Photo: Elaine Thompson/AP Photo

Go inside the labs where researchers are battling deadly superbugs

The answer could be hidden anywhere—in any plant, any animal, any spore, mold, fungus or pathogen. The planet is teeming with potential, a writhing black box whose secrets are waiting to be discovered, assayed, and tested again and again and again. Maybe the answer is in a worm. A nematode worm, to be specific, a microscopic thread-like parasite which is among the most abundant lifeforms on the planet. Hidden inside this legion could be the key to beating back bacteria resistant to our current antibiotics, lethal pathogens dubbed “superbugs.”

The scale and severity of the problem began to take focus for Philippe Villain-Guillot while he was earning his doctorate. Before beginning his PhD studies at the University of Montpellier, he had been aware of the rise of superbugs. But the scope of the problem came into focus as he studied the academic literature and later started to share his own work. He kept running into people who had been infected themselves.

“This is really frightening, actually,” Dr. Villain-Guillot said by Skype from his native France. “The fact that anybody now can be infected by such bacteria.”

Finding new antimicrobial compounds is crucial for stopping the superbugs. Imagine the pathogen, Villain-Guillot said, as a castle under siege; access can be gained by inserting the right key into the right door. If the castle-dwellers know the plan of attack, however, they can break a key in the keyhole and hold fast. What is needed are new keys and new doors, avenues of attack that we have not yet discovered.

Working with another University of Montpellier doctoral candidate, Dr. Maxime Gualtieri, they began searching for new forms of antibiotics to check the growing scourge. Misuse of antibiotics—incomplete dosing regimens and reckless deployment chief among them—and a period of time wherein antibiotic research, supposedly secure in its defeat of one corner of the microscopic kingdom, laid fallow, all boosted the rise of drug-resistant superbugs. These bacteria were the survivors of humanity’s war on disease, which had endured their encounters with modern medicine by some twist of genetic fate, and would go on to profligate, passing on their resilience, to future iterations. Their unimaginably immense population size and rapid accrual of generations causes bacteria to evolve far faster than most life forms, and superbugs are now threatening to tip the balance in the war on infectious disease.

“This is really frightening, actually. The fact that anybody now can be infected by such bacteria.”

The two founded Nosopharm, of which Villain-Guillot is CEO and Gualtieri CSO, to specifically focus on research and development of antimicrobials for hospital-based infections and drug-resistant pathogens.

“We felt that natural products—I mean the microbial biodiversity—was a rich source of potential antibiotics,” Villain-Guillot said. Using a list of microbial candidates for antibiotics from the French National Institute of Agricultural Research which had not been thoroughly analyzed, the pair focused on a bacteria found in the parasitic nematode worm, which Gualtieri was already familiar with from his previous work.

Nematodes, also known as roundworms, are among the most abundant multicellular life forms on earth. Many are parasitic, infecting insects, plants and animals alike, and their microscopic, string-like bodies can be found in most any environment, many thousands of them in a fistful of soil. A symbiotic bacteria inside the nematode helps it to infect and kill the insects the worm inhabits for food, while an antibiotic the bacteria produces then helps protect the nematode—and, by extension, the bacteria—from becoming infected itself. This parasitic matryoshka revealed to the Nosopharm team odilorhabdins, the antibiotic agent the nematode’s partner creates.

Beginning with a collection of strains, the scientists cultured and screened them for antibiotic activity.

“We created hundreds and hundreds of samples from the growth media against the relevant pathogens,” Villain-Guillot said. “When we have a positive result, we have to purify and identify the molecules that are responsible for the antibiotic activity.” It was painstaking work that promised no quick satisfaction; even if a molecule was identified, there was no guarantee that it would be worth the time, effort, and capital required of further research.

Nosopharm, founded by CEO Villain-Guillot and chief science officer Maxime Gualtieri, focuses on research and development of antimicrobials for hospital-based infections and drug-resistant pathogens.

The odilorhabdins, or ODLs, proved effective against a wide array of resistant bacteria.

“When you have these results, you are far from a drug,” Villain-Guillot said. “It’s really when you go to the first experiment in a mouse; when you see that you are able to cure an infection within a complex, living animal.”

As the mice were cured of various infections—in their blood, their urinary tracts, their lungs—enthusiasm for the potential of their new compound grew. ODLs seemed not to provoke any serious side effects. What’s more, it worked slightly better than the standard they required to consider working with it further.

The ODLs had a new chemical structure for an antibiotic, meaning chances were good for a new mechanism of action. Nosopharm knew that the ODLs attacked the ribosomes of the bacteria. Ribosomes are a cell’s protein factory, taking genetic information and using it to create the proteins needed for proper biologic function. By corrupting the ribosome, an antibiotic corrupts the proteins, killing the cell. The ODLs are a bactericidal antibiotic—cidal antibiotics actively kill organisms, while static ones inhibit them until the immune system can finish the job. ODLs kill.

Nosopharm now knew how they were killing bacteria, but they did not know where. If the ODLs were attaching to a new binding site on the ribosome that no other antibiotic currently utilized, it could mean an important new front opening in the war on infectious disease, one which had not yet been sealed off by the legions of bacteria.

“We knew the key,” Villain-Guillot said. “We didn’t have the keyhole.”


Up a DNA double helix staircase in the University of Illinois at Chicago’s brutalist Molecular Biology Research building, sits an unassuming lab belonging to Drs. Alexandr Mankin and Yury Polikanov. The Muscovites are ribosome experts; if anyone could find out where the ODLs were binding, it would be them.

The scientists used radioactivity to trace the product of the reactions, and the results surprised them: The ribosomes would not stop making proteins, but cranked out erroneous ones poisonous to the bacteria. Their ODL hypothesis was not proven right or wrong.

“Possibility number three is probably the most exciting,” Mankin said. “Which is when you get a result that does not confirm, or not confirm, your hypothesis. You get something that you completely did not expect to get.”

To see where the ODL was attaching to the ribosomes, another technique would be required: x-ray crystallography. The results were compounded into crystals, which Polikanov flash froze with liquid nitrogen and stored in “pucks.” The pucks were then taken to the Advanced Photon Source at the Argonne National Laboratory, where they were exposed to powerful x-rays. Once shot through the crystal, the rays diffract into points, which can be used to create a three-dimensional model.

“The first time that you ever saw something … that was the most amazing thing. You’re dealing with tiny little molecules that are just unimaginably small,” Polikanov said. “We cannot comprehend. It’s not tangible.”

What Polikanov’s images showed now was that the ODLs were binding to a site on the ribosome that no antibiotic had used before. In other words, Nosopharm’s drug has the potential to attack superbugs in a whole new way.

Years of study remain to determine whether odilorhabdins will cure new or drug-resistant diseases in humans or are merely a tantalizing hint at the antimicrobials around us.

“It’s like you’re trying to escape from jail,” Mankin says of the daunting challenges science provides. “You start digging the tunnel not knowing whether you are digging in the right direction. Sometimes the tunnel collapses and you have to start digging it anew. Sometimes you come out of the tunnel and find that you are still in jail.”

But the successes, and their potential positive impact on the world, are worth it.

“One of your attempts will be successful, and you will be able to get the light of morn.”
