Optimizing Bacteriophage Surface Densities for Bacterial Capture and Sensing in Quartz Crystal Microbalance with Dissipation Monitoring

Bacteriophage-Based Bioanalysis

Bacteriophages, which are viral predators of bacteria, have evolved to efficiently recognize, bind, infect, and lyse their host, resulting in the release of tens to hundreds of propagated viruses. These abilities have attracted biosensor developers who have developed new methods to detect bacteria. Recently, several comprehensive reviews have covered many of the advances made regarding the performance of phage-based biosensors. Therefore, in this review, we first describe the landscape of phage-based biosensors and then cover advances in other aspects of phage biology and engineering that can be used to make high-impact contributions to biosensor development. Many of these advances are in fields adjacent to analytical chemistry such as synthetic biology, machine learning, and genetic engineering and will allow those looking to develop phage-based biosensors to start taking alternative approaches, such as a bottom-up design and synthesis of custom phages with the singular task of detecting their host.

Anisotropic Particle Deposition Kinetics from Quartz Crystal Microbalance Measurements: Beyond the Sphere Paradigm

Deposition kinetics of polymer particles characterized by a prolate spheroid shape on gold sensors modified by the adsorption of poly(allylamine) was investigated using a quartz crystal microbalance and atomic force microscopy. Reference measurements were also performed for polymer particles of a spherical shape and the same diameter as the spheroid shorter axis. Primarily, the frequency and dissipation shifts for various overtones were measured as a function of time. These kinetic data were transformed into the dependence of the complex impedance, scaled up by the inertia impedance, upon the particle size to the hydrodynamic boundary layer ratio. The results obtained for low particle coverage were interpolated, which enabled the derivation of Sauerbrey-like equations, yielding the real particle coverage using the experimental frequency or dissipation (bandwidth) shifts. Experiments carried out for a long deposition time confirmed that, for spheroids, the imaginary and real impedance components were equal to each other for all overtones and for a large range of particle coverage. This result was explained in terms of a hydrodynamic, lubrication-like contact of particles with the sensor, enabling their sliding motion. In contrast, the experimental data obtained for spheres, where the impedance ratio was a complicated function of overtones and particle coverage, showed that the contact was rather stiff, preventing their motion over the sensor. It was concluded that results obtained in this work can be exploited as useful reference systems for a quantitative interpretation of bioparticle, especially bacteria, deposition kinetics on macroion-modified surfaces.

Living virus-based nanohybrids for biomedical applications

Living viruses characterized by distinctive biological functions including specific targeting, gene invasion, immune modulation, and so forth have been receiving intensive attention from researchers worldwide owing to their promising potential for producing numerous theranostic modalities against diverse pathological conditions. Nevertheless, concerns during applications, such as rapid immune clearance, altering immune activation modes, insufficient gene transduction efficiency, and so forth, highlight the crucial issues of excessive therapeutic doses and the associated biosafety risks. To address these concerns, synthetic nanomaterials featuring unique physical/chemical properties are frequently exploited as efficient drug delivery vehicles or treatments in biomedical domains. By constant endeavor, researchers nowadays can create adaptable living virus-based nanohybrids (LVN) that not only overcome the limitations of virotherapy, but also combine the benefits of natural substances and nanotechnology to produce novel and promising therapeutic and diagnostic agents. In this review, we discuss the fundamental physiochemical properties of the viruses, and briefly outline the basic construction methodologies of LVN. We then emphasize their distinct diagnostic and therapeutic performances for various diseases. Furthermore, we survey the foreseeable challenges and future perspectives in this interdisciplinary area to offer insights. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Enzymatic and Microbial Electrochemistry: Approaches and Methods

The coupling of enzymes and/or intact bacteria with electrodes has been vastly investigated due to the wide range of existing applications. These span from biomedical and biosensing to energy production purposes and bioelectrosynthesis, whether for theoretical research or pure applied industrial processes. Both enzymes and bacteria offer a potential biotechnological alternative to noble/rare metal-dependent catalytic processes. However, when developing these biohybrid electrochemical systems, it is of the utmost importance to investigate how the approaches utilized to couple biocatalysts and electrodes influence the resulting bioelectrocatalytic response. Accordingly, this tutorial review starts by recalling some basic principles and applications of bioelectrochemistry, presenting the electrode and/or biocatalyst modifications that facilitate the interaction between the biotic and abiotic components of bioelectrochemical systems. Focus is then directed toward the methods used to evaluate the effectiveness of enzyme/bacteria-electrode interaction and the insights that they provide. The basic concepts of electrochemical methods widely employed in enzymatic and microbial electrochemistry, such as amperometry and voltammetry, are initially presented to later focus on various complementary methods such as spectroelectrochemistry, fluorescence spectroscopy and microscopy, and surface analytical/characterization techniques such as quartz crystal microbalance and atomic force microscopy. The tutorial review is thus aimed at students and graduate students approaching the field of enzymatic and microbial electrochemistry, while also providing a critical and up-to-date reference for senior researchers working in the field.

Bacteriophage-Based Biosensors: A Platform for Detection of Foodborne Bacterial Pathogens from Food and Environment

Foodborne microorganisms are an important cause of human illness worldwide. Two-thirds of human foodborne diseases are caused by bacterial pathogens throughout the globe, especially in developing nations. Despite enormous developments in conventional foodborne pathogen detection methods, progress is limited by the assay complexity and a prolonged time-to-result. The specificity and sensitivity of assays for live pathogen detection may also depend on the nature of the samples being analyzed and the immunological or molecular reagents used. Bacteriophage-based biosensors offer several benefits, including specificity to their host organism, the detection of only live pathogens, and resistance to extreme environmental factors such as organic solvents, high temperatures, and a wide pH range. Phage-based biosensors are receiving increasing attention owing to their high degree of accuracy, specificity, and reduced assay times. These characteristics, coupled with their abundant supply, make phages a novel bio-recognition molecule in assay development, including biosensors for the detection of foodborne bacterial pathogens to ensure food safety. This review provides comprehensive information about the different types of phage-based biosensor platforms, such as magnetoelastic sensors, quartz crystal microbalance, and electrochemical and surface plasmon resonance for the detection of several foodborne bacterial pathogens from various representative food matrices and environmental samples.

Molecular Interactions of Tannic Acid with Proteins Associated with SARS-CoV-2 Infectivity

The overall impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on our society is unprecedented. The identification of small natural ligands that could prevent the entry and/or replication of the coronavirus remains a pertinent approach to fight the coronavirus disease (COVID-19) pandemic. Previously, we showed that the phenolic compounds corilagin and 1,3,6-tri-O-galloyl-β-D-glucose (TGG) inhibit the interaction between the SARS-CoV-2 spike protein receptor binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 target receptor on the cell membrane of the host organism. Building on these promising results, we now assess the effects of these phenolic ligands on two other crucial targets involved in SARS-CoV-2 cell entry and replication, respectively: transmembrane protease serine 2 (TMPRSS2) and 3-chymotrypsin like protease (3CLpro) inhibitors. Since corilagin, TGG, and tannic acid (TA) share many physicochemical and structural properties, we investigate the binding of TA to these targets. In this work, a combination of experimental methods (biochemical inhibition assays, surface plasmon resonance, and quartz crystal microbalance with dissipation monitoring) confirms the potential role of TA in the prevention of SARS-CoV-2 infectivity through the inhibition of extracellular RBD/ACE2 interactions and TMPRSS2 and 3CLpro activity. Moreover, molecular docking prediction followed by dynamic simulation and molecular mechanics Poisson–Boltzmann surface area (MMPBSA) free energy calculation also shows that TA binds to RBD, TMPRSS2, and 3CLpro with higher affinities than TGG and corilagin. Overall, these results suggest that naturally occurring TA is a promising candidate to prevent and inhibit the infectivity of SARS-CoV-2.

Overview of Rapid Detection Methods for Salmonella in Foods: Progress and Challenges

Salmonella contamination in food production and processing is a serious threat to consumer health. More and more rapid detection methods have been proposed to compensate for the inefficiency of traditional bacterial cultures to suppress the high prevalence of Salmonella more efficiently. The contamination of Salmonella in foods can be identified by recognition elements and screened using rapid detection methods with different measurable signals (optical, electrical, etc.). Therefore, the different signal transduction mechanisms and Salmonella recognition elements are the key of the sensitivity, accuracy and specificity for the rapid detection methods. In this review, the bioreceptors for Salmonella were firstly summarized and described, then the current promising Salmonella rapid detection methods in foodstuffs with different signal transduction were objectively summarized and evaluated. Moreover, the challenges faced by these methods in practical monitoring and the development prospect were also emphasized to shed light on a new perspective for the Salmonella rapid detection methods applications.

Soft Viscoelastic Particles in Contact with a Quartz Crystal Microbalance (QCM): A Frequency-Domain Lattice Boltzmann Simulation

Shifts of frequency and bandwidth of a quartz crystal microbalance (QCM) in contact with a structured, viscoelastic sample have been computed with a linearized version of the lattice Boltzmann method (LBM). The algorithm operates in the frequency domain and covers viscoelasticity. The different domains are characterized by different values of the complex viscosity, η, equivalent to different values of the shear modulus, G. Stiff particles are given large |η_Sph|, where |η_Sph| must be less than ∼100 η_bulk with η_bulk the viscosity of the ambient liquid. Critical to the computational efficiency is a match of the LBM populations at the upper boundary of the simulation box to an analytical solution of the Stokes equation in the bulk above the box. The application example is a test of the ΔΓ/(-Δf)-extrapolation scheme, where Δf and ΔΓ are the shifts in resonance frequency and half bandwidth, respectively. For adsorbed particles, plots of ΔΓ/(-Δf) versus - Δf/n (with n the overtone order) show almost straight lines. The extrapolation of these lines to zero yields a frequency shift, which, after conversion to a thickness with the Sauerbrey equation, closely agrees with the height of the particles. Plots of Δf/n and ΔΓ/n versus n look similar to the corresponding plots obtained for viscoelastic films, where the parameters, which would usually be extracted from those plots (apparent mass and apparent compliance), depend on the geometry and the sample's viscoelasticity in a nontrivial way.

Strategies for Surface Immobilization of Whole Bacteriophages: A Review

Bacteriophage immobilization is a key unit operation in emerging biotechnologies, enabling new possibilities for biodetection of pathogenic microbes at low concentration, production of materials with novel antimicrobial properties, and fundamental research on bacteriophages themselves. Wild type bacteriophages exhibit extreme binding specificity for a single species, and often for a particular subspecies, of bacteria. Since their specificity originates in epitope recognition by capsid proteins, which can be altered by chemical or genetic modification, their binding specificity may also be redirected toward arbitrary substrates and/or a variety of analytes in addition to bacteria. The immobilization of bacteriophages on planar and particulate substrates is thus an area of active and increasing scientific interest. This review assembles the knowledge gained so far in the immobilization of whole phage particles, summarizing the main chemistries, and presenting the current state-of-the-art both for an audience well-versed in bioconjugation methods as well as for those who are new to the field.

Formulations for Bacteriophage Therapy and the Potential Uses of Immobilization

The emergence of antibiotic-resistant pathogens is becoming increasingly problematic in the treatment of bacterial diseases. This has led to bacteriophages receiving increased attention as an alternative form of treatment. Phages are effective at targeting and killing bacterial strains of interest and have yielded encouraging results when administered as part of a tailored treatment to severely ill patients as a last resort. Despite this, success in clinical trials has not always been as forthcoming, with several high-profile trials failing to demonstrate the efficacy of phage preparations in curing diseases of interest. Whilst this may be in part due to reasons surrounding poor phage selection and a lack of understanding of the underlying disease, there is growing consensus that future success in clinical trials will depend on effective delivery of phage therapeutics to the area of infection. This can be achieved using bacteriophage formulations instead of purely liquid preparations. Several encapsulation-based strategies can be applied to produce phage formulations and encouraging results have been observed with respect to efficacy as well as long term phage stability. Immobilization-based approaches have generally been neglected for the production of phage therapeutics but could also offer a viable alternative.

Biosensors for rapid detection of Salmonella in food: A review

Salmonella is one of the main causes of foodborne infectious diseases, posing a serious threat to public health. It can enter the food supply chain at various stages of production, processing, distribution, and marketing. High prevalence of Salmonella necessitates efficient and effective approaches for its identification, detection, and monitoring at an early stage. Because conventional methods based on plate counting and real-time polymerase chain reaction are time-consuming and laborious, novel rapid detection methods are urgently needed for in-field and on-line applications. Biosensors provide many advantages over conventional laboratory assays in terms of sensitivity, specificity, and accuracy, and show superiority in rapid response and potential portability. They are now recognized as promising alternative tools and one of the most on-site applicable and end user-accessible methods for rapid detection. In recent years, we have witnessed a flourishing of studies in the development of robust and elaborate biosensors for detection of Salmonella in food. This review aims to provide a comprehensive overview on Salmonella biosensors by highlighting different signal-transducing mechanisms (optical, electrochemical, piezoelectric, etc.) and critically analyzing its recent trends, particularly in combination with nanomaterials, microfluidics, portable instruments, and smartphones. Furthermore, current challenges are emphasized and future perspectives are discussed.

Disparity of Cytochrome Utilization in Anodic and Cathodic Extracellular Electron Transfer Pathways of Geobacter sulfurreducens Biofilms

Extracellular electron transfer (EET) in microorganisms is prevalent in nature and has been utilized in functional bioelectrochemical systems. EET of Geobacter sulfurreducens has been extensively studied and has been revealed to be facilitated through c-type cytochromes, which mediate charge between the electrode and G. sulfurreducens in anodic mode. However, the EET pathway of cathodic conversion of fumarate to succinate is still under debate. Here, we apply a variety of analytical methods, including electrochemistry, UV-vis absorption and resonance Raman spectroscopy, quartz crystal microbalance with dissipation, and electron microscopy, to understand the involvement of cytochromes and other possible electron-mediating species in the switching between anodic and cathodic reaction modes. By switching the applied bias for a G. sulfurreducens biofilm coupled to investigating the quantity and function of cytochromes, as well as the emergence of Fe-containing particles on the cell membrane, we provide evidence of a diminished role of cytochromes in cathodic EET. This work sheds light on the mechanisms of G. sulfurreducens biofilm growth and suggests the possible existence of a nonheme, iron-involving EET process in cathodic mode.

Materials Nanoarchitectonics for Mechanical Tools in Chemical and Biological Sensing

In this Focus Review, nanoarchitectonic approaches for mechanical-action-based chemical and biological sensors are briefly discussed. In particular, recent examples of piezoelectric devices, such as quartz crystal microbalances (QCM and QCM-D) and a membrane-type surface stress sensor (MSS), are introduced. Sensors need well-designed nanostructured sensing materials for the sensitive and selective detection of specific targets. Nanoarchitectonic approaches for sensing materials, such as mesoporous materials, 2D materials, fullerene assemblies, supported lipid bilayers, and layer-by-layer assemblies, are highlighted. Based on these sensing approaches, examples of bioanalytical applications are presented for toxic gas detection, cell membrane interactions, label-free biomolecular assays, anticancer drug evaluation, complement activation-related multiprotein membrane attack complexes, and daily biodiagnosis, which are partially supported by data analysis, such as machine learning and principal component analysis.

Bacterial biosensing: Recent advances in phage-based bioassays and biosensors

In nature, different types of bacteria including pathogenic and beneficial ones exist in different habitats including environment, plants, animals, and humans. Among these, the pathogenic bacteria should be detected at earlier stages of infection; however, the conventional bacterial detection procedures are complex and time-consuming. In contrast, the advanced molecular approaches such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) have significantly reduced the detection time; nevertheless, such approaches are not acceptable to a large extent and are mostly laborious and expensive. Therefore, the development of fast, inexpensive, sensitive, and specific approaches for pathogen detection is essential for different applications in food industry, clinical diagnosis, biological defense and counter-terrorism. To this end, the novel sensing approaches involving bacteriophages as recognition elements are receiving immense consideration owing to their high degree of specificity, accuracy, and reduced assay times. Besides, the phages are easily produced and are tolerant to extreme pH, temperature, and organic solvents as compared to antibodies. To date, several phage-based assays and sensors have been developed involving different systems such as quartz crystal microbalance, magnetoelastic platform, surface plasmon resonance, and electrochemical methods. This review highlights different taxonomic species and genera of phages infecting eight common disease-causing bacterial genera. It further overviews the most recent advancements in phage-based sensing assays and sensors. Likewise, it elaborates various whole-phage and phage components-based assays. Overall, this review emphasizes the importance of electrochemical biosensors as simple, reliable, cost-effective, and accurate tools for bacterial detection.

Physisorption and chemisorption of T4 bacteriophages on amino functionalized silica particles

Bacteriophages, or phages, are receiving increasing interest as recognition tools for the design of bioactive surfaces. However, to maintain the activity of surface-bound phages, the immobilization strategy must provide the right orientation and not compromise the phages' integrity. The objectives of this study were to characterize the phage sorption capacity and the immobilized phage activity for aminated silica particles functionalized with T4 phages. Two functionalization strategies were compared; physisorption, based on electrostatic adhesion, and chemisorption, where the phage and the particle are coupled using a carbodiimide cross-linker. We report that chemisorption, at maximum adsorption conditions on 1 µm particles, yielded 16 functional phages per particle, which is 2.5 times more than by the physisorption method. Particle diameter is shown to have an important impact on phage attachment and 1.8 µm particles were found to have ∼4 times more phages per surface area than 0.5 µm particles. Higher surface coverage is attributed to the lower steric hindrance on bigger particles. These findings provide important guidelines for the design of phage-functionalized particles for environmental, biomedical, or sensing applications.

Recent advances in bacteriophage-based methods for bacteria detection

Fast and reliable bacteria detection is crucial for lowering the socioeconomic burden related to bacterial infections (e.g., in healthcare, industry or security). Bacteriophages (i.e., viruses with bacterial hosts) pose advantages such as great specificity, robustness, toughness and cheap preparation, making them popular biorecognition elements in biosensors and other assays for bacteria detection. There are several possible designs of bacteriophage-based biosensors. Here, we focus on developments based on whole virions as recognition agents. We divide the review into sections dealing with phage lysis as an analytical signal, phages as capturing elements in assays and phage-based sensing layers, putting the main focus on development reported within the past three years but without omitting the fundamentals.

Recent advances in therapeutic delivery systems of bacteriophage and bacteriophage-encoded endolysins

Antibiotics have been the cornerstone of clinical management of bacterial infection since their discovery in the early 20th century. However, their widespread and often indiscriminate use has now led to reports of multidrug resistance becoming globally commonplace. Bacteriophage therapy has undergone a recent revival in battle against pathogenic bacteria, as the self-replicating and co-evolutionary features of these predatory virions offer several advantages over conventional therapeutic agents. In particular, the use of targeted bacteriophage therapy from specialized delivery platforms has shown particular promise owing to the control of delivery location, administration conditions and dosage of the therapeutic cargo. This review presents an overview of the recent formulations and applications of such delivery vehicles as an innovative and elegant tool for bacterial control.

Probing the Interaction between Nanoparticles and Lipid Membranes by Quartz Crystal Microbalance with Dissipation Monitoring

There is increasing interest in using quartz crystal microbalance with dissipation monitoring (QCM-D) to investigate the interaction of nanoparticles (NPs) with model surfaces. The high sensitivity, ease of use and the ability to monitor interactions in real-time has made it a popular technique for colloid chemists, biologists, bioengineers, and biophysicists. QCM-D has been recently used to probe the interaction of NPs with supported lipid bilayers (SLBs) as model cell membranes. The interaction of NPs with SLBs is highly influenced by the quality of the lipid bilayers. Unlike many surface sensitive techniques, by using QCM-D, the quality of SLBs can be assessed in real-time, hence QCM-D studies on SLB-NP interactions are less prone to the artifacts arising from bilayers that are not well formed. The ease of use and commercial availability of a wide range of sensor surfaces also have made QCM-D a versatile tool for studying NP interactions with lipid bilayers. In this review, we summarize the state-of-the-art on QCM-D based techniques for probing the interactions of NPs with lipid bilayers.

Bacteriophage-based tools: recent advances and novel applications

Bacteriophages (phages) are viruses that infect bacterial hosts, and since their discovery over a century ago they have been primarily exploited to control bacterial populations and to serve as tools in molecular biology. In this commentary, we highlight recent diverse advances in the field of phage research, going beyond bacterial control using whole phage, to areas including biocontrol using phage-derived enzybiotics, diagnostics, drug discovery, novel drug delivery systems and bionanotechnology.