Label-free visual biosensor based on cascade amplification for the detection of Salmonella

Aptamer-mediated double strand displacement amplification with microchip electrophoresis for ultrasensitive detection of Salmonella typhimurium

Rapid and quantitative detection of foodborne bacteria is of great significance to public health. In this work, an aptamer-mediated double strand displacement amplification (SDA) strategy was first explored to couple with microchip electrophoresis (MCE) for rapid and ultrasensitive detection of Salmonella typhimurium (S. Typhimurium). In double-SDA, a bacteria-identified probe consisting of the aptamer (Apt) and trigger sequence (Tr) was ingeniously designed. The aptamer showed high affinity to the S. Typhimurium, releasing the Tr sequence from the probe. The released Tr hybridized with template C1 chain, initiating the first SDA to produce numerous output strands (OS). The second SDA process was induced with the hybridization of the liberated OS and template C2 sequence, generating a large number of reporter strands (RS), which were separated and quantified through MCE. Cascade signal amplification and rapid separation of nucleic acids could be realized by the proposed double-SDA method with MCE, achieving the limit of detection for S. typhimurium down to 6 CFU/mL under the optimal conditions. Based on the elaborate design of the probes, the double-SDA assisted MCE strategy achieved better amplification performance, showing high separation efficiency and simple operation, which has satisfactory expectation for bacterial disease diagnosis.

Recombinase Polymerase Amplification-Based Biosensors for Rapid Zoonoses Screening

Recent, outbreaks of new emergency zoonotic diseases have prompted an urgent need to develop fast, accurate, and portable screening assays for pathogen infections. Recombinase polymerase amplification (RPA) is sensitive and specific and can be conducted at a constant low temperature with a short response time, making it especially suitable for on-site screening and making it a powerful tool for preventing or controlling the spread of zoonoses. This review summarizes the design principles of RPA-based biosensors as well as various signal output or readout technologies involved in fluorescence detection, lateral flow assays, enzymatic catalytic reactions, spectroscopic techniques, electrochemical techniques, chemiluminescence, nanopore sequencing technologies, microfluidic digital RPA, and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems. The current status and prospects of the application of RPA-based biosensors in zoonoses screening are highlighted. RPA-based biosensors demonstrate the advantages of rapid response, easy-to-read result output, and easy implementation for on-site detection, enabling development toward greater portability, automation, and miniaturization. Although there are still problems such as high cost with unstable signal output, RPA-based biosensors are increasingly becoming one of the most important means of on-site pathogen screening in complex samples involving environmental, water, food, animal, and human samples for controlling the spread of zoonotic diseases.

Applications of Terminal Deoxynucleotidyl Transferase Enzyme in Biotechnology

The use of polymerase enzymes in biotechnology has allowed us to gain unprecedented control over the manipulation of DNA, opening up new and exciting applications in areas such as biosensing, polynucleotide synthesis, and DNA storage, aptamer development and DNA-nanotechnology. One of the most intriguing enzymes which has gained prominence in the last decade is terminal deoxynucleotidyl transferase (TdT), which is one of the only polymerase enzymes capable of catalysing the template independent stepwise addition of nucleotides onto an oligonucleotide chain. This unique enzyme has seen a significant increase in a variety of different applications. In this review, we give a comprehensive discussion of the unique properties and applications of TdT as a biotechnology tool, and the application in the enzymatic synthesis of poly/oligonucleotides. Finally, we look at the increasing role of TdT enzyme in biosensing, DNA storage, synthesis of DNA nanostructures and aptamer development, and give a future outlook for this technology.

Low-cost, point-of-care biomarker quantification

Low-cost, point-of-care (POC) devices that allow fast, on-site disease diagnosis could have a major global health impact, particularly if they can provide quantitative measurement of molecules indicative of a diseased state (biomarkers). Accurate quantification of biomarkers in patient samples is already challenging when research-grade, sophisticated equipment is available; it is even more difficult when constrained to simple, cost-effective POC platforms. Here, we summarize the main challenges to accurate, low-cost POC biomarker quantification. We also review recent efforts to develop and implement POC tools beyond qualitative readouts, and we conclude by identifying important future research directions.

Colorimetric detection of Salmonella typhimurium based on hexadecyl trimethyl ammonium bromide-induced supramolecular assembly of β-cyclodextrin-capped gold nanoparticles

We developed an effective and specific colorimetric strategy to detect Salmonella typhimurium (S. typhimurium) based on hexadecyl trimethyl ammonium bromide (CTAB)-induced supramolecular assembly of β-cyclodextrin-capped gold nanoparticles (β-CD-AuNPs). In this study, ssDNA aptamer of S. typhimurium could combine with CTAB to form the supramolecular ssDNA-CTAB composite, so the ssDNA aptamer was applied to control the concentration of CTAB. In the presence of S. typhimurium, ssDNA aptamers selectively bound to S. typhimurium but not to CTAB, leading to the host-guest chemistry reaction of CTAB and β-CD resulting in β-CD-AuNP supramolecular assembly aggregation with an obvious color change. The ratio of absorption at 650 and 520 nm (A_650nm/A_520nm) has a linear correlation to the log scale of the concentration of the bacteria (1 × 10²-1 × 10⁷ CFU/mL) with a low limit of detection (LOD) of 13 CFU/mL. In addition, this optical sensor has good selectivity and practicability. In milk samples, the recovery was 93.55-111.32%, which suggested its potential application in real samples.

Recombinase polymerase amplification in the molecular diagnosis of microbiological targets and its applications

Since the introduction of the polymerase chain reaction (PCR) technique in 1983, nucleic acid amplification has permeated all fields of biological science, particularly clinical research. Despite its importance, PCR has been restricted to specialized centers and its use in laboratories with few resources is limited. In recent decades, there has been a notable increase in the development of new isothermal technologies for molecular diagnosis with the hope of overcoming the traditional limitations of the laboratory. Among these technologies, recombinase polymerase amplification (RPA) has a wide application potential because it does not require thermocyclers and has high sensitivity, specificity, simplicity, and detection speed. This technique has been used for DNA and RNA amplification in various pathogenic organisms such as viruses, bacteria, and parasites. In addition, RPA has been successfully implemented in different detection strategies, making it a promising alternative for performing diagnoses in environments with scarce resources and a high burden of infectious diseases. In this study, we present a review of the use of RPA in clinical settings and its implementation in various research areas.

Biosensor Technologies in Medicine: from Detection of Biochemical Markers to Research into Molecular Targets (Review)

Infections are a major cause of premature death. Fast and accurate laboratory diagnostics of infectious diseases is a key condition for the timely initiation and success of treatment. Potentially, it can reduce morbidity, as well as prevent the outbreak and spread of dangerous epidemics. The traditional methods of laboratory diagnostics of infectious diseases are quite time- and labour-consuming, require expensive equipment and trained personnel, which is crucial within limited resources. The fast biosensor-based methods that combine the diagnostic capabilities of biomedicine with modern technological advances in microelectronics, optoelectronics, and nanotechnology make an alternative.

The modern achievements in the development of label-free biosensors make them promising diagnostic tools that combine rapid detection of specific molecular markers, simplicity, ease-of-use, efficiency, accuracy, and cost-effectiveness with the tendency to the development of portable platforms. These qualities exceed the generally accepted standards of microbiological and immunological diagnostics and open up broad prospects for using these analytical systems in clinical practice directly at the site of medical care provision (point-of-care, POC concept).

A wide variety of modern biosensor designs are based on the use of diverse formats of analytical and technological strategies, identification of various regulatory and functional molecular markers associated with infectious pathogens. The solution to the existing problems in biosensing will open up great prospects for these rapidly developing diagnostic biotechnologies.

The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.

Biosensors Coupled with Signal Amplification Technology for the Detection of Pathogenic Bacteria: A Review

Foodborne disease caused by foodborne pathogens is a very important issue in food safety. Therefore, the rapid screening and sensitive detection of foodborne pathogens is of great significance for ensuring food safety. At present, many research works have reported the application of biosensors and signal amplification technologies to achieve the rapid and sensitive detection of pathogenic bacteria. Thus, this review summarized the use of biosensors coupled with signal amplification technology for the detection of pathogenic bacteria, including (1) the development, concept, and principle of biosensors; (2) types of biosensors, such as electrochemical biosensors, optical biosensors, microfluidic biosensors, and so on; and (3) different kinds of signal amplification technologies applied in biosensors, such as enzyme catalysis, nucleic acid chain reaction, biotin-streptavidin, click chemistry, cascade reaction, nanomaterials, and so on. In addition, the challenges and future trends for pathogenic bacteria based on biosensor and signal amplification technology were also discussed and summarized.

Recent advances in visual detection for cancer biomarkers and infectious pathogens

It is an urgency to detect infectious pathogens or cancer biomarkers using rapid, simple, convenient and cost-effective methods in complex biological samples. Many existing approaches (traditional virus culture, ELISA or PCR) for the pathogen and biomarker assays face several challenges in the clinical applications that require lengthy time, sophisticated sample pre-treatment and expensive instruments. Due to the simple and rapid detection manner as well as no requirement of expensive equipment, many visual detection methods have been considered to resolve the aforementioned problems. Meanwhile, various new materials and colorimetric/fluorescent methods have been tried to construct new biosensors for infectious pathogens and biomarkers. However, the recent progress of these aspects is rarely reviewed, especially in terms of integration of new materials, microdevice and detection mechanism into the visual detection systems. Herein, we provide a broad field of view to discuss the recent progress in the visual detection of infectious pathogens and cancer biomarkers along with the detection mechanism, new materials, novel detection methods, special targets as well as multi-functional microdevices and systems. The novel visual approaches for the infectious pathogens and biomarkers, such as bioluminescence resonance energy transfer (BRET), metal-induced metallization and clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensors, are discussed. Additionally, recent advancements in visual assays utilizing various new materials for proteins, nucleic acids, viruses, exosomes and small molecules are comprehensively reviewed. Future perspectives on the visual sensing systems for infectious pathogens and cancers are also proposed.

Integration of a Thermoelectric Heating Unit with Ionic Wind-Induced Droplet Centrifugation Chip to Develop Miniaturized Concentration Device for Rapid Determination of Salmonella on Food Samples Using Antibody-Functionalized SERS Tags

When a centrifugation-enriched sample of 100 μL containing the surface-enhanced Raman scattering (SERS) tag-bound bacteria (Salmonella in this study) is siphoned onto a glass slide next to an embedded thermoelectric heating chip, such a sessile droplet is quickly evaporated. As the size of the sample droplet is significantly reduced during the heating process, ionic wind streams from a corona discharge needle, stationed above the sample, sweep across the liquid surface to produce centrifugal vortex flow. Tag-bound Salmonella in the sample are then dragged and trapped at the center of droplet bottom. Finally, when the sample is dried, unlike the "coffee ring" effect, the SERS tag-bound Salmonella is concentrated in one small spot to allow sensitive detection of a Raman signal. Compared with our previous electrohydrodynamic concentration device containing only a corona discharge needle, this thermoelectric evaporation-assisted device is more time-effective, with the time of concentrating and drying about 100 μL sample reduced from 2 h to 30 min. Hence, sample throughput can be accelerated with this device for practical use. It is also more sensitive, with SERS detection of a few cells of Salmonella in neat samples achievable. We also evaluated the feasibility of using this device to detect Salmonella in food samples without performing the culturing procedures. Having spiked a few Salmonella cells into ice cubes and lettuce leaves, we use filtration and ultracentrifugation steps to obtain enriched tag-bound Salmonella samples of 200 μL. After loading an aliquot of 100 μL of sample onto this concentration device, the SERS tag signals from samples of 100 g ice cubes containing two Salmonella cells and 20 g lettuce leaf containing 5 Salmonella cells can be successfully detected.

Single universal primer recombinase polymerase amplification-based lateral flow biosensor (SUP-RPA-LFB) for multiplex detection of genetically modified maize

In this study, an isothermal paper biosensor, combining single universal primer recombinase polymerase amplification (SUP-RPA) and the lateral flow technique was developed for the multiplex detection of genetically modified maize (GMM). In pre-amplification stage, the event-specific primers contain a universal sequence at the 5' end, with a biotin-labeled deoxycytidine triphosphate (dCTP) deoxynucleotide providing additional amplification, which improves their amplification ability and ensures consistent multiplex amplification efficiency. In the signal recognition strategy, the SUP-RPA products are identified visually using the lateral flow biosensor (LFB) through dual hybridization. The accumulation of gold nanoparticles (AuNPs) produces a characteristic red band. Through this biosensor, a limit of detection of at least 50 copies was achieved, which is sensitive enough to detect MON810, MON863 and MON89034 simultaneously. The entire process of analysis was completed within 30 min and without any large-scale instrumentation. This biosensor, therefore, provides a novel rapid and portable multiple detection method for point-of-care applications, especially genetically modified organism (GMO) event-specific detection.

Combining impedance biosensor with immunomagnetic separation for rapid screening of Salmonella in poultry supply chains

Salmonella screening is a key to ensure food safety in poultry supply chains. Currently available Salmonella detection methods including culture, polymerase chain reaction and enzyme-linked immuno-sorbent assay could not achieve rapid, sensitive, and in-field detection. In this study, different strategies for separation and detection of Salmonella were proposed, compared, and improved based on our previous studies on immunomagnetic separation and impedance biosensor. First, the coaxial capillary for immunomagnetic separation of target bacteria was improved with less contamination, and 3 strategies based on the improved capillary and immunomagnetic nanoparticles were compared to separate the target bacteria from sample and form the magnetic bacteria. The experimental results showed that the strategy of capture in tube and separation in capillary was the most suitable with separation efficiency of approximately 88%. Then, the immune gold nanoparticles coated with urease were used to label the magnetic bacteria, resulting in the formation of enzymatic bacteria, which were injected into the capillary. After the urea was catalyzed by the urease on the enzymatic bacteria in the capillary, different electrodes were compared to measure the impedance of the catalysate and the screen-printed electrode with higher sensitivity and better stability was the most suitable. This impedance biosensor-based bacterial detection strategy was able to detect Salmonella as low as 102 CFU/mL in 2 h without complex operations. Compared to the gold standard culture method for practical screening of Salmonella in poultry supply chains, this proposed strategy had an accuracy of approximately 90% for 75 real poultry samples.

Label-Free Biosensors for Laboratory-Based Diagnostics of Infections: Current Achievements and New Trends

Infections pose a serious global public health problem and are a major cause of premature mortality worldwide. One of the most challenging objectives faced by modern medicine is timely and accurate laboratory-based diagnostics of infectious diseases. Being a key factor of timely initiation and success of treatment, it may potentially provide reduction in incidence of a disease, as well as prevent outbreak and spread of dangerous epidemics. The traditional methods of laboratory-based diagnostics of infectious diseases are quite time- and labor-consuming, require expensive equipment and qualified personnel, which restricts their use in case of limited resources. Over the past six decades, diagnostic technologies based on lateral flow immunoassay (LFIA) have been and remain true alternatives to modern laboratory analyzers and have been successfully used to quickly detect molecular ligands in biosubstrates to diagnose many infectious diseases and septic conditions. These devices are considered as simplified formats of modern biosensors. Recent advances in the development of label-free biosensor technologies have made them promising diagnostic tools that combine rapid pathogen indication, simplicity, user-friendliness, operational efficiency, accuracy, and cost effectiveness, with a trend towards creation of portable platforms. These qualities exceed the generally accepted standards of microbiological and immunological diagnostics and open up a broad range of applications of these analytical systems in clinical practice immediately at the site of medical care (point-of-care concept, POC). A great variety of modern nanoarchitectonics of biosensors are based on the use of a broad range of analytical and constructive strategies and identification of various regulatory and functional molecular markers associated with infectious bacterial pathogens. Resolution of the existing biosensing issues will provide rapid development of diagnostic biotechnologies.

Rapid strand replacement primer thermostat visual sensor based on Bst DNA polymerase and pyrophosphatase for detecting Vibrio parahaemolyticus

Vibrio parahaemolyticus is a major hidden danger of food safety. To develop a rapid, sensitive and on-site detecting method of Vibrio parahaemolyticus (V. parahaemolyticus), a strand replacement primer thermostat phosphate (SRPP) visual sensor was proposed, based on Bst DNA polymerase and pyrophosphatase. The novel strand replacement primer (SRP) facilitates chain substitution and to open a self-folding hairpin by adding region at its 3' end. Under the action of the SRP, a pair of external primers and two inner primers, target DNA is specifically amplified at 63 °C relies mainly on the hairpin. Many pyrophosphates (PPi) are simultaneously generated as by-products, which can be converted into phosphates (Pi) by pyrophosphatase for phosphomolybdate blue visual detection within 5 min. The proposed biosensor can detect 1.29 × 10³ copies of V. parahaemolyticus within 35 min.

Continuous-Flow Separation and Efficient Concentration of Foodborne Bacteria from Large Volume Using Nickel Nanowire Bridge in Microfluidic Chip

Separation and concentration of target bacteria has become essential to sensitive and accurate detection of foodborne bacteria to ensure food safety. In this study, we developed a bacterial separation system for continuous-flow separation and efficient concentration of foodborne bacteria from large volume using a nickel nanowire (NiNW) bridge in the microfluidic chip. The synthesized NiNWs were first modified with the antibodies against the target bacteria and injected into the microfluidic channel to form the NiNW bridge in the presence of the external arc magnetic field. Then, the large volume of bacterial sample was continuous-flow injected to the channel, resulting in specific capture of the target bacteria by the antibodies on the NiNW bridge to form the NiNW–bacteria complexes. Finally, these complexes were flushed out of the channel and concentrated in a lower volume of buffer solution, after the magnetic field was removed. This bacterial separation system was able to separate up to 74% of target bacteria from 10 mL of bacterial sample at low concentrations of ≤10² CFU/mL in 3 h, and has the potential to separate other pathogenic bacteria from large volumes of food samples by changing the antibodies.