Pathogen detection: A perspective of traditional methods and biosensors

Graphene and graphene oxide for bio-sensing: General properties and the effects of graphene ripples

The use of Graphene based materials, such as graphene oxide (GO), in biosensing applications is gaining significant interest, due to high signal output, with strong potential for high industrial growth rate. Graphene's excellent conduction and mechanical properties (such as toughness and elasticity) coupled with high reactivity to chemical molecules are some of its appealing properties. The presence of ripples on the surface (whether indigenous or induced) represents another property/variable that provide enormous potential if harnessed properly. In this article, we review the current knowledge regarding the use of graphene for biosensing. We discuss briefly the general topic of using graphene for biosensing applications with special emphasis on wearable graphene-based biosensors. The intrinsic ripples of graphene and their effect on graphene biosensing capabilities are thoroughly discussed. We dedicate a section also for the manipulation of intrinsic ripples. Then we review the use of Graphene oxide (GO) in biosensing and discuss the effect of ripples on its properties. We present a review of the current biosensor devices made out of GO for detection of different molecular targets. Finally, we present some thoughts for future perspectives and opportunities of this field. STATEMENT OF SIGNIFICANCE: Biosensors are tools that detect the presence and amount of a chemical substance, such as pregnancy tests and glucose monitoring devices. They are general portable, have short response times and are sensitive, making them highly effective. Gold and silver are used in biosensors and more recently, graphene.  Graphene is sheets of carbon atoms and is the only two-dimensional crystal in nature. It has unique features allowing its effective use in biosensing applications, including the presence of ripples (non-flat areas that give it its electronic properties). The last comprehensive review of this topic was published in 2016. This paper reviews the current knowledge of graphene based biosensors, with a focus on ripples and their effect on graphene biosensing capabilities.

Wide-Range, Rapid, and Specific Identification of Pathogenic Bacteria by Surface-Enhanced Raman Spectroscopy

Sensitive, selective, rapid, and label-free detection of pathogenic bacteria with high generality is of great importance for clinical diagnosis, biosecurity, and public health. However, most traditional approaches, such as microbial cultures, are time-consuming and laborious. To circumvent these problems, surface-enhanced Raman spectroscopy (SERS) appears to be a powerful technique to characterize bacteria at the single-cell level. Here, by SERS, we report a strategy for the rapid and specific detection of 22 strains of common pathogenic bacteria. A novel and high-quality silver nanorod SERS substrate, prepared by the facile interface self-assembly method, was utilized to acquire the chemical fingerprint information of pathogens with improved sensitivity. We also applied the mathematical analysis methods, such as the t-test and receiver operating characteristic method, to determine the Raman features of these 22 strains and demonstrate the clear identification of most bacteria (20 strains) from the rest and also the reliability of this SERS sensor. This rapid and specific strategy for wide-range bacterial detection offers significant advantages over existing approaches and sets the base for automated and onsite detection of pathogenic bacteria in a complex real-life situation.

Strategies of Detecting Bacteria Using Fluorescence-Based Dyes

Identification of bacterial strains is critical for the theranostics of bacterial infections and the development of antibiotics. Many organic fluorescent probes have been developed to overcome the limitations of conventional detection methods. These probes can detect bacteria with "off-on" fluorescence change, which enables the real-time imaging and quantitative analysis of bacteria in vitro and in vivo. In this review, we outline recent advances in the development of fluorescence-based dyes capable of detecting bacteria. Detection strategies are described, including specific interactions with bacterial cell wall components, bacterial and intracellular enzyme reactions, and peptidoglycan synthesis reactions. These include theranostic probes that allow simultaneous bacterial detection and photodynamic antimicrobial effects. Some examples of other miscellaneous detections in bacteria have also been described. In addition, this review demonstrates the validation of these fluorescent probes using a variety of biological models such as gram-negative and -positive bacteria, antibiotic-resistant bacteria, infected cancer cells, tumor-bearing, and infected mice. Prospects for future research are outlined by presenting the importance of effective in vitro and in vivo detection of bacteria and development of antimicrobial agents.

Biosensors based on aptamer-conjugated gold nanoparticles: A review

Simply synthetized gold nanoparticles have been highly used in medicine and biotechnology as a result of their biocompatibility, conductivity, and being easily functionalized with biomolecules such as aptamer. Aptamer-conjugated gold nanoparticle structures synergically possess characteristics of both aptamer and gold nanoparticles including high binding affinity, high biocompatibility, enhanced target selectivity, and long circulatory half-life. Aptamer-conjugated gold nanoparticles have extensively gained considerable attention for designing of biosensing systems due to their interesting optical and electrochemical features. Moreover, biosensors based on aptamer-gold nanoparticles are easy to use, with fast response, and inexpensive which make them ideal in individualized medicine, disease markers detection, food safety, and so forth. Moreover, due to high selectivity and biocompatibility of aptamer-gold nanoparticles, these biosensing platforms are ideal tools for targeted drug delivery systems. The application of this nanostructure as diagnostic and therapeutic tool has been developed for detection of cancer in the early stage by detecting cancer biomarkers, pathogens, proteins, toxins, antibiotics, adenosine triphosphate, and other small molecules. This review obviously demonstrates that this nanostructure effectively is applicable in the field of biomedicine and possesses potential of commercialization aims.

Emerging materials for the electrochemical detection of COVID-19

The SARS-CoV-2 virus is still causing a dramatic loss of human lives worldwide, constituting an unprecedented challenge for the society, public health and economy, to overcome. The up-to-date diagnostic tests, PCR, antibody ELISA and Rapid Antigen, require special equipment, hours of analysis and special staff. For this reason, many research groups have focused recently on the design and development of electrochemical biosensors for the SARS-CoV-2 detection, indicating that they can play a significant role in controlling COVID disease. In this review we thoroughly discuss the transducer electrode nanomaterials investigated in order to improve the sensitivity, specificity and response time of the as-developed SARS-CoV-2 electrochemical biosensors. Particularly, we mainly focus on the results appeard on Au-based and carbon or graphene-based electrodes, which are the main material groups recently investigated worldwidely. Additionally, the adopted electrochemical detection techniques are also discussed, highlighting their pros and cos. The nanomaterial-based electrochemical biosensors could enable a fast, accurate and without special cost, virus detection. However, further research is required in terms of new nanomaterials and synthesis strategies in order the SARS-CoV-2 electrochemical biosensors to be commercialized.

Biomarker imprinted magnetic core-shell nanoparticles for rapid, culture free detection of pathogenic bacteria

Rapid and selective detection of microorganisms in complex biological systems draws huge attention to address the rising issue of antimicrobial resistance. Diagnostics based on the identification of whole microorganisms are laborious, time-consuming and costly, thus alternative strategies for early clinical diagnosis include biomarker based microbial detection. This paper describes a low-cost, easy-to-use method for the detection of Pseudomonas aeruginosa infections by specifically identifying a biomarker pyocyanin, using surface-molecularly imprinted nanoparticles or "plastibodies". The selective nanopockets are created by templating pyocyanin onto 20 nm allyl-functionalized magnetic nanoparticles coated with a thin layer of the acrylamide-based polymer. This functional material with an impressive imprinting factor (IF) of 5 and a binding capacity of ∼2.5 mg g-1 of polymers can be directly applied for the detection of bacteria in complex biological samples based on the presence of pyocyanin. These MIPs are highly selective and sensitive to pyocyanin and can consistently bind with pyocyanin in repeated use. Finally, the facile and efficient capture of pyocyanin has versatile applications ranging from biomarker based culture free detection of P. aeruginosa to monitoring of the therapeutic regime, in addition to developing a new class of antibiotics.

A guanidinium-rich polymer as a new universal bioreceptor for multiplex detection of bacteria from environmental samples

Protamine, a guanidinium rich polymer, is proposed as a universal bioreceptor for bacteria, towards rapid and handheld bacteria detection from complex environmental water samples without the need for specific antibodies or primers. Escherichia coli K12, Salmonella Typhimurium, and Staphylococcus aureus (MSSA) were assayed, representing gram-negative, gram-positive, rod- and round-shaped bacteria. Samples and the protamine conjugated fluorescent particles were sequentially loaded to the paper microfluidic chips and flowed through the channels spontaneously via capillary action. The particles were aggregated via protamine-bacteria membrane interactions and unbound particles were rinsed via capillary action. A low-cost smartphone fluorescence microscope was designed, fabricated, and imaged the paper channels. A unique image processing algorithm isolated only the aggregated particles to detect all three bacteria (p < 0.05) with a detection limit of 10¹-10² CFU/mL. Protamine did not induce any particle aggregation with a model protein, algae, and virus. Successful bacteria detection was also demonstrated with environmental field water samples. Total assay time was < 10 min with neither extraction nor enrichment steps. In summary, a guanidinium-rich polymer showed a promise as a universal bioreceptor for bacteria and can be used on a paper microfluidic chip and smartphone quantification towards rapid and handheld detection.

Rapid detection and enumeration of aerobic mesophiles in raw foods using dielectrophoresis

The concept of dielectrophoresis (DEP), which involves the movement of neutral particles by induced polarization in nonuniform electric fields, has been exploited in various biological applications. However, only a few studies have investigated the use of DEP for detecting and enumerating microorganisms in foodstuffs. Therefore, we aimed to evaluate the accuracy and efficiency of a DEP-based method for enumerating viable bacteria in three raw foods: freshly cut lettuce, chicken breast, and minced pork. The DEP separation of bacterial cells was conducted at 20 V of output voltage and 6000 to 9000 kHZ of frequency with sample conductivity of 30-70 μS/cm. The accuracy and validity of the DEP method for enumerating viable bacteria were compared with those of the conventional culture method; no significant variation was observed. We found a high correlation between the data obtained using DEP and the conventional aerobic plate count culture method, with a high coefficient of determination (R2 > 0.90) regardless of the food product; the difference in cell count data between both methods was within 1.0 log CFU/mL. Moreover, we evaluated the efficiency of the DEP method for enumerating bacterial cells in chicken breasts subjected to either freezing or heat treatment. After thermal treatment at 55 °C and 60 °C, the viable cell counts determined via the DEP method were found to be lower than those obtained using the conventional culture method, which implies that the DEP method may not be suitable for the direct detection of injured cells. In addition to its high accuracy and efficiency, the DEP method enables the determination of viable cell counts within 30 min, compared to 48 h required for the conventional culture method. In conclusion, the DEP method may be a potential alternative tool for rapid determination of viable bacteria in a variety of foodstuffs.

Thread-based isotachophoresis for DNA extraction and purification from biological samples

A rapid, low-cost, and disposable microfluidic thread-based isotachophoresis method was developed for the purification and preconcentration of nucleic acids from biological samples, prior to their extraction and successful analysis using quantitative polymerase chain reaction (qPCR). This approach extracts and concentrates protein-free DNA from the terminating electrolyte buffer, via a continuous sampling approach, resulting in significant focussing of the extracted DNA upon a 6 cm length nylon thread. The platform was optimised using the preconcentration of a fluorescent dye, showing a 600-fold concentration capacity within <5 min. The system was then applied to the one-step extraction of lambda DNA - an E. coli bacteriophage - spiked into whole blood, exhibiting the exclusion of PCR inhibitors. The extraction efficiency from the thread material following concentration was consistent, between 94.4-113.9%. The determination of lambda DNA in whole blood was achieved within a linear range of 1.0-1 × 105 fg μL-1 (20-2 × 106 copies per μL). This technique demonstrates great potential for the development of thread-based affordable analytical and diagnostic devices based upon DNA and RNA isolation.

Gold nanoparticles-mediated fluorescent chemical nose sensor for pathogenic diagnosis and phenotype

Pathogens are one of the important factors affecting national economic construction. An ideal detection system for pathogen control with excellent sensitivity, high specificity, and time-saving is needed. Here, we reported a method for bacterial detection using gold nanoparticles-mediated fluorescent "chemical nose" sensors (GFCEs). The technique consists of gold nanoparticles-coated magnetic particle using benzaldehyde, octyl aldehyde, and pyrimidine-4-formaldehyde modified, respectively. And these positively charged nanocompound interacting with three different fluorescent proteins (FPs) to form three kinds of GFCEs, respectively, named GFCE1, GFCE2, and GFCE3. Upon binding with pathogenic cells, functionalized gold nanoparticles could identify patches on hydrophobic/functional surfaces of microorganisms, and self-assemble with living bacteria by complementary electrostatic interactions. The binding ability between GFCEs and bacteria determines the change of fluorescence response of three FPs from GFCEs. These feature fluorescent level are pathogen-specific, highly repeatable, and can be analyzed by Linear Discriminant Analysis (LDA). The combination of GFCE1 and GFCE2 has the best performance when detecting pathogens with concentrations of 10⁶  cfu mL^-1 . The first discriminant within 15 minutes is 93.8%, which could be used for subsequent identification of unknown samples. The commonly applicable system provides a simple way for the rapid bacterial detection without preprocessing procedures.

3' Tth Endonuclease Cleavage Polymerase Chain Reaction (3TEC-PCR) Technology for Single-Base-Specific Multiplex Pathogen Detection using a Two-Oligonucleotide System

Polymerase chain reaction (PCR) is the standard in nucleic acid amplification technology for infectious disease pathogen detection and has been the primary diagnostic tool employed during the global COVID-19 pandemic. Various PCR technology adaptations, typically using two-oligonucleotide dye-binding methods or three-oligonucleotide hydrolysis probe systems, enable real-time multiplex target detection or single-base specificity for the identification of single-nucleotide polymorphisms (SNPs). A small number of two-oligonucleotide PCR systems facilitating both multiplex detection and SNP identification have been reported; however, these methods often have limitations in terms of target specificity, production of variable or false-positive results, and the requirement for extensive optimisation or post-amplification analysis. This study introduces 3' Tth endonuclease cleavage PCR (3TEC-PCR), a two-oligonucleotide PCR system incorporating a modified primer/probe and a thermostable cleavage enzyme, Tth endonuclease IV, for real-time multiplex detection and SNP identification. Complete analytical specificity, low limits of detection, single-base specificity, and simultaneous multiple target detection have been demonstrated in this study using 3TEC-PCR to identify bacterial meningitis associated pathogens. This is the first report of a two-oligonucleotide, real-time multiplex PCR technology with single-base specificity using Tth endonuclease IV.

Tailoring metal-organic frameworks-based nanozymes for bacterial theranostics

Nanozymes are next-generation artificial enzymes having distinguished features such as cost-effective, enhanced surface area, and high stability. However, limited selectivity and moderate activity of nanozymes in the biochemical environment hindered their usage and encouraged researchers to seek alternative catalytic materials. Recently, metal-organic frameworks (MOFs) characterized by distinct crystalline porous structures with large surface area, tunable pores, and uniformly dispersed active sites emerged, that filled the gap between natural enzymes and nanozymes. Moreover, by selecting suitable metal ions and organic linkers, MOFs can be designed for effective bacterial theranostics. In this review, we briefly presented the design and fabrication of MOFs. Then, we demonstrated the applications of MOFs in bacterial theranostics and their safety considerations. Finally, we proposed the major obstacles and opportunities for further development in research on the interface of nanozymes and MOFs. We expect that MOFs based nanozymes with unique physicochemical and intrinsic enzyme-mimicking properties will gain broad interest in both fundamental research and biomedical applications.

Acoustofluidic device for acoustic capture of Bacillus anthracis spore analogues at low concentration

A portable device for the rapid concentration of Bacillus subtilis var niger spores, also known as Bacillus globigii (BG), using a thin-reflector acoustofluidic configuration is described. BG spores form an important laboratory analog for the Bacillus anthracis spores, a serious health and bioterrorism risk. Existing systems for spore detection have limitations on detection time and detection that will benefit from the combination with this technology. Thin-reflector acoustofluidic devices can be cheaply and robustly manufactured and provide a more reliable acoustic force than previously explored quarter-wave resonator systems. The system uses the acoustic forces to drive spores carried in sample flows of 30 ml/h toward an antibody functionalized surface, which captures and immobilizes them. In this implementation, spores were fluorescently labeled and imaged. Detection at concentrations of 100 CFU/ml were demonstrated in an assay time of 10 min with 60% capture. We envisage future systems to incorporate more advanced detection of the concentrated spores, leading to rapid, sensitive detection in the presence of significant noise.

Recent progress in fluorescent probes for bacteria

Food fermentation, antibiotics, and pollutant degradation are closely related to bacteria. Bacteria play an irreplaceable role in life. However, some bacteria seriously threaten human health and cause large-scale infectious diseases. Therefore, there is a pressing need to develop strategies to accurately monitor bacteria. Technology based on molecular probes and fluorescence imaging is noninvasive, results in little damage, and has high specificity and sensitivity, so it has been widely applied in the detection of bacteria. In this review, we summarize the recent progress in bacterial detection using fluorescence. In particular, we generalize the mechanisms commonly used to design organic fluorescent probes for detecting and imaging bacteria. Moreover, a perspective regarding fluorescent probes for bacterial detection is discussed.

Recent advances in biosensors for detecting viruses in water and wastewater

As there is a considerable number of virus particles in wastewater which cause numerous infectious diseases, it is necessary to eliminate viruses from domestic wastewater before it is released in the environment. In addition, on-site detection of viruses in wastewater can provide information on possible virus exposures in the community of a given wastewater catchment. For this purpose, the pre-detection of different strains of viruses in wastewaters is an essential environmental step. Epidemiological studies illustrate that viruses are the most challenging pathogens to be detected in water samples because of their nano sizes, discrete distribution, and low infective doses. Over the past decades, several methods have been applied for the detection of waterborne viruses which include polymerase chain reaction-based methods (PCR), enzyme-linked immunosorbent assay (ELISA), and nucleic acid sequence-based amplification (NASBA). Although they have shown acceptable performance in virus measurements, their drawbacks such as complicated and time-consuming procedures, low sensitivity, and high analytical cost call for alternatives. Although biosensors are still in an early stage for practical applications, they have shown great potential to become an alternative means for virus detection in water and wastewater. This comprehensive review addresses the different types of viruses found in water and the recent development of biosensors for detecting waterborne viruses.

Human sensor-inspired supervised machine learning of smartphone-based paper microfluidic analysis for bacterial species classification

Bacteria identification has predominantly been conducted using specific bioreceptors such as antibodies or nucleic acid sequences. This approach may be inappropriate for environmental monitoring when the user does not know the target bacterial species and for screening complex water samples with many unknown bacterial species. In this work, we investigate the supervised machine learning of the bacteria-particle aggregation pattern induced by the peptide sets identified from the biofilm-bacteria interface. Each peptide is covalently conjugated to polystyrene particles and loaded together with bacterial suspensions onto paper microfluidic chips. Each peptide interacts with bacterial species to a different extent, leading to varying sizes of particle aggregation. This aggregation changes the surface tension and viscosity of the liquid flowing through the paper pores, altering the flow velocity at different extents. A smartphone camera captures this flow velocity without being affected by ambient and environmental conditions, towards a low-cost, rapid, and field-ready assay. A collection of such flow velocity data generates a unique fingerprinting profile for each bacterial species. Support vector machine is utilized to classify the species. At optimized conditions, the training model can predict the species at 93.3% accuracy out of five bacteria: Escherichia coli, Staphylococcus aureus, Salmonella Typhimurium, Enterococcus faecium, and Pseudomonas aeruginosa. Flow rates are monitored for less than 6 s and the sample-to-answer assay time is less than 10 min. The demonstrated method can open a new way of analyzing complex biological and environmental samples in a biomimetic manner with machine learning classification.

Fluorescence nucleobase analogue-based strategy with high signal-to-noise ratio for ultrasensitive detection of food poisoning bacteria

We developed a simple and ultrasensitive strategy for the identification of foodborne pathogens utilizing a fluorescent nucleobase analogue [2-aminopurine (2-AP)]-containing split G-quadruplex that binds blocker DNA. Compared to a previous strategy that did not use blocker DNA, this strategy showed a significant increase in the signal-to-noise ratio-by approximately 300%-owing to the displacement of the blocker DNA by the target DNA that induces the formation of an active G-quadruplex structure, thereby leading to a substantial increase in the 2-AP fluorescence signal. The proposed strategy was rationally combined with polymerase chain reaction, which resulted in the successful determination of genomic DNA (within the range of 10-106 copies) derived from the food poisoning bacterium Escherichia coli, with a limit of detection of 5.2 copies and high selectivity. In addition, the practical applicability of this method was demonstrated by analyzing E. coli-spiked lettuce samples.

Fast and Sensitive Bacteria Detection by Boronic Acid Modified Fluorescent Dendrimer

This study reports a novel, fast, easy, and sensitive detection method for bacteria which is urgently needed to diagnose infections in their early stages. Our work presents a complex of poly(amidoamine) dendrimer modified by phenylboronic acid and labeled by a fluorescent dansyl group (Dan-B8.5-PAMAM). Our system detects bacteria in 20 min with a sensitivity of approximately 10⁴ colony-forming units (CFU)·mL⁻¹. Moreover, it does not require any peculiar technical skills or expensive materials. The driving force for bacteria recognition is the binding between terminal phenylboronic acids on the probe and bacteria’s surface glycolipids, rather than electrostatic interactions. The aggregation caused by such binding reduces fluorescence. Even though our recognition method does not distinguish between live or dead bacteria, it shows selective antibacterial activity towards Gram-negative bacteria. This study may potentially contribute a new method for the convenient detection and killing of bacteria.

Detection of Bacterial Metabolic Volatile Indole Using a Graphene-Based Field-Effect Transistor Biosensor

The existence of bacteria is a great threat to food safety. Volatile compounds secreted by bacteria during their metabolic process can be dissected to evaluate bacterial contamination. Indole, as a major volatile molecule released by Escherichia coli (E. coli), was chosen to examine the presence of E. coli in this research. In this work, a graphene field-effect transistor (G-FET) was employed to detect the volatile molecule-indole based on a π-π stacking interaction between the indole and the graphene. The exposure of G-FET devices to the indole provokes a change in electrical signal, which is ascribed to the adsorption of the indole molecule onto the graphene surface via π-π stacking. The adsorption of the indole causes a charge rearrangement of the graphene-indole complex, which leads to changes in the electrical signal of G-FET biosensors with a different indole concentration. Currently, the indole biosensor can detect indole from 10 ppb to 250 ppb and reach a limit of detection of 10 ppb for indole solution detection. We believe that our detection strategy for detecting bacterial metabolic gas molecules will pave a way to developing an effective platform for bacteria detection in food safety monitoring.

Theranostic platforms for specific discrimination and selective killing of bacteria

Bacterial infections are serious threats to public health due to lack of advanced techniques to rapidly and accurately diagnose these infections in clinics. Although bacterial infections can be treated with broad-spectrum antibiotics based on empirical judgment, the emergence of antimicrobial resistance has attracted global attention due to long-term misuse and abuse of antibiotics by humans in recent decades. Therefore, it is imperative to selectively discriminate and precisely eliminate pathogenic bacteria. Herein, in addition to the conventional methods for bacterial identification, we comprehensively reviewed the recently developed theranostic platforms for specific discrimination and selective killing of bacteria according to their different interactions with the target bacteria, such as electrostatic and hydrophobic interactions, molecular recognition, microenvironment response, metabolic labeling, bacteriophage targeting, and others. These theranostic agents not only benefit from improved therapeutic efficiency but also present limited susceptibility to induce bacterial resistance. The strategies summarized in this review will open up new avenues in developing effective antimicrobial materials to accurately diagnose and treat bacterial infections in the post-antibiotic era. STATEMENT OF SIGNIFICANCE: Bacterial infections are difficult to be rapidly and accurately diagnosed, and are generally treated with broad-spectrum antibiotics, which leads to the development of drug resistance. By integrating imaging modalities and therapeutic methods in a single treatment, various theranostic agents have been developed to address the abovementioned issues. Therefore, the emerging theranostic platforms for selective identification and elimination of bacteria based on the distinct interactions of the theranostic agents with the target bacteria are summarized in this review. We believe that the information provided in this review will guide researchers in designing advanced antibacterial theranostics for practical applications in the post-antibiotic era.

Nanotheranostic Interface Based on Antibiotic-Loaded Conducting Polymer Nanoparticles for Real-Time Monitoring of Bacterial Growth Inhibition

Conducting polymers have been increasingly used as biologically interfacing electrodes for biomedical applications due to their excellent and fast electrochemical response, reversible doping-dedoping characteristics, high stability, easy processability, and biocompatibility. These advantageous properties can be used for the rapid detection and eradication of infections associated to bacterial growth since these are a tremendous burden for individual patients as well as the global healthcare system. Herein, a smart nanotheranostic electroresponsive platform, which consists of chloramphenicol (CAM)-loaded in poly(3,4-ethylendioxythiophene) nanoparticles (PEDOT/CAM NPs) for concurrent release of the antibiotic and real-time monitoring of bacterial growth is presented. PEDOT/CAM NPs, with an antibiotic loading content of 11.9 ± 1.3% w/w, are proved to inhibit the growth of Escherichia coli and Streptococcus sanguinis due to the antibiotic release by cyclic voltammetry. Furthermore, in situ monitoring of bacterial activity is achieved through the electrochemical detection of β-nicotinamide adenine dinucleotide, a redox active specie produced by the microbial metabolism that diffuse to the extracellular medium. According to these results, the proposed nanotheranostic platform has great potential for real-time monitoring of the response of bacteria to the released antibiotic, contributing to the evolution of the personalized medicine.

Quantum Plasmonic Sensors

The extraordinary sensitivity of plasmonic sensors is well-known in the optics and photonics community. These sensors exploit simultaneously the enhancement and the localization of electromagnetic fields close to the interface between a metal and a dielectric. This enables, for example, the design of integrated biochemical sensors at scales far below the diffraction limit. Despite their practical realization and successful commercialization, the sensitivity and associated precision of plasmonic sensors are starting to reach their fundamental classical limit given by quantum fluctuations of light-known as the shot-noise limit. To improve the sensing performance of these sensors beyond the classical limit, quantum resources are increasingly being employed. This area of research has become known as "quantum plasmonic sensing", and it has experienced substantial activity in recent years for applications in chemical and biological sensing. This review aims to cover both plasmonic and quantum techniques for sensing, and it shows how they have been merged to enhance the performance of plasmonic sensors beyond traditional methods. We discuss the general framework developed for quantum plasmonic sensing in recent years, covering the basic theory behind the advancements made, and describe the important works that made these advancements. We also describe several key works in detail, highlighting their motivation, the working principles behind them, and their future impact. The intention of the review is to set a foundation for a burgeoning field of research that is currently being explored out of intellectual curiosity and for a wide range of practical applications in biochemistry, medicine, and pharmaceutical research.

Designing of Nanomaterials-Based Enzymatic Biosensors: Synthesis, Properties, and Applications

Among the many biological entities employed in the development of biosensors, enzymes have attracted the most attention. Nanotechnology has been fostering excellent prospects in the development of enzymatic biosensors, since enzyme immobilization onto conductive nanostructures can improve characteristics that are crucial in biosensor transduction, such as surface-to-volume ratio, signal response, selectivity, sensitivity, conductivity, and biocatalytic activity, among others. These and other advantages of nanomaterial-based enzymatic biosensors are discussed in this work via the compilation of several reports on their applications in different industrial segments. To provide detailed insights into the state of the art of this technology, all the relevant concepts around the topic are discussed, including the properties of enzymes, the mechanisms involved in their immobilization, and the application of different enzyme-derived biosensors and nanomaterials. Finally, there is a discussion around the pressing challenges in this technology, which will be useful for guiding the development of future research in the area.

Covalent capture and electrochemical quantification of pathogenic E. coli

Pathogenic E. coli pose a significant threat to public health, as strains of this species cause both foodborne illnesses and urinary tract infections. Using a rapid bioconjugation reaction, we selectively capture E. coli at a disposable gold electrode from complex solutions and accurately quantify the pathogenic microbes using electrochemical impedance spectroscopy.

Electrical Characterization of Cellulose-Based Membranes towards Pathogen Detection in Water

Paper substrates are promising for development of cost-effective and efficient point-of-care biosensors, essential for public healthcare and environmental diagnostics in emergency situations. Most paper-based biosensors rely on the natural capillarity of paper to perform qualitative or semi-quantitative colorimetric detections. To achieve quantification and better sensitivity, technologies combining paper-based substrates and electrical detection are being developed. In this work, we demonstrate the potential of electrical measurements by means of a simple, parallel-plate electrode setup towards the detection of whole-cell bacteria captured in nitrocellulose (NC) membranes. Unlike current electrical sensors, which are mostly integrated, this plug and play system has reusable electrodes and enables simple and fast bacterial detection through impedance measurements. The characterized NC membrane was subjected to (i) a biofunctionalization, (ii) different saline solutions modelling real water samples, and (iii) bacterial suspensions of different concentrations. Bacterial detection was achieved in low conductivity buffers through both resistive and capacitive changes in the sensed medium. To capture Bacillus thuringiensis, the model microorganism used in this work, the endolysin cell-wall binding domain (CBD) of Deep-Blue, a bacteriophage targeting this bacterium, was integrated into the membranes as a recognition bio-interface. This experimental proof-of-concept illustrates the electrical detection of 10⁷ colony-forming units (CFU) mL⁻¹ bacteria in low-salinity buffers within 5 min, using a very simple setup. This offers perspectives for affordable pathogen sensors that can easily be reconfigured for different bacteria. Water quality testing is a particularly interesting application since it requires frequent testing, especially in emergency situations.

An Engineered Reporter Phage for the Fluorometric Detection of Escherichia coli in Ground Beef

Despite enhanced sanitation implementations, foodborne bacterial pathogens still remain a major threat to public health and generate high costs for the food industry. Reporter bacteriophage (phage) systems have been regarded as a powerful technology for diagnostic assays for their extraordinary specificity to target cells and cost-effectiveness. Our study introduced an enzyme-based fluorescent assay for detecting the presence of E. coli using the T7 phage engineered with the lacZ operon which encodes beta-galactosidase (β-gal). Both endogenous and overexpressed β-gal expression was monitored using a fluorescent-based method with 4-methylumbelliferyl β-d-galactopyranoside (MUG) as the substrate. The infection of E. coli with engineered phages resulted in a detection limit of 10 CFU/mL in ground beef juice after 7 h of incubation. In this study, we demonstrated that the overexpression of β-gal coupled with a fluorogenic substrate can provide a straightforward and sensitive approach to detect the potential biological contamination in food samples. The results also suggested that this system can be applied to detect E. coli strains isolated from environmental samples, indicating a broader range of bacterial detection.

SHERLOCK and DETECTR: CRISPR-Cas Systems as Potential Rapid Diagnostic Tools for Emerging Infectious Diseases

Infectious diseases are one of the most intimidating threats to human race, responsible for an immense burden of disabilities and deaths. Rapid diagnosis and treatment of infectious diseases offers a better understanding of their pathogenesis. According to the World Health Organization, the ideal approach for detecting foreign pathogens should be rapid, specific, sensitive, instrument-free, and cost-effective. Nucleic acid pathogen detection methods, typically PCR, have numerous limitations, such as highly sophisticated equipment requirements, reagents, and trained personnel relying on well-established laboratories, besides being time-consuming. Thus, there is a crucial need to develop novel nucleic acid detection tools that are rapid, specific, sensitive, and cost-effective, particularly ones that can be used for versatile point-of-care diagnostic applications. Two new methods exploit unpredicted in vitro properties of CRISPR-Cas effectors, turning activated nucleases into basic amplifiers of a specific nucleic acid binding event. These effectors can be attached to a diversity of reporters and utilized in tandem with isothermal amplification approaches to create sensitive identification in multiple deployable field formats. Although still in their beginning, SHERLOCK and DETECTR technologies are potential methods for rapid detection and identification of infectious diseases, with ultrasensitive tests that do not require complicated processing. This review describes SHERLOCK and DETECTR technologies and assesses their properties, functions, and prospective to become the ultimate diagnostic tools for diagnosing infectious diseases and curbing disease outbreaks.

Imprinted Polymers as Synthetic Receptors in Sensors for Food Safety

Foodborne illnesses represent high costs worldwide in terms of medical care and productivity. To ensure safety along the food chain, technologies that help to monitor and improve food preservation have emerged in a multidisciplinary context. These technologies focus on the detection and/or removal of either biological (e.g., bacteria, virus, etc.) or chemical (e.g., drugs and pesticides) safety hazards. Imprinted polymers are synthetic receptors able of recognizing both chemical and biological contaminants. While numerous reviews have focused on the use of these robust materials in extraction and separation applications, little bibliography summarizes the research that has been performed on their coupling to sensing platforms for food safety. The aim of this work is therefore to fill this gap and highlight the multidisciplinary aspects involved in the application of imprinting technology in the whole value chain ranging from IP preparation to integrated sensor systems for the specific recognition and quantification of chemical and microbiological contaminants in food samples.

Label-Free Protein Analysis Using Liquid Chromatography with Gravimetric Detection

The detection and analysis of proteins in a label-free manner under native solution conditions is an increasingly important objective in analytical bioscience platform development. Common approaches to detect native proteins in solution often require specific labels to enhance sensitivity. Dry mass sensing approaches, by contrast, using mechanical resonators, can operate in a label-free manner and offer attractive sensitivity. However, such approaches typically suffer from a lack of analyte selectivity as the interface between standard protein separation techniques and micro-resonator platforms is often constrained by qualitative mechanical sensor performance in the liquid phase. Here, we describe a strategy that overcomes this limitation by coupling liquid chromatography with a quartz crystal microbalance (QCM) platform by using a microfluidic spray dryer. We explore a strategy which allows first to separate a protein mixture in a physiological buffer solution using size exclusion chromatography, permitting specific protein fractions to be selected, desalted, and subsequently spray-dried onto the QCM for absolute mass analysis. By establishing a continuous flow interface between the chromatography column and the spray device via a flow splitter, simultaneous protein mass detection and sample fractionation is achieved, with sensitivity down to a 100 μg/mL limit of detection. This approach for quantitative label-free protein mixture analysis offers the potential for detection of protein species under physiological conditions.

Molecular diagnostic of toxigenic Corynebacterium diphtheriae strain by DNA sensor potentially suitable for electrochemical point-of-care diagnostic

The presented study is focused on the development of electrochemical genosensor for detection of tox gene fragment of toxigenic Corynebacterium diphtheriae strain. Together with our previous studies it fulfils the whole procedure for fast and accurate diagnostic of diphtheria at its early stage of infection with the use of electrochemical methods. The developed DNA sensor potentially can be used in more sophisticated portable device. After the electrochemical stem-loop probe structure optimization the conditions for real asymmetric PCR (aPCR) product detection were selected. As was shown it was crucial to optimize the magnesium and organic solvent concentrations in detection buffer. Under optimal conditions it was possible to selectively detect as low as 20.8 nM of complementary stand in 5 min or 0.5 nM in 30 min with sensitivity of 12.81 and 0.24 1⋅μM^-1 respectively. The unspecific biosensor response was elucidated with the use of new electrode blocking agent, diethyldithiocarbamate. Its application in electrochemical genosensors lead to significant higher current values and the biosensor response even in conditions with magnesium ion depletion. The developed biosensor selectivity was examined using samples containing genetic material originated from a number of non-target bacterial species which potentially can be present in the human upper respiratory tract.

A Review on Biosensors and Recent Development of Nanostructured Materials-Enabled Biosensors

A biosensor is an integrated receptor-transducer device, which can convert a biological response into an electrical signal. The design and development of biosensors have taken a center stage for researchers or scientists in the recent decade owing to the wide range of biosensor applications, such as health care and disease diagnosis, environmental monitoring, water and food quality monitoring, and drug delivery. The main challenges involved in the biosensor progress are (i) the efficient capturing of biorecognition signals and the transformation of these signals into electrochemical, electrical, optical, gravimetric, or acoustic signals (transduction process), (ii) enhancing transducer performance i.e., increasing sensitivity, shorter response time, reproducibility, and low detection limits even to detect individual molecules, and (iii) miniaturization of the biosensing devices using micro-and nano-fabrication technologies. Those challenges can be met through the integration of sensing technology with nanomaterials, which range from zero- to three-dimensional, possessing a high surface-to-volume ratio, good conductivities, shock-bearing abilities, and color tunability. Nanomaterials (NMs) employed in the fabrication and nanobiosensors include nanoparticles (NPs) (high stability and high carrier capacity), nanowires (NWs) and nanorods (NRs) (capable of high detection sensitivity), carbon nanotubes (CNTs) (large surface area, high electrical and thermal conductivity), and quantum dots (QDs) (color tunability). Furthermore, these nanomaterials can themselves act as transduction elements. This review summarizes the evolution of biosensors, the types of biosensors based on their receptors, transducers, and modern approaches employed in biosensors using nanomaterials such as NPs (e.g., noble metal NPs and metal oxide NPs), NWs, NRs, CNTs, QDs, and dendrimers and their recent advancement in biosensing technology with the expansion of nanotechnology.

One-Dimensional Flow of Bacteria on an Electrode Rail by Dielectrophoresis: Toward Single-Cell-Based Analysis

Many applications in biotechnology and medicine, among other disciplines, require the rapid enumeration of bacteria, preferably using miniaturized portable devices. Microfluidic technology is expected to solve this miniaturization issue. In the enumeration of bacteria in microfluidic devices, the technique of aligning bacteria in a single line prior to counting is the key to an accurate count at single-bacterium resolution. Here, we describe the numerical and experimental evaluation of a device utilizing a dielectrophoretic force to array bacteria in a single line, allowing their facile numeration. The device comprises a channel to flow bacteria, two counter electrodes, and a capture electrode several microns or less in width for arranging bacteria in a single line. When the capture electrode is narrower than the diameter of a bacterium, the entrapment efficiency of the one-dimensional array is 80% or more within 2 s. Furthermore, since some cell-sorting applications require bacteria to move against the liquid flow, we demonstrated that bacteria can move in a single line in the off-axial direction tilted 30° from the flow direction. Our findings provide the basis for designing miniature, portable devices for evaluating bacteria with single-cell accuracy.

Porous Silicon Biosensor for the Detection of Bacteria through Their Lysate

Porous silicon (PSi) has been widely used as a biosensor in recent years due to its large surface area and its optical properties. Most PSi biosensors consist in close-ended porous layers, and, because of the diffusion-limited infiltration of the analyte, they lack sensitivity and speed of response. In order to overcome these shortcomings, PSi membranes (PSiMs) have been fabricated using electrochemical etching and standard microfabrication techniques. In this work, PSiMs have been used for the optical detection of Bacillus cereus lysate. Before detection, the bacteria are selectively lysed by PlyB221, an endolysin encoded by the bacteriophage Deep-Blue targeting B. cereus. The detection relies on the infiltration of bacterial lysate inside the membrane, which induces a shift of the effective optical thickness. The biosensor was able to detect a B. cereus bacterial lysate, with an initial bacteria concentration of 105 colony forming units per mL (CFU/mL), in only 1 h. This proof-of-concept also illustrates the specificity of the lysis before detection. Not only does this detection platform enable the fast detection of bacteria, but the same technique can be extended to other bacteria using selective lysis, as demonstrated by the detection of Staphylococcus epidermidis, selectively lysed by lysostaphin.

Microcapillary LAMP for rapid and sensitive detection of pathogen in bovine semen

A microcapillary-based loop-mediated isothermal amplification (µcLAMP) has been described for specific detection of infectious reproductive pathogens in semen samples of cattle without sophisticated instrumentation. Brucella abortus, Leptospira interrogans serovar Pomona and bovine herpesvirus 1 (BoHV-1) cultures were mixed in bovine semen samples. The µcLAMP assay is portable, user-friendly, cost-effective, and suitable to be performed as a POC diagnostic test. We have demonstrated high sensitivity and specificity of µcLAMP for detection of Brucella, Leptospira, and BoHV-1 in bovine semen samples comparable to PCR and qPCR assays. Thus, µcLAMP would be a promising field-based test for monitoring various infectious pathogens in biological samples.HighlightsDetect infectious organism in bovines semenReduction in carryover contamination is an important attribute, which may reduce the false-positive reaction.µcLAMP is a miniaturized form, which could be performed with a minimum volume of reagents.The µcLAMP assay is portable, user-friendly, and suitable to be performed as a POC diagnostic test.

Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance

Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy.

Integration of FISH and Microfluidics

Suitable molecular methods for a faster microbial identification in food and clinical samples have been explored and optimized during the last decades. However, most molecular methods still rely on time-consuming enrichment steps prior to detection, so that the microbial load can be increased and reach the detection limit of the techniques.In this chapter, we describe an integrated methodology that combines a microfluidic (lab-on-a-chip) platform, designed to concentrate cell suspensions and speed up the identification process in Saccharomyces cerevisiae , and a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) protocol optimized and adapted to microfluidics. Microfluidic devices with different geometries were designed, based on computational fluid dynamics simulations, and subsequently fabricated in polydimethylsiloxane by soft lithography. The microfluidic designs and PNA-FISH procedure described here are easily adaptable for the detection of other microorganisms of similar size.

Ultrasensitive biosensors based on waveguide-coupled long-range surface plasmon resonance (WC-LRSPR) for enhanced fluorescence spectroscopy

We investigated the coupling phenomenon between plasmonic resonance and waveguide modes through theoretical and experimental parametric analyses on the bimetallic waveguide-coupled long-range surface plasmon resonance (Bi-WCLRSPR) structure.

Application of lectin-based biosensor technology in the detection of foodborne pathogenic bacteria: a review

Foodborne diseases caused by pathogenic bacteria pose a serious threat to human health.

Selective Butyrate Esterase Probe for the Rapid Colorimetric and Fluorogenic Identification of Moraxella catarrhalis

Clinical identification of the pathogenic bacterium Moraxella catarrhalis in cultures relies on the detection of bacterial butyrate esterase (C4-esterase) using a coumarin-based fluorogenic substrate, 4-methylumbelliferyl butyrate. However, this classical probe may give false-positive responses because of its poor stability and lack of specificity. Here, we report a new colorimetric and fluorogenic probe design employing a meso-ester-substituted boron dipyrromethene (BODIPY) dye for the specific detection of C4-esterase activity expressed by M. catarrhalis. This new probe has resistance to nonspecific hydrolysis that is far superior to the classical probe and also selectively responds to esterase with rapid colorimetric and fluorescence signal changes and large "turn-on" ratios. The probe was successfully applied to the specific detection of M. catarrhalis with high sensitivity.

AIEgens for microbial detection and antimicrobial therapy

Pathogenic microbes can cause infections or diseases in hosts and they pose ongoing threats to human health. Antibiotics have been taken an active role in treating a wide variety of infections or diseases since they were first introduced in the 1940s. However, the emergence of antibiotic-resistant microbes makes these previously effective drugs invalid regrettably. So it is urgently needed to accelerate research and development for new antimicrobial systems and strategies. Recently, luminogens with aggregation-induced emission characteristics (AIEgens) have emerged as powerful fluorescent tools for microbial detection and antimicrobial therapy. In this review, we highlighted the latest advancements of AIEgen-based biofunctional materials and systems in this research field. AIE fluorescent probes have the advantages of excellent sensitivity and rapid response, which make them useful for ultrafast bacterial imaging, bacteria classification, and pathogen discrimination. Early microbial detection and identification could help us study the mechanism of antibiotic resistance more scientifically. Moreover, the AIEgens-based photosensitizers (AIE-PSs) with strong photosensitization show good performance on the efficient elimination of multidrug-resistant bacteria and intracellular bacteria. At the end of the review, a short perspective on aggregate science is concluded.

Portable Device for Quick Detection of Viable Bacteria in Water

(1) Background: Access to clean water is a very important factor for human life. However, pathogenic microorganisms in drinking water often cause diseases, and convenient/inexpensive testing methods are urgently needed. (2) Methods: The reagent contains 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and phenazine methosulfate (PMS) and can react with succinate dehydrogenase within bacterial cell membranes to produce visible purple crystals. The colorimetric change of the reagent after reaction can be measured by a sensor (AS7262). (3) Results: Compared with traditional methods, our device is simple to operate and can provide rapid (i.e., 5 min) semi-quantitative results regarding the concentration of bacteria within a test sample. (4) Conclusions: This easy-to-use device, which employs MTT-PMS reagents, can be regarded as a potential and portable tool for rapid water quality determination.

The Application of Bacteriophage Diagnostics for Bacterial Pathogens in the Agricultural Supply Chain: From Farm-to-Fork

Bacteriophages (phages) have great potential not only as therapeutics but as diagnostics. Indeed, they have been developed and used to diagnose and detect bacterial infections, primarily in human clinical settings. The ability to rapidly detect and control bacterial pathogens in agriculture is of primary importance to maintain food security, improve animal health, and prevent the passage of zoonotic pathogens into the human population. Culture-based detection methods are often labor-intensive, and require further confirmatory tests, increasing costs and processing times needed for diagnostics. Molecular detection methods such as polymerase chain reaction are commonly used to determine the safety of food, however, a major drawback is their inability to differentiate between viable and nonviable bacterial pathogens in food. Phage diagnostics have been proven to be rapid, capable of identifying viable pathogens and do not require cultivation to detect bacteria. Phage detection takes advantage of the specificity of interaction between phage and their hosts. Furthermore, phage detection is cost effective, which is vitally important in agricultural supply chains where there is a drive to keep costs down to ensure that the cost of food does not increase. The full potential of phage detection/diagnostics is not wholly realized or commercialized. This review explores the current use and potential future scope of phage diagnostics and their application to various bacterial pathogens across agriculture and food supply chains.

A Systematic Review of Food Allergy: Nanobiosensor and Food Allergen Detection

Several individuals will experience accidental exposure to an allergen. In this sense, the industry has invested in the processes of removing allergenic compounds in food. However, accidental exposure to allergenic proteins can result from allergenic substances not specified on labels. Analysis of allergenic foods is involved in methods based on immunological, genetic, and mass spectrometry. The traditional methods have some limitations, such as high cost. In recent years, biosensor and nanoparticles combined have emerged as sensitive, selective, low-cost, and time-consuming techniques that can replace classic techniques. Nevertheless, each nanomaterial has shown a different potential to specific allergens or classes. This review used Preferred Reporting Items for Systematic Reviews and the Meta-Analysis guidelines (PRISMA) to approach these issues. A total of 104 articles were retrieved from a standardized search on three databases (PubMed, Scopus and Web of Science). The systematic review article is organized by the category of allergen detection and nanoparticle detection. This review addresses the relevant biosensors and nanoparticles as gold, carbon, graphene, quantum dots to allergen protein detection. Among the selected articles it was possible to notice a greater potential application on the allergic proteins Ah, in peanuts and gold nanoparticle-base as a biosensor. We envision that in our review, the association between biosensor and nanoparticles has shown promise in the analysis of allergenic proteins present in different food samples.