Tetracycline—a powerful antibiotic—came from the soil. Researchers isolated the drug, used to treat everything from sexually transmitted diseases to bacterial pneumonia, from the soil-dwelling microbe Septomyces aureofaciens, which produces tetracycline to kill its microbe neighbors. So it comes as no surprise that other soil microbes have evolved ways to resist this antibiotic
But a new genetic analysis has revealed that soil microbes and clinical pathogens—the kinds of microbes that make people sick—have been swapping the genes necessary to resist humanity's arsenal of antibiotics. According to research published in Science on August 31, scientists found that identical genes that confer resistance to a suite of 12 different antibiotics are found in both U.S. soil microbes and pathogens from around the globe.
Eighteen of the resistance genes found in sick people in every inhabited continent directly match genes found in soil microbes from Massachusetts, Minnesota and Pennsylvania. This identical match, including even the parts that play no known biological role, suggests that soil microbes and the microbes that cause sickness have been swapping genes recently, not developing such resistance on their own, though it's unclear which way the genes flowed.
As part of their analysis, the researchers detected 110 different genes that could confer resistance to one or more of the nine major classes of antibiotics. (More than half of these genes had never been identified before.)
The soil microbes are not only evolving resistance to the antibiotics naturally present in their environment, they seem to be developing ways to protect themselves from man-made antibiotics ranging from ciprofloxacin to penicillins. That evolutionary process has likely been speeded along by the widespread use of various antibiotics in farming.
How exactly the genes are getting from soil microbes to sickness microbes or vice versa remains unclear. One suggestion is that soil microbes and pathogens mingle in the human gut, swapping genes that allow both to prosper. It is also likely that microbes are evolving antibiotic resistance in other environments contaminated with excess antibiotics, such as rivers, lakes, streams and even the seas.
But, just as over-reliance on antibiotics has helped foster microbial resistance, microbial over-reliance on the same set of genes may prove a fatal flaw, if new antibiotics or treatments can be found. The place to start may be in the dirt.