Rapid detection of bacterial resistance to antibiotics using AFM cantilevers as nanomechanical sensors

Rapid and Sensitive Quantification of Bacterial Viability Using Ratiometric Fluorescence Sensing

Bacterial viability assessment plays an important role in food-borne pathogen detection and antimicrobial drug development. Here, we first used GelRed as a DNA-binding stain for a bacterial viability assessment. It was found that live bacteria were able to exclude GelRed, which however could easily penetrate dead ones and be absorbed nonspecifically on the bacterial periplasm. Cations were used to reduce the nonspecific adsorption and greatly increase the red fluorescence ratio of dead to live bacteria. Combined with SYTO 9 (a membrane-permeable dye) for double-staining, a ratiometric fluorescent method was established. Using Escherichia coli O157:H7 as a bacteria model, the ratiometric fluorescent method can probe dead bacteria as low as 0.1%. A linear correlation between the ratiometric fluorescence and the theoretical ratio of dead bacteria was acquired, with a correlation coefficient R2 of 0.97. Advantages in sensitivity, accuracy, and safety of the GelRed/SYTO9-based ratiometric fluorescent method against traditional methods were demonstrated. The established method was successfully applied to the assessment of germicidal efficacy of different heat treatments. It was found that even 50 °C treatment could lead to the death of minor bacteria. The as-developed method has many potential applications in microbial researches, and we believe it could be expanded to the viability assessment of mammalian cells.

Development of a microcantilever-based biosensor for detecting Programmed Death Ligand 1

The ongoing global concern of cancer worldwide necessitates the development of advanced diagnostic and therapeutic strategies. The majority of recent detection strategies involve the employment of biomarkers. A critical biomarker for cancer immunotherapy efficacy and patient prognosis is Programmed Death Ligand 1 (PD-L1), which is a key immune checkpoint protein. PD-L1 can be particularly linked to cancer progression and therapy response. Current detection methods, such as enzyme-linked immunosorbent assay (ELISA), face limitations like high cost, time consumption, and complexity. This study introduces a microcantilever-based biosensor designed for the detection of soluble PD-L1 (sPD-L1), which has a specific association with PD-L1. The biosensor utilizes anti-PD-L1 as the sensing layer, capitalizing on the specific binding affinity between anti-PD-L1 and sPD-L1. The presence of the sensing layer was confirmed through Atomic Force Microscopy (AFM) and contact angle measurements. Binding between sPD-L1 and anti-PD-L1 induces a shift in the microcantilever's resonance frequency, which is proportional to the PD-L1 concentration. Notably, the resonance frequency shift demonstrates a robust linear relationship with the increasing biomarker concentration, ranging from 0.05 ng/ml to 500 ng/ml. The detection limit of the biosensor was determined to be approximately 10 pg/ml. The biosensor demonstrates excellent performance in detecting PD-L1 with high specificity even in complex biological matrices. This innovative approach not only provides a promising tool for early cancer diagnosis but also holds potential for monitoring immunotherapy efficacy, paving the way for personalized and effective cancer treatments.

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.

An Optical Fiber-Based Nanomotion Sensor for Rapid Antibiotic and Antifungal Susceptibility Tests

The emergence of antibiotic and antifungal resistant microorganisms represents nowadays a major public health issue that might push humanity into a post-antibiotic/antifungal era. One of the approaches to avoid such a catastrophe is to advance rapid antibiotic and antifungal susceptibility tests. In this study, we present a compact, optical fiber-based nanomotion sensor to achieve this goal by monitoring the dynamic nanoscale oscillation of a cantilever related to microorganism viability. High detection sensitivity was achieved that was attributed to the flexible two-photon polymerized cantilever with a spring constant of 0.3 N/m. This nanomotion device showed an excellent performance in the susceptibility tests of Escherichia coli and Candida albicans with a fast response in a time frame of minutes. As a proof-of-concept, with the simplicity of use and the potential of parallelization, our innovative sensor is anticipated to be an interesting candidate for future rapid antibiotic and antifungal susceptibility tests and other biomedical applications.

A simplified version of rapid susceptibility testing of bacteria and yeasts using optical nanomotion detection

We present a novel optical nanomotion-based rapid antibiotic and antifungal susceptibility test. The technique consisted of studying the effects of antibiotics or antifungals on the nanometric scale displacements of bacteria or yeasts to assess their sensitivity or resistance to drugs. The technique relies on a traditional optical microscope, a video camera, and custom-made image analysis software. It provides reliable results in a time frame of 2-4 h and can be applied to motile, non-motile, fast, and slowly growing microorganisms. Due to its extreme simplicity and low cost, the technique can be easily implemented in laboratories and medical centers in developing countries.

Machine learning method for the classification of the state of living organisms' oscillations

The World Health Organization highlights the urgent need to address the global threat posed by antibiotic-resistant bacteria. Efficient and rapid detection of bacterial response to antibiotics and their virulence state is crucial for the effective treatment of bacterial infections. However, current methods for investigating bacterial antibiotic response and metabolic state are time-consuming and lack accuracy. To address these limitations, we propose a novel method for classifying bacterial virulence based on statistical analysis of nanomotion recordings. We demonstrated the method by classifying living Bordetella pertussis bacteria in the virulent or avirulence phase, and dead bacteria, based on their cellular nanomotion signal. Our method offers significant advantages over current approaches, as it is faster and more accurate. Additionally, its versatility allows for the analysis of cellular nanomotion in various applications beyond bacterial virulence classification.

Hydrodynamic function and spring constant calibration of FluidFM micropipette cantilevers

Fluidic force microscopy (FluidFM) fuses the force sensitivity of atomic force microscopy with the manipulation capabilities of microfluidics by using microfabricated cantilevers with embedded fluidic channels. This innovation initiated new research and development directions in biology, biophysics, and material science. To acquire reliable and reproducible data, the calibration of the force sensor is crucial. Importantly, the hollow FluidFM cantilevers contain a row of parallel pillars inside a rectangular beam. The precise spring constant calibration of the internally structured cantilever is far from trivial, and existing methods generally assume simplifications that are not applicable to these special types of cantilevers. In addition, the Sader method, which is currently implemented by the FluidFM community, relies on the precise measurement of the quality factor, which renders the calibration of the spring constant sensitive to noise. In this study, the hydrodynamic function of these special types of hollow cantilevers was experimentally determined with different instruments. Based on the hydrodynamic function, a novel spring constant calibration method was adapted, which relied only on the two resonance frequencies of the cantilever, measured in air and in a liquid. Based on these results, our proposed method can be successfully used for the reliable, noise-free calibration of hollow FluidFM cantilevers.

Relative quantification of the recA gene for antimicrobial susceptibility testing in response to ciprofloxacin for pathogens of concern

Antimicrobial resistance (AR) is one of the greatest threats to global health and is associated with higher treatment costs, longer hospital stays, and increased mortality. Current gold standard antimicrobial susceptibility tests (AST) rely on organism growth rates that result in prolonged time-to-answer for slow growing organisms. Changes in the cellular transcriptome can be rapid in the presence of stressors such as antibiotic pressure, providing the opportunity to develop AST towards transcriptomic signatures. Here, we show that relative quantification of the recA gene is an indicator of pathogen susceptibly when select species are challenged with relevant concentrations of ciprofloxacin. We demonstrate that ciprofloxacin susceptible strains of Y. pestis and B. anthracis have significant increases in relative recA gene expression after 15 min of exposure while resistant strains show no significant differences. Building upon this data, we designed and optimized seven duplex RT-qPCR assays targeting the recA and 16S rRNA gene, response and housekeeping genes, respectively, for multiple biothreat and ESKAPE pathogens. Final evaluation of all seven duplex assays tested against 124 ciprofloxacin susceptible and resistant strains, including Tier 1 pathogens, demonstrated an overall categorical agreement compared to microbroth dilution of 97% using a defined cutoff. Testing pathogen strains commonly associated with urinary tract infections in contrived mock sample sets demonstrated an overall categorical agreement of 96%. These data indicate relative quantification of a single highly conserved gene accurately determines susceptibility for multiple bacterial species in response to ciprofloxacin.

Deep-Learning-Based Nanomechanical Vibration for Rapid and Label-Free Assay of Epithelial Mesenchymal Transition

Cancer is a profound danger to our life and health. The classification and related studies of epithelial and mesenchymal phenotypes of cancer cells are key scientific questions in cancer research. Here, we investigated cancer cell colonies from a mechanical perspective and developed an assay for classifying epithelial/mesenchymal cancer cell colonies using the biomechanical fingerprint in the form of "nanovibration" in combination with deep learning. The classification method requires only 1 s of vibration data and has a classification accuracy of nearly 92.5%. The method has also been validated for the screening of anticancer drugs. Compared with traditional methods, the method has the advantages of being nondestructive, label-free, and highly sensitive. Furthermore, we proposed a perspective that subcellular structure influences the amplitude and spectrum of nanovibrations and demonstrated it using experiments and numerical simulation. These findings allow internal changes in the cell colony to be manifested by nanovibrations. This work provides a perspective and an ancillary method for cancer cell phenotype diagnosis and promotes the study of biomechanical mechanisms of cancer progression.

Rapid and visual identification of β-lactamase subtypes for precision antibiotic therapy

The abuse of antibiotics urgently requires rapid identification of drug-resistant bacteria at the point of care (POC). Here we report a visual paper sensor that allows rapid (0.25-3 h) discrimination of the subtypes of β-lactamase (the major cause of bacterial resistance) for precision antibiotic therapy. The sensor exhibits high performance in identifying antibiotic-resistant bacteria with 100 real samples from patients with diverse bacterial infections, demonstrating 100% clinical sensitivity and specificity. Further, this sensor can enhance the accuracy of antibiotic use from 48% empirically to 83%, and further from 50.6% to 97.6% after eliminating fungal infection cases. Our work provides a POC testing platform for guiding effective management of bacterial infections in both hospital and community settings.

Antimicrobial susceptibility testing using infrared attenuated total reflection (IR-ATR) spectroscopy to monitor metabolic activity

Fast and accurate detection of antimicrobial resistance in pathogens remains a challenge, and with the increase in antimicrobial resistance due to mis- and overuse of antibiotics, it has become an urgent public health problem. We demonstrate how infrared attenuated total reflection (IR-ATR) can be used as a simple method for assessment of bacterial susceptibility to antibiotics. This is achieved by monitoring the metabolic activities of bacterial cells via nutrient consumption and using this as an indicator of bacterial viability. Principal component analysis of the obtained spectra provides a tool for fast and simple discrimination of antimicrobial resistance in the acquired data. We demonstrate this concept using four bacterial strains and four different antibiotics, showing that the change in glucose concentration in the growth medium after 2 h, as monitored by IR-ATR, can be used as a spectroscopic diagnostic technique, to reduce detection time and to improve quality in the assessment of antimicrobial resistance in pathogens.

Mechanical Properties and Nanomotion of BT-20 and ZR-75 Breast Cancer Cells Studied by Atomic Force Microscopy and Optical Nanomotion Detection Method

Cells of two molecular genetic types of breast cancer-hormone-dependent breast cancer (ZR-75 cell line) and triple-negative breast cancer (BT-20 cell line)-were studied using atomic force microscopy and an optical nanomotion detection method. Using the Peak Force QNM and Force Volume AFM modes, we revealed the unique patterns of the dependence of Young's modulus on the indentation depth for two cancer cell lines that correlate with the features of the spatial organization of the actin cytoskeleton. Within a 200-300 nm layer just under the cell membrane, BT-20 cells are stiffer than ZR-75 cells, whereas in deeper cell regions, Young's modulus of ZR-75 cells exceeds that of BT-20 cells. Two cancer cell lines also displayed a difference in cell nanomotion dynamics upon exposure to cytochalasin D, a potent actin polymerization inhibitor. The drug strongly modified the nanomotion pattern of BT-20 cells, whereas it had almost no effect on the ZR-75 cells. We are confident that nanomotion monitoring and measurement of the stiffness of cancer cells at various indentation depths deserve further studies to obtain effective predictive parameters for use in clinical practice.

Intracellular Dynamics-Resolved Label-Free Scattering Reveals Real-Time Metabolism of Single Bacteria

Nanoscopic investigation of bacterial cells is essential to reveal their physiological status, impacting all cellular functions. Currently, this requires labeled probes or targeted staining procedures. Herein, we report a new bacterial feature, intracellular dynamics-resolved Rayleigh scattering (IDRS), that visualizes spatiotemporal cytoplasmic transitions in unlabeled bacteria and characterizes their real-time physiological status in 10 s. From single-bacterium IDRS signals, we discovered unique spatial patterns and their multiple transitions in Gram-negative and Gram-positive bacteria. The magnitude of IDRS signal variation highly correlated with the metabolic status of bacteria, differentiating persistent subpopulations. This is also the first report demonstrating distinct real-time metabolic conditions of unlabeled drug-resistant bacteria that are exposed to different doses of antibiotics. Our strategy opens up a way to simultaneously trace in situ metabolic and antibiotic resistance statuses, which can be applied in single-cell level control of bacterial metabolism and efficacy with a heterogeneous nature.

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.

Cavity Quantum Optomechanical Nonlinearities and Position Measurement beyond the Breakdown of the Linearized Approximation

Several optomechanics experiments are now entering the highly sought nonlinear regime where optomechanical interactions are large even for low light levels. Within this regime, new quantum phenomena and improved performance may be achieved; however, a corresponding theoretical formalism of cavity quantum optomechanics that captures the nonlinearities of both the radiation-pressure interaction and the cavity response is needed to unlock these capabilities. Here, we develop such a nonlinear cavity quantum optomechanical framework, which we then utilize to propose how position measurement can be performed beyond the breakdown of the linearized approximation. Our proposal utilizes optical general-dyne detection, ranging from single to dual homodyne, to obtain mechanical position information imprinted onto both the optical amplitude and phase quadratures and enables both pulsed and continuous modes of operation. These cavity optomechanical nonlinearities are now being confronted in a growing number of experiments, and our framework will allow a range of advances to be made in, e.g., quantum metrology, explorations of the standard quantum limit, and quantum measurement and control.

Correlating nanoscale motion and ATP production in healthy and favism erythrocytes: a real-time nanomotion sensor study

Introduction

Red blood cells (RBCs) are among the simplest, yet physiologically relevant biological specimens, due to their peculiarities, such as their lack of nucleus and simplified metabolism. Indeed, erythrocytes can be seen as biochemical machines, capable of performing a limited number of metabolic pathways. Along the aging path, the cells' characteristics change as they accumulate oxidative and non-oxidative damages, and their structural and functional properties degrade.

Methods

In this work, we have studied RBCs and the activation of their ATP-producing metabolism using a real-time nanomotion sensor. This device allowed time-resolved analyses of the activation of this biochemical pathway, measuring the characteristics and the timing of the response at different points of their aging and the differences observed in favism erythrocytes in terms of the cellular reactivity and resilience to aging. Favism is a genetic defect of erythrocytes, which affects their ability to respond to oxidative stresses but that also determines differences in the metabolic and structural characteristic of the cells.

Results

Our work shows that RBCs from favism patients exhibit a different response to the forced activation of the ATP synthesis compared to healthy cells. In particular, the favism cells, compared to healthy erythrocytes, show a greater resilience to the aging-related insults which was in good accord with the collected biochemical data on ATP consumption and reload.

Conclusion

This surprisingly higher endurance against cell aging can be addressed to a special mechanism of metabolic regulation that permits lower energy consumption in environmental stress conditions.

Fiber-integrated cantilever-based nanomechanical biosensors as a tool for rapid antibiotic susceptibility testing

There is an urgent need for developing rapid and affordable antibiotic susceptibility testing (AST) technologies to inhibit the overuse of antibiotics. In this study, a novel microcantilever nanomechanical biosensor based on Fabry-Pérot interference demodulation was developed for AST. To construct the biosensor, a cantilever was integrated with the single mode fiber in order to form the Fabry-Pérot interferometer (FPI). After the attachment of bacteria on the cantilever, the fluctuations of cantilever caused by the bacterial movements were detected by monitoring the changes of resonance wavelength in the interference spectrum. We applied this methodology to Escherichia coli and Staphylococcus aureus, showing the amplitude of cantilever's fluctuations was positively related on the quantity of bacteria immobilized on the cantilever and associated with the bacterial metabolism. The response of bacteria to antibiotics was dependent on the types of bacteria, the types and concentrations of antibiotics. Moreover, the minimum inhibitory and bactericidal concentrations for Escherichia coli were obtained within 30 minutes, demonstrating the capacity of this method for rapid AST. Benefiting from the simplicity and portability of the optical fiber FPI-based nanomotion detection device, the developed nanomechanical biosensor in this study provides a promising technique for AST and a more rapid alternative for clinical laboratories.

Magneto-Nanomechanical Array Biosensor for Ultrasensitive Detection of Oncogenic Exosomes for Early Diagnosis of Cancers

Exosomes are a class of nanoscale vesicles secreted by cells, which contain abundant information closely related to parental cells. The ultrasensitive detection of cancer-derived exosomes is highly significant for early non-invasive diagnosis of cancer. Here, an ultrasensitive nanomechanical sensor is reported, which uses a magnetic-driven microcantilever array to selectively detect oncogenic exosomes. A magnetic force, which can produce a far greater deflection of microcantilever than that produced by the intermolecular interaction force even with very low concentrations of target substances, is introduced. This method reduced the detection limit to less than 10 exosomes mL^-1 . Direct detection of exosomes in the serum of patients with breast cancer and in healthy people showed a significant difference. This work improved the sensitivity by five orders of magnitude as compared to that of traditional nanomechanical sensing based on surface stress mode. This method can be applied parallelly for highly sensitive detection of other microorganisms (such as bacteria and viruses) by using different probe molecules, which can provide a supersensitive detection approach for cancer diagnosis, food safety, and SARS-CoV-2 infection.

Achieving Ultrasensitive Chromogenic Probes for Rapid, Direct Detection of Carbapenemase-Producing Bacteria in Sputum

Carbapenemase-producing bacteria (CPB) stand as the most dangerous "superbugs" in the clinic. Rapid point-of-care (POC) detection of CPB in clinical samples is key to timely and effective infection management. We herein report the first ultrasensitive chromogenic probe that allows direct POC detection of CPB in clinical sputum samples at a sample-to-result time of less than 15 min. This chromogenic probe is modularly designed by conjugating the carbapenem core with a benzene derivative bearing an electronegativity-tunable substituent. Unexpectedly high sensitivity was achieved simply by choosing strong electron-withdrawing substituents, such as -N⁺(CH₃)₃, without resorting to complex molecular design. Through integrating the probes with a portable paper chip, 24 out of 80 clinical sputum samples from sepsis patients with lung infections were quickly diagnosed as CPB-positive, exhibiting 100% clinical sensitivity and specificity. This low-cost paper chip assay can be readily performed on-site, breaking through the dilemma of rapid CPB detection, especially in resource-limited settings.

Differences in bacteria nanomotion profiles and neutrophil nanomotion during phagocytosis

The main goal of this work is to highlight the connection between nanomotion and the metabolic activity of living cells. We therefore monitored the nanomotion of four different clinical strains of bacteria (prokaryotes) and the bacterial phagocytosis by neutrophil granulocytes (eukaryotes). All clinical strains of bacteria, regardless of their biochemical profile, showed pronounced fluctuations. Importantly, the nature of their nanomotions was different for the different strains. Flagellated bacteria (Escherichia coli, Proteus mirabilis) showed more pronounced movements than the non-flagellated forms (Staphylococcus aureus, Klebsiella pneumoniae). The unprimed neutrophil did not cause any difference in cantilever oscillations with control. However, in the process of phagocytosis of S. aureus (metabolically active state), a significant activation of neutrophil granulocytes was observed and cell nanomotions were maintained at a high level for up to 30 min of observation. These preliminary results indicate that nanomotion seems to be specific to different bacterial species and could be used to monitor, in a label free manner, basic cellular processes.

Mitochondrial nanomotion measured by optical microscopy

Nanometric scale size oscillations seem to be a fundamental feature of all living organisms on Earth. Their detection usually requires complex and very sensitive devices. However, some recent studies demonstrated that very simple optical microscopes and dedicated image processing software can also fulfill this task. This novel technique, termed as optical nanomotion detection (ONMD), was recently successfully used on yeast cells to conduct rapid antifungal sensitivity tests. In this study, we demonstrate that the ONMD method can monitor motile sub-cellular organelles, such as mitochondria. Here, mitochondrial isolates (from HEK 293 T and Jurkat cells) undergo predictable motility when viewed by ONMD and triggered by mitochondrial toxins, citric acid intermediates, and dietary and bacterial fermentation products (short-chain fatty acids) at various doses and durations. The technique has superior advantages compared to classical methods since it is rapid, possesses a single organelle sensitivity, and is label- and attachment-free.

Modulation of the nanoscale motion rate of Candida albicans by X-rays

Introduction

Patients undergoing cancer treatment by radiation therapy commonly develop Candida albicans infections (candidiasis). Such infections are generally treated by antifungals that unfortunately also induce numerous secondary effects in the patient. Additional to the effect on the immune system, ionizing radiation influences the vital activity of C. albicans cells themselves; however, the reaction of C. albicans to ionizing radiation acting simultaneously with antifungals is much less well documented. In this study, we explored the effects of ionizing radiation and an antifungal drug and their combined effect on C. albicans.

Methods

The study essentially relied on a novel technique, referred to as optical nanomotion detection (ONMD) that monitors the viability and metabolic activity of the yeast cells in a label and attachment-free manner.

Results and discussion

Our findings demonstrate that after exposure to X-ray radiation alone or in combination with fluconazole, low-frequency nanoscale oscillations of whole cells are suppressed and the nanomotion rate depends on the phase of the cell cycle, absorbed dose, fluconazole concentration, and post-irradiation period. In a further development, the ONMD method can help in rapidly determining the sensitivity of C. albicans to antifungals and the individual concentration of antifungals in cancer patients undergoing radiation therapy.

Half-wet nanomechanical sensors for cellular dynamics investigations

Testing devices based on cell tracking are particularly interesting as diagnostic tools in medicine for antibiotics susceptibility testing and in vitro chemotherapeutic screening. In this framework, the application of nanomechanical sensors has attracted much attention, although some crucial aspects such as the effects of the viscous damping, when operating in physiological conditions environment, still need to be properly solved. To address this problem, we have designed and fabricated a nanomechanical force sensor that operates at the interface between liquid and air. Our sensor consists of a silicon chip including a 500 μm wide Si₃N₄ suspended membrane where three rectangular silicon nitride cantilevers are defined by a lithographically etched gap. The cantilevers can be operated in air, fully immersed in a liquid environment and in half wetting condition, with one side in contact with the solution and the opposite one in air. The formation of a water meniscus in the gap prevents the leakage of medium to the opposite side, which remained dry and is used to reflect a laser to measure the cantilever deflection. This configuration enables to keep the cells in physiological environment while operating the sensor in dry conditions. The performance of the sensor has been applied to monitor the motion and measures the forces developed by migrating breast cancer cell. The functionalization of one side of the cantilever and the use of a purposely designed chamber of measurements enable the confinement of the cell only on one side of the cantilever. Our data demonstrate that this approach can distinguish the adhesion and contraction forces developed by different cell lines and may represents valuable tool for a fast and quantitative in-vitro screening of new chemotherapeutic drugs targeting cancer cell adhesion and motility.

Investigating nanomotion-based technology (Resistell AST) for rapid antibiotic susceptibility testing among adult patients admitted to a tertiary-care hospital with Gram-negative bacteraemia: protocol for a prospective, observational, cross-sectional, single-arm study

INTRODUCTION

Effective treatment of bloodstream infections (BSIs) is relying on rapid identification of the causing pathogen and its antibiotic susceptibility. Still, most commercially available antibiotic susceptibility testing (AST) methods are based on monitoring bacterial growth, thus impacting the time to results. The Resistell AST is based on a new technology measuring the nanomotion caused by physiologically active bacterial cells and detecting the changes in nanomotion caused by the exposure to a drug.

METHODS AND ANALYSIS

This is a single-centre, prospective, cross-sectional, single-arm diagnostic accuracy study to determine the agreement of the Resistell AST on Gram-negative bacteria isolated from blood cultures among patients admitted to a tertiary-care hospital with the reference method. Up to 300 patients will be recruited. Starting with a pilot phase, enrolling 10%-20% of the subjects and limited to Escherichia coli BSI tested for ceftriaxone susceptibility, the main phase will follow, extending the study to Klebsiella pneumoniae and ciprofloxacin.

ETHICS AND DISSEMINATION

This study has received ethical approval from the Swiss Ethics Committees (swissethics, project 2020-01622). All the case report forms and clinical samples will be assigned a study code by the local investigators and stored anonymously at the reference centre (Lausanne University Hospital). The results will be broadly distributed through conference presentations and peer-reviewed publications.

TRIAL REGISTRATION NUMBER

ClinicalTrials.gov Registry (NCT05002413).

Rapid Bacteria Detection from Patients' Blood Bypassing Classical Bacterial Culturing

Sepsis is a life-threatening condition mostly caused by a bacterial infection resulting in inflammatory reaction and organ dysfunction if not treated effectively. Rapid identification of the causing bacterial pathogen already in the early stage of bacteremia is therefore vital. Current technologies still rely on time-consuming procedures including bacterial culturing up to 72 h. Our approach is based on ultra-rapid and highly sensitive nanomechanical sensor arrays. In measurements we observe two clearly distinguishable distributions consisting of samples with bacteria and without bacteria respectively. Compressive surface stress indicates the presence of bacteria. For this proof-of-concept, we extracted total RNA from EDTA whole blood samples from patients with blood-culture-confirmed bacteremia, which is the reference standard in diagnostics. We determined the presence or absence of bacterial RNA in the sample through 16S-rRNA hybridization and species-specific probes using nanomechanical sensor arrays. Via both probes, we identified two clinically highly-relevant bacterial species i.e., Escherichia coli and Staphylococcus aureus down to an equivalent of 20 CFU per milliliter EDTA whole blood. The dynamic range of three orders of magnitude covers most clinical cases. We correctly identified all patient samples regarding the presence or absence of bacteria. We envision our technology as an important contribution to early and sensitive sepsis diagnosis directly from blood without requirement for cultivation. This would be a game changer in diagnostics, as no commercial PCR or POCT device currently exists who can do this.

Hemolysis-Inspired, Highly Sensitive, Label-Free IgM Detection Using Erythrocyte Membrane-Functionalized Nanomechanical Resonators

Immunoglobulin detection is important for immunoassays, such as diagnosing infectious diseases, evaluating immune status, and determining neutralizing antibody concentrations. However, since most immunoassays rely on labeling methods, there are limitations on determining the limit of detection (LOD) of biosensors. In addition, although the antigen must be immobilized via complex chemical treatment, it is difficult to precisely control the immobilization concentration. This reduces the reproducibility of the biosensor. In this study, we propose a label-free method for antibody detection using microcantilever-based nanomechanical resonators functionalized with erythrocyte membrane (EM). This label-free method focuses on the phenomenon of antibody binding to oligosaccharides (blood type antigen) on the surface of the erythrocyte. We established a method for extracting the EM from erythrocytes and fabricated an EM-functionalized microcantilever (MC), termed EMMC, by surface-coating EM layers on the MC. When the EMMC was treated with immunoglobulin M (IgM), the bioassay was successfully performed in the linear range from 2.2 pM to 22 nM, and the LOD was 2.0 pM. The EMMC also exhibited excellent selectivity compared to other biomolecules such as serum albumin, γ-globulin, and IgM with different paratopes. These results demonstrate that EMMC-based nanotechnology may be utilized in criminal investigations to identify blood types with minimal amounts of blood or to evaluate individual immunity through virus-neutralizing antibody detection.

Microfluidics for antibiotic susceptibility testing

The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.

Measuring Single Bacterial Viability in Optical Traps with a Power Sweeping Technique

Assessing bacterial viability is crucial in public health, food safety, environmental microbiology, and other relevant fields. The classical agar plate counting method and the popular dye-based assays have shown their strengths, but they also have limitations including high time consumption, relatively complex sample preparations, and cytotoxicity. In this work, we present a new bacterial viability assay based on optical tweezers utilizing a power sweeping strategy. By monitoring and analyzing bacterial nanomotion in optical traps under different trapping laser powers, the slope of the proportionality between the quantified extent of motion and the trapping laser power was defined as the mobility restriction coefficient (MRC) to quantify bacterial viability. We first established a firm correlation between the viability and MRC by measuring alive and dead Escherichia coli and Photobacterium phosphoreum. Then the capability of real-time long-term characterization of the assay was validated by measuring the viability of individual P. phosphoreum while regulating the viability with an inactivation light. Notably, a 'spinning-induced stabilization' mechanism was proposed to explain the surprising increase of apparent bacterial mobility after inactivation. Overall, the assay was proved to be a reliable label-free bacterial viability assay at a single-cell level, which holds potential in antibiotic susceptibility testing, drug screening, and rapid diagnostics.

Stress Analysis and Q-Factor of Free-Standing (La,Sr)MnO3 Oxide Resonators

High-sensitivity nanomechanical sensors are mostly based on silicon technology and related materials. The use of functional materials, such as complex oxides having strong interplay between structural, electronic, and magnetic properties, may open possibilities for developing new mechanical transduction schemes and for further enhancement of the device performances. The integration of these materials into micro/nano-electro-mechanical systems (MEMS/NEMS) is still at its very beginning and critical basic aspects related to the stress state and the quality factors of mechanical resonators made from epitaxial oxide thin films need to be investigated. Here, suspended micro-bridges are realized from single-crystal thin films of (La_0.7 ,Sr_0.3 )MnO₃ (LSMO), a prototypical complex oxide showing ferromagnetic ground state at room temperature. These devices are characterized in terms of resonance frequency, stress state, and Q-factor. LSMO resonators are highly stressed, with a maximum value of ≈260 MPa. The temperature dependence of their mechanical resonance is discussed considering both thermal strain and the temperature-dependent Young's modulus. The measured Q-factors reach few tens of thousands at room temperature, with indications of further improvements by optimizing the fabrication protocols. These results demonstrate that complex oxides are suitable to realize high Q-factor mechanical resonators, paving the way toward the development of full-oxide MEMS/NEMS sensors.

Rapid and label-free identification of single foodborne pathogens using microfluidic pore sensors

Foodborne pathogenic microorganisms have become major threats that endanger human life and health. The current technology cannot perform rapid screening of foodborne pathogenic bacteria, and fail to timely control food safety risks. Here, we develop a novel microfluidic sensor for real-time and label-free bacteria classification at the single-cell level. Concretely, a low-aspect-ratio SiN micropore with PDMS coating was fabricated, which could significantly reduce the noise of the sensing system, and makes the microfluidic pore sensor sensitive to bacteria discrimination. The prepared SiN micropore equipped with the high temporal-spatial resolution was applied to observe bacterial translocation “events” and the current pulse signals could be obtained, which depend on the size, charge, and morphology of the target bacteria. According to the variation of the current pulse signals produced by different bacteria across the micropore, three common foodborne pathogens such as Salmonella enteric, Listeria monocytogenes, and Escherichia coli were identified. Due to convenience, rapidity, and accuracy, the label-free method we report here has great potential for the identification of diverse foodborne microorganisms at single-cell sensitivity.

Living Sample Viability Measurement Methods from Traditional Assays to Nanomotion

Living sample viability measurement is an extremely common process in medical, pharmaceutical, and biological fields, especially drug pharmacology and toxicology detection. Nowadays, there are a number of chemical, optical, and mechanical methods that have been developed in response to the growing demand for simple, rapid, accurate, and reliable real-time living sample viability assessment. In parallel, the development trend of viability measurement methods (VMMs) has increasingly shifted from traditional assays towards the innovative atomic force microscope (AFM) oscillating sensor method (referred to as nanomotion), which takes advantage of the adhesion of living samples to an oscillating surface. Herein, we provide a comprehensive review of the common VMMs, laying emphasis on their benefits and drawbacks, as well as evaluating the potential utility of VMMs. In addition, we discuss the nanomotion technique, focusing on its applications, sample attachment protocols, and result display methods. Furthermore, the challenges and future perspectives on nanomotion are commented on, mainly emphasizing scientific restrictions and development orientations.

Performance Evaluation of the Quantamatrix QMAC-dRAST System for Rapid Antibiotic Susceptibility Testing Directly from Blood Cultures

Objectives: Rapid antibiotic susceptibility testing (AST) for positive blood cultures can improve patient clinical outcomes if the time to an effective antimicrobial therapy is shortened. In this study, we tested the Quantamatrix dRAST system (QMAC-dRAST), a rapid AST system based on time-lapse microscopic imagery of bacterial colony formation in agarose. Methods: Evaluation of the QMAC-dRAST was performed from 250 monobacterial blood cultures including 130 Enterobacterales, 20 non-fermentative Gram-negative bacteria, 69 staphylococci and 31 enterococci. Blood cultures were recovered from anonymous patients or from spiking experiments to enrich our study with bacterial species and resistant strains. Categorical agreement (CA), minor errors (me), major errors (ME) and very major errors (VME) were calculated in comparison to the results obtained from the BD Phoenix™ M50. Discrepancies between the Phoenix™ M50 and QMAC-dRAST results were investigated using the gradient strip method. The repeatability and reproducibility performance of the QMAC-dRAST was assessed for 16 strains, each strain being tested five times from a spiked blood culture. Results: The overall CAs for Enterobacterales, non-fermentative Gram-negative bacteria, staphylococci and enterococci were 95.1%, 91.2%, 93.4% and 94.5%, respectively. The VME percentage was below 4% for all the groups except for staphylococci, which showed a VME rate of 7%. The median time to result was 6.7 h (range: 4.7–7.9). Repeatability and reproducibility assays showed a high reliability of AST results with best and worst ratios of 98.8% and 99.6% and 95.0% and 98.3%, respectively. Conclusions: The QMAC-dRAST is a fast and reliable system to determine AST directly from monobacterial blood cultures with a major TAT reduction compared to conventional AST testing.

Nanotechnology Approaches for Rapid Detection and Theranostics of Antimicrobial Resistant Bacterial Infections

As declared by WHO, antimicrobial resistance (AMR) is a high priority issue with a pressing need to develop impactful technologies to curb it. The rampant and inappropriate use of antibiotics due to the lack of adequate and timely diagnosis is a leading cause behind AMR evolution. Unfortunately, populations with poor economic status and those residing in densely populated areas are the most affected ones, frequently leading to emergence of AMR pathogens. Classical approaches for AMR diagnostics like phenotypic methods, biochemical assays, and molecular techniques are cumbersome and resource-intensive and involve a long turnaround time to yield confirmatory results. In contrast, recent emergence of nanotechnology-assisted approaches helps to overcome challenges in classical approaches and offer simpler, more sensitive, faster, and more affordable solutions for AMR diagnostics. Nanomaterial platforms (metallic, quantum-dot, carbon-based, upconversion, etc.), nanoparticle-based rapid point-of-care platforms, nano-biosensors (optical, mechanical, electrochemical), microfluidic-assisted devices, and importantly, nanotheranostic devices for diagnostics with treatment of AMR infections are examples of rapidly growing nanotechnology approaches used for AMR management. This review comprehensively summarizes the past 10 years of research progress on nanotechnology approaches for AMR diagnostics and for estimating antimicrobial susceptibility against commonly used antibiotics. This review also highlights several bottlenecks in nanotechnology approaches that need to be addressed prior to considering their translation to clinics.

Ultrasensitive detection of local acoustic vibrations at room temperature by plasmon-enhanced single-molecule fluorescence

Sensitive detection of local acoustic vibrations at the nanometer scale has promising potential applications involving miniaturized devices in many areas, such as geological exploration, military reconnaissance, and ultrasound imaging. However, sensitive detection of weak acoustic signals with high spatial resolution at room temperature has become a major challenge. Here, we report a nanometer-scale system for acoustic detection with a single molecule as a probe based on minute variations of its distance to the surface of a plasmonic gold nanorod. This system can extract the frequency and amplitude of acoustic vibrations with experimental and theoretical sensitivities of 10 pm Hz^−1/2 and 10 fm Hz^−1/2, respectively. This approach provides a strategy for the optical detection of acoustic waves based on molecular spectroscopy without electromagnetic interference. Moreover, such a small nano-acoustic detector with 40-nm size can be employed to monitor acoustic vibrations or read out the quantum states of nanomechanical devices.

.Sensitive detection of weak acoustic signals at nanometer scale is challenging. Here, the authors present an acoustic detection system based on a single molecule as a probe, where frequency and amplitude of acoustic vibrations can be extracted from its minute variations in distance to the surface of a plasmonic gold nanorod.

Probing nanomotion of single bacteria with graphene drums

Motion is a key characteristic of every form of life¹. Even at the microscale, it has been reported that colonies of bacteria can generate nanomotion on mechanical cantilevers², but the origin of these nanoscale vibrations has remained unresolved^3,4. Here, we present a new technique using drums made of ultrathin bilayer graphene, where the nanomotion of single bacteria can be measured in its aqueous growth environment. A single Escherichia coli cell is found to generate random oscillations with amplitudes of up to 60 nm, exerting forces of up to 6 nN to its environment. Using mutant strains that differ by single gene deletions that affect motility, we are able to pinpoint the bacterial flagella as the main source of nanomotion. By real-time tracing of changes in nanomotion on administering antibiotics, we demonstrate that graphene drums can perform antibiotic susceptibility testing with single-cell sensitivity. These findings deepen our understanding of processes underlying cellular dynamics, and pave the way towards high-throughput and parallelized rapid screening of the effectiveness of antibiotics in bacterial infections with graphene devices.

Measurement of the low-frequency charge noise of bacteria

Bacteria meticulously regulate their intracellular ion concentrations and create ionic concentration gradients across the bacterial membrane. These ionic concentration gradients provide free energy for many cellular processes and are maintained by transmembrane transport. Given the physical dimensions of a bacterium and the stochasticity in transmembrane transport, intracellular ion concentrations and hence the charge state of a bacterium are bound to fluctuate. Here we investigate the charge noise of hundreds of nonmotile bacteria by combining electrical measurement techniques from condensed matter physics with microfluidics. In our experiments, bacteria in a microchannel generate charge density fluctuations in the embedding electrolyte due to random influx and efflux of ions. Detected as electrical resistance noise, these charge density fluctuations display a power spectral density proportional to 1/f^{2} for frequencies 0.05Hz≤f≤1Hz. Fits to a simple noise model suggest that the steady-state charge of a bacterium fluctuates by ±1.30×10^{6}e(e≈1.60×10^{-19}C), indicating that bacterial ion homeostasis is highly dynamic and dominated by strong charge noise. The rms charge noise can then be used to estimate the fluctuations in the membrane potential; however, the estimates are unreliable due to our limited understanding of the intracellular concentration gradients.

The Dynamics of Single-Cell Nanomotion Behaviour of Saccharomyces cerevisiae in a Microfluidic Chip for Rapid Antifungal Susceptibility Testing

The fast emergence of multi-resistant pathogenic yeasts is caused by the extensive—and sometimes unnecessary—use of broad-spectrum antimicrobial drugs. To rationalise the use of broad-spectrum antifungals, it is essential to have a rapid and sensitive system to identify the most appropriate drug. Here, we developed a microfluidic chip to apply the recently developed optical nanomotion detection (ONMD) method as a rapid antifungal susceptibility test. The microfluidic chip contains no-flow yeast imaging chambers in which the growth medium can be replaced by an antifungal solution without disturbing the nanomotion of the cells in the imaging chamber. This allows for recording the cellular nanomotion of the same cells at regular time intervals of a few minutes before and throughout the treatment with an antifungal. Hence, the real-time response of individual cells to a killing compound can be quantified. In this way, this killing rate provides a new measure to rapidly assess the susceptibility of a specific antifungal. It also permits the determination of the ratio of antifungal resistant versus sensitive cells in a population.

d-Amino Acid-Based Metabolic Labeling Enables a Fast Antibiotic Susceptibility Test of Both Isolated Bacteria and Bronchoalveolar Lavage Fluid

The threat of multidrug-resistant bacteria has escalated rapidly, increasing the demand for accurate antibiotic susceptibility tests (ASTs). Traditional bacterial growth yield-based ASTs often take overnight to report, delaying the timely guidance of antibiotic use. Here, a fluorescent d-amino acid (FDAA) labeling-based AST (FaAST) is reported, which can quickly provide accurate minimum inhibitory concentrations (MICs). The FDAA-labeling signals that reflect the bacterial metabolic status underlie the flow cytometry-based strategy for MIC determination. Resistant bacteria show a reluctant decline in FDAA-labeling (inhibited metabolism) after treatment with the corresponding antibiotics, whereas susceptible bacteria demonstrate quick responses to low doses of drugs. The MICs are determined based on the changing trends in labeling. After testing 23 clinical isolates and laboratory strains of the most critical drug-resistant bacteria against a panel of representative antibiotics, FaAST shows a high susceptibility category with an accuracy of 98.13%. Moreover, FaAST can also make quick and accurate diagnosis against bronchoalveolar lavage fluids collected from hospital-acquired pneumonia patients, saving 2-4 days in guiding antibiotic use for this life-threatening infection. Thus, the speed, accuracy, and broad applicability of FaAST will be valuable in informing antibiotic decisions when treating critical infections caused by drug-resistant bacteria.

Direct Color Observation of Light-Driven Molecular Conformation-Induced Stress

Although usually complex to handle, nanomechanical sensors are exceptional, label-free tools for monitoring molecular conformational changes, which makes them of paramount importance in understanding biomolecular interactions. Herein, a simple and inexpensive mechanical imaging approach based on low-stiffness cantilevers with structural coloration (mechanochromic cantilevers (MMC)) is demonstrated, able to monitor and quantify molecular conformational changes with similar sensitivity to the classical optical beam detection method of cantilever-based sensors (≈4.6 × 10^-3  N m^-1 ). This high sensitivity is achieved by using a white light and an RGB camera working in the reflection configuration. The sensor performance is demonstrated by monitoring the UV-light induced reversible conformational changes of azobenzene molecules coating. The trans-cis isomerization of the azobenzene molecules induces a deflection of the cantilevers modifying their diffracted color, which returns to the initial state by cis-trans relaxation. Interestingly, the mechanical imaging enables a simultaneous 2D mapping of the response thus enhancing the spatial resolution of the measurements. A tight correlation is found between the color output and the cantilever's deflection and curvature angle (sensitivities of 5 × 10^-3  Hue µm^-1 and 1.5 × 10^-1  Hue (°)^-1 ). These findings highlight the suitability of low-stiffness MMC as an enabling technology for monitoring molecular changes with unprecedented simplicity, high-throughput capability, and functionalities.

Biosensors and Point-of-Care Devices for Bacterial Detection: Rapid Diagnostics Informing Antibiotic Therapy

With an exponential rise in antimicrobial resistance and stagnant antibiotic development pipeline, there is, more than ever, a crucial need to optimize current infection therapy approaches. One of the most important stages in this process requires rapid and effective identification of pathogenic bacteria responsible for diseases. Current gold standard techniques of bacterial detection include culture methods, polymerase chain reactions, and immunoassays. However, their use is fraught with downsides with high turnaround time and low accuracy being the most prominent. This imposes great limitations on their eventual application as point-of-care devices. Over time, innovative detection techniques have been proposed and developed to curb these drawbacks. In this review, a systematic summary of a range of biosensing platforms is provided with a strong focus on technologies conferring high detection sensitivity and specificity. A thorough analysis is performed and the benefits and drawbacks of each type of biosensor are highlighted, the factors influencing their potential as point-of-care devices are discussed, and the authors' insights for their translation from proof-of-concept systems into commercial medical devices are provided.

Combinatorial nanodroplet platform for screening antibiotic combinations

The emergence and spread of multidrug resistant bacterial strains and concomitant dwindling of effective antibiotics pose worldwide healthcare challenges. To address these challenges, advanced engineering tools are developed to personalize antibiotic treatments by speeding up the diagnostics that is critical to prevent antibiotic misuse and overuse and make full use of existing antibiotics. Meanwhile, it is necessary to investigate novel antibiotic strategies. Recently, repurposing mono antibiotics into combinatorial antibiotic therapies has shown great potential for treatment of bacterial infections. However, widespread adoption of drug combinations has been hindered by the complexity of screening techniques and the cost of reagent consumptions in practice. In this study, we developed a combinatorial nanodroplet platform for automated and high-throughput screening of antibiotic combinations while consuming orders of magnitude lower reagents than the standard microtiter-based screening method. In particular, the proposed platform is capable of creating nanoliter droplets with multiple reagents in an automatic manner, tuning concentrations of each component, performing biochemical assays with high flexibility (e.g., temperature and duration), and achieving detection with high sensitivity. A biochemical assay, based on the reduction of resazurin by the metabolism of bacteria, has been characterized and employed to evaluate the combinatorial effects of the antibiotics of interest. In a pilot study, we successfully screened pairwise combinations between 4 antibiotics for a model Escherichia coli strain.

A Cascaded Droplet Microfluidic Platform Enables High-Throughput Single Cell Antibiotic Susceptibility Testing at Scale

The global threat of antibiotic resistance underscores critical but unmet needs for rapid antibiotic susceptibility testing (AST) technologies. To this end, droplet microfluidic-based single-cell AST offers promise by achieving unprecedented rapidity, but its potential for clinical use is marred by the capacity of testing one to few antibiotic conditions per device, which falls short from the required scale in clinically relevant scenarios. To lift the scalability constraint in rapid single-cell AST technologies, a new cascaded droplet microfluidic platform that can streamline bacteria/antibiotic mixing, single-cell encapsulation within picoliter droplets, incubation, and detection in a continuous, assembly-line-like workflow is developed. The scalability of the platform is demonstrated by generating 32 groups of ≈10 000 droplets with custom antibiotic conditions within a single device, from which a new statistics-based method is used to analyze the single cell data and produce clinically useful antibiograms with minimum inhibitory concentrations in ≈90 min for the first antibiotic, plus 2 min for each subsequent antibiotic condition. Potential clinical utility of this platform is demonstrated by testing three clinical isolates and eight urine specimens against four frequently used antibiotics, and 100% and 93.8% categorical agreements are achieved compared to laboratory-based results that became available after 48 h.

Antimicrobial susceptibility testing by measuring bacterial oxygen consumption on an integrated platform

Cellular respiration is a fundamental feature of metabolic activity and oxygen consumption can be considered as a reliable indicator of bacterial aerobic respiration, including for facultative anaerobic bacteria like E. coli. Addressing the emerging global health challenge of antimicrobial resistance, we performed antimicrobial susceptibility testing using the bacterial oxygen consumption rate (OCR) as a phenotypic indicator. We demonstrated that microbial exposure to antibiotics showed systematic OCR variations, which enabled determining minimum inhibitory concentrations for three clinically relevant antibiotics, ampicillin, ciprofloxacin, and gentamicin, within a few hours. Our study was performed by using photoluminescence-based oxygen sensing in a microchamber format, which enabled reducing the sample volume to a few hundred microliters. OCR modeling based on exponential bacterial growth allowed estimating the bacterial doubling time for various culture conditions (different types of media, different culture temperature and antibiotic concentrations). Furthermore, correlating metabolic heat production data, as obtained by nanocalorimetry in the same type of microchamber, and OCR measurements provided further insight on the actual metabolic state and activity of a microbial sample. This approach represents a new path towards more comprehensive microbiological studies performed on integrated miniaturized systems.

Advances in Antimicrobial Resistance Monitoring Using Sensors and Biosensors: A Review

The indiscriminate use and mismanagement of antibiotics over the last eight decades have led to one of the main challenges humanity will have to face in the next twenty years in terms of public health and economy, i.e., antimicrobial resistance. One of the key approaches to tackling antimicrobial resistance is clinical, livestock, and environmental surveillance applying methods capable of effectively identifying antimicrobial non-susceptibility as well as genes that promote resistance. Current clinical laboratory practices involve conventional culture-based antibiotic susceptibility testing (AST) methods, taking over 24 h to find out which medication should be prescribed to treat the infection. Although there are techniques that provide rapid resistance detection, it is necessary to have new tools that are easy to operate, are robust, sensitive, specific, and inexpensive. Chemical sensors and biosensors are devices that could have the necessary characteristics for the rapid diagnosis of resistant microorganisms and could provide crucial information on the choice of antibiotic (or other antimicrobial medicines) to be administered. This review provides an overview on novel biosensing strategies for the phenotypic and genotypic determination of antimicrobial resistance and a perspective on the use of these tools in modern health-care and environmental surveillance.

Color-Coded Droplets and Microscopic Image Analysis for Multiplexed Antibiotic Susceptibility Testing

Since the discovery of antibiotics, the emergence of antibiotic resistance has become a global issue that is threatening society. In the era of antibiotic resistance, finding the proper antibiotics through antibiotic susceptibility testing (AST) is crucial in clinical settings. However, the current clinical process of AST based on the broth microdilution test has limitations on scalability to expand the number of antibiotics that are tested with various concentrations. Here, we used color-coded droplets to expand the multiplexing of AST regarding the kind and concentration of antibiotics. Color type and density differentiate the kind of antibiotics and concentration, respectively. Microscopic images of a large view field contain numbers of droplets with different testing conditions. Image processing analysis detects each droplet, decodes color codes, and measures the bacterial growth in the droplet. Testing E. coli ATCC 25922 with ampicillin, gentamicin, and tetracycline shows that the system can provide a robust and scalable platform for multiplexed AST. Furthermore, the system can be applied to various drug testing systems, which require several different testing conditions.

Nanomotion Spectroscopy as a New Approach to Characterize Bacterial Virulence

Atomic force microscopy (AFM)-based nanomotion detection is a label-free technique that has been used to monitor the response of microorganisms to antibiotics in a time frame of minutes. The method consists of attaching living organisms onto an AFM cantilever and in monitoring its nanometric scale oscillations as a function of different physical-chemical stimuli. Up to now, we only used the cantilever oscillations variance signal to assess the viability of the attached organisms. In this contribution, we demonstrate that a more precise analysis of the motion pattern of the cantilever can unveil relevant medical information about bacterial phenotype. We used B. pertussis as the model organism, it is a slowly growing Gram-negative bacteria which is the agent of whooping cough. It was previously demonstrated that B. pertussis can expresses different phenotypes as a function of the physical-chemical properties of the environment. In this contribution, we highlight that B. pertussis generates a cantilever movement pattern that depends on its phenotype. More precisely, we noticed that nanometric scale oscillations of B. pertussis can be correlated with the virulence state of the bacteria. The results indicate a correlation between metabolic/virulent bacterial states and bacterial nanomotion pattern and paves the way to novel rapid and label-free pathogenic microorganism detection assays.

Nanomechanical sensor for rapid and ultrasensitive detection of tumor markers in serum using nanobody

Early cancer diagnosis requires ultrasensitive detection of tumor markers in blood. To this end, we develop a novel microcantilever immunosensor using nanobodies (Nbs) as receptors. As the smallest antibody (Ab) entity comprising an intact antigen-binding site, Nbs achieve dense receptor layers and short distances between antigen-binding regions and sensor surfaces, which significantly elevate the generation and transmission of surface stress. Owing to the inherent thiol group at the C-terminus, Nbs are covalently immobilized on microcantilever surfaces in directed orientation via one-step reaction, which further enhances the stress generation. For microcantilever-based nanomechanical sensor, these advantages dramatically increase the sensor sensitivity. Thus, Nb-functionalized microcantilevers can detect picomolar concentrations of tumor markers with three orders of magnitude higher sensitivity, when compared with conventional Ab-functionalized microcantilevers. This proof-of-concept study demonstrates an ultrasensitive, label-free, rapid, and low-cost method for tumor marker detection. Moreover, interestingly, we find Nb inactivation on sensor interfaces when using macromolecule blocking reagents. The adsorption-induced inactivation is presumably caused by the change of interfacial properties, due to binding site occlusion upon complex coimmobilization formations. Our findings are generalized to any coimmobilization methodology for Nbs and, thus, for the construction of high-performance immuno-surfaces.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (experimental section, HER2 detection using anti-HER2-mAb-functionalized microcantilevers) is available in the online version of this article at 10.1007/s12274-021-3588-4.

Multimodal real-time frequency tracking of cantilever arrays in liquid environment for biodetection: Comprehensive setup and performance analysis

We present a nanomechanical platform for real-time quantitative label-free detection of target biomolecules in a liquid environment with mass sensitivity down to few pg. Newly fabricated arrays of up to 18 cantilevers are integrated in a micromachined fluidic chamber, connected to software-controlled fluidic pumps for automated sample injections. We discuss two functionalization approaches to independently sensitize the interface of different cantilevers. A custom piezo-stack actuator and optical readout system enable the measurement of resonance frequencies up to 2 MHz. We implement a new measurement strategy based on a phase-locked loop (PLL), built via in-house developed software. The PLL allows us to track, within the same experiment, the evolution of resonance frequency over time of up to four modes for all the cantilevers in the array. With respect to the previous measurement technique, based on standard frequency sweep, the PLL enhances the estimated detection limit of the device by a factor of 7 (down to 2 pg in 5 min integration time) and the time resolution by more than threefold (below 15 s), being on par with commercial gold-standard techniques. The detection limit and noise of the new setup are investigated via Allan deviation and standard deviation analysis, considering different resonance modes and interface chemistries. As a proof-of-concept, we show the immobilization and label-free in situ detection of live bacterial cells (E. coli), demonstrating qualitative and quantitative agreement in the mechanical response of three different resonance modes.