Listening to the sound of a single bacterium with graphene

Ever wondered how a single bacterium sounds like? We used the exquisite sensing capabilities of graphene to listen to the sound of a single E. coli in its growth medium and used that to perform antibiotic sensitivity tests at the single cell level
Published in Materials
Listening to the sound of a single bacterium with graphene
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The discovery of graphene, and the ability to fabricate atomically thin membranes, marked the start of a new era in mechanical sensing that not so long ago was only dreamed of. During my research project performed in the framework of the European Research Council Starting Grant (ENIGMA), we developed a novel procedure for measuring nanomechanical vibrations of ultrathin (<1 nm) suspended graphene drums, in collaboration with Peter Steeneken, professor at my department at TU Delft. We used light to read-out the motion of graphene with extreme sensitivities in a large range, from Brownian fluctuations up to nonlinear dynamics.

 In 2019, we got the idea to use this read-out system for measuring forces that are generated by micro-organisms such as bacteria. To do this, we needed a method that could probe bacterial forces in a growth medium. This would unfortunately discard utilizing graphene’s resonant response since the damped aqueous environment of bacteria makes detecting and correlating bacterial forces to resonance frequency changes of graphene practically impossible, yet we could perhaps measure those bugs. Indeed, we realized instead that cell populations transduce random-like nanoscale oscillations to their environment as a result of their biological processes, and were wondering if graphene could resolve these oscillations at the single bacterium level.

 To explore this route, we initiated a collaboration with the group of Cees Dekker, a professor and pioneer in nanoscale biology at TU Delft, to aid us with sample preparation and conceiving experiments with bacterial cells. He was enthusiastic about the idea and so we teamed up. Together with highly motivated PhD student Irek Roslon and postdoctoral fellow Dr. Aleksandre Japaridze, we performed our first measurements in a cuvette containing live E. coli in its growth medium, and used the laser motion detection system to determine the time-dependent deflection of graphene in the presence of E. coli. The outcome of our first measurements was mind-blowing! We were able to detect nanoscale forces generated by a single bacterium! Our results also made us think, what could be the source of these nanoscale forces? And can graphene act as a single-cell antibiotic sensitivity platform?

 The answer to these questions is given in our Nature Nanotechnology article published today, where we show that a single E. coli can transduce average forces in the order of 6 nN to graphene with major contribution from its flagella (tails on the cell surface that propel the bacteria). To understand how tiny these flagellar beats on graphene are, its worth saying that they are at least 10 billion times smaller than a boxer’s punch when reaching a punch bag. Yet,  These nanoscale beats can be even converted to sound tracks and listened to- and how cool is that!

Graphene to fight antibiotic resistance

Using graphene to detect nanoscale forces of single bacteria not only has substantial implications for our understanding of mechanobiology of bacterial cells, but can also offer a unique way for monitoring the efficacy of antibiotics. To prove this, we traced the nanomechanical fluctuations of a single-bacterium in the presence of antibiotics with different modes of action and showed that these oscillations diminish in the presence of antibiotics within 1 hour. Interestingly, when the bacteria were resistant to antibiotic, we did not observe a change in nanomotion, suggesting that graphene can detect the antibiotic resistance of even a single cell. This opens the door to very fast antibiotic testing, which may greatly help doctors in a hospital.

 For the future we aim at optimizing our graphene antibiotic sensitivity platform by enhancing its throughput, developing faster read-out schemes, and validating it against a variety of pathogenic samples, so that eventually it can be used as an effective diagnostic toolkit for fast detection of antibiotic resistance in clinical practice. This becomes very crucial when knowing that antibiotic resistance is one of the biggest threats that the global community will face in the future, endangering millions of lives.

 To that end, I also decided to start a company, which is a new experience for me. In addition to research at university, we plan to bring this technology closer to market with the help of our valorization partners. With the significant reduction in size, increase in speed, and great enhancement of the sensitivity offered by graphene, we envision that graphene nanomotion-based antibiotic sensitivity devices can shift current paradigms in diagnostics by providing a faster and much more sensitive method for diagnosis of bacterial infections and fighting antibiotic resistance.

Artist's impression of a single bacterium nanomotion detection using graphene drums (Credit: Irek Roslon, TU Delft)

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