Scientists from EPFL and Vrije Universiteit Brussel have been working for several years on a new nanomotion based method to detect bacterial sensitivity to antibiotics. In essence, it involves “watching the bacteria dance”. Joining Stéphane Gabioud and journalist, Cécile Guérin, on Swiss radio show CQFD to discuss this new method is Professor Gilbert Greub, Chief Physician of Diagnostic Laboratories at the University Hospital of Vaud (CHUV) and scientific advisor to Resistell, the company commercializing this novel detection method.
When you suffer from a bacterial infection, it is important to determine which bacterium is involved and which antibiotics will be effective in eliminating it. Indeed, precisely targeting the treatment is essential to overcome the infection and prevent antibiotic resistance. This represents a major public health challenge, as has been known for a few years. Physicists and microbiologists in Lausanne are currently working on a new, faster method to accurately detect bacterial sensitivity to antibiotics. In summary, the method involves observing the movements of the bacteria. Is that correct?
In summary, the oscillations of bacteria at the nanoscale are compared before and after the use of antibiotics. When the bacteria cease to move, it means that the antibiotic has eliminated it and is therefore effective. This method provides a response within a few hours, compared to the conventional methods used in hospitals where one has to wait for the bacteria to grow and react to the antibiotic, which typically takes a day. Saving time is crucial, especially in the case of bloodstream infections, as it allows for faster treatment with the appropriate antibiotic. This method, called nanoscale optical detection, now needs to be validated in a hospital environment, particularly in the microbiology laboratory at CHUV (Centre Hospitalier Universitaire Vaudois).
One laboratory you are familiar with is that of Professor Gilbert Greub. Professor Greub is the head physician of the diagnostic laboratories at CHUV and also serves as a scientific advisor at Resistell AG, a company that commercializes an optical detection method. It would be interesting to hear the story of the discovery of observing dancing bacteria, i.e., the observation of nanoscale vibrations of bacteria.
So, the idea was born in the minds of physicists, mainly Prof. Giovanni Dietler, Dr. Giovanni Longo, and Dr. Sandor Kasas, whom all work at EPFL. They started by studying eukaryotic cells, such as mammalian cells, and noticed that they were able to measure their movements. Then they had the idea to focus on something smaller: bacteria. In 2013, they obtained the first evidence of observed movements in bacteria. Starting in 2015, we collaborated together to explore its use in the context of bloodstream infections, specifically bacteremia, which refers to the presence of bacteria in the blood and can lead to severe sepsis. Our goal was to reduce the turnaround time for results.
So, how does it work to determine if a bacterium will be susceptible or resistant to an antibiotic?
In practice, the technology that was initially used in 2015 involved setting up a small device called a cantilever or quantum lever. This device is very small, measuring a few millimeters in length. Just like when we stand on a diving board at a swimming pool, even without jumping, the diving board can experience slight movements due to our trembling, anxiety, or dizziness. The same goes for bacteria. Some flagellated bacteria, capable of actively moving in their environment, were attached to this device, and the movement of the flagellum acts as an engine to create movements. Even bacteria that normally do not move can generate movements, perhaps due to osmotic variations or changes in the cell wall, for example. Thus, all these movements can be measured, which indicates if the bacterium is alive. Additionally, if we fix them with a fixing agent such as formaldehyde, a derivative of formalin, to kill the bacteria, the movements cease completely. Therefore, we can distinguish the living from the non-living without waiting for bacterial growth, that is, without waiting for 2, 4, or 8-cell divisions to observe a signal.
So, you place your bacteria at the end of the diving board and administer an antibiotic to them, right?
The idea is to place liquid around the chamber where the diving board is located. This liquid contains doses of antibiotics. If the bacterium continues to move despite the antibiotic’s presence, it is resistant. On the other hand, if it stops moving, it indicates that it is susceptible to the antibiotic.
Are there currently clinical trials underway with real patients at the hospital, where the bacterial strains responsible for their illness are finally analyzed?
Yes, there are three ongoing studies. Two of them specifically focus on blood diseases. The first one is being conducted exclusively in Lausanne and is almost finished. We have included over 170 patients. The second study was recently launched and is multicenter, with the participation of two other centers to enrich the sample in case of resistance. In Switzerland, we are fortunate to have few cases of resistance, so we have asked our colleagues in Madrid to contribute since they encounter more resistance. This will allow us to more precisely evaluate the sensitivity of the test. We know that this test is very specific, but this collaboration will help us determine its sensitivity. Lastly, the third study focuses on urinary tract infections. In this case, we work directly with the sample. For example, in a kidney infection, the presence of leukocytes and nitrites usually indicates a significant urinary tract infection with a high presence of bacteria. So, we can directly place this urine sample into the chamber where the small lever (or diving board) is located and observe if there is movement of the diving board.
Cécile mentioned that this optical detection method saves valuable hours compared to a traditional antibiogram. Why is it crucial to save these hours?
Time is truly crucial because inadequate treatment can lead to a significant increase in mortality. Therefore, when a bloodstream infection occurs with bacteria circulating in the blood, doctors are well aware of the danger of this situation. As a precautionary measure, they tend to use a broad spectrum of antibiotics, even though in 90% of cases, a narrower spectrum would have been sufficient. Indeed, only a minority of bacteria exhibit resistance. However, the frequent use of these broad-spectrum antibiotics, such as carbapenems or similar molecules, leads to the emergence of resistance. Additionally, in some cases, if you are not sure, it may be necessary to use a combination of antibiotics, but this combination can be more toxic than targeted treatment.
So, will this method actually change the way infections are treated? Does it mean that you will be truly targeted because you will quickly know which antibiotics work or not?
Well, we have already made significant advancements for a long time now, as we are able to quickly detect the presence of bacteria in the blood through blood cultures. We are also able to rapidly identify the name of the bacteria, which already guides us toward specific treatments. These advancements have already revolutionized the field compared to the past. However, we are now facing a new stage that could further reduce the turnaround time for results. I say “could” because we are still in the stage of studies.
Yes, the only downside is that these machines are still in development and are very expensive. So, they are highly sophisticated equipment. Today, what applications could they be used for?
So, today, it would primarily work for blood diseases when bacteria are circulating in the blood and causing sepsis. Because it is serious enough to require a rapid response. Additionally, for bacteria that grow slowly, such as the agent of tuberculosis, it would save considerable time. We wouldn’t have to wait for their growth, which would allow us to work on the diagnosis of resistance to anti-tuberculosis drugs in our high-security laboratory located in our institute.
And last week, Dr. Sandor Kasas from EPFL, the physicist who came up with this method, published a paper on even cheaper methods, still based on the same principle. This time, he uses only an optical microscope and a camera. It could be interesting to consider in what applications this method can be used. What do you think?
Well, it’s very interesting indeed. It’s a completely different approach. The first one is very sophisticated, with a cantilever, lasers, mirrors, and all that. On the other hand, this one simply involves observing bacteria under an optical microscope, which provides a magnification of 1000 times. This allows us to see bacteria that are usually around 1 micron in size as if they were about 1 mm. They appear as small moving dots or small rods if they are bacilli. This technique has the advantage of potentially being more easily exportable and less costly. So, it’s an approach that should also be pursued because it’s really novel. We have discussed it with Dr. Sandor Kasas, and we will also study this second technique. We have a series of Escherichia coli mutants, and we will observe their movements using these different mutants. There is a whole field of study to compare the two approaches, which will be very interesting. Indeed, we are not measuring the same movements. There are movements such as the respiration of bacteria, where they expand and contract due to osmotic pressure. These movements are already measured with the small cantilevers. However, with this new technique, we can see how they move and the paths they take, which will provide us with additional information. So, by combining the two types of information obtained through these two technologies, both stemming from the mind of this physicist, we are making significant progress. It helps us better understand these bacteria, their biology and represents a step forward for research.
And you are passionate about bacteria and microbiology, so seeing them move at this nanoscale level is really new. Does that mean we thought they didn’t move?
Yes, indeed, one of them is Chlamydia. When they are in the form of elementary infectious bodies, it was thought that they were metabolically inactive, at least that’s what is mentioned in the old texts. However, what we have documented with the small cantilever is that they do move. We have also conducted preliminary tests with Dr. Sandor Kasas’ method, although these results have not been published yet, but we can observe that they also move with this small microscope.
And what does it mean for you to know that they move?
It means that we can already attack them at their elementary stage if they are metabolically inactive. However, we cannot attack them at this stage; we have to wait for them to enter the cells. And there it becomes more complicated because the molecule must penetrate the host cell, whether it is a human cell or a mammalian cell. On the other hand, we now know that it is possible to attack them even outside the cells, which represents interesting concepts. Furthermore, if we observe the mutants and study what makes them move, we can identify essential proteins and genes and target those proteins.
Could this same observation technique be useful in other fields, for example, viruses?
Yes, for example, phages are viruses that infect bacteria, so we are still in the field of bacteria.
Are these viruses that eat bacteria or rather attack them?
They can integrate into the genome of bacteria and remain relatively inactive or lyse them. Thus, for studying phages, this technology is also very useful. It is also used in Lausanne, at the CHUV, where we have several research projects focusing on Chlamydia, mycobacteria, etc.
Professor Gilbert Greub, we mentioned it, we will finish with that. You are the director of the Institute of Microbiology at the University of Lausanne, and at the same time, you are also a medical advisor for the startup Resistell AG, which commercializes this optical detection method. How do you manage conflicts of interest?
Well, it is very important to manage them well. Between 2015 and 2018, we received funding from the National Front with Giovanni Dietler, but that ended, and we had to move on to the next step. That meant figuring out how this technology, for which we had demonstrated its effectiveness in a scientific publication and through basic projects, could evolve. It was necessary to have identical machines to ensure reproducibility between different machines, institutes, and laboratories. This meant having professionals such as engineers and bioinformaticians, among others. The only way to achieve this was to create a startup, and for my part, I stayed outside of the startup in terms of financing, etc. We discussed it with the lawyers at CHUV and simply created a research agreement for the projects we carry out, as described earlier. As for the role of scientific and medical advisor, it is another contract where we agreed on a package to compensate for the time I spend as an advisor to the startup.
Watch the bacteria move on a small cantilever. It’s a faster method to detect the sensitivity of these bacteria to antibiotics! Thank you very much to Professor Gilbert Greub, guest of Cécile Guérin.
