Researchers have figured out how some soil bacteria turn antibiotic drugs into food. Credit: Michael Worful.

You might have heard all about how many bacterial strains are becoming resistant to even our strongest antibiotics. The most immediate (and frightening) consequence is that humanity risks reverting to a dark age of medicine where unstoppable infectious diseases spread like wildfire. What’s truly mindboggling is that not only have some strains become resistant to antibiotics, they’ve learned to embrace them, consuming them for food.

Researchers at the Washington University School of Medicine in St. Louis have investigated what freaky biology allows bacteria to ingest as food what would normally be poison for them. Writing in the journal Nature Chemical Biology, the authors say that three distinct set of genes become active in trials when the bacteria ate penicillin but stayed inactive while the bacteria ate sugar.

The researchers worked with four distinct species of soil bacteria. These species likely gained antibiotic resistance due to the unregulated dumping of antibiotic-laden waste into local waterways, which also ends up in the soil. Because bacteria easily share genetic material, the antibiotic-resistant genes quickly spread through the community.

Each of the three genes identified by the researchers corresponds to one of three steps the bacteria take in order to consume antibiotics as food. First, the bacteria neutralize the dangerous part of the antibiotic which is toxic to them. With the toxin disarmed, the bacteria are then free to consume the matter which is essentially just like any other carbon-based food at this point.

“Ten years ago we stumbled onto the fact that bacteria can eat antibiotics, and everyone was shocked by it,” said senior author Gautam Dantas in a statement. “But now it’s beginning to make sense. It’s just carbon, and wherever there’s carbon, somebody will figure out how to eat it. Now that we understand how these bacteria do it, we can start thinking of ways to use this ability to get rid of antibiotics where they are causing harm.”

Antibiotic resistance is no joke. Whenever bacteria survive an antibiotic onslaught, it can acquire resistant through mutation of the genetic material or by ‘borrowing’ pieces of DNA that code for the resistance to antibiotics from other bacteria, like those from livestock. Moreover, the DNA that codes the resistance is grouped in an easily transferable package which enables the germs to become resistant to many antimicrobial agents.

In a previous long-form article, I wrote:

“Before Alexander Fleming discovered penicillin in 1928, there was no effective treatment for infections such as pneumonia, gonorrhea or rheumatic fever. Fleming’s discovery kicked off a golden age of antimicrobial research with many pharmaceutical companies developing new drugs that would save countless lives. Some doctors in the 1940s would famously prophesize that antibiotics would finally eradicate the infectious diseases that had plagued humankind throughout history. Almost a hundred years later since Fleming made his milestone discovery not only are bacterial infections still common, the misuse and overuse of antibiotics are threatening to undo all of this medical progress.”

According to the CDC, the following bacterial strains have developed the most resistance such that they’ve been listed as urgent hazards:

• Clostridium difficile. Causes severe diarrhea, especially in older people and those who have serious illnesses.
• Enterobacteriaceae. These normally live in the digestive tract but can invade other parts of the body, like the urinary tract, and cause infections.
• Neisseria gonorrhoeae. Causes gonorrhea, a sexually transmitted infection. In 2016, the WHO said gonorrhea might soon become untreatable. 

However, although antibiotic-munching bacteria sound terrifying, the authors of the new study say their adapted abilities could be exploited in our favor. One of the reasons so many bacteria develop resistance in the first place is due to poor waste management. In China and India — the world’s most important producers of pharmaceuticals — it’s common practice for waste leftover from the antibiotic manufacturing process to end up in waterways. So, why not use the antibiotic-resistant bacteria to clean up such dumps? That would be one primary application of the recent findings.

“Of course, the benefits of any such bioremediation program would need to be weighed against the risk of releasing a genetically modified bacterium into the environment and the potential spread of antibiotic resistance/degradation genes to other organisms,” the authors wrote.

“Before starting this project, we already knew that a lot of bacteria in the soil could eat antibiotics, and we all would have been very surprised if it had turned out they were somehow doing this without using antibiotic resistance genes in some way. So I think that it is mostly good news that, while resistance is part of this pathway, we now have the blueprints for how bacteria eat an antibiotic. We actually used this knowledge to design a benign strain of laboratory E. coli to do an even better job eating penicillin,” Terence Crofts, first author of the new paper and a researcher at the University of Washington, told ZME Science.

One major challenge is that the soil bacteria capable of eating antibiotics are difficult to work with and the rate at which they consume the drugs is far too slow to make an impact. The researchers, however, are confident that they can engineer E. coli, which is a well-studied bacteria and a far more tractable species, for this purpose. In experiments, the Washington University researchers showed that they could give E. coli antibiotic-eating abilities, allowing it to thrive on penicillin. The bacteria usually requires sugar to survive, but due to genetic modifications and the presence of a key protein, the E. coli survived on a sugar-free diet of penicillin.

“I think an important take-away from this paper is how we look at antibiotics. We (humans) see antibiotics just as a medicine we get from the clinic, but most of our antibiotics are actually chemicals that are made by or based on compounds that soil bacteria and fungi use to compete against their neighbors. So from the point of view of soil microbes, antibiotics are just another type of carbon-based molecule that while sometimes toxic are fair game for eating if they can be detoxified. When we consider antibiotics as being by and for bacteria, it makes sense that antibiotic resistance and antibiotic degradation/eating are widespread in the soil,” Crofts concluded.