May 2025

If you are lucky enough to have had regular medical care in the United States, odds are good that, at some point, you’ve taken antibiotics. Maybe you had strep throat, pink eye, an infected cut, or another of the range of bacterial infections that antibiotics can stamp out. Or perhaps yours was one of the full 25% of antibiotic prescriptions inappropriately given to fight a viral infection. Either way, you likely took the course of medication within a couple weeks, got better, and moved on. But new research reveals that your normal gut bacteria may not have moved on as quickly …

Where's the evolution?

Scientists and doctors have long known that bacteria can rapidly evolve resistance to antibiotics with exposure to these drugs. This happens through the process of natural selection. It works like this. The population of bacteria that cause, say, a strep throat infection, are not all identical to one another because random mutation causes new genetic variants to occur. Many of these mutations are harmful to the bacterium, some have no effect, and a few might be helpful, at least in certain situations. Imagine that one of the bacteria in the strep population happens to have a mutation that makes it more likely than others to survive to reproduce in the presence of antibiotics. When the infection is treated with antibiotics, that bacterium will leave behind more descendants than other bacteria. And those descendants will have inherited the trait of antibiotic resistance. Over many bacterial generations (i.e., a few days), an easily treated bacterial infection can evolve into an antibiotic-resistant strain. If that strain spreads, the previously used medicine will be less effective or ineffective against the new strep cases.

Of course, when a patient takes an antibiotic, it’s not just the illness-causing bacteria that are exposed to the drug. Other “good” bacteria that normally inhabit our bodies and help keep us healthy could also experience natural selection favoring the evolution of resistant strains.  The researchers behind the new study wondered what happens to the good bacteria that normally live inside the human gut when someone takes a course of a common antibiotic. To find out, they collected gut bacteria samples from 60 healthy study volunteers before, during, and after a five-day course of the antibiotic ciprofloxacin. They then sequenced the bacterial genomes to learn whether they evolved resistance to the antibiotic.

The scientists found that the rise of resistant mutations was common. In fact, in about 10% of the thousands of bacterial populations, variants carrying one particular resistance mutation took over the population in what’s known as a selective sweep. This is an example of convergent evolution, when the same sort of selection pressure—in this case exposure to the same antibiotic—causes distinct groups or species to evolve similar adaptations.

Even more concerning was the observation that populations didn’t tend to evolve back into susceptible strains after the antibiotic was stopped. Many resistance mutations remained common more than nine weeks after the last dose. An intuitively appealing hypothesis suggests that having an adaptation that is beneficial in a particular environment, like a resistance mutation that is advantageous in the presence of antibiotics, comes at a fitness cost to the individual in other environments. In other words, there is a tradeoff. Perhaps the mutation causes antibiotic resistance through a cellular mechanism that also reduces the ability of the bacterium to move around or slows its ability to produce the proteins it needs. It makes intuitive sense that a bacterium couldn’t get something (e.g., resistance) for nothing. However, if this idea were true of the resistance mutations in the recent research on human gut bacteria, then we’d expect susceptible forms to outcompete resistant forms once people stopped taking the antibiotic, and for the gut populations to evolve back into susceptible strains. But that’s not what happened. Resistant forms remained common in the gut for many months, supporting the idea that bacterial resistance is often “low cost.”

The new study is just one of many that underscores the threat of antibiotic resistance and the need to manage our use of antibiotics to slow the evolution of resistance. Even a short course of antibiotics can have a lasting impact, not just on the illness-causing pathogen, but on other helpful bacteria as well – ones that live in our bodies or even in ecosystems where our wastewater is released.