said. When those antibiotics get into food and are then consumed, they can still cause resistance among bacteria. She points out that antibiotics and antibiotic resistance are everywhere - possibly even in Mason's garden.

Levy sees a simple answer to antibiotic resistance: decrease the use of antibiotics.

"I think the solution is to use antibiotics in a more responsible way," resistance-expert Levy said. "Respect these drugs for the purpose in which they were developed."

That's what the European Union did. There, the use of antibiotics as livestock growth promoters is illegal. In light of this, McKinney's results are both reassuring and troubling. They suggest that decreasing the antibiotic use lowers the introduction of new resistant genes to the environment. But previously existing genes will persist.

In the U.S., reducing antibiotic use has been politically difficult. The EPA and USDA have regulations for manure, but they are designed to keep bacteria like E. coli and nutrients like phosphorous and nitrates from running off into waterways, where they can cause harm.

About antibiotics, Ron Jepson of the Colorado Department of Public Health and Environment's Agriculture Program said, "there are no regulations in place currently that address that."
For Colorado to regulate agricultural antibiotic use, "it would depend on what the scientific evidence shows," Jepson said.

In the meantime, practices like active manure management, pioneered by Storteboom, are dirty yet feasible stopgap solutions to antibiotic resistance.