Cantilever Sensors for Rapid Optical Antimicrobial Sensitivity Testing

Ultra-Sensitive Biosensors for Medical Applications Based on Nanomechanics: From Detection of Synthetic Biomolecules to Analysis of Sepsis in Pediatric Patients

Recent advancements in nanomechanical microcantilever biosensors open new possibilities for clinical applications, permitting precise analysis of molecular interactions. The technology enables tracking gene expression, molecular conformational changes, antibody binding and antibiotic resistance. In particular, hybridization of DNA or RNA extracted from biopsies and whole blood from patients has led to significant advancements in diagnostics of critical medical conditions, e.g., cancer, bacteraemia and sepsis, utilizing rapid, sensitive, and label-free detection. Direct diagnosis from patient samples is a decisive advantage over competitive methods circumventing elaborate and time-consuming purification, amplification and cultivation procedures prior to analysis. Here, recent developments are presented from simple DNA hybridization of synthesized oligonucleotides to RNA material obtained from patients' blood samples, highlighting technological advancements in diagnostic applications, such as detection of pathogens and disease biomarkers. We envisage our method to be a significant input to rapid, early and sensitive diagnosis directly from patients' blood without requirements for amplification or cultivation. This would represent a paradigm shift in diagnostics, as no competing method currently exists.

Next-generation rapid phenotypic antimicrobial susceptibility testing

Slow progress towards implementation of conventional clinical bacteriology in low resource settings and strong interest in greater speed for antimicrobial susceptibility testing (AST) more generally has focused attention on next-generation rapid AST technologies. In this Review, we systematically synthesize publications and submissions to regulatory agencies describing technologies that provide phenotypic AST faster than conventional methods. We characterize over ninety technologies in terms of underlying technical innovations, technology readiness level, extent of clinical validation, and time-to-results. This work provides a guide for technology developers and clinical microbiologists to understand the rapid phenotypic AST technology landscape, current development pipeline, and AST-specific validation milestones.

Label-free single-cell antimicrobial susceptibility testing in droplets with concentration gradient generation

Bacterial communities exhibit significant heterogeneity, resulting in the emergence of specialized phenotypes that can withstand antibiotic exposure. Unfortunately, the existence of subpopulations resistant to antibiotics often goes unnoticed during treatment initiation. Thus, it is crucial to consider the concept of single-cell antibiotic susceptibility testing (AST) to tackle bacterial infections. Nevertheless, its practical application in clinical settings is hindered by its inability to conduct AST efficiently across a wide range of antibiotics and concentrations. This study introduces a droplet-based microfluidic platform designed for rapid single-cell AST by creating an antibiotic concentration gradient. The advantage of a microfluidic platform is achieved by executing bacteria and antibiotic mixing, cell encapsulation, incubation, and enumeration of bacteria in a seamless workflow, facilitating susceptibility testing of each antibiotic. Firstly, we demonstrate the rapid determination of minimum inhibitory concentration (MIC) of several antibiotics with Gram-negative E. coli and Gram-positive S. aureus, which enables us to bypass the time-consuming bacteria cultivation, speeding up the AST in 3 h from 1 to 2 days of conventional methods. Additionally, we assess 10 clinical isolates including methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant Staphylococcus aureus (MDRSA) against clinically important antibiotics for analyzing the MIC, compared to the gold standard AST method from the United States Clinical and Laboratory Standards Institute (CLSI), which becomes available only after 48 h. Furthermore, by monitoring single cells within individual droplets, we have found a spectrum of resistance levels among genetically identical cells, revealing phenotypic heterogeneity within isogenic populations. This discovery not only advances clinical diagnostics and treatment strategies but also significantly contributes to the field of antibiotic stewardship, underlining the importance of our approach in addressing bacterial resistance.

Mass and Stiffness Deconvolution in Nanomechanical Resonators for Precise Mass Measurement and In Vivo Biosensing

Nanomechanical sensors, due to their small size and high sensitivity to the environment, hold significant promise for various sensing applications. These sensors enable rapid, highly sensitive, and selective detection of biological and biochemical entities as well as mass spectrometry by utilizing the frequency shift of nanomechanical resonators. Nanomechanical systems have been employed to measure the mass of cells and biomolecules and study the fundamentals of surface science such as phase transitions and diffusion. Here, we develop a methodology using both experimental measurements and numerical simulations to explore the characteristics of nanomechanical resonators when the detection entities are absorbed on the cantilever surface and quantify the mass, density, and Young's modulus of adsorbed entities. Moreover, based on this proposed concept, we present an experimental method for measuring the mass of molecules and living biological entities in their physiological environment. This approach could find applications in predicting the behavior of bionanoelectromechanical resonators functionalized with biological capture molecules, as well as in label-free, nonfunctionalized micro/nanoscale biosensing and mass spectrometry of living bioentities.

Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria

Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The method is based on measuring intensity fluctuations of a reflected laser focused on a bacterium in reflective microwells. Using numerical simulations, we show that both refraction and absorption of light by the bacterium contribute to the observed signal. By administering antibiotics that kill the bacteria, we show that the variance of the detected fluctuations vanishes within 1 h, indicating the potential of this technique for rapid sensing of bacterial antibiotic susceptibility. We envisage the use of this method for massively parallelizable AST tests and fast detection of drug-resistant pathogens.

Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria

Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.

Electroacoustic Biosensor Systems for Evaluating Antibiotic Action on Microbial Cells

Antibiotics are widely used to treat infectious diseases. This leads to the presence of antibiotics and their metabolic products in the ecosystem, especially in aquatic environments. In many countries, the growth of pathogen resistance to antibiotics is considered a threat to national security. Therefore, methods for determining the sensitivity/resistance of bacteria to antimicrobial drugs are important. This review discusses the mechanisms of the formation of antibacterial resistance and the various methods and sensor systems available for analyzing antibiotic effects on bacteria. Particular attention is paid to acoustic biosensors with active immobilized layers and to sensors that analyze antibiotics directly in liquids. It is shown that sensors of the second type allow analysis to be done within a short period, which is important for timely treatment.

Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers

The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.

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.

Single-cell pathogen diagnostics for combating antibiotic resistance

Bacterial infections and antimicrobial resistance are a major cause for morbidity and mortality worldwide. Antimicrobial resistance often arises from antimicrobial misuse, where physicians empirically treat suspected bacterial infections with broad-spectrum antibiotics until standard culture-based diagnostic tests can be completed. There has been a tremendous effort to develop rapid diagnostics in support of the transition from empirical treatment of bacterial infections towards a more precise and personalized approach. Single-cell pathogen diagnostics hold particular promise, enabling unprecedented quantitative precision and rapid turnaround times. This Primer provides a guide for assessing, designing, implementing and applying single-cell pathogen diagnostics. First, single-cell pathogen diagnostic platforms are introduced based on three essential capabilities: cell isolation, detection assay and output measurement. Representative results, common analysis methods and key applications are highlighted, with an emphasis on initial screening of bacterial infection, bacterial species identification and antimicrobial susceptibility testing. Finally, the limitations of existing platforms are discussed, with perspectives offered and an outlook towards clinical deployment. This Primer hopes to inspire and propel new platforms that can realize the vision of precise and personalized bacterial infection treatments in the near future.

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.

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.

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.

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.

Biosensing, Characterization of Biosensors, and Improved Drug Delivery Approaches Using Atomic Force Microscopy: A Review

Since its invention, atomic force microscopy (AFM) has come forth as a powerful member of the “scanning probe microscopy” (SPM) family and an unparallel platform for high-resolution imaging and characterization for inorganic and organic samples, especially biomolecules, biosensors, proteins, DNA, and live cells. AFM characterizes any sample by measuring interaction force between the AFM cantilever tip (the probe) and the sample surface, and it is advantageous over other SPM and electron micron microscopy techniques as it can visualize and characterize samples in liquid, ambient air, and vacuum. Therefore, it permits visualization of three-dimensional surface profiles of biological specimens in the near-physiological environment without sacrificing their native structures and functions and without using laborious sample preparation protocols such as freeze-drying, staining, metal coating, staining, or labeling. Biosensors are devices comprising a biological or biologically extracted material (assimilated in a physicochemical transducer) that are utilized to yield electronic signal proportional to the specific analyte concentration. These devices utilize particular biochemical reactions moderated by isolated tissues, enzymes, organelles, and immune system for detecting chemical compounds via thermal, optical, or electrical signals. Other than performing high-resolution imaging and nanomechanical characterization (e.g., determining Young’s modulus, adhesion, and deformation) of biosensors, AFM cantilever (with a ligand functionalized tip) can be transformed into a biosensor (microcantilever-based biosensors) to probe interactions with a particular receptors of choice on live cells at a single-molecule level (using AFM-based single-molecule force spectroscopy techniques) and determine interaction forces and binding kinetics of ligand receptor interactions. Targeted drug delivery systems or vehicles composed of nanoparticles are crucial in novel therapeutics. These systems leverage the idea of targeted delivery of the drug to the desired locations to reduce side effects. AFM is becoming an extremely useful tool in figuring out the topographical and nanomechanical properties of these nanoparticles and other drug delivery carriers. AFM also helps determine binding probabilities and interaction forces of these drug delivery carriers with the targeted receptors and choose the better agent for drug delivery vehicle by introducing competitive binding. In this review, we summarize contributions made by us and other researchers so far that showcase AFM as biosensors, to characterize other sensors, to improve drug delivery approaches, and to discuss future possibilities.

Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains

The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.

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.

Gradient-Based Microfluidic Platform for One Single Rapid Antimicrobial Susceptibility Testing

Antimicrobial resistance is a growing problem, necessitating rapid antimicrobial susceptibility testing (AST) to enable effective in-clinic diagnostic testing and treatment. Conventional AST using broth microdilution or the Kirby-Bauer disk diffusion are time-consuming (e.g., 24-72 h), labor-intensive, and costly and consume reagents. Here, we propose a novel gradient-based microchamber microfluidic (GM²) platform to perform AST assay for a wide range of antibiotic concentrations plus zero (positive control) and maximum (negative control) concentrations all in a single test. Antibiotic lateral diffusion within enriched to depleted (C_max and zero, respectively) cocurrent flowing fluids, moving alongside a micron-sized main channel, is led to form an antibiotic concentration profile in microchambers, connected to the depleted side of the main channel. We examined the tunability of the GM² platform, in terms of producing a wide range of antibiotic concentrations in a gradient mode between two consecutive microchambers with changing either the loading fluids' flow rates or their initial concentrations. We also tested the GM² platform for profiling bacteria associated with human Crohn's disease and bovine mastitis. Time to result for performing a complete AST assay was ∼ 3-4 h in the GM² platform. Lastly, the GM² platform tracked the bacterial growth independent of an antibiotic mechanism of action or bacterial species in a robust and easy-to-implement fashion.

Nanomotion Detection-Based Rapid Antibiotic Susceptibility Testing

Rapid antibiotic susceptibility testing (AST) could play a major role in fighting multidrug-resistant bacteria. Recently, it was discovered that all living organisms oscillate in the range of nanometers and that these oscillations, referred to as nanomotion, stop as soon the organism dies. This finding led to the development of rapid AST techniques based on the monitoring of these oscillations upon exposure to antibiotics. In this review, we explain the working principle of this novel technique, compare the method with current ASTs, explore its application and give some advice about its implementation. As an illustrative example, we present the application of the technique to the slowly growing and pathogenic Bordetella pertussis bacteria.

Microfluidic Technology for Antibacterial Resistance Study and Antibiotic Susceptibility Testing: Review and Perspective

A review on microfluidic technology for antibacterial resistance study and antibiotic susceptibility testing (AST) is presented here. Antibiotic resistance has become a global health crisis in recent decades, severely threatening public health, patient care, economic growth, and even national security. It is extremely urgent that antibiotic resistance be well looked into and aggressively combated in order for us to survive this crisis. AST has been routinely utilized in determining bacterial susceptibility to antibiotics and identifying potential resistance. Yet conventional methods for AST are increasingly incompetent due to unsatisfactory test speed, high cost, and deficient reliability. Microfluidics has emerged as a powerful and very promising platform technology that has proven capable of addressing the limitation of conventional methods and advancing AST to a new level. Besides, potential technical challenges that are likely to hinder the development of microfluidic technology aimed at AST are observed and discussed. To conclude, it is noted that (1) the translation of microfluidic innovations from laboratories to be ready AST platforms remains a lengthy journey and (2) ensuring all relevant parties engaged in a collaborative and unified mode is foundational to the successful incubation of commercial microfluidic platforms for AST.