“Yet here they were in a soil organism, in the exact same orientation as you find in the genome of VRE,” Wright says. “That sure gave us a head-slap moment. If only we had done this experiment 15 years ago, when vancomycin came into widespread use, we might have understood exactly what kind of resistance mechanisms would follow the drug into our clinics and hospitals.” If nothing else, that foreknowledge might have prepared doctors for the inevitable resistance they would encounter soon after vancomycin was broadly prescribed.
Image courtesy of the USDA
Wright wondered what else he might find in a shovelful of dirt. So he handed out plastic bags to students departing on break, telling them to bring back soil samples. Over two years his lab amassed a collection that spanned the continent. It even included a thawed slice of tundra mailed by Wright’s brother, a provincial policeman stationed on the northern Ontario-Manitoba border.
By 2005 Wright’s team had combed through the genes of nearly 500 streptomyces strains and species, many never before identified. Every one proved resistant to multiple antibiotics, not just their own signature chemicals. On average, each could neutralize seven or eight drugs, and many could shrug off 14 or 15. In all, the researchers found resistance to every one of the 21 antibiotics they tested, including Ketek and Zyvox, two synthetic new drugs.
“These genes clearly didn’t jump directly from streptomyces into disease-causing bacteria,” Wright says. He had noted subtle variations between the resistance genes he pulled out of soil organisms and their doppelgängers in disease-causing bacteria. As in a game of telephone, each time a gene gets passed from one microbe to another, slight differences develop that reflect the DNA dialect of its new host. The resistance genes bedeviling doctors had evidently passed through many intermediaries on their way from soil to critically ill patients.
Wright suspects that the antibiotic-drenched environment of commercial livestock operations is prime ground for such transfer. “You’ve got the genes encoding for resistance in the soil beneath these operations,” he says, “and we know that the majority of the antibiotics animals consume get excreted intact.” In other words, the antibiotics fuel the rise of resistant bacteria both in the animals’ guts and in the dirt beneath their hooves, with ample opportunity for cross-contamination.
Nobody knows how long free-floating DNA might persist in the water.
A 2001 study by University of Illinois microbiologist Roderick Mackie documented this flow. When he looked for tetracycline resistance genes in groundwater downstream from pig farms, he also found the genes in local soil organisms like Microbacterium and Pseudomonas, which normally do not contain them. Since then, Mackie has found that soil bacteria around conventional pig farms, which use antibiotics, carry 100 to 1,000 times more resistance genes than do the same bacteria around organic farms.
“These animal operations are real hot spots,” he says. “They’re glowing red in the concentrations and intensity of these genes.” More worrisome, perhaps, is that Mackie pulled more resistance genes from his deepest test wells, suggesting that the genes percolated down toward the drinking water supplies used by surrounding communities.
An even more direct conduit into the environment may be the common practice of irrigating fields with wastewater from livestock lagoons. About three years ago, David Graham, a University of Kansas environmental engineer, was puzzled in the fall by a dramatic spike in resistance genes in a pond on a Kansas feedlot he was studying. “We didn’t know what was going on until I talked with a large-animal researcher,” he recalls. At the end of the summer, feedlots receive newly weaned calves from outlying ranches. To prevent the young animals from importing infections, the feedlot operators were giving them five-day “shock doses” of antibiotics. “Their attitude had been, cows are big animals, they’re pretty tough, so you give them 10 times what they need,” Graham says.
The operators cut back on the drugs when Graham showed them that they were coating the next season’s alfalfa crop with highly drug-resistant bacteria. “Essentially, they were feeding resistance genes back to their animals,” Graham says. “Once they realized that, they started being much more conscious. They still used antibiotics, but more discriminately.”
While livestock operations are an obvious source of antibiotic resistance, humans also take a lot of antibiotics—and their waste is another contamination stream. Bacteria make up about one-third of the solid matter in human stool, and Scott Weber, of the State University of New York at Buffalo, studies what happens to the antibiotic resistance genes our nation flushes down its toilets.
Conventional sewage treatment skims off solids for landfill disposal, then feeds the liquid waste to sewage-degrading bacteria. The end result is around 5 billion pounds of bacteria-rich slurry, or waste sludge, each year. Around 35 percent of this is incinerated or put in a landfill. Close to 65 percent is recycled as fertilizer, much of it ending up on croplands.
