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Routes of Resistance

Our focus on using antibiotics to kill bacteria has blinded us to their diverse functions in the organisms that make these chemicals

Robert L. Dorit

The Rise of Resistance

It did not take long for antibiotic resistance to emerge once the drugs entered the arsenal of modern medicine. Penicillin, discovered in 1929, came into widespread use on the battlefield during World War II: Some 100 million doses were produced between 1943 and 1945. But even before the end of the war, the first penicillin-resistant strains of bacteria appeared. Over the next five decades, the pattern repeated numerous times. The discovery of every new antibiotic class created excitement by promising to bring bacterial infections to heel. Inevitably, however, the edge of this new tool for the treatment of infections became blunt with overuse as resistant strains grew common. The useful clinical life of new antibiotics, defined as the time between clinical introduction and the rise of resistant strains, is often no more than a matter of three to five years. Over the past decade, moreover, antibiotic resistance, once only a public-health concern, has morphed into a measurable cause of death. Conservatively, untreatable bacterial infections result in some 100,000 deaths per year in the United States. The early promise of the age of antibiotics—an end to infectious diseases—now seems absurdly naive.

But every day, in clinics and hospitals around the world, doctors are forced to administer antibiotics to clear up bacterial infections that threaten the lives of patients. And every day, the bacteria—both the pathogens we are targeting and the innocent bystanders that end up as collateral damage—respond by evolving mechanisms to resist the antibiotics. Each dose is a skirmish in a larger war. Yet, focused as we are on what we see as an epic battle between humans and pathogens, we forget that both antibiotics and antibiotic resistance have been part of the microbial world for the past 3 billion years. Yes, the widespread use of antibiotics to combat infections has had profound implications for the evolution of infectious disease, but it is a mere blip in the history of the microbial world.

Four out of five antibiotics in use today are based on naturally occurring compounds produced by bacteria and fungi. The organisms that produce antibiotics have not, of course, been doing so over billions of years just so that we might discover them and put them to therapeutic use in the 21st century. So what are antibiotics doing for the organisms that produce them? The explanation most obvious to us, of course, is to see these compounds as part of the competitive arsenal of the bacteria that produce them. In this model, antibiotic-producing bacteria kill their competitors and make ecological space available for themselves and their genetic kin. Seen this way, antibiotics in microbial ecosystems and antibiotics in the clinic do one and the same thing: kill bacteria.

To be sure, naturally produced antibiotics in intact microbial ecosystems enable producing strains to kill other bacteria. Some antibiotics, such as a class of proteins called the bacteriocins, are not subtle: A single molecule entering a target cell will kill it. These molecules are designed to kill and nothing more. But the concentrations of many other antibiotics in natural ecosystems seem consistently too low to kill surrounding organisms effectively. Why would bacteria bother to produce antibiotics—which are expensive molecules to synthesize—at concentrations too low to reap the benefits? It now appears that at lower concentrations, antibiotics may well, to the bacteria, mean something utterly different than they do at the massive concentrations encountered in the clinic. In their original context, antibiotics may not be killers at all, but instead messengers enabling cell-to-cell communication both within and across bacterial species boundaries.

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