Development of an AFM-based nanomotion detection device for microbiological samples

The main goals of this thesis pertain to the development of a device capable of detecting microorganism viability through monitoring the oscillations of a microscopic cantilever transducer, to improve the presently used device and to attempt to explain in physical terms the underlying cause of the observed effect. The thesis begins with a brief introduction about the antimicrobial resistance, atomic force microscopy and application of the presented method in antimicrobial susceptibility testing. The state of the art for assessing antimicrobial susceptibility (so called gold standard) and the emerging methods in antimicrobial susceptibility testing follows. A special emphasis was given to cantilever – based techniques. Afterwards a theoretical description of the observed effect is attempted by evaluating the possible contributing phenomena. Those phenomena are divided into two groups: ones that contribute to the effect positively and ones that are mimicking viable microorganisms. All the contributing phenomena are quantified using model calculations and evaluated based on the significance of the contribution to the total effect. The development of the devices and controlling software is given in the subsequent chapter. The construction of the devices is described in detail. The operation and procedures regarding the utilization of the device are characterized. The software that manages the preparation of the device before the experiment and the data acquisition during the experiments is demonstrated. Experimental results are reported in the following chapters. First section is devoted to introduce the technique, its basic procedures and methodology. The following section is briefly presenting the calibration procedure. Afterwards a section describes the application of the method to slow-growing bacteria as an extreme case of rapid antimicrobial susceptibility testing. Subsequent section elaborates on the utilization of the technique to assess the metabolic activity of mitochondria. The discussion of the results and possible effects are presented in the penultimate chapter. The final chapter concludes the thesis.