Survival of the smartest: Superbugs defeated with evolutionary trick

With an old drug, researchers dupe drug-resistant bacteria into tossing resistance.

Beth Mole – Sep 26, 2016 5:53 pm | 44

Bacteria are wizzes at developing resistance to our most powerful antibiotics. This unfortunate skill leads to millions of difficult-to-treat infections worldwide and growing fears that bacteria may one day become unstoppable. But these microbes’ evolutionary prowess can just as easily be their downfall, scientists reported last week in Nature Chemical Biology.

By gaming the evolutionary system, researchers have fooled drug-resistant Escherichia coli into tossing their resistance. Then, with a shot of the drug that the bacteria could previously withstand, the E. coli met their end. Though the study was just done in lab dishes, the authors, led by researchers at Harvard, are hopeful that the one-two punch could be useful in reversing drug resistance and restoring the effectiveness of life-saving antibiotics.

This strategy could “add valuable tools to our antimicrobial arsenal,” they conclude.

To pull off the evolutionary bamboozle, the researchers started the study knowing that some types of drug resistance come with exploitable drawbacks. That is, not all drug resistance is equal—and it depends on the type of antibiotic the bacteria have evolved to dodge.

Some antibiotics, such as ciprofloxacin and other fluoroquinolones, work by effectively tossing a wrench into bacterial cell division, while others, such as penicillin and its ilk, sabotage bacterial cell walls, leading to a leaky mess. Still others, such as tetracyclines and aminoglycosides (eg. Streptomycin), foul up protein production in bacteria, bringing the microbes’ essential biological processes to a grinding halt.

Bacteria have evolved clever defenses against almost all types of drugs. Some bacteria have used mutations to mask a drug’s primary target. For instance, some germs resist penicillin by disguising the cell wall component that the drug blocks. Other bacteria have enzymes to degrade specific antibiotics or have actual pumps (efflux pumps) that forcibly toss drugs out of a bacterial cell before they can do any damage.

Occasionally, these resistance strategies arise through new mutations that offer an advantage when a bacterial population gets a non-lethal dose of a drug. However, much resistance stems from already highly evolved and specialized genes that bacteria can share with each other, such as those on transferrable rings of DNA called plasmids or transposable elements, aka “jumping genes.”

Weakness in antibiotic armor

Knowing all the particulars about a bacterial population’s resistance can be key to finding a weakness, the authors argue. For instance, some drug-dissolving enzymes may require a lot of energy to make. Thus, if a bacterium is strapped for resources and in a place where it’s not being bombarded by drugs, it may quickly ditch the plasmid carrying the enzyme’s blueprints. Additionally, there are the resistance genes that inadvertently make bacteria immune to one drug but more sensitive another—a scenario first reported in 1952, dubbed collateral sensitivity.

Since then, researchers have found many instances of collateral sensitivity in bacteria with new, drug-resistant mutations. But they’ve found only a few instances of collateral sensitivity in bacteria that carry around one of those specialized and highly evolved drug-resistance genes. The authors set out to find some more—then use it to reverse evolution.

They focused on E. coli that had become resistant to tetracycline (tet) by way of an efflux pump, the genetic code for which is on a transposon (jumping gene). Tetracycline resistance is widespread in clinical and agricultural settings, rendering it useless in many cases. And the transposon-embedded efflux pump is a common source of that resistance.

The researchers set up a high-volume screen to sort through a chemical library of 19,769 compounds, looking for any that would kill off tet-resistant E. coli but leave regular old E. coli relatively unscathed. They found two such compounds: Disulfiram, an FDA-approved drug (Antabuse) for treating alcoholism; and β-Thujaplicin, known to have antifungal and antibacterial activity.

β-Thujaplicin was the better, more selective killer of the two, so the researchers moved forward with it alone. They next grew eight replicate populations of tet-resistant E. coli for a week, giving each a non-lethal dose of β-Thujaplicin. Because the tet-resistance made the bacteria more sensitive to β-Thujaplicin, there was selective pressure to scrap their transposon-based resistance—which they mostly did. At the end, seven of the eight populations had completely lost their tet-resistance due to mutations that messed up the transposable element. The bacteria were easily killed with a tetracycline antibiotic.

In the one population that didn’t completely lose tet-resistance, they found a bacterium that had a mutation that rendered it resistant to both tet and β-Thujaplicin. While such dual resistance would ruin the evolutionary trick, the researchers noted that this mutation was exceedingly rare. Other snags are that a two-phase antibiotic course would make for a long treatment, which may not work for patients with severe infections. “Despite these difficulties,” the authors concluded, “we hope these findings will inspire future therapeutic paradigms that can reverse the evolution of resistance.”

Nature Chemical Biology, 2016. DOI: 10.1038/nchembio.2176 (About DOIs).