Thesis defense Wouter Beenker ‘Alternatives to antibiotics: the potential of silencing bacterial chat’

Since the discovery of penicillin, an antibiotic derived from a fungus, many different antibiotics have come on the market to treat bacterial infections. A recurring problem is resistance: bacteria become insensitive to the agent used. This complicates the treatment of the infection with that agent and makes it necessary to find an alternative. Treatment is usually still possible with other antibiotics. However, as the problem of antibiotic resistance grows, alternatives will become increasingly necessary in the future. One of the possible alternatives is to target quorum sensing, a form of bacterial communication.

Silencing bacteria

During his PhD, Beenker investigated whether inhibition of quorum sensing could be used to fight bacterial infections. He explains: “Quorum sensing works through signaling molecules that bacteria send to each other. When one bacterium receives such a signal from the other, it adjusts its activity. In this way, quorum sensing allows bacteria to work together when there are many of them. Then they can start to produce virulence factors, for example. These are molecules that damage our tissues, which makes us feel sick when we have an infection. In addition, quorum sensing is also involved in the formation of biofilms. This means that bacteria stick together, which makes them much less sensitive to antibiotics. That is why it could be interesting to block quorum sensing, so that the bacteria can no longer ‘talk’ to each other. With the aim, of course, to make them less pathogenic or more sensitive to antibiotics.”

Searching the fungal library

Beenker and his colleagues therefore started looking for compounds that can inhibit quorum sensing. Because fungi produce all kinds of useful substances, such as penicillin, their search began in a fungal library. Beenker: “Even before I started my PhD, a library with filtrates of more than 10,000 fungi had been set up together with the Westerdijk Institute. A filtrate contains all of the substances that a fungus excretes. Among other substances, we identified paecilomycone, a compound that inhibited quorum sensing in multiple types of bacteria. This also caused a decrease in the production of virulence factors and biofilm formation. Because this is an interesting starting point for a possible new treatment, we now have a patent application pending for this compound.”

Infected mini lungs

Because little was known about the role of quorum sensing during a bacterial infection in humans, Beenker decided to investigate this further. For this he collaborated with Cayetano Pleguezuelos from the Organoid group. “Together we developed an infection model, in order to mimic a bacterial infection in human lungs in the lab. We used Pseudomonas aeruginosa, bacteria mostly known for causing lung infections in people with cystic fibrosis. We infected airway organoidsMiniature organs that can be cultured in the laboratory. Organoids mimic the shape and function of an actual organ. Researchers use the structures to, for example, study the effects of medication on diseased organs. with these bacteria. That sounds easier than it is. It took more than two years to get it working properly. One of the best days of my PhD was when it finally worked and we saw the bacteria swimming around in the organoids,” says Beenker. The researchers then studied the role of quorum sensing during the infection, by switching off this process in the bacteria. “The effect of quorum sensing turned out to be quite small in this model. Still, setting up this method was not in vain. Currently, much of the research in this field is done with animals or isolated bacteria from patients. Both methods have many disadvantages, so a better infection model for further research is essential. Hopefully, our organoid model can contribute to the discovery of new antibiotics or alternatives. Whether that will also include quorum sensing inhibitors? Time will tell,” says Beenker.

Positive experience

Beenker looks back positively on his PhD. “You don’t just learn much about your topic, but also about yourself. It is a unique opportunity to get a lot of freedom in a project.” At the same time, that freedom can sometimes be difficult, especially in the beginning. “You have just finished your studies and you don’t have much experience yet, but you have a great responsibility. You often find yourself wondering whether you are doing things right.” He would therefore advise other PhD students to share their frustrations and insecurities with each other. “My PhD was partly during covid, so sometimes I thought I was the only one struggling. But when you talk to others, you find out that everyone is in the same boat.” He also advises not to make a PhD more important than it is. “That’s easier said than done, but as important as a PhD may sometimes seem, it is just work in the end. If at times nothing seems to work, don’t try to work even harder. Just go home and do something fun. Treat it like work, not like your whole life.” Now that he is done, Beenker concludes: “I can be proud of myself: I did it.”