Advances in aptamer-based biosensors for monitoring foodborne pathogens

Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05889-8.

Microfluidic paper analytic device (μPAD) technology for food safety applications

Foodborne pathogens, food adulterants, allergens, and toxic chemicals in food can cause major health hazards to humans and animals. Stringent quality control measures at all stages of food processing are required to ensure food safety. There is, therefore, a global need for affordable, reliable, and rapid tests that can be conducted at different process steps and processing sites, spanning the range from the sourcing of food to the end-product acquired by the consumer. Current laboratory-based food quality control tests are well established, but many are not suitable for rapid on-site investigations and are costly. Microfluidic paper analytical devices (μPADs) are a fast-growing field in medical diagnostics that can fill these gaps. In this review, we describe the latest developments in the applications of microfluidic paper analytic device (μPAD) technology in the food safety sector. State-of-the-art μPAD designs and fabrication methods, microfluidic assay principles, and various types of μPAD devices with food-specific applications are discussed. We have identified the prominent research and development trends and future directions for maximizing the value of microfluidic technology in the food sector and have highlighted key areas for improvement. We conclude that the μPAD technology is promising in food safety applications by using novel materials and improved methods to enhance the sensitivity and specificity of the assays, with low cost.

Paper-Based Aptasensors: Working Principles, Detection Modes, and Applications

Aptamers are short oligonucleotides designed to possess high binding affinity towards specific target compounds (ions, molecules, or cells). Due to their function and unique advantages, aptamers are considered viable alternatives to antibodies as biorecognition elements in bioassays and biosensors. On the other hand, paper-based devices (PADs) have emerged as a promising and powerful technology for the fabrication of low-cost analytical tools, mainly intended for on-site and point-of-care applications. The present work aims to provide a comprehensive overview of paper-based aptasensors. The review describes the fabrication methods and working principles of paper-based devices, the properties of aptamers as bioreceptors, the different modes of detection used in conjunction with aptasensing PADs, and representative applications for the detection of ions, small molecules, proteins, and cells. The future challenges and prospects of these devices are also discussed.

Recent Progress and Challenges on the Microfluidic Assay of Pathogenic Bacteria Using Biosensor Technology

Microfluidic technology is one of the new technologies that has been able to take advantage of the specific properties of micro and nanoliters, and by reducing the costs and duration of tests, it has been widely used in research and treatment in biology and medicine. Different materials are often processed into miniaturized chips containing channels and chambers within the microscale range. This review (containing 117 references) demonstrates the significance and application of nanofluidic biosensing of various pathogenic bacteria. The microfluidic application devices integrated with bioreceptors and advanced nanomaterials, including hyperbranched nano-polymers, carbon-based nanomaterials, hydrogels, and noble metal, was also investigated. In the present review, microfluid methods for the sensitive and selective recognition of photogenic bacteria in various biological matrices are surveyed. Further, the advantages and limitations of recognition methods on the performance and efficiency of microfluidic-based biosensing of photogenic bacteria are critically investigated. Finally, the future perspectives, research opportunities, potential, and prospects on the diagnosis of disease related to pathogenic bacteria based on microfluidic analysis of photogenic bacteria are provided.

Microfluidic Paper-Based Analytical Devices for the Determination of Food Contaminants: Developments and Applications

Food safety is an issue that cannot be ignored at any time because of the great impact of food contaminants on people's daily life, social production, and the economy. Because of the extensive demand for high-quality food, it is necessary to develop rapid, reliable, and efficient devices for food contaminant detection. Microfluidic paper-based analytical devices (μPADs) have been applied in a variety of detection fields owing to the advantages of low-cost, ease of handling, and portability. This review systematically discusses the latest progress of μPADs, including the fundamentals of fabrication as well as applications in the detection of chemical and biological hazards in foods, hoping to provide suitable screening strategies for contaminants in foods and accelerating the technology transformation of μPADs from the lab into the field.

Nanomaterial-assisted microfluidics for multiplex assays

Simultaneous detection of different biomarkers from a single specimen in a single test, allowing more rapid, efficient, and low-cost analysis, is of great significance for accurate diagnosis of disease and efficient monitoring of therapy. Recently, developments in microfabrication and nanotechnology have advanced the integration of nanomaterials in microfluidic devices toward multiplex assays of biomarkers, combining both the advantages of microfluidics and the unique properties of nanomaterials. In this review, we focus on the state of the art in multiplexed detection of biomarkers based on nanomaterial-assisted microfluidics. Following an overview of the typical microfluidic analytical techniques and the most commonly used nanomaterials for biochemistry analysis, we highlight in detail the nanomaterial-assisted microfluidic strategies for different biomarkers. These highly integrated platforms with minimum sample consumption, high sensitivity and specificity, low detection limit, enhanced signals, and reduced detection time have been extensively applied in various domains and show great potential in future point-of-care testing and clinical diagnostics.

ASSURED Point-of-Need Food Safety Screening: A Critical Assessment of Portable Food Analyzers

Standard methods for chemical food safety testing in official laboratories rely largely on liquid or gas chromatography coupled with mass spectrometry. Although these methods are considered the gold standard for quantitative confirmatory analysis, they require sampling, transferring the samples to a central laboratory to be tested by highly trained personnel, and the use of expensive equipment. Therefore, there is an increasing demand for portable and handheld devices to provide rapid, efficient, and on-site screening of food contaminants. Recent technological advancements in the field include smartphone-based, microfluidic chip-based, and paper-based devices integrated with electrochemical and optical biosensing platforms. Furthermore, the potential application of portable mass spectrometers in food testing might bring the confirmatory analysis from the laboratory to the field in the future. Although such systems open new promising possibilities for portable food testing, few of these devices are commercially available. To understand why barriers remain, portable food analyzers reported in the literature over the last ten years were reviewed. To this end, the analytical performance of these devices and the extent they match the World Health Organization benchmark for diagnostic tests, i.e., the Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable to end-users (ASSURED) criteria, was evaluated critically. A five-star scoring system was used to assess their potential to be implemented as food safety testing systems. The main findings highlight the need for concentrated efforts towards combining the best features of different technologies, to bridge technological gaps and meet commercialization requirements.

A novel microfluidic system for the sensitive and cost-effective detection of okadaic acid in mussels

Okadaic acid (OA) is produced by marine dinoflagellates and it can be easily accumulated in shellfish, causing intoxications when consumed by humans. Consequently, there is a need for sensitive, reliable and cost-effective methods to detect OA in real samples. In this work, we developed a novel and affordable microfluidic system to detect OA based on the protein phosphatase 1 inhibition colorimetric assay. This enzyme was immobilized in a microfluidic chamber by physisorption in an alumina sol-gel. The results show good enzyme stability over time when maintained at 4 °C. The developed system was sensitive for OA standard solutions, presenting a limit of detection (LOD) of 11.6 nM over a large linear range (43.4 to 3095.8 nM). Our method revealed an LOD as low as 0.2 μg kg-1 and a linear range between 1.47 and 506 μg kg-1 for extracted mussel matrix, detecting OA concentrations in contaminated mussels much lower than the regulated limit (160 μg kg-1). The enzyme stability and reusability along with the simplicity and low cost associated with microfluidics systems make this method very interesting from a commercial point of view.

Microfluidic thread-based electrochemical aptasensor for rapid detection of Vibrio parahaemolyticus

Vibrio parahaemolyticus is one of the foodborne bacteria that widely present in seafood as well as the leading cause of seafood-associated bacterial gastroenteritis. Traditional identification of such pathogens mainly relies on culturing methods, ELISA or PCR. These methods are usually laborious, time-consuming with poor diagnosis competences, or require costly and bulky equipment though of high sensitivity. In this study, a thread-based microfluidic electrochemical aptasensor was designed, fabricated and tested by using label-free aptamer immunosensing technology for rapid and highly sensitive detection of Vibrio parahaemolyticus in seafood. Both the microfluidic channels and electrodes were simply fabricated on threads. Molybdenum disulfide (MoS₂) nanosheets were used to obtain enhanced sensitivity of the electrochemical measurement. When used in detecting Vibrio parahaemolyticus, the proposed aptasensor has a dynamic detection range of 10-10⁶ CFU mL^-1 with a detection limit of 5.74 CFU mL^-1. Compared with traditional plate counting method, the proposed aptasensor has higher detection sensitivity and less assay time (30 min), while high specificity and accuracy are kept. The proposed microfluidic thread-based electrochemical aptasensor grabs the potential to detect other pathogens by simply functionalizing the threaded electrodes with aptamers for targeted biological substances.

Graphene-Based FRET Aptasensors

Graphene-based FRET aptasensors can be realized only by unique combinations of aptamer that can be freely functionalized by chemical modification, and graphene/graphene oxide that works as an excellent fluorescence acceptor at the same time as aptamer adsorbates. This review describes the principles of the sensor, several applications to microchannel devices, improvement of the sensing performance by molecular design of the aptamer and remarks on future prospects based on an introduction of recent works and achievements, including the author's paper. The sensor employs DNA modified with graphene/graphene oxide at the terminal as the molecular probe. This system is supported by the excellent property of DNA that does not lose the molecular recognition ability even due to a chemical modification at the terminal. I hope that this review will be useful for developing research on higher performance of graphene aptasensors in the future.

Application of Multiplexed Aptasensors in Food Contaminants Detection

The existence of contaminants in food poses a serious threat to human health. In recent years, aptamer sensors (aptasensors) have been developed rapidly for the detection of food contaminants because of their high specificity, design flexibility, and high efficiency. However, the development of high-throughput, highly sensitive, on-site, and cost-effective methods for simultaneous detection of food contaminants is still restricted due to multiple signal overlap or mutual interference and cross-reaction between different analytes with similar molecular structures. To overcome these problems, this Review summarizes some effective strategies from the articles published in recent years about multiplexed aptasensors for the simultaneous detection of food contaminants. This work focuses on the application of multiplexed aptasensors to simultaneously detect antibiotics, pathogens, and mycotoxins in food. These aptasensors mainly contain fluorescent aptasensors, electrochemical aptasensors, surface-enhanced Raman scattering-based aptasensors, microfluidic chip aptasensors, and paper-based multiplexed aptasensors. In addition, this Review also covers the application of nucleic acid cycle amplification and nanomaterial amplification strategies to improve the detection sensitivity. Finally, the limitations and challenges in the design of multiplexed aptasensor are also taken into account.

Recent progress in micro/nano biosensors for shellfish toxin detection

Shellfish toxins, as one kind of marine toxin, have attracted worldwide attention due to their severe threat to food safety and human health. Therefore, it is highly essential and urgent to develop a low-cost and convenient method to detect these toxins. With the rapid advance in microfabrication processes, micro/nano biosensors provide novel approaches to address this issue. In addition to their features of low cost, portability, easy operation, high efficiency and high bioactivity, micro/nano biosensors have great potential to realize on-the-spot, rapid detection of shellfish toxins. This review focuses on the most recent advances in the development of micro/nano biosensors for shellfish toxin detection. These biosensors are mainly classified into five categories according to their transducer detection principles, which include optical devices, electrochemical sensors, electrochemiluminescence, field-effect transistors, and acoustic devices. Sensor strategies, toxin analytes, biosensitive elements, coupling methods and field detection performance are highlighted to discuss the applications of shellfish toxin detection. With advances in sensor technology, biomaterials, microfabrication and miniaturized electronics, micro/nano biosensors applied to in-field fast detection of shellfish toxins are expected to play a critical role in food safety, environmental monitoring, and foreign trade in the foreseeable future. Finally, the current challenges and future development trends of micro/nano biosensors for shellfish toxin detection are discussed.

Paper-based microfluidic aptasensors

For in-situ disease markers detection, point-of-care (POC) diagnosis has great advantages in speed and cost compared with traditional techniques. The rapid diagnosis, prognosis, and surveillance of diseases can significantly reduce disease-related mortality and trauma. Therefore, increasing attention has been paid to the POC diagnosis devices due to their excellent diagnosis speed and portability. Over the past ten years, paper-based microfluidic aptasensors have emerged as a class of critical POC diagnosis devices and various aptasensors have been proposed to detect various disease markers. However, most aptasensors need further improvement before they can actually enter the market and be widely used. There is thus an urgent need to sort out the key points of preparing the aptasensors and the direction that needs to be invested in. This review summarizes the representative articles in the development of paper-based microfluidic aptasensors. These works can be divided into paper-based optical aptasensors and paper-based electrochemical aptasensors according to their output signals. Significant focus is applied to these works according to the following three parts: (1) The ingenious design of device structure; (2) Application and synthesis of nanomaterial; (3) The detection principle of the proposed aptasensor. This is a detailed and comprehensive review of paper-based microfluidic aptasensors. The accomplishments and shortcomings of the current aptasensors are outlined, the development direction and the future prospective are given. It is hoped that the research in this review can provide a reference for further development of more advanced, more effective paper-based microfluidic aptasensors for POC disease markers diagnosis.

Lab-on-a-Chip Systems for Aptamer-Based Biosensing

Aptamers are oligonucleotides or peptides that are selected from a pool of random sequences that exhibit high affinity toward a specific biomolecular species of interest. Therefore, they are ideal for use as recognition elements and ligands for binding to the target. In recent years, aptamers have gained a great deal of attention in the field of biosensing as the next-generation target receptors that could potentially replace the functions of antibodies. Consequently, it is increasingly becoming popular to integrate aptamers into a variety of sensing platforms to enhance specificity and selectivity in analyte detection. Simultaneously, as the fields of lab-on-a-chip (LOC) technology, point-of-care (POC) diagnostics, and personal medicine become topics of great interest, integration of such aptamer-based sensors with LOC devices are showing promising results as evidenced by the recent growth of literature in this area. The focus of this review article is to highlight the recent progress in aptamer-based biosensor development with emphasis on the integration between aptamers and the various forms of LOC devices including microfluidic chips and paper-based microfluidics. As aptamers are extremely versatile in terms of their utilization in different detection principles, a broad range of techniques are covered including electrochemical, optical, colorimetric, and gravimetric sensing as well as surface acoustics waves and transistor-based detection.

Thread-based isoelectric focusing coupled with desorption electrospray ionization mass spectrometry

Efficient ‘on-thread’ isoelectric focusing of proteins, with direct on-thread detection using desorption electrospray ionisation mass spectrometry.

Microfluidic-Based Approaches for Foodborne Pathogen Detection

Food safety is of obvious importance, but there are frequent problems caused by foodborne pathogens that threaten the safety and health of human beings worldwide. Although the most classic method for detecting bacteria is the plate counting method, it takes almost three to seven days to get the bacterial results for the detection. Additionally, there are many existing technologies for accurate determination of pathogens, such as polymerase chain reaction (PCR), enzyme linked immunosorbent assay (ELISA), or loop-mediated isothermal amplification (LAMP), but they are not suitable for timely and rapid on-site detection due to time-consuming pretreatment, complex operations and false positive results. Therefore, an urgent goal remains to determine how to quickly and effectively prevent and control the occurrence of foodborne diseases that are harmful to humans. As an alternative, microfluidic devices with miniaturization, portability and low cost have been introduced for pathogen detection. In particular, the use of microfluidic technologies is a promising direction of research for this purpose. Herein, this article systematically reviews the use of microfluidic technology for the rapid and sensitive detection of foodborne pathogens. First, microfluidic technology is introduced, including the basic concepts, background, and the pros and cons of different starting materials for specific applications. Next, the applications and problems of microfluidics for the detection of pathogens are discussed. The current status and different applications of microfluidic-based technologies to distinguish and identify foodborne pathogens are described in detail. Finally, future trends of microfluidics in food safety are discussed to provide the necessary foundation for future research efforts.

Improving quantitative control and homogeneous distribution of samples on paper-based analytical devices via drop-on-demand inkjet printing

A standard desktop printer with multiple ink cartridges can accurately deposit a broad variety of biomaterials on microfluidic paper-based analytical devices (μPADs) which have been extensively applied to environmental monitoring and screening of food and beverage contamination. Finding ways to realize sample quantitative control by tuning the CMYK value, however, remains challenging. Herein, we studied the influence of the CMYK value on the ink volume jetted by ink cartridges. The regularity research on a single-color and two-colors was performed in two print mode-grayscale printing and color printing. The results demonstrated that the number of ink dots increased with the increase of the gray value and opacity value, which means that the amount of the bio-ink increases with the increase of the CMYK value. The 3,3',5,5'-tetramethylbenzidine-horseradish peroxidase-hydrogen peroxide, glucose oxidase-horseradish peroxidase and bull serum albumin-citrate buffer-tetrabromophenol blue systems were chosen as examples to prove the print regularity. Samples and assay reagents can be quantitatively deposited on a substrate by adjusting the CMYK value with as many as four ink cartridges. The present approach has been successfully applied to assay the targets in real serum samples, showing the potential application of the most common office piezoelectric printer in μPADs.

Recent advances in thread-based microfluidics for diagnostic applications

Over the past decades, researchers have been seeking attractive substrate materials to keep microfluidics improving to outbalance the drawbacks and issues. Cellulose substrates, including thread, paper and hydrogels are alternatives due to their distinct structural and mechanical properties for a number of applications. Thread have gained considerable attention and become promising powerful tool due to its advantages over paper-based systems thus finds numerous applications in the development of diagnostic systems, smart bandages and tissue engineering. To the best of our knowledge, no comprehensive review articles on the topic of thread-based microfluidics have been published and it is of significance for many scientific communities working on Microfluidics, Biosensors and Lab-on-Chip. This review gives an overview of the advances of thread-based microfluidic diagnostic devices in a variety of applications. It begins with an overall introduction of the fabrication followed by an in-depth review on the detection techniques in such devices and various applications with respect to effort and performance to date. A few perspective directions of thread-based microfluidics in its development are also discussed. Thread-based microfluidics are still at an early development stage and further improvements in terms of fabrication, analytical strategies, and function to become low-cost, low-volume and easy-to-use point-of-care (POC) diagnostic devices that can be adapted or commercialized for real world applications.

Phosphorene-gold nanocomposite based microfluidic aptasensor for the detection of okadaic acid

Okadaic acid (OA) is one of the most prevalent and largely distributed bio-toxin in the world. Consumption of OA results in a series of digestive ailments such as nausea and diarrhea. This study demonstrates the preparation and functioning of an electrochemical microfluidic biochip for the detection of OA. The screen-printed carbon electrode (SPCE) was modified by phosphorene-gold nanocomposite onto which an aptamer specific to OA was immobilized. BP-Au nanocomposites were synthesized by an in-situ, one-step method without the use of a reducing agent. Potassium ferro-ferri cyanide was used as a redox pair to quantify signal strength. To improve reaction time, increase sensitivity and portability, a microfluidic platform was designed and developed. This device comprised of channels identified for specific purposes such as sample mixing and incubation. Overall, the integrated system consisted of a polydimethylsiloxane microfluidic chip housing an aptamer modified SPCE, as a single detection module for Okadaic acid. The nanomaterials and the microfluidic channels prepared were spectroscopically and electrochemically analyzed. Differential pulse voltammograms revealed a detection limit of 8 pM, while a linear range was found between 10 nM-250 nM. Selectivity studies were also performed with spiked mussel samples and other interfering species. This point-of-care device can be deployed to perform on-farm assays in fishing units.

Microfluidic technology for plankton research

Plankton produces numerous chemical compounds used in cosmetics and functional foods. They also play a key role in the carbon budget on the Earth. In a context of global change, it becomes important to understand the physiological response of these microorganisms to changing environmental conditions. Their adaptations and the response to specific environmental conditions are often restricted to a few active cells or individuals in large populations. Using analytical capabilities at the subnanoliter scale, microfluidic technology has also demonstrated a high potential in biological assays. Here, we review recent advances in microfluidic technologies to overcome the current challenges in high content analysis both at population and the single cell level.

Recent Microdevice-Based Aptamer Sensors

Since the systematic evolution of ligands by exponential enrichment (SELEX) method was developed, aptamers have made significant contributions as bio-recognition sensors. Microdevice systems allow for low reagent consumption, high-throughput of samples, and disposability. Due to these advantages, there has been an increasing demand to develop microfluidic-based aptasensors for analytical technique applications. This review introduces the principal concepts of aptasensors and then presents some advanced applications of microdevice-based aptasensors on several platforms. Highly sensitive detection techniques, such as electrochemical and optical detection, have been integrated into lab-on-a-chip devices and researchers have moved towards the goal of establishing point-of-care diagnoses for target analyses.

Detecting Chemical Hazards in Foods Using Microfluidic Paper-Based Analytical Devices (μPADs): The Real-World Application

Food safety remains one of the most important issues in most countries and the detection of food hazards plays a key role in the systematic approach to ensuring food safety. Rapid, easy-to-use and low-cost analytical tools are required to detect chemical hazards in foods. As a promising candidate, microfluidic paper-based analytical devices (μPADs) have been rarely applied to real food samples for testing chemical hazards, although numerous papers have been published in this field in the last decade. This review discusses the current status and concerns of the μPAD applications in the detection of chemical hazards in foods from the perspective of food scientists, mainly for an audience with a background in mechanical and chemical engineering who may have interests in exploring the potential of μPAD to address real-world food safety issues.