Accurate and rapid antibiotic susceptibility testing using a machine learning-assisted nanomotion technology platform

Antimicrobial resistance (AMR) is a major public health threat, reducing treatment options for infected patients. AMR is promoted by a lack of access to rapid antibiotic susceptibility tests (ASTs). Accelerated ASTs can identify effective antibiotics for treatment in a timely and informed manner. We describe a rapid growth-independent phenotypic AST that uses a nanomotion technology platform to measure bacterial vibrations. Machine learning techniques are applied to analyze a large dataset encompassing 2762 individual nanomotion recordings from 1180 spiked positive blood culture samples covering 364 Escherichia coli and Klebsiella pneumoniae isolates exposed to cephalosporins and fluoroquinolones. The training performances of the different classification models achieve between 90.5 and 100% accuracy. Independent testing of the AST on 223 strains, including in clinical setting, correctly predict susceptibility and resistance with accuracies between 89.5% and 98.9%. The study shows the potential of this nanomotion platform for future bacterial phenotype delineation.

Nanomotion technology in combination with machine learning: a new approach for a rapid antibiotic susceptibility test for Mycobacterium tuberculosis

Nanomotion technology is a growth-independent approach that can be used to detect and record the vibrations of bacteria attached to cantilevers. We have developed a nanomotion-based antibiotic susceptibility test (AST) protocol for Mycobacterium tuberculosis (MTB). The protocol was used to predict strain phenotype towards isoniazid (INH) and rifampicin (RIF) using a leave-one-out cross-validation (LOOCV) and machine learning techniques. This MTB-nanomotion protocol takes 21 h, including cell suspension preparation, optimized bacterial attachment to functionalized cantilever, and nanomotion recording before and after antibiotic exposure. We applied this protocol to MTB isolates (n = 40) and were able to discriminate between susceptible and resistant strains for INH and RIF with a maximum sensitivity of 97.4% and 100%, respectively, and a maximum specificity of 100% for both antibiotics when considering each nanomotion recording to be a distinct experiment. Grouping recordings as triplicates based on source isolate improved sensitivity and specificity to 100% for both antibiotics. Nanomotion technology can potentially reduce time-to-result significantly compared to the days and weeks currently needed for current phenotypic ASTs for MTB. It can further be extended to other anti-TB drugs to help guide more effective TB treatment.

In Vitro Activity of Ebselen and Diphenyl Diselenide Alone and in Combination with Drugs against Trichophyton mentagrophytes Strains

Background: Dermatophytoses are one of the most prevalent infectious diseases in the world for which the pace of developing new drugs has not kept pace with the observed therapeutic problems. Thus, searching for new antifungals with an alternative and novel mechanism of action is necessary. Objective: This study aimed to evaluate the antifungal activity of ebselen and diphenyl diselenide against Trichophyton mentagrophytes clinical isolates. Methods: In vitro antifungal susceptibility was assessed for organoselenium compounds used alone or in combination with allylamines and azoles according to the 3rd edition of the CLSI M38 protocol. Results: Ebselen demonstrated high antifungal activity with MIC_GM equal to 0.442 μg/mL and 0.518 μg/mL in the case of human and animal origin strains, respectively. The values of MIC_GM of diphenyl diselenide were higher: 17.36 μg/mL and 13.45 μg/mL for the human and animal isolates, respectively. Synergistic or additive effects between terbinafine and ebselen or diphenyl diselenide were observed in the case of 12% and 20% strains, respectively. In turn, the combination of itraconazole with diphenyl diselenide showed a synergistic effect only in the case of 6% of the tested strains, whereas no synergism was shown in the combination with ebselen. Conclusions: The results highlight the promising activity of organoselenium compounds against Trichophyton mentagrophytes. However, their use in combinational therapy with antifungal drugs seems to be unjustified due to the weak synergistic effect observed.

Quartz tuning fork mass change sensing for FIB/SEM technology

In this paper we present a metrological method for determination of mass density of focused ion beam induced deposition (FIBID) materials using quartz tuning fork (QTF) mass change sensors. Dimension and density determination of FIBID deposited nanostructures is necessary to develop and reliable and repeatable microfabribrication technology of the highest versatility. The proposed metrological methodology allows to determine mass change with 5 pg resolution and accuracy below 5 % if density is considered. The described method is suitable for precise FIBID precursor parameters determination conducted during the deposition as actuation and signal read-out of the applied QTF can be performed electrically. High accuracy, resolution and stability are ensured due to excellent properties of quartz forming the sensor structure.

Influence of Production Parameters on the Content of Polyphenolic Compounds in Extruded Porridge Enriched with Chokeberry Fruit (Aronia melanocarpa (Michx.) Elliott)

Chokeberry fruit (Aronia melanocarpa (Michx.) Elliott) is known for its antioxidant properties and generally beneficial impact on human health. The aim of the research was to produce innovative corn porridge with a different content of chokeberry fruit percentage-wise and to test it to determine the content of polyphenolic compounds, including flavonoids and individual free phenolic acids, and determine the antioxidant properties of analysed extracts. One of the objectives was also to identify the optimum porridge production parameters, including, among other things, the rotational speed of the extruder screw during the extrusion process.

Obtained results showed that an increased content of chokeberry fruit in porridge enhances its antioxidant properties, as well the content of polyphenols, flavonoids, and free phenolic acids. The greatest free radicals scavenging activity by all extracts was reported after 10 minutes of the process. The results of the above study demonstrate that extruded porridge enriched with chokeberry fruit have a potential for becoming a good source of natural antioxidants, and the extrusion process at 80 rpm does not degrade the tested active compounds.

Contact atomic force microscopy using piezoresistive cantilevers in load force modulation mode

Scanning probe microscopy (SPM) encompasses several techniques for imaging of the physical and chemical material properties at nanoscale. The scanning process is based on the detection of the deflection of the cantilever, which is caused by near field interactions, while the tip runs over the sample's surface. The variety of deflection detection methods including optical, piezoresistive, piezoelectric technologies has been developed and applied depending on the measurement mode and measurement environment. There are many advantages (compactness, vacuum compatibility, etc.) of the piezoresistive detection method, which makes it very attractive for almost all SPM experiments. Due to the technological limitations the stiffness of the piezoresistive beams is usually higher than the stiffness of the cantilever detected using optical methods. This is the basic constraint for the application of the piezoresistive beams in contact mode (CM) atomic force microscopy (AFM) investigations performed at low load forces (usually less than 20 nN). Drift of the deflection signal, which is related to thermal fluctuations of the measurement setup, causes that the microscope controller compensates the fluctuations instead of compensating the strength of tip-surface interactions. Therefore, it is quite difficult to keep near field interaction precisely at the setpoint level during the whole scanning process. This can lead to either damage of the cantilever's tip and material surface or loosing the contact with the investigated sample and making the measurement unreliable. For these reasons, load force modulation (LoFM) scanning mode, in which the interaction at the tip is precisely controlled at every point of the sample surface, is proposed to enable precise AFM surface investigations using the piezoresistive cantilevers. In this article we describe the developed measurement algorithm as well as proposed and introduced hardware and software solutions. The results of the experiments confirm strong reduction of the AFM entire setup drift. The results demonstrating contactless tip lateral movements are presented. It is common knowledge that such a scanning reduces tip wear.

Carrier density distribution in silicon nanowires investigated by scanning thermal microscopy and Kelvin probe force microscopy

The use of scanning thermal microscopy (SThM) and Kelvin probe force microscopy (KPFM) to investigate silicon nanowires (SiNWs) is presented. SThM allows imaging of temperature distribution at the nanoscale, while KPFM images the potential distribution with AFM-related ultra-high spatial resolution. Both techniques are therefore suitable for imaging the resistance distribution. We show results of experimental examination of dual channel n-type SiNWs with channel width of 100 nm, while the channel was open and current was flowing through the SiNW. To investigate the carrier distribution in the SiNWs we performed SThM and KPFM scans. The SThM results showed non-symmetrical temperature distribution along the SiNWs with temperature maximum shifted towards the contact of higher potential. These results corresponded to those expressed by the distribution of potential gradient along the SiNWs, obtained using the KPFM method. Consequently, non-uniform distribution of resistance was shown, being a result of non-uniform carrier density distribution in the structure and showing the pinch-off effect. Last but not least, the results were also compared with results of finite-element method modeling.

Studies of ferroelectric properties of collagen

Dielectric hysteresis loop and differential thermal analysis (DTA) studies of collagen were performed for temperatures ranging from a room temperature to 393 K. The material studied was collagen from Achilles tendon of a bullock, which contained 10% of water. The DTA curve for collagen with 10% of water showed a clear minimum at 353 K. The character of the curve proved that around 353 K an endothermic transformation of collagen took place which could be connected with the transition spiral-ball. A hypothetical dielectric hysteresis loop shows a maximum shift along the direction of the electric field applied in the vicinity of 375 K. Low frequencies of the applied electric field are connected with a great dielectric loss influencing the interpretation of collagen ferroelectricity.