Rewriting Life

How Pathogens Fight Drugs

“Death galaxy” chip shows bacteria evolve antibiotic resistance at a surprising pace.

When attacked with antibiotics, bacteria can mutate rapidly in order to survive—it’s what makes, for instance, the staph infection MRSA so dangerous. New research suggests that such bacterial evolution occurs even faster, and in a more predictable fashion, than anyone thought. Using a novel type of microfluidics chip, researchers have shown that bacteria can develop antibiotic resistance in less than 10 hours.

Death on a chip: This microfluidics chip consists of over 1,000 chambers, with nutrients circulating along half of the perimeter (artificially colored yellow here) and an antibiotic solution circulating along the other half (colored red). The resulting gradient, from habitable to toxic, proves fertile ground for bacterial evolution.

Rather than taking the conventional approach of testing the bacteria in a test tube, Robert Austin, a biophysicist at Princeton University, designed a microfluidics chip to simulate the complex chemical environments that bacteria experience in the real world. The chip contains over 1,000 tiny hexagonal chambers, each one a microhabitat connected to others by long, slim corridors. 

Austin flowed nutrients around one side of the chip and a solution of the antibiotic ciprofloxacin around the other. The solutions diffused into the inner hexagons through nano-sized slits, building a landscape of different ecologies. “I call it the ‘death galaxy’—a galaxy of different environments designed to be very stressful,” Austin says. “And the question is, if we apply very high levels of antibiotics to this funny world, would we see the rapid evolution of resistance?”

Austin and colleagues began to see resistant strains emerge within five hours. After 10 hours, the resistant strains  were populating even the most Cipro-saturated chambers.

The researchers also discovered that the evolution occurred predictably. Every time they ran the experiment, they got the same result, with the same four resistance-conferring mutations emerging over and over again. “It’s surprising that it happens so quickly and in such a logical and repeatable manner,” he says.

If Austin’s chip can help researchers understand how bacteria develop resistance and predict the changes they will undergo, it could be invaluable in antibiotic development. Says Susan Rosenberg, a molecular geneticist specializing in bacterial and cancer cell evolution at Baylor University, in Houston, “We’re in an evolutionary arms race against pathogenic bacteria. But if we understand how they become resistant, we might think about designing smarter drugs, ones that attack the process of resistance acquisition instead of just changing antibiotics when resistance happens.”

Patterned evolution: Bacteria labeled with a green fluorescent protein were placed on the chip. As they evolved greater resistance to the antibiotic, they colonized outward, toward increasing concentrations of antibiotic and nutrient, in distinct patterns.

The chip has other potential applications as well. It might be used to improve strains of beneficial bacteria that degrade pollutants. Cancer research could likely make use of it too. Tumor cells can develop rapid resistance to chemotherapy, much as bacteria develop resistance to antibiotics. “The mechanism they’ve identified may also be a mechanism of change in cancer, and it could lead to tests to identify resistance before you even start administering drugs,” says Anna Barker, director of Arizona State University’s Transformative Healthcare Networks, who specializes in complex systems like cancer.

Cancer is indeed where Austin is headed next: he is already adapting his death galaxy for cancer cells. “Breast cancer and multiple myeloma are both existing in complex microenvironments,” he says, “and my hope is that they might be most susceptible to my approach.”