Highly specific and cost-efficient detection of Salmonella Paratyphi A combining aptamers with single-walled carbon nanotubes

Wastewater-born eviruses and bacteria, surveillance and biosensors at the interface of academia and field deployment

Wastewater is a complex, but an ideal, matrix for disease monitoring and surveillance as it represents the entire load of enteric pathogens from a local catchment area. It captures both clinical and community disease burdens. Global interest in wastewater surveillance has been growing rapidly for infectious diseases monitoring and for providing an early warning of potential outbreaks. Although molecular detection methods show high sensitivity and specificity in pathogen monitoring from wastewater, they are strongly limited by challenges, including expensive laboratory settings and prolonged sample processing and analysis. Alternatively, biosensors exhibit a wide range of practical utility in real-time monitoring of biological and chemical markers. However, field deployment of biosensors is primarily challenged by prolonged sample processing and pathogen concentration steps due to complex wastewater matrices. This review summarizes the role of wastewater surveillance and provides an overview of infectious viral and bacterial pathogens with cutting-edge technologies for their detection. It emphasizes the practical utility of biosensors in pathogen monitoring and the major bottlenecks for wastewater surveillance of pathogens, and overcoming approaches to field deployment of biosensors for real-time pathogen detection. Furthermore, the promising potential of novel machine learning algorithms to resolve uncertainties in wastewater data is discussed.

Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification

Early and accurate diagnoses of pathogenic microorganisms is essential to correctly identify diseases, treating infections, and tracking disease outbreaks associated with microbial infections, to develop precautionary measures that allow a fast and effective response in epidemics and pandemics, thus improving public health. Aptamers are a class of synthetic nucleic acid molecules with the potential to be used for medical purposes, since they can be directed towards any target molecule. Currently, the use of aptamers has increased because they are a useful tool in the detection of specific targets. We present a brief review of the use of aptamers to detect and identify bacteria or even some toxins with clinical importance. This work describes the advances in the technology of aptamers, with the purpose of providing knowledge to develop new aptamers for diagnoses and treatment of different diseases caused by infectious microorganisms.

Future of Nanotechnology in Food Industry: Challenges in Processing, Packaging, and Food Safety

Over the course of the last several decades, nanotechnology has garnered a growing amount of attention as a potentially valuable technology that has significantly impacted the food industry. Nanotechnology helps in enhancing the properties of materials and structures that are used in various fields such as agriculture, food, pharmacy, and so on. Applications of nanotechnology in the food market have included the encapsulation and distribution of materials to specific locations, the improvement of flavor, the introduction of antibacterial nanoparticles into food, the betterment of prolonged storage, the detection of pollutants, enhanced storage facilities, locating, identifying, as well as consumer awareness. Labeling food goods with nano barcodes helps ensure their security and may also be used to track their distribution. This review article presents a discussion about current advances in nanotechnology along with its applications in the field of food-tech, food packaging, food security, enhancing life of food products, etc. A detailed description is provided about various synthesis routes of nanomaterials, that is, chemical, physical, and biological methods. Nanotechnology is a rapidly improving the field of food packaging and the future holds great opportunities for more enhancement via the development of new nanomaterials and nanosensors.

Aptamer-Assisted Proximity Ligation Assay for Sensitive Detection of Infectious Bronchitis Coronavirus

Infectious bronchitis virus (IBV) is a coronavirus responsible for major health problems in the poultry industry. New virus strains continue to appear, causing large economic losses. To develop a rapid and accurate new quantitative assay for diagnosis of the virus without DNA extraction, we selected highly specific single-stranded DNA (ssDNA) aptamers with a high affinity to IBV, using the systematic evolution of ligands by exponential enrichment (SELEX) technology for aptamer screening, followed by high-throughput sequencing technology. Two of these aptamers, AptIBV5 and AptIBV2, were used to establish homogenous and solid-phase proximity ligation assays (PLAs). The developed assays were evaluated for their sensitivity and specificity using collected field samples and then compared to the newly developed sandwich enzyme-linked aptamer assay (ELAA) and reverse transcription-quantitative PCR (qRT-PCR), as the gold-standard method. The solid-phase PLA showed a lower limit of detection and a broader dynamic range than the two other assays. The developed technique may serve as an alternative assay for the diagnosis of IBV, with the potential to be extended to the detection of other important animal or human viruses. IMPORTANCE Infectious bronchitis virus (IBV) causes high morbidity and mortality and large economic losses in the poultry industry. The virus has the ability to genetically mutate into new IBV strains, causing devastating disease and outbreaks. To better monitor the emergence of this virus, the development of a rapid and highly sensitive diagnostic method should be implemented. For this, we generated aptamers with high affinity and specificity to the IBV in an ssDNA library. Using two high-affinity aptamers, we developed a sandwich ELAA and a very sensitive aptamer-based proximity ligation assay (PLA). The new assay showed high sensitivity and specificity and was used to detect IBV in farm samples. The PLA was compared to the newly developed sandwich ELAA and qRT-PCR, as the gold-standard technique.

Nanomaterials for optical biosensors in forensic analysis

Biosensors are compact analytical devices capable of transducing a biological interaction event into a measurable signal outcome in real-time. They can provide sensitive and affordable analysis of samples without the need for additional laboratory equipment or complex preparation steps. Biosensors may be beneficial for forensic analysis as they can facilitate large-scale high-throughput, sensitive screening of forensic samples to detect target molecules that are of high evidential value. Nanomaterials are gaining attention as desirable components of biosensors that can enhance detection and signal efficiency. Biosensors that incorporate nanomaterials within their design have been widely reported and developed for medical purposes but are yet to find routine employment within forensic science despite their proven potential. In this article, key examples of the use of nanomaterials within optical biosensors designed for forensic analysis are outlined. Their design and mechanism of detection are both considered throughout, discussing how nanomaterials can enhance the detection of the target analyte. The critical evaluation of the optical biosensors detailed within this review article should help to guide future optical biosensor design via the incorporation of nanomaterials, for not only forensic analysis but alternative analytical fields where such biosensors may prove a valuable addition to current workflows.

Aptamer-based NanoBioSensors for seafood safety

Chemical and biological contaminants are of primary concern in ensuring seafood safety. Rapid detection of such contaminants is needed to keep us safe from being affected. For over three decades, immunoassay (IA) technology has been used for the detection of contaminants in seafood products. However, limitations inherent to antibody generation against small molecular targets that cannot elicit an immune response, along with the instability of antibodies under ambient conditions greatly limit their wider application for developing robust detection and monitoring tools, particularly for non-biomedical applications. As an alternative, aptamer-based biosensors (aptasensors) have emerged as a powerful yet robust analytical tool for the detection of a wide range of analytes. Due to the high specificity of aptamers in recognising targets ranging from small molecules to large proteins and even whole cells, these have been suggested to be viable molecular recognition elements (MREs) in the development of new diagnostic and biosensing tools for detecting a wide range of contaminants including heavy metals, antibiotics, pesticides, pathogens and biotoxins. In this review, we discuss the recent progress made in the field of aptasensors for detection of contaminants in seafood products with a view of effectively managing their potential human health hazards. A critical outlook is also provided to facilitate translation of aptasensors from academic laboratories to the mainstream seafood industry and consumer applications.

Advances, applications, and limitations of portable and rapid detection technologies for routinely encountered foodborne pathogens

Traditional foodborne pathogen detection methods are highly dependent on pre-treatment of samples and selective microbiological plating to reliably screen target microorganisms. Inherent limitations of conventional methods include longer turnaround time and high costs, use of bulky equipment, and the need for trained staff in centralized laboratory settings. Researchers have developed stable, reliable, sensitive, and selective, rapid foodborne pathogens detection assays to work around these limitations. Recent advances in rapid diagnostic technologies have shifted to on-site testing, which offers flexibility and ease-of-use, a significant improvement from traditional methods' rigid and cumbersome steps. This comprehensive review aims to thoroughly discuss the recent advances, applications, and limitations of portable and rapid biosensors for routinely encountered foodborne pathogens. It discusses the major differences between biosensing systems based on the molecular interactions of target analytes and biorecognition agents. Though detection limits and costs still need further improvement, reviewed technologies have high potential to assist the food industry in the on-site detection of biological hazards such as foodborne pathogens and toxins to maintain safe and healthy foods. Finally, this review offers targeted recommendations for future development and commercialization of diagnostic technologies specifically for emerging and re-emerging foodborne pathogens.

Aptamers: A prospective tool for infectious diseases diagnosis

It is well known that people's health is seriously threatened by various pathogens (such as Mycobacterium tuberculosis, Treponema pallidum, Novel coronavirus, HIV, Mucor, etc.), which leads to heavy socioeconomic burdens. Therefore, early and accurate pathogen diagnosis is essential for timely and effective therapies. Up to now, diagnosing human contagious diseases at molecule and nano levels is remarkably difficult owing to insufficient valid probes when it comes to determining the biological markers of pathogens. Aptamers are a set of high‐specificity and high‐sensitivity plastic oligonucleotides screened in vitro via the selective expansion of ligands by exponential enrichment (SELEX). With the advent of aptamer‐based technologies, their merits have aroused mounting academic interest. In recent years, as new detection and treatment tools, nucleic acid aptamers have been extensively utilized in the field of biomedicine, such as pathogen detection, new drug development, clinical diagnosis, nanotechnology, etc. However, the traditional SELEX method is cumbersome and has a long screening cycle, and it takes several months to screen out aptamers with high specificity. With the persistent development of SELEX‐based aptamer screening technologies, the application scenarios of aptamers have become more and more extensive. The present research briefly reviews the research progress of nucleic acid aptamers in the field of biomedicine, especially in the diagnosis of contagious diseases.

SELEX against whole-cell bacteria resulted in lipopolysaccharide binding aptamers

Nucleic acid aptamers are target-specific oligonucleotides selected from combinatorial libraries through an iterative in vitro screening process known as Systemic Evolution of Ligands by Exponential Enrichment (SELEX). In this report, the selection of bacteria differentiating ssDNA aptamer candidates from a combinatorial library through the whole-cell SELEX method was performed. The enriched SELEX pool was sequenced using Illumina Next-Generation Sequencing (NGS) technology and analyzed for the most abundant sequences using CLC Genomics Workbench. The sequencing data resulted in several oligonucleotide families from which three individual sequences were chosen per SELEX based on the copy numbers. The binding performance of the selected aptamers was assessed by flow cytometry and fluorescence spectroscopy, and the binding constants were estimated using binding saturation curves. Varying results were obtained from two independent SELEX procedures where the SELEX against the model gram-negative bacterium Escherichia coli provided more selective sequences while the SELEX library used against gram-positive bacterium Listeria monocytogenes did not evolve as expected. The sequences that emerged from E. coli SELEX were shown to bind Lipopolysaccharide residues (LPS) and inhibit LPS-induced macrophage polarization. Thus, it can be said that, performed whole-cell SELEX could be resulted as the selection of aptamers which can bind LPS and inhibit LPS induced inflammation response and thus can be candidates for the inhibition of bacterial infections. In future studies, the selected aptamer sequences could be structurally and chemically modified and exploited as potential diagnostic tools and therapeutic agents as LPS antagonists.

Aptamer-conjugated carbon-based nanomaterials for cancer and bacteria theranostics: A review

Aptamers are single-stranded oligonucleotides that link to various substrates with great affinity and selectivity, including small molecules, peptides, proteins, cells, and tissues. For this reason, they can be used as imaging agents for cancer imaging techniques. Multifunctional nanomaterials combined with imaging probes and drugs are promising cancer diagnosis and treatment candidates. On the other hand, carbon-based nanomaterials (CNMs), including such as fullerene, carbon nanotubes, carbon-based quantum dots, carbon nanohorns, graphene oxide and its derivatives carbon nanodots, and nanodiamonds, are sort of smart materials that can be used in a variety of theranostic applications, including photo-triggered therapies. The remarkable physical characteristics, functionalizable chemistry, biocompatibility, and optical properties of these nanoparticles have enabled their utilization in less-invasive therapies. The theranostic agents that emerged by combining aptamers with CNMs have opened a novel alternative for personified medicine of cancer, target-specific imaging, and label-free diagnosis of a broad range of cancers, as well as pathogens. Aptamer-functionalized CNMs have been used as nanovesicles for targeted delivery of anti-cancer agents (i.e., doxorubicin and 5-fluorouracil) to tumor sites. Furthermore, these CNMs conjugated with aptamers have shown great advantages over standard CNMs to sensitively detect Mycobacterium tuberculosis, Escherichia coli, staphylococcus aureus, Vibrio parahaemolyticus, Salmonella typhimurium, Pseudomonas aeruginosa, and Citrobacter freundii. Regrettably, CNMs can form compounds defined as NOAA (nano-objects, and their aggregates and agglomerates larger than 100 nm), that accumulate in the body and cause toxic effects. Surface modification and pretreatment with albumin avoid agglomeration and increase the dispersibility of CNMs, so it is needed to guarantee the desirable interactions between functionalized CNMs and blood plasma proteins. This preliminary review aimed to comprehensively discuss the features and uses of aptamer-conjugated CNMs to manage cancer and bacterial infections.

DNA aptamers specific for Legionella pneumophila: systematic evolution of ligands by exponential enrichment in whole bacterial cells

Legionella pneumophila is the major causative agent of Legionnaires' disease and Pontiac fever, which pose major public health problems. Rapid detection of L. pneumophila is important for global control of these diseases. Aptamers, short oligonucleotides that bind to targets with high affinity and specificity, have great potential for use in pathogenic bacterium detection, diagnostics, and therapy. Here, we used a whole-cell SELEX (systematic evolution of ligands by exponential enrichment) method to isolate and characterize single-stranded DNA (ssDNA) aptamers against L. pneumophila. A total of 60 ssDNA sequences were identified after 17 rounds of selection. Other bacterial species (Escherichia coli, Bacillus subtilis, Pseudomonas syringae, Staphylococcus aureus, Legionella quateirensis, and Legionella adelaidensis) were used for counterselection to enhance the specificity of ssDNA aptamers against L. pneumophila. Four ssDNA aptamers showed strong affinity and high selectivity for L. pneumophila, with K_d values in the nanomolar range. Bioinformatic analysis of the most specific aptamers revealed predicted conserved secondary structures that might bind to L. pneumophila cell walls. In addition, the binding of these four fluorescently labeled aptamers to the surface of L. pneumophila was observed directly by fluorescence microscopy. These aptamers identified in this study could be used in the future to develop medical diagnostic tools and public environmental detection assays for L. pneumophila.

Nano-engineered materials for sensing food pollutants: Technological advancements and safety issues

Food spoilage and safety are key concerns of the modern food sector. Among them, several types of polluting agents are the prime grounds of food deterioration. In this context, nanotechnology-based measures are setting new frontiers to strengthen food applications. Herein, we summarize the nanotechnological dimension of the food industry for both processing and packaging applications. Active bioseparation, smart delivery, nanoencapsulation, nutraceuticals, and nanosensors for biological detection are a few emerging topics of nanobiotechnology in the food sector. The development of functional foods is another milestone set by food nanotechnology by building the link between humans and diet. However, the establishment of optimal intake, product formulations, and delivery matrices, the discovery of beneficial compounds are a few of the key challenges that need to be addressed. Nanotechnology provides effective solutions for the aforementioned problem giving various novel nanomaterials and methodologies. Various nanodelivery systems have been designed, e.g., cochleate, liposomes, multiple emulsions, and polysaccharide-protein coacervates. However, their real applications in food sciences are very limited. This review also provides the status and outlook of nanotechnological systems for future food applications.

Nucleic Acid-Based Nanobiosensor (NAB) Used for Salmonella Detection in Foods: A Systematic Review

Salmonella bacteria is a foodborne pathogen found mainly in food products causing severe symptoms in the individual, such as diarrhea, fever, and abdominal cramps after consuming the infected food, which can be fatal in some severe cases. Rapid and selective methods to detect Salmonella bacteria can prevent outbreaks when ingesting contaminated food. Nanobiosensors are a highly sensitive, simple, faster, and lower cost method for the rapid detection of Salmonella, an alternative to conventional enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) techniques. This study systematically searched and analyzed literature data related to nucleic acid-based nanobiosensors (NABs) with nanomaterials to detect Salmonella in food, retrieved from three databases, published between 2010 and 2021. We extracted data and critically analyzed the effect of nanomaterial functionalized with aptamer or DNA at the limit of detection (LOD). Among the nanomaterials, gold nanoparticles (AuNPs) were the most used nanomaterial in studies due to their unique optical properties of the metal, followed by magnetic nanoparticles (MNPs) of Fe₃O₄, copper nanoparticles (CuNPs), and also hybrid nanomaterials multiwalled carbon nanotubes (c-MWCNT/AuNP), QD/UCNP-MB (quantum dotes upconverting nanoparticle of magnetic beads), and cadmium telluride quantum dots (CdTe QDs@MNPs) showed excellent LOD values. The transducers used for detection also varied from electrochemical, fluorescent, surface-enhanced Raman spectroscopy (SERS), RAMAN spectroscopy, and mainly colorimetric due to the possibility of visualizing the detection result with the naked eye. Furthermore, we show the magnetic separation system capable of detecting the target amplification of the genetic material. Finally, we present perspectives, future research, and opportunities to use point-of-care (POC) diagnostic devices as a faster and lower cost approach for detecting Salmonella in food as they prove to be viable for resource-constrained environments such as field-based or economically limited conditions.

Assays to Estimate the Binding Affinity of Aptamers

Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.

New analytical methods using carbon-based nanomaterials for detection of Salmonella species as a major food poisoning organism in water and soil resources

Salmonella is one of the most prevalent causing agents of food- and water-borne illnesses, posing an ongoing public health threat. These food-poisoning bacteria contaminate the resources at different stages such as production, aggregation, processing, distribution, as well as marketing. According to the high incidence of salmonellosis, effective strategies for early-stage detection are required at the highest priority. Since traditional culture-dependent methods and polymerase chain reaction are labor-intensive and time-taking, identification of early and accurate detection of Salmonella in food and water samples can prevent significant health economic burden and lessen the costs. The immense potentiality of biosensors in diagnosis, such as simplicity in operation, the ability of multiplex analysis, high sensitivity, and specificity, have driven research in the evolution of nanotechnology, innovating newer biosensors. Carbon nanomaterials enhance the detection sensitivity of biosensors while obtaining low levels of detection limits due to their possibility to immobilize huge amounts of bioreceptor units at insignificant volume. Moreover, conjugation and functionalization of carbon nanomaterials with metallic nanoparticles or organic molecules enables surface functional groups. According to these remarkable properties, carbon nanomaterials are widely exploited in the development of novel biosensors. To be specific, carbon nanomaterials such as carbon nanotubes, graphene and fullerenes function as transducers in the analyte recognition process or surface immobilizers for biomolecules. Herein the potential application of carbon nanomaterials in the development of novel Salmonella biosensors platforms is reviewed comprehensively. In addition, the current problems and critical analyses of the future perspectives of Salmonella biosensors are discussed.

Advancement in Salmonella Detection Methods: From Conventional to Electrochemical-Based Sensing Detection

Large-scale food-borne outbreaks caused by Salmonella are rarely seen nowadays, thanks to the advanced nature of the medical system. However, small, localised outbreaks in certain regions still exist and could possess a huge threat to the public health if eradication measure is not initiated. This review discusses the progress of Salmonella detection approaches covering their basic principles, characteristics, applications, and performances. Conventional Salmonella detection is usually performed using a culture-based method, which is time-consuming, labour intensive, and unsuitable for on-site testing and high-throughput analysis. To date, there are many detection methods with a unique detection system available for Salmonella detection utilising immunological-based techniques, molecular-based techniques, mass spectrometry, spectroscopy, optical phenotyping, and biosensor methods. The electrochemical biosensor has growing interest in Salmonella detection mainly due to its excellent sensitivity, rapidity, and portability. The use of a highly specific bioreceptor, such as aptamers, and the application of nanomaterials are contributing factors to these excellent characteristics. Furthermore, insight on the types of biorecognition elements, the principles of electrochemical transduction elements, and the miniaturisation potential of electrochemical biosensors are discussed.

Aptamers and Aptamer-Coupled Biosensors to Detect Water-Borne Pathogens

Aptamers can serve as efficient bioreceptors for the development of biosensing detection platforms. Aptamers are short DNA or RNA oligonucleotides that fold into specific structures, which enable them to selectively bind to target analytes. The method used to identify aptamers is Systematic Evolution of Ligands through Exponential Enrichment (SELEX). Target properties can have an impact on aptamer efficiencies. Therefore, characteristics of water-borne microbial targets must be carefully considered during SELEX for optimal aptamer development. Several aptamers have been described for key water-borne pathogens. Here, we provide an exhaustive overview of these aptamers and discuss important microbial aspects to consider when developing such aptamers.

Highly adaptable and sensitive FRET-based aptamer assay for the detection of Salmonella paratyphi A

Here we demonstrate a facile and versatile fluorescence resonance energy transfer (FRET) based aptasensor for rapid detection of Salmonella paratyphi A. The assay shows a detection limit up to 10 cfu·mL^-1 with no cross-reactivity with other bacterial species. Less than 8% of inter-assay coefficient variance and recovery rate between 85 and 102% attests the assay reliability. The advantages of FRET-based aptamer assay over the conventional immunoassay formats such as ELISA are the specificity, speed, reliability, and simplicity of the assay. The ssDNA aptamers specific towards pathogenic Salmonella paratyphi A were generated via whole-cell SELEX. The aptamer was conjugated onto quantum dot (QD) that served as the molecular beacon and graphene oxide (GO) was used as a fluorescence quencher. Thus the proposed method enables detection of target pathogen using FRET-based assay. Further interaction of aptamer with pathogen protein DNA gyrase was explored using classical molecular dynamics simulation.

Aptamers used for biosensors and targeted therapy

Aptamers are single-stranded nucleic acid sequences that can bind to target molecules with high selectivity and affinity. Most aptamers are screened in vitro by a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers were discovered in the 1990s, they have attracted considerable attention and have been widely used in many fields owing to their unique advantages. In this review, we present an overview of the advancements made in aptamers used for biosensors and targeted therapy. For the former, we will discuss multiple aptamer-based biosensors with different principles detected by various signaling methods. For the latter, we will focus on aptamer-based targeted therapy using aptamers as both biotechnological tools for targeted drug delivery and as targeted therapeutic agents. Finally, challenges and new perspectives associated with these two regions were further discussed. We hope that this review will help researchers interested in aptamer-related biosensing and targeted therapy research.

Carbon Nanomaterials as Versatile Platforms for Biosensing Applications

A biosensor is defined as a measuring system that includes a biological receptor unit with distinctive specificities toward target analytes. Such analytes include a wide range of biological origins such as DNAs of bacteria or viruses, or proteins generated from an immune system of infected or contaminated living organisms. They further include simple molecules such as glucose, ions, and vitamins. One of the major challenges in biosensor development is achieving efficient signal capture of biological recognition-transduction events. Carbon nanomaterials (CNs) are promising candidates to improve the sensitivity of biosensors while attaining low detection limits owing to their capability of immobilizing large quantities of bioreceptor units at a reduced volume, and they can also act as a transduction element. In addition, CNs can be adapted to functionalization and conjugation with organic compounds or metallic nanoparticles; the creation of surface functional groups offers new properties (e.g., physical, chemical, mechanical, electrical, and optical properties) to the nanomaterials. Because of these intriguing features, CNs have been extensively employed in biosensor applications. In particular, carbon nanotubes (CNTs), nanodiamonds, graphene, and fullerenes serve as scaffolds for the immobilization of biomolecules at their surface and are also used as transducers for the conversion of signals associated with the recognition of biological analytes. Herein, we provide a comprehensive review on the synthesis of CNs and their potential application to biosensors. In addition, we discuss the efforts to improve the mechanical and electrical properties of biosensors by combining different CNs.

Mathematical approaches in estimating aptamer-target binding affinity

The performance of aptamers as versatile tools in numerous analytical applications is critically dependent on their high target binding specificity and selectivity. However, only the technical or methodological aspects of measuring aptamer-target binding affinities are focused, ignoring the equally important mathematical components that play pivotal roles in affinity measurements. In this study, we aim to provide a comprehensive review regarding the utilization of different mathematical models and equations, along with a detailed description of the computational steps involved in mathematically deriving the binding affinity of aptamers against their specific target molecules. Mathematical models ranging from one-site binding to multiple aptameric binding site-based models are explained in detail. Models applied in several different approaches of affinity measurements such as thermodynamics and kinetic analysis, including cooperativity and competitive-assay based mathematical models have been elaborately discussed. Mathematical models incorporating factors that could potentially affect affinity measurements are also further scrutinized.

Aptamers coupled to nanoparticles in the diagnosis and treatment of microbial infections

There are nanoparticles with remarkable antibacterial characteristics and aptamers able to recognize specific pathogenic bacteria with high affinity and specificity. The combination of both systems has been used to design rapid bacterial detection methods with excellent detection limits. Likewise, the synergism between aptamers and nanoparticles have allowed to optimize the antimicrobial activity of antibiotics and other nanostructures providing them with activity bacterium-specific, turning into attractive and promising tools to fight against bacteria resistant to multiple antimicrobials.

New strategies for the enumeration of enteric pathogens in water

Water quality standards for drinking water and recreational waters have long been based on the enumeration of faecal coliforms in the various water supplies, with 0 CFU Escherichia coli/100 ml for drinking water and <126 CFU generic E. coli/100 ml for recreational waters. Irrigation water will soon undergo the same scrutiny in the United States. For over 50 years the most probable number method has been used by laboratories to estimate the level of viable bacteria in a sample, but this method is labour intensive and slow, especially if large numbers of samples need to be tested. In this review, we describe some recent innovations in methods to enumerate enteric pathogens in water. These methods are based on different reasoning schemes that can be categorized as biosensors and nucleic acid-based methods. All the methods described here used natural water sources. Several were also used to survey the bacterial levels in naturally contaminated samples. The different methods vary in their limits of detection, ease of use, and potential portability. Some combine very good limits of detection with the ability to overcome technical challenges; however, there is considerable room for improvement, as none of the methods are without shortcomings.

Detection of pathogenic bacteria via nanomaterials-modified aptasensors

Detection and identification of special cells via aptamer-based nano-conjugates sensors have been revolutionized over the past few years. These sensing platforms rely on selecting aptamers using systematic evolution of ligands by exponential enrichment (SELEX) in vitro, which allows for sensitive detection of cells. Integration of the aptamer-based sensors (aptasensors) with nanomaterials offers enhanced specificity and sensitivity, which in turn, offers great promise for numerous applications, spanning from bioanalysis to biomedical applications. Accordingly, the demand for using aptamer-conjugated nanomaterials for various applications has progressively increased over the past years. In light of this, this Review seeks to highlight the recent advances in the development of aptamer-conjugated nanomaterials and their utilization for the detection of various pathogens involved in infectious diseases and food contamination.

Detection of Gram-negative bacterial outer membrane vesicles using DNA aptamers

Infection of various pathogenic bacteria causes severe illness to human beings. Despite the research advances, current identification tools still exhibit limitations in detecting Gram-negative bacteria with high accuracy. In this study, we isolated single-stranded DNA aptamers against multiple Gram-negative bacterial species using Toggle-cell-SELEX (systemic evolution of ligands by exponential enrichment) and constructed an aptamer-based detection tool towards bacterial secretory cargo released from outer membranes of Gram-negative bacteria. Three Gram-negative bacteria, Escherichia coli DH5α, E. coli K12, and Serratia marcescens, were sequentially incubated with the pool of random DNA sequences at each SELEX loop. Two aptamers selected, GN6 and GN12, were 4.2-times and 3.6-times higher binding to 10⁸ cells of Gram-negative bacteria than to Gram-positive bacteria tested, respectively. Using GN6 aptamer, we constructed an Enzyme-linked aptamer assay (ELAA) to detect bacterial outer membrane vesicles (OMVs) of Gram-negative bacteria, which contain several outer membrane proteins with potent immunostimulatory effects. The GN6-ELAA showed high sensitivity to detect as low as 25 ng/mL bacterial OMVs. Aptamers developed in this study show a great potential to facilitate medical diagnosis and early detection of bacterial terrorism, based on the ability to detect bacterial OMVs of multiple Gram-negative bacteria.

Detection of Salmonella in Food Matrices, from Conventional Methods to Recent Aptamer-Sensing Technologies

Rapid detection of the foodborne pathogen Salmonella in food processing is of crucial importance to prevent food outbreaks and to ensure consumer safety. Detection and quantification of Salmonella species in food samples is routinely performed using conventional culture-based techniques, which are labor intensive, involve well-trained personnel, and are unsuitable for on-site and high-throughput analysis. To overcome these drawbacks, many research teams have developed alternative methods like biosensors, and more particularly aptasensors, were a nucleic acid is used as biorecognition element. The increasing interest in these devices is related to their high specificity, convenience, and relative rapid response. This review aims to present the advances made in these last years in the development of biosensors for the detection and the quantification of Salmonella, highlighting applications on meat from the chicken food chain.

Simultaneous Colorimetric Detection of a Variety of Salmonella spp. in Food and Environmental Samples by Optical Biosensing Using Oligonucleotide-Gold Nanoparticles

Optical biosensors for rapid detection of significant foodborne pathogens are steadily gaining popularity due to its simplicity and sensitivity. While nanomaterials such as gold nanoparticles (AuNPs) are commonly used as signal amplifiers for optical biosensors, AuNPs can also be utilized as a robust biosensing platform. Many reported optical biosensors were designed for individual pathogen detection in a single assay and have high detection limit (DL). Salmonella spp. is one of the major causative agents of foodborne sickness, hospitalization and deaths. Unfortunately, there are around 2,000 serotypes of Salmonella worldwide, and rapid and simultaneous detection of multiple strains in a single assay is lacking. In this study, a comprehensive and highly sensitive simultaneous colorimetric detection of nineteen (19) environmental and outbreak Salmonella spp. strains was achieved by a novel optical biosensing platform using oligonucleotide-functionalized AuNPs. A pair of newly designed single stranded oligonucleotides (30-mer) was displayed onto the surface of AuNPs (13 nm) as detection probes to hybridize with a conserved genomic region (192-bases) of ttrRSBCA found on a broad range of Salmonella spp. strains. The sandwich hybridization (30 min, 55°C) resulted in a structural formation of highly stable oligonucleotide/AuNPs-DNA complexes which remained undisturbed even after subjecting to an increased salt concentration (2 M, final), thus allowing a direct discrimination via color change of target (red color) from non-target (purplish-blue color) reaction mixtures by direct observation using the naked eye. In food matrices (blueberries and chicken meat), nineteen different Salmonella spp. strains were concentrated using immunomagnetic separation and then simultaneously detected in a 96-well microplate by oligonucleotide-functionalized AuNPs after DNA preparation. Successful oligonucleotide/AuNPs-DNA hybridization was confirmed by gel electrophoresis while AuNPs aggregation in non-target and control reaction mixtures was verified by both spectrophotometric analysis and TEM images. Results showed that the optical AuNP biosensing platform can simultaneously screen nineteen (19) viable Salmonella spp. strains tested with 100% specificity and a superior detection limit of <10 CFU/mL or g for both pure culture and complex matrices setups. The highly sensitive colorimetric detection system can significantly improve the screening and detection of viable Salmonella spp. strains present in complex food and environmental matrices, therefore reducing the risks of contamination and incidence of foodborne diseases.

Ultrasensitive Colorimetric Detection of Murine Norovirus Using NanoZyme Aptasensor

Human norovirus (NoV) remains the most common cause of viral gastroenteritis and the leading cause of viral foodborne outbreaks globally. NoV is highly pathogenic with an estimated median viral infective dose (ID₅₀) ranging from 18 to 1015 genome copies. For NoV detection, the only reliable and sensitive method available for detection and quantification is reverse transcription quantitative polymerase chain reaction (RTqPCR). NoV detection in food is particularly challenging, requiring matrix specific concentration of the virus and removal of inhibitory compounds to detection assays. Hence, the RTqPCR method poses some challenges for rapid in-field or point-of-care diagnostic applications. We propose a new colorimetric NanoZyme aptasensor strategy for rapid (10 min) and ultrasensitive (calculated Limit of Detection (LoD) of 3 viruses per assay equivalent to 30 viruses/mL of sample and experimentally demonstrated LoD of 20 viruses per assay equivalent to 200 viruses/mL) detection of the infective murine norovirus (MNV), a readily cultivable surrogate for NoV. Our approach combines the enzyme-mimic catalytic activity of gold nanoparticles with high target specificity of an MNV aptamer to create sensor probes that produce a blue color in the presence of this norovirus, such that the color intensity provides the virus concentrations. Overall, our strategy offers the most sensitive detection of norovirus or a norovirus surrogate achieved to date using a biosensor approach, enabling for the first time, the detection of MNV virion corresponding to the lower end of the ID₅₀ for NoV. We further demonstrate the robustness of the norovirus NanoZyme aptasensor by testing its performance in the presence of other nontarget microorganisms, human serum and shellfish homogenate, supporting the potential of detecting norovirus in complex matrices. This new assay format can, therefore, be of significant importance as it allows ultrasensitive norovirus detection rapidly within minutes, while also offering the simplicity of use and need for nonspecialized laboratory infrastructure.

Point-of-care microfluidic devices for pathogen detection

The rapid diagnosis of pathogens is crucial in the early stages of treatment of diseases where the choice of the correct drug can be critical. Although conventional cell culture-based techniques have been widely utilized in clinical applications, newly introduced optical-based, microfluidic chips are becoming attractive. The advantages of the novel methods compared to the conventional techniques comprise more rapid diagnosis, lower consumption of patient sample and valuable reagents, easy application, and high reproducibility in the detection of pathogens. The miniaturized channels used in microfluidic systems simulate interactions between cells and reagents in microchannel structures, and evaluate the interactions between biological moieties to enable diagnosis of microorganisms. The overarching goal of this review is to provide a summary of the development of microfluidic biochips and to comprehensively discuss different applications of microfluidic biochips in the detection of pathogens. New types of microfluidic systems and novel techniques for viral pathogen detection (e.g. HIV, HVB, ZIKV) are covered. Next generation techniques relying on high sensitivity, specificity, lower consumption of precious reagents, suggest that rapid generation of results can be achieved via optical based detection of bacterial cells. The introduction of smartphones to replace microscope based observation has substantially improved cell detection, and allows facile data processing and transfer for presentation purposes.

Prospects of using nanotechnology for food preservation, safety, and security

The rapid development of nanotechnology has transformed many domains of food science, especially those that involve the processing, packaging, storage, transportation, functionality, and other safety aspects of food. A wide range of nanostructured materials (NSMs), from inorganic metal, metal oxides, and their nanocomposites to nano-organic materials with bioactive agents, has been applied to the food industry. Despite the huge benefits nanotechnology has to offer, there are emerging concerns regarding the use of nanotechnology, as the accumulation of NSMs in human bodies and in the environment can cause several health and safety hazards. Therefore, safety and health concerns as well as regulatory policies must be considered while manufacturing, processing, intelligently and actively packaging, and consuming nano-processed food products. This review aims to provide a basic understanding regarding the applications of nanotechnology in the food packaging and processing industries and to identify the future prospects and potential risks associated with the use of NSMs.

Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases

The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.

Whole-bacterium SELEX of DNA aptamers for rapid detection of E.coli O157:H7 using a QCM sensor

The rapid detection of foodborne pathogens is critical to ensure food safety. The objective of this study is to select aptamers specifically bound to Escherichia coli O157:H7 using the whole-bacterium SELEX (Systematic Evolution of Ligands by Exponential Enrichment) and apply the selected aptamer to a QCM (quartz crystal microbalance) sensor for rapid and sensitive detection of target bacteria. A total of 19 rounds of selection against live E. coli O157:H7 and 6 rounds of counter selection against a mixture of Staphylococcus aureus, Listeria monocytogenes, and Salmonella Typhimurium, were performed. The aptamer pool from the last round was cloned and sequenced. One sequence S1 that appeared 16 times was characterized and a dissociation constant (K_d) of 10.30nM was obtained. Subsequently, a QCM aptasensor was developed for the rapid detection of E. coli O157:H7. The limit of detection (LOD) and the detection time of the aptasensor was determined to be 1.46×10³ CFU/ml and 50min, respectively. This study demonstrated that the ssDNA aptamer selected by the whole-bacterium SELEX possessed higher sensitivity than previous work and the potential use of the constructed QCM aptasensor in rapid screening of foodborne pathogens.

Ensuring food safety using aptamer based assays: Electroanalytical approach

Aptamers, are being increasingly employed as favorable receptors for constructing highly sensitive biosensors, for their remarkable affinities towards certain targets including a wide scope of biological or chemical substances, and their superiority over other biologic receptors. The selectivity and affinity of the aptamers have been integrated with the wise design of the assay, applying suitable modifications, such as nanomaterials on the electrode surface, employing oligonucleotide-specific amplification strategies or, their combinations. After successful performance of the electrochemical aptasensors for biomedical applications, the food sector with its direct implication for human health, which demands rapid and sensitive and economic analytical solutions for determination of health threatening contaminants in all stages of production process, is the next field of research for developing efficient electrochemical aptasensors. The aim of this review is to categorize and introduce food hazards and summarize the recent electrochemical aptasensors that have been developed to address these contaminants.

Application of aptamers in diagnostics, drug-delivery and imaging

Aptamers are small, single-stranded oligonucleotides (DNA or RNA) that bind to their target with high specificity and affinity. Although aptamers are analogous to antibodies for a wide range of target recognition and variety of applications, they have significant advantages over antibodies. Since aptamers have recently emerged as a class of biomolecules with an application in a wide array of fields, we need to summarize the latest developments herein. In this review we will discuss about the latest developments in using aptamers in diagnostics, drug delivery and imaging. We begin with diagnostics, discussing the application of aptamers for the detection of infective agents itself, antigens/ toxins (bacteria), biomarkers (cancer), or a combination. The ease of conjugation and labelling of aptamers makes them a potential tool for diagnostics. Also, due to the reduced off-target effects of aptamers, their use as a potential drug delivery tool is emerging rapidly. Hence, we discuss their use in targeted delivery in conjugation with siRNAs, nanoparticles, liposomes, drugs and antibodies. Finally, we discuss about the conjugation strategies applicable for RNA and DNA aptamers for imaging. Their stability and self-assembly after heating makes them superior over protein-based binding molecules in terms of labelling and conjugation strategies.

Design and optimization of an ultra-sensitive hairpin DNA aptasensor for Salmonella detection

A simple scheme using a hairpin DNA aptasensor was established to detectSalmonellaTyphimurium (S.Typhimurium).

QCM-based aptamer selection and detection of Salmonella typhimurium

In this study, quartz crystal microbalance (QCM) was used to select aptamers against Salmonella typhimurium. To increase the success rate of Systematic Evolution of Ligands Exponential Enrichment (SELEX), the affinity of DNA pool in each round was simultaneously tracked using QCM in order to avoid the loss of high-quality aptamers. When the frequency change reached a maximum value after several rounds of selection and counter-selection, the candidate pool was cloned and sequenced. Out of three aptamer candidates, aptamer B5 showed high specificity and binding affinity with dissociation constant (K_d value) of 58.5nM, and was chosen for further studies. Subsequently, a QCM-based aptasensor was developed to detect S. typhimurium. This aptasensor was able to detect 10³CFU/mL of S. typhimurium with less than 1h. This study demonstrated QCM-based selection could be more effective selection of aptamers and QCM-based aptasensor could be more sensitive in detecting S. typhimurium.

Nano-materials for use in sensing of salmonella infections: Recent advances

Salmonella infectious diseases spreading every day through food have become a life-threatening problem for millions of people and growing menace to society. Health expert's estimate that the yearly cost of all the food borne diseases is approximately $5-6 billion. Traditional methodologies for salmonella analysis provide high reliability and very low limits of detection. Among them immunoassays and Nucleic acid-based assays provide results within 24h, but they are expensive, tedious and time consuming. So, there is an urgent need for development of rapid, robust and cost-effective alternative technologies for real-time monitoring of salmonella. Several biosensors have been designed and commercialized for detection of this pathogen in food and water. In this overview, we have updated the literature concerning novel biosensing methods such as various optical and electrochemical biosensors and newly developed nano- and micro-scaled and aptamers based biosensors for detection of salmonella pathogen. Furthermore, attention has been focused on the principal concepts, applications, and examples that have been achieved up to diagnose salmonella. In addition, commercial biosensors and foreseeable future trends for onsite detecting salmonella have been summarized.

Selection and Characterization of Aptamers Using a Modified Whole Cell Bacterium SELEX for the Detection of Salmonella enterica Serovar Typhimurium

This study describes the selection of single-stranded DNA (ssDNA) aptamers against Salmonella enterica serovar Typhimurium using a modified whole cell systematic evolution of ligands by exponential enrichment (whole cell SELEX). For evolving specific aptamers, ten rounds of selection to live Salmonella cells, alternating with negative selection against a cocktail of related pathogens, were performed. The resulting highly enriched oligonucleotide pools were sequenced and clustered into eight groups based on primary sequence homology and predicted secondary structure similarity. Fifteen sequences from different groups were selected for further characterization. The binding affinity and specificity of aptamers were determined by fluorescence binding assays. Aptamers (SAL 28, SAL 11, and SAL 26) with dissociation constants of 195 ± 46, 184 ± 43, and 123 ± 23 nM were used to develop a nanogold-based colorimetric detection method and a sedimentation assay. The former showed a better sensitivity limit of 10(2) CFU/mL using aptamer SAL 26. This approach should enable further refinement of diagnostic methods for the detection of Salmonella enterica serovar Typhimurium and of other microbial pathogens.

Aptamer-nanobody based ELASA for specific detection of Acinetobacter baumannii isolates

Acinetobacter baumannii has turned into an important threat in nosocomial outbreak infections and multidrug resistance leading to high mortality rates in the 21st century. In recent years its mortality has increased by 15% which in part could be due to lack of a rapid and sensitive diagnostic test. In this work we introduced a new detection test for A. baumannii with two highly specific aptamer and nanobody molecules. High binding affinity DNA oligonucleotide aptamers toward A. baumannii were selected through 12 rounds of whole cell System Evolution of Ligands by EXponential enrichment process (SELEX). The SELEX procedures was monitored by flow cytometry. The dissociation constant and binding efficiency of the selected aptamer Aci49 was 7.547±1:353pM and 47.50%, respectively. A sandwich enzyme linked aptamer sorbent assay (ELASA) was designed with the biotinylated Aci49 aptamer and our previously developed nanobody against biofilm associated protein (Bap). The assay system was optimized with A. baumannii (ATCC 19606) and 47 clinical isolates of A. baumannii were tested. The threshold of detection in sandwich ELASA process was10(3) CFU/ml. The sensitivity of test toward the clinical isolates was 95.47%. Our results reveal that the sandwich ELASA is sensitive and specific enough for the rapid detection of A. baumannii from clinical isolates.

Isolation of an Aptamer that Binds Specifically to E. coli

Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. Aptamers are short oligonucleotides that bind to targets with high affinity and specificity, and have great potential for use in diagnostics and therapy. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. Fluorescently labeled aptamers label the surface of E. coli cells, as viewed by fluorescent microscopy. Specificity tests with twelve different bacterial species showed that one of the aptamers–called P12-31—is highly specific for E. coli. Importantly, this aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies.

SELEX Modifications and Bioanalytical Techniques for Aptamer-Target Binding Characterization

The quest to improve the detection of biomolecules and cells in health and life sciences has led to the discovery and characterization of various affinity bioprobes. Libraries of synthetic oligonucleotides (ssDNA/ssRNA) with randomized sequences are employed during Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to select highly specific affinity probes called aptamers. With much focus on the generation of aptamers for a variety of target molecules, conventional SELEX protocols have been modified to develop new and improved SELEX protocols yielding highly specific and stable aptamers. Various techniques have been used to analyze the binding interactions between aptamers and their cognate molecules with associated merits and limitations. This article comprehensively reviews research advancements in the generation of aptamers, analyses physicochemical conditions affecting their binding characteristics to cellular and biomolecular targets, and discusses various field applications of aptameric binding. Biophysical techniques employed in the characterization of the molecular and binding features of aptamers to their cognate targets are also discussed.

Dual-excitation upconverting nanoparticle and quantum dot aptasensor for multiplexed food pathogen detection

In this report, a dual-excitation sensing method was developed using aptamer-functionalized quantum dots and upconverting nanoparticles, exhibiting Stokes and anti-Stokes type excitation profiles, respectively. Conjugation of the aptamer-functionalized luminescent nanoparticles with the magnetic beads, comprising short DNA sequences that were partially complementary to the aptamer sequences, enabled facile separation of the analyte-free conjugates for fluorescent measurement. UV-Visible spectroscopy, Circular Dichroism spectroscopy, Dynamic Light Scattering and Polyacrylamide Gel Electrophoresis techniques were used to characterize the aptamer probes developed. The target-specific luminescent conjugates were applied for multiplex detection of model food pathogens, Salmonella typhimurium, and Staphylococcus aureus, in which the fluorescent emission spectra were obtained under UV excitation at 325nm for quantum dots and NIR excitation at 980nm for upconverting nanoparticles, respectively. The dual-excitation strategy was aimed to minimize cross-talk between the luminescent signals for multiplexed detection, and yielded limit of detection values of 16 and 28cfumL(-1) for Staphylococcus aureus, and Salmonella typhimurium, respectively. By employing a greater number of quantum dots and upconverting nanoparticles with non-overlapping fluorescent emissions, the proposed methodology might be exploited further to detect several analytes, simultaneously.