Selection and identification of a DNA aptamer targeted to Vibrio parahemolyticus

Isolation and characterization of ssDNA aptamers against BipD antigen of Burkholderia pseudomallei

BACKGROUND

Melioidosis is difficult to diagnose due to its wide range of clinical symptoms. The culture method is time-consuming and less sensitive, emphasizing the importance of rapid and accurate diagnostic tests for melioidosis. Burkholderia invasion protein D (BipD) of Burkholderia pseudomallei is a potential diagnostic biomarker. This study aimed to isolate and characterize single-stranded DNA aptamers that specifically target BipD.

METHODS

The recombinant BipD protein was produced, followed by isolation of BipD-specific aptamers using Systematic Evolution of Ligands by EXponential enrichment. The binding affinity and specificity of the selected aptamers were evaluated using Enzyme-Linked Oligonucleotide Assay.

RESULTS

The fifth SELEX cycle showed a notable enrichment of recombinant BipD protein-specific aptamers. Sequencing analysis identified two clusters with a total of seventeen distinct aptamers. AptBipD1, AptBipD13, and AptBipD50 were chosen based on their frequency. Among them, AptBipD1 exhibited the highest binding affinity with a Kd value of 1.0 μM for the recombinant BipD protein. Furthermore, AptBipD1 showed significant specificity for B. pseudomallei compared to other tested bacteria.

CONCLUSION

AptBipD1 is a promising candidate for further development of reliable, affordable, and efficient point-of-care diagnostic tests for melioidosis.

Construction of Aptamer-Functionalized DNA Hydrogels for Effective Inhibition of Shiga Toxin II Toxicity

Bacterial infections have been seriously endangering public health and life, making it imperative to explore novel anti-infection strategies for their control. Herein, we constructed a DNA hydrogel encoded with aptamers (Apt-hydrogel) to inhibit Shiga toxin II (Stx2) toxicity, thereby alleviating Escherichia coli (EHEC) infection. The Apt-hydrogel was formed by two Y-shaped DNA scaffolds through rational design, where one end of Y was encoded with an aptamer sequence targeting the B subunit of Shiga toxin II (Stx2B). The Apt-hydrogel not only retained the high affinity of the aptamer but also provided protection for the aptamer, endowing it with better stability and biocompatibility. The results from in vitro and in vivo demonstrated good mediation effects of the Apt-hydrogel on Stx2 toxicity and confirmed its excellent inhibition activity. We hypothesized that the mechanism could be attributed to the high affinity of Apt-hydrogel for Stx2B, which effectively occupies the active site of Stx2B and its receptor Gb3. This interaction enhanced steric hindrance, thereby mediating their interaction and preventing Stx2 from entering the cell to exert toxicity. We anticipate that the novel Apt-hydrogel will expand the usage of aptamers and provide a new dimension for the Apt-hydrogel as a promising blocking assistant to inhibit Shiga toxin infections via a strong steric hindrance effect.

Research progress on the detection of foodborne pathogens based on aptamer recognition

Foodborne diseases caused by bacterial contamination are a serious threat to food safety and human health. The classical plate culture method has the problems of long detection cycle, low sensitivity and specificity, and complicated operation, which cannot meet the growing demand for rapid quantitative detection of pathogenic bacteria. The frequent outbreak of foodborne diseases has put forward higher requirements for rapid and simple detection technology of foodborne pathogens. Aptamer is a kind of oligonucleotide fragment that can recognize targets with the advantages of high affinity and good specificity. The target can be range from proteins, small molecules, cells bacteria, and even viruses. Herein, the latest advances in sensitive and rapid detection of foodborne pathogens based on aptamer recognition was reviewed. Special attention has been paid to the obtained sequences of aptamers to various foodborne pathogens, the optimization of sequences, and the mechanism of aptamer recognition. Then, the research progress of biosensors for the detection of pathogenic bacteria based on aptamer recognition were summarized. Some challenges and prospects for the detection of foodborne pathogens based on aptamer recognition were prospected. In summary, with the further deepening of aptamer research and improvement of detection technology, aptamer-based recognition can meet the needs of rapid, sensitive, and accurate detection in practical applications.

Mesoporous Silica Nanoparticles-Enhanced Microarray Technology for Highly Sensitive Simultaneous Detection of Multiplex Foodborne Pathogens

Ensuring food safety is paramount for the food industry and global health concerns. In this study, we have developed a method for the detection of prevalent foodborne pathogenic bacteria, including Escherichia coli, Salmonella spp., Listeria spp., Shigella spp., Campylobacter spp., Clostridium spp., and Vibrio spp., utilizing antibody-aptamer arrays. To enhance the fluorescence signals on the microarray, the mesoporous silica nanoparticles (MSNs) conjugated with fluorescein, streptavidin, and seven detection antibodies-biotin were employed, forming fluorescein doped mesoporous silica nanoparticles conjugated with detection antibodies (MSNs-Flu-SA-Abs) complexes. The array pattern was designed for easy readability and enabled the simultaneous detection of all seven foodborne pathogens, referred to as the 7FP-biochip. Following the optimization of MSNs-Flu-SA-Abs complexes attachment and enhancement of the detection signal in fluorescent immunoassays, a high level of sensitivity was achieved. The detection limits for the seven pathogens in both buffer and food samples were 102 CFU/mL through visual screening, with fluorescent intensity quantification achieving levels as low as 20-34 CFU/g were achieved on the antibody-aptamer arrays. Our antibody-aptamer array offers several advantages, including significantly reduced nonspecific binding with no cross-reaction between bacteria. Importantly, our platform detection exhibited no cross-reactivity among the tested bacteria in this study. The multiplex detection of foodborne pathogens in canned tuna samples with spiked bacteria was successfully demonstrated in real food measurements. In conclusion, our study presents a promising method for detecting multiple foodborne pathogens simultaneously. With its high sensitivity and specificity, the developed antibody-aptamer array holds great potential for enhancing food safety and public health.

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.

Detection of Vibrio parahaemolyticus Based on Magnetic and Upconversion Nanoparticles Combined with Aptamers

Vibrio parahaemolyticus is a halophilic and heat-labile gram-negative bacterium and is the most prevalent foodborne bacterium in seafood. In order to develop a rapid and sensitive method for detecting the foodborne pathogenic bacterium Vibrio parahaemolyticus, an aptamer-modified magnetic nanoparticle and an aptamer-modified upconversion nanoparticle were synthesised and used as a capture probe and a signal probe, respectively. The aptamer-modified magnetic nanoparticle, V. parahaemolyticus cell, and aptamer-modified upconversion nanoparticle formed a sandwich-like complex, which was rapidly separated from a complex matrix using a magnetic force, and the bacterial concentration was determined by fluorescence intensity analysis. The results showed that the fluorescence intensity signal correlated positively with the concentration of V. parahaemolyticus in the range of 3.2 × 102 to 3.2 × 105 CFU/mL, with a linear equation of y = 296.40x - 217.67 and a correlation coefficient of R2 = 0.9610. The detection limit of the developed method was 4.4 CFU/mL. There was no cross-reactivity with other tested foodborne pathogens. This method is highly specific and sensitive for the detection of V. parahaemolyticus, and can achieve the qualitative detection of this bacterium in a complex matrix.

Advanced diagnostic methods for identification of bacterial foodborne pathogens: contemporary and upcoming challenges

It is a public health imperative to have safe food and water across the population. Foodborne infections are one of the primary causes of sickness and mortality in both developed and developing countries. An estimated 100 million foodborne diseases and 120 000 foodborne illness-related fatalities occur each year in India. Several factors affect foodborne illness, such as improper farming methods, poor sanitary and hygienic conditions at all levels of the food supply chain, the lack of preventative measures in the food processing industry, the misuse of food additives, as well as improper storage and handling. In addition, chemical and microbiological combinations also play a key role in disease development. But recent disease outbreaks indicated that microbial pathogens played a major role in the development of foodborne diseases. Therefore, prompt, rapid, and accurate detection of high-risk food pathogens is extremely vital to warrant the safety of the food items. Conventional approaches for identifying foodborne pathogens are labor-intensive and cumbersome. As a result, a range of technologies for the rapid detection of foodborne bacterial pathogens have been developed. Presently, many methods are available for the instantaneous detection, identification, and monitoring of foodborne pathogens, such as nucleic acid-based methods, biosensor-based methods, and immunological-based methods. The goal of this review is to provide a complete evaluation of several existing and emerging strategies for detecting food-borne pathogens. Furthermore, this review outlines innovative methodologies and their uses in food testing, along with their existing limits and future possibilities in the detection of live pathogens in food.

Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections

The continuous evolution and spread of common pathogenic bacteria is a major challenge in diagnosis and treatment with current biotechnology and modern molecular medicine. To confront this challenge, scientists urgently need to find alternatives for traditional antimicrobial agents. Various bacteriostatic aptamers obtained through SELEX screening are one of the most promising strategies. These bacteriostatic aptamers can reduce bacterial infection by blocking bacterial toxin infiltration, inhibiting biofilm formation, preventing bacterial invasion of immune cells, interfering with essential biochemical processes, and other mechanisms. In addition, aptamers may also help enhance the function of other antibacterial materials/drugs when used in combination. This paper has reviewed the bacteriostatic aptamers in the treatment of common pathogenic bacteria infections. For this aspect, first, bacteriostatic aptamers and their screening strategies are summarized. Then, the effect of molecular tailoring and modification on the performance of the bacteriostatic aptamer is analyzed, and the antibacterial mechanism and antibacterial strategy based on aptamers are introduced. Finally, the key technical challenges and their development prospects in clinical treatment are also carefully discussed.

Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation

Introduction: Aptamers are valuable for bioassays, but aptamer-target binding is susceptible to reaction conditions. In this study, we combined thermofluorimetric analysis (TFA) and molecular dynamics (MD) simulations to optimize aptamer-target binding, explore underlying mechanisms and select preferred aptamer. Methods: Alpha-fetoprotein (AFP) aptamer AP273 (as the model) was incubated with AFP under various experimental conditions, and melting curves were measured in a real-time PCR system to select the optimal binding conditions. The intermolecular interactions of AP273-AFP were analysed by MD simulations with these conditions to reveal the underlying mechanisms. A comparative study between AP273 and control aptamer AP-L3-4 was performed to validate the value of combined TFA and MD simulation in selecting preferred aptamers. Results: The optimal aptamer concentration and buffer system were easily determined from the dF/dT peak characteristics and the melting temperature (Tm) values on the melting curves of related TFA experiments, respectively. A high Tm value was found in TFA experiments performed in buffer systems with low metal ion strength. The molecular docking and MD simulation analyses revealed the underlying mechanisms of the TFA results, i.e., the binding force and stability of AP273 to AFP were affected by the number of binding sites, frequency and distance of hydrogen bonds, and binding free energies; these factors varied in different buffer and metal ion conditions. The comparative study showed that AP273 was superior to the homologous aptamer AP-L3-4. Conclusion: Combining TFA and MD simulation is efficient for optimizing the reaction conditions, exploring underlying mechanisms, and selecting aptamers in aptamer-target bioassays.

Molecular Targets for Foodborne Pathogenic Bacteria Detection

The detection of foodborne pathogenic bacteria currently relies on their ability to grow on chemically defined liquid and solid media, which is the essence of the classical microbiological approach. Such procedures are time-consuming and the quality of the result is affected by the selectivity of the media employed. Several alternative strategies based on the detection of molecular markers have been proposed. These markers may be cell constituents, may reside on the cell envelope or may be specific metabolites. Each marker provides specific advantages and, at the same time, suffers from specific limitations. The food matrix and chemical composition, as well as the accompanying microbiota, may also severely compromise detection. The aim of the present review article is to present and critically discuss all available information regarding the molecular targets that have been employed as markers for the detection of foodborne pathogens. Their strengths and limitations, as well as the proposed alleviation strategies, are presented, with particular emphasis on their applicability in real food systems and the challenges that are yet to be effectively addressed.

Fluorescent aptasensor for detection of live foodborne pathogens based on multicolor perovskite-quantum-dot-encoded DNA probes and dual-stirring-bar-assisted signal amplification

In this study, a fluorescent (FL) aptasensor was developed for on-site detection of live Salmonella typhimurium (S.T.) and Vibrio parahaemolyticus (V.P.). Complementary DNA (cDNA) of aptamer (Apt)-functionalized multicolor polyhedral oligomeric silsesquioxane-perovskite quantum dots (cDNA-POSS-PQDs) were used as encoded probes and combined with dual-stirring-bar-assisted signal amplification for pathogen quantification. In this system, bar 1 was labeled with the S.T. and V.P. Apts, and then bar 2 was functionalized with cDNA-POSS-PQDs. When S.T. and V.P. were introduced, pathogen-Apt complexes would form and be released into the supernatant from bar 1. Under agitation, the two complexes reached bar 2 and subsequently reacted with cDNA-POSS-PQDs, which were immobilized on MXene. Then, the encoded probes would be detached from bar 2 to generate FL signals in the supernatant. Notably, the pathogens can resume their free state and initiate next cycle. They swim between the two bars, and the FL signals can be gradually enhanced to maximum after several cycles. The FL signals from released encoded probes can be used to detect the analytes. In particular, live pathogens can be distinguished from dead ones by using an assay. The detection limits and linear range for S.T. and V.P. were 30 and 10 CFU/mL and 10²-10⁶ CFU/mL, respectively. Therefore, this assay has broad application potential for simultaneous on-site detection of various live pathogenic bacteria in water.

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.

The Magnetosome Protein, Mms6 from Magnetospirillum magneticum Strain AMB-1, Is a Lipid-Activated Ferric Reductase

Magnetosomes of magnetotactic bacteria consist of magnetic nanocrystals with defined morphologies enclosed in vesicles originated from cytoplasmic membrane invaginations. Although many proteins are involved in creating magnetosomes, a single magnetosome protein, Mms6 from Magnetospirillum magneticum strain AMB-1, can direct the crystallization of magnetite nanoparticles in vitro. The in vivo role of Mms6 in magnetosome formation is debated, and the observation that Mms6 binds Fe³⁺ more tightly than Fe²⁺ raises the question of how, in a magnetosome environment dominated by Fe³⁺, Mms6 promotes the crystallization of magnetite, which contains both Fe³⁺ and Fe²⁺. Here we show that Mms6 is a ferric reductase that reduces Fe³⁺ to Fe²⁺ using NADH and FAD as electron donor and cofactor, respectively. Reductase activity is elevated when Mms6 is integrated into either liposomes or bicelles. Analysis of Mms6 mutants suggests that the C-terminal domain binds iron and the N-terminal domain contains the catalytic site. Although Mms6 forms multimers that involve C-terminal and N-terminal domain interactions, a fusion protein with ubiquitin remains a monomer and displays reductase activity, which suggests that the catalytic site is fully in the monomer. However, the quaternary structure of Mms6 appears to alter the iron binding characteristics of the C-terminal domain. These results are consistent with a hypothesis that Mms6, a membrane protein, promotes the formation of magnetite in vivo by a mechanism that involves reducing iron.

Advances in magnetic nanoparticles for the separation of foodborne pathogens: Recognition, separation strategy, and application

Foodborne pathogens contamination is one of the main sources of food safety problems. Although the existing detection methods have been developed for a long time, the complexity of food samples is still the main factor affecting the detection time and sensitivity, and the rapid separation and enrichment of pathogens is still an objective to be studied. Magnetic separation strategy based on magnetic nanoparticles (MNPs) is considered to be an effective tool for rapid separation and enrichment of foodborne pathogens in food. Therefore, this study comprehensively reviews the development of MNPs in the separation of foodborne pathogens over the past decade. First, various biorecognition reagents for identification of foodborne pathogens and their modifications on the surface of MNPs are introduced. Then, the factors affecting the separation of foodborne pathogens, including the size of MNPs, modification methods, separation strategies and separation forms are discussed. Finally, the application of MNPs in integrated detection methods is reviewed. Moreover, current challenges and prospects of MNPs for the analysis of foodborne pathogens are discussed. Further research should focus on the design of multifunctional MNPs, the processing of large-scale samples, the simultaneous analysis of multiple targets, and the development of all-in-one small analytical device with separation and detection.

In vitro selection and characterization of a DNA aptamer targeted to Prorocentrum minimum-A common harmful algae

Prorocentrum minimum is a common diarrhetic shellfish toxins-producing marine microalga that may seriously endanger marine resources and cause great economic losses. The development of a novel rapid detection technique is of great importance for the prevention and control of the damage caused by P. minimum. In this study, the aptamer against P. minimum was for the first time generated from an artificially synthesized single-stranded DNA library by systematic evolution of ligand by exponential enrichment (SELEX), using P. minimum and P. minimum-related species, including Prorocentrum donghaiense, Prorocentrum lima and Prorocentrum micans as target and counter-screening species, respectively. The aptamer library was successfully obtained at the end of 18 rounds of SELEX-screening by continuously monitoring the binding ratio of the resultant ssDNA from each round. Three sequences (Apt 1, Apt 2 and Apt 3) with the highest frequency in the aptamer library resulted from high-throughput sequencing were first selected as candidate aptamers. The secondary structure of these sequences was predicted and analyzed. In addition, the specificity and affinity of these candidate aptamers were determined by flow cytometry analysis. The results indicated that these aptamers had high specificity and affinity, with a K_D of (224.6 ± 8.8) nM (Apt 1), (286.6 ± 13.9) nM (Apt 2) and (388.5 ± 44.6) nM (Apt 3), respectively. Apt 1 was therefore chosen as the best aptamer against P. minimum. Finally, the fluorescence microscopic examination further confirmed that Apt 1 can well bind to P. minimum. In summary, Apt 1 may be promising for being used as a novel molecular recognition element for P. minimum.

Generation and Selection of Specific Aptamers Targeting Brucella Species through an Enhanced Cell-SELEX Methodology

Brucellae are Gram-negative, aerobic, non-motile coccobacilli causing brucellosis in man and animals. The disease is one of the most significant yet neglected global zoonoses. Especially in developing countries, brucellosis is causing public health problems and economic losses to private animal owners and national revenues. Composed of oligonucleotides, aptamers are chemical analogues of antibodies that are promising components for developing aptamer-based rapid, sensitive, and specific tests to identify the Brucella group of bacteria. For this purpose, aptamers were generated and selected by an enhanced protocol of cell systematic evolution of ligands by exponential enrichment (cell-SELEX). This enhanced cell-SELEX procedure involved the combination of both conventional and toggle cell-SELEX to boost the specificity and binding affinity to whole Brucella cells. This procedure, combined with high-throughput sequencing of the resulting aptamer pools, comprehensive bioinformatics analysis, and wet lab validation assays, led to the selection of a highly sensitive and specific aptamer for those Brucella species known to circulate in Egypt. The isolated candidate aptamer showed dissociation constant (K_D) values of 43.5 ± 11, 61.5 ± 8, and 56 ± 10.8 nM for B. melitensis, B. abortus, and B. suis, respectively. This is the first development of a Brucella-specific aptamer using an enhanced combination of conventional and toggle cell-SELEX to the authors’ best knowledge.

Aptamers against Pathogenic Bacteria: Selection Strategies and Apta-assay/Aptasensor Application for Food Safety

Pathogenic bacteria are primarily kinds of detrimental agents that cause mankind illness via contaminated food with traits of multiple types, universality, and low content. In view of the detection demands for rapidity, aptamer recognition factors emerged as a substitution for antibodies, which are short single strands of nucleic acid selected via in vitro. They display certain superiorities over antibodies, such as preferable stability, liable modification, and cost-efficiency. Taking advantage of the situation, numerous aptamers against pathogenic bacteria have been successfully selected and applied, yet there are still restrictions on commercial availability. In this review, the strategies/approaches to key sections in pathogen aptamers SELEX and post-SELEX are summarized and sorted out. Recently, optical, electrochemical, and piezoelectric aptamer-based assays or sensors dedicated to pathogen detection have been critically reviewed. Ultimately, the existing challenges and future trends in this field are proposed to further promote development prospects.

Selection, truncation and fluorescence polarization based aptasensor for Weissella viridescens detection

Weissella viridescens is a spoilage bacterium commonly found in low-temperature meat products. In this work, after fifteen rounds including three counter selection rounds of whole-cell systemic evolution of ligands by exponential enrichment (SELEX) in vitro, a novel aptamer L3 that can specifically recognize W. viridescens was obtained with a dissociation constant (K_d) value of 68.25 ± 5.32 nM. The sequence of aptamer L3 was optimized by truncation and a new aptamer sequence TL43 was obtained with a lower K_d value of 32.11 ± 3.01 nM. Finally, a simple and rapid fluorescence polarization (FP) platform was constructed to detect W. viridescens, in which FAM-labeled complementary sequence (FAM-cDNA) was employed to generate FP signal and streptavidin was used to amplify FP signal. In the presence of target bacteria, FP value decreased owning to the dissociation of FAM-cDNA from streptavidin/biotin-TL43/FAM-cDNA complex. Under optimal conditions, the concentration of W. viridescens and FP value displayed a good linear relationship with the detection range from 10² to 10⁶ cfu/mL. Moreover, the designed detection system had a good recovery rate of 90.6%-107.7% in smoked ham samples compared with classical plate counting method, indicating the great potential of the selected and truncated aptamer in practical biosensing applications.

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.

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.

Lateral flow colorimetric biosensor for detection of Vibrio parahaemolyticus based on hybridization chain reaction and aptamer

Vibrio parahaemolyticus (V. parahaemolyticus) is the causative agent for acute hepatopancreatic necrosis disease (AHPND) of shrimp, and it is also a common seafood-borne pathogen for humans. Rapid and accurate identification of V. parahaemolyticus is helpful to diagnose the AHPND and ensure food safety. Common detection methods suffer the deficiency of time-consuming and complexed operation. Based on the increased development of aptamer and our previous study, a new detection assay of V. parahaemolyticus was introduced, in which the aptamer combined with magnetic nanoparticles (MNPs) was the recognizer, hybridization chain reaction (HCR) was the signal amplifier, and lateral flow nucleotide biosensor (LFNB) was the signal exporter. The assay possessed high specificity of distinguishing the target with other bacteria, and the calculated limit of detection was 2.6 × 10³ cells. Furthermore, the whole process just needs 67 min, free of thermocycle instruments and signal readout instruments, which means it is suitable for low-resource laboratories or districts.

The systemic characterization of aptamer cocktail for bacterial detection studied by graphene oxide-based fluorescence resonance energy transfer aptasensor

Aptamers have gained significant attention as the molecular recognition element to replace antibodies in sensor development and target delivery. Nevertheless, it is noteworthy that unlike the wide application of polyvalent antibodies, existing researches on the combined use of heterologous aptamers with similar recognition affinity and specificity for target detection were sporadic. Herein, first, the wide existence of polyaptamer for bacteria was revealed through the summary of existing literature. Furthermore, based on the establishment of a sensitive aptamer cocktail/graphene oxide fluorescence resonance energy transfer polyaptasensor with a detection limit as low as 10 CFU/ml, the systemic characterization of aptamer cocktails in bacterial detection was carried out by taking E. coli, Vi. parahemolyticus, S. typhimurium, and C. sakazakii as the assay targets. It was turned out that the polyaptasensors for C. sakazakii and S. typhimurium owned prevalence in the broader concentration range of target bacteria. While the polyaptasensors for E. coli and V. parahemolyticus outperformed monoaptasensor mainly in the lower concentration of target bacteria. The linear relationships between fluorescence recovery and the concentration of bacteria were also discussed. The different characteristics of the bacterial cellular membrane, including the binding affinity and the robustness to variation, are analyzed to be the main reason for the diverse detection performance of aptasensors. The study here enhances a sensor detection strategy with super sensitivity. More importantly, this systemic study on the aptamer cocktail in reference to antibodies will advance the in-depth understanding and rational design of aptamer based biological recognition, detection, and targeting.

Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases

Infectious diseases are considered as a pressing challenge to global public health. Accurate and rapid diagnostics tools for early recognition of the pathogen, as well as individualized precision therapy are essential for controlling the spread of infectious diseases. Aptamers, which were screened by systematic evolution of ligands by exponential enrichment (SELEX), can bind to targets with high affinity and specificity so that have exciting potential in both diagnosis and treatment of infectious diseases. In this review, we provide a comprehensive overview of the latest development of SELEX technology and focus on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.

Oligonucleotide aptamers for pathogen detection and infectious disease control

During an epidemic or pandemic, the primary task is to rapidly develop precise diagnostic approaches and effective therapeutics. Oligonucleotide aptamer-based pathogen detection assays and control therapeutics are promising, as aptamers that specifically recognize and block pathogens can be quickly developed and produced through simple chemical synthesis. This work reviews common aptamer-based diagnostic techniques for communicable diseases and summarizes currently available aptamers that target various pathogens, including the SARS-CoV-2 virus. Moreover, this review discusses how oligonucleotide aptamers might be leveraged to control pathogen propagation and improve host immune system responses. This review offers a comprehensive data source to the further develop aptamer-based diagnostics and therapeutics specific for infectious diseases.

Selection and Characterization of Cell Surface Specific Aptamer and Development of Fluorescence Assay for Detection of Shigella flexneri from Water Samples

The present study demonstrates, development of ssDNA aptamers against whole cell of S. flexneri employing a whole bacterium-based Systemic Evolution of Ligands by Exponential Enrichment (SELEX). After ten rounds of SELEX, cell surface specific aptamer pool was cloned, sequenced and divided based on sequence similarities and secondary structure. Binding affinity of FITC labelled aptamer from different group were carried out by flow cytometry analysis. The dissociation constant (Kd) values for specific and higher binder were evaluated to range from 144 to 329 nM. Six high binding aptamers with lower dissociation constant was chosen for selectivity study. Aptamer SHI 23, SHI 37 and SHI 42 showed higher selectivity towards S. flexneri in comparison with other related bacteria. Further applicability of selected aptamer was proven by fluorescence assay for convenience detection of target cell from spiked water sample and natural contaminated water samples. Altogether, aptamer generated in this study can be alternative DNA ligands for detection of S. flexneri compared to available ligands.

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.

Generation and characterization of aptamers against grass carp reovirus infection for the development of rapid detection assay

Grass carp reovirus (GCRV) causes devastating viral haemorrhagic disease in farmed grass carp (Ctenopharyngon idellus). As novel molecular probes, aptamers have been widely applied in rapid diagnosis and efficient therapies against virus or diseases. In this study, three single-stranded DNA (ssDNA) aptamers were selected against GCRV-infected CIK cells via SELEX (systematic evolution of ligands by exponential enrichment technology). Secondary structures predicted by MFOLD indicated that aptamers formed stem-loop structures, and GVI-11 had the lowest ΔG value of -30.84 KJ/mol. Three aptamers could specifically recognize GCRV-infected CIK cells, with calculated dissociation constants (Kd) of 220.86, 176.63 and 278.66 nM for aptamers GVI-1, GVI-7 and GVI-11, respectively, which indicated that they could serve as specific delivery system for antiviral therapies. The targets of aptamers GVI-1, GVI-7 and GVI-11 on the surface of GCRV-infected cells could be membrane proteins, which were trypsin-sensitive. Furthermore, FAM-labelled aptamer GVI-7 could be applied to detect GCRV infection in vivo. It is the first time to generate and characterize aptamers against GCRV-infected cells. These aptamers have great potentials in development of rapid diagnosis technology and antiviral agents against GCRV infection in aquaculture.

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.

DNA aptamers against bacterial cells can be efficiently selected by a SELEX process using state-of-the art qPCR and ultra-deep sequencing

DNA aptamers generated by cell-SELEX against bacterial cells have gained increased interest as novel and cost-effective affinity reagents for cell labelling, imaging and biosensing. Here we describe the selection and identification of DNA aptamers for bacterial cells using a combined approach based on cell-SELEX, state-of-the-art applications of quantitative real-time PCR (qPCR), next-generation sequencing (NGS) and bioinformatic data analysis. This approach is demonstrated on Enterococcus faecalis (E. faecalis), which served as target in eleven rounds of cell-SELEX with multiple subtractive counter-selections against non-target species. During the selection, we applied qPCR-based analyses to evaluate the ssDNA pool size and remelting curve analysis of qPCR amplicons to monitor changes in pool diversity and sequence enrichment. Based on NGS-derived data, we identified 16 aptamer candidates. Among these, aptamer EF508 exhibited high binding affinity to E. faecalis cells (K_D-value: 37 nM) and successfully discriminated E. faecalis from 20 different Enterococcus and non-Enterococcus spp. Our results demonstrate that this combined approach enabled the rapid and efficient identification of an aptamer with both high affinity and high specificity. Furthermore, the applied monitoring and assessment techniques provide insight into the selection process and can be highly useful to study and improve experimental cell-SELEX designs to increase selection efficiency.

An Aptamer Linked Immobilized Sorbent Assay (ALISA) to Detect Circulatory IFN-α, an Inflammatory Protein among Tuberculosis Patients

Dysregulation of IFN-α is the basis for pathogenesis of autoimmune as well as infectious diseases. Identifying inflammatory signatures in peripheral blood of patients is an approach for monitoring active infection. Hence, estimation of type I IFNs as an inflammatory biomarker to scrutinize disease status after treatment is useful. Accordingly, an Aptamer Linked Immobilized Sorbent Assay (ALISA) for the detection of IFN-α in serum samples was developed. Sixteen aptamers were screened for their ability to bind IFN-α. Aptamer IFNα-3 exhibited specificity for IFN-α with no cross-reactivity with interferons β and γ and human serum albumin. The disassociation constant (K_d) was determined to be 3.96 ± 0.36 nM, and the limit of detection was ∼2 ng. The characterized IFNα-3 aptamer was used in ALISA to screen tuberculosis (TB) patients' sera. An elevated IFN-α level in sera derived from untreated TB patients (median = 0.31), compared to nontuberculous household contacts (median = 0.13) and healthy volunteers (median = 0.12), and further a decline in IFN-α level among treated patients (median = 0.13) were seen. The ALISA assay facilitates direct estimation of inflammatory protein(s) in circulation unlike mRNA estimation by real time PCR. Designing of aptamers similar to the IFNα-3 aptamer provides a novel approach to assess other inflammatory protein(s) in patients before, during, and after completion of treatment and would denote clinical improvement in successfully treated patients.

Simple Colorimetric Assay for Vibrio parahaemolyticus Detection Using Aptamer-Functionalized Nanoparticles

Simple, rapid, and sensitive screening methods are the key to prevent and control the spread of foodborne diseases. In this study, a simple visual colorimetric assay using magnetic nanoparticles (MNPs) and gold nanoparticles (AuNPs) was developed for the detection of Vibrio parahaemolyticus. First, the aptamer responding to V. parahaemolyticus was conjugated onto the surface of MNPs and used as a specific magnetic separator. In addition, the aptamer was also immobilized on the surface of AuNPs and used as a colorimetric detector. In the presence of V. parahaemolyticus, a sandwich structure of MNP-aptamer-bacteria-aptamer-AuNPs is formed through specific recognition of the aptamer and V. parahaemolyticus. The magnetic separation technique was then applied to generate a detection signal. Owing to the optical properties of AuNPs, a visual signal could be observed, resulting in an instrument-free colorimetric detection. Under optimal conditions, this assay shows a linear response toward V. parahaemolyticus concentration through the range of 10-106 cfu/mL, with a limit of detection of 2.4 cfu/mL. This method was also successfully applied for V. parahaemolyticus detection in spiked raw shrimp samples.

Recent advances on functional nucleic acid-based biosensors for detection of food contaminants

It has seen increasing development of reliable, robust, and flexible biosensors for rapid food-safety analysis in the past few decades. Recently, functional nucleic acid-based biosensors have attracted attention because of their programmability, bottom-up characteristics, and structural switches. However, few systematic reviews devoted to categorizing the potential of DNA nanostructures and devices were found for detecting food contaminants. Hence, the applications of functional nucleic acid-based biosensors were reviewed for analyzing food contaminants, including foodborne pathogen bacteria, biotoxins, heavy metals, and et al. In addition to categorizing the various biosensors, multiple signal readout strategies, such as optical, electrochemical, and mass-based signals were also examined. Finally, the future changes and potential opportunities, as well as practical applications of functional nucleic acid-based biosensors were discussed.

Detection Strategies of Zearalenone for Food Safety: A Review

Zearalenone (ZEN) is a toxic compound produced by the metabolism of fungi (genus Fusarium) that threaten the food and agricultural industry belonging to the in foods and feeds. ZEN has toxic effects on human and animal health due to its mutagenicity, teratogenicity, carcinogenicity, nephrotoxicity, immunotoxicity, and genotoxicity. To ensure food safety, rapid, precise, and reliable analytical methods can be developed for the detection of toxins such as ZEN. Different selective molecular diagnostic elements are used in conjunction with different detection strategies to achieve this goal. In this review, the use of electrochemical, colorimetric, fluorometric, refractometric as well as other strategies were discussed for ZEN detection. The success of the sensors in analytical performance depends on the development of receptors with increased affinity to the target. This requirement has been met with different immunoassays, aptamer-assays, and molecular imprinting techniques. The immobilization techniques and analysis strategies developed with the combination of nanomaterials provided high precision, reliability, and convenience in ZEN detection, in which electrochemical strategies perform the best.

Selection of aptamers targeted to food-borne pathogenic bacteria Vibrio parahaemolyticus

Vibrio parahaemolyticus (Vp) is a common marine halophilic food-borne pathogen, mainly found in seafood and food with a high salt content. Gastrointestinal reactions such as diarrhea, headache, vomiting, nausea, and abdominal cramps may occur after eating food infected with Vp. This study aimed to screen for high-affinity aptamers that specifically recognize Vp. A high-affinity modified aptamer screening kit was used to rapidly screen aptamers of the food-borne Vp. The first round of screening involved release of target aptamers from the microspheres. The "false-positive" aptamers were eliminated after specific binding to and elution of Vp in the second round. The second round of screening of the aptamers involved polymerase chain reaction (PCR), and the abundance of a sequence was determined using next-generation sequencing. Nine high-affinity aptamer sequences were obtained, and the first eight modified aptamer sequences were derived using a cloud-based intelligent software of the American AM Biotech Co. Escherichia coli (E. coli) was used as a control, and aptamer ID 12 with the highest affinity for Vp was selected using real-time PCR. According to the principle of color change caused by nano-gold condensing under salt induction, Salmonella, Listeria monocytogenes (L. monocytogenes), and E. coli were used as counter-screening bacteria, and the aptamer ID12 was combined with nano-gold. The results showed that aptamer ID12 has strong specificity for Vp. Based on these findings, this study developed a simple, innovative, and rapid method for screening Vp aptamers.

An overview and future prospects on aptamers for food safety

Introduction

Many bacteria are responsible for infections in humans and plants, being found in vegetables, water, and medical devices. Most bacterial detection methods are time-consuming and take days to give the result. Aptamers are a promising alternative for a quick and reliable measurement technique to detect bacteria present in food products. Selected aptamers are DNA or RNA oligonucleotides that can bind with bacteria or other molecules with affinity and specificity for the target cells by the SELEX or cell-SELEX technique. This method is based on some rounds to remove the non-ligand oligonucleotides, leaving the aptamers specific to bind to the selected bacteria. Compared with conventional methodologies, the detection approach using aptamers is a rapid, low-cost form of analysis.

Objective

This review summarizes obtention methods and applications of aptamers in the food industry and biotechnology. Besides, different techniques with aptamers are presented, which enable more effective target detection.

Conclusion

Applications of aptamers as biosensors, or the association of aptamers with nanomaterials, may be employed in analyses by colorimetric, fluorescence, or electrical devices. Additionally, more efficient ways of sample preparation are presented, which can support food safety to provide human health, with a low-cost method for contaminant detection.

Key points • Aptamers are promising for detecting contaminants outbreaks. • Studies are needed to identify aptamers for different targets.

Aptamer Hybrid Nanocomplexes as Targeting Components for Antibiotic/Gene Delivery Systems and Diagnostics: A Review

With the passage of time and more advanced societies, there is a greater emergence and incidence of disease and necessity for improved treatments. In this respect, nowadays, aptamers, with their better efficiency at diagnosing and treating diseases than antibodies, are at the center of attention. Here, in this review, we first investigate aptamer function in various fields (such as the detection and remedy of pathogens, modification of nanoparticles, antibiotic delivery and gene delivery). Then, we present aptamer-conjugated nanocomplexes as the main and efficient factor in gene delivery. Finally, we focus on the targeted co-delivery of genes and drugs by nanocomplexes, as a new exciting approach for cancer treatment in the decades ahead to meet our growing societal needs.

A SERS aptasensor for simultaneous multiple pathogens detection using gold decorated PDMS substrate

An aptamer-based sensitive method was developed here for detection of multiple foodborne pathogens in food matrix by surface-enhanced Raman scattering (SERS) technology. Polydimethylsiloxane (PDMS) film was first prepared and then coated with gold nanoparticles (AuNP) to act as an active substrate for the enhancement of Raman scattering. The as-prepared Au-PDMS film was functionalized with specific pathogen aptamers (Apt) to capture the targets. In addition, aptamers functionalized AuNP integrated with Raman reporters (4-Mercaptobenzoic acid (4-MBA)/Nile blue A (NBA)) were fabricated as pathogen-specific SERS probes. In this scheme, pathogens were first captured by Apt-Au-PDMS film and then bind with SERS probes to allow the formation of a sandwich assay to complete the sensor module for the detection of multiple pathogens. With Vibrio parahaemolyticus and Salmonella typhimurium as model targets, this protocol can selectively detect 18 cfu/mL and 27 cfu/mL, respectively. Furthermore, this platform can be successfully applied to detect pathogens in seafood samples with recoveries ranging from 82.9% to 95.1%.

Rapid and Accurate Quantification of Paramylon Produced from Euglena gracilis Using an ssDNA Aptamer

The functional ingredients of microalgal biomass are receiving substantial recognition as the global demands for health supplements produced from natural sources are on the rise. Paramylon, a conglomerate of β-1,3-glucans, is one of the major valuable sources derived from Euglena gracilis having multiple applications, thus necessitating the development of an efficient quantification method. Here, we employed a DNA aptamer to quantify the amount of paramylon produced by E. gracilis. Paramylon-specific aptamers were isolated by the systematic evolution of ligands by exponential enrichment (SELEX) process. To evaluate the potential aptamers, the binding affinity between aptamer candidates and paramylon granules was confirmed by a confocal laser scanning microscope and the dissociation constants of the selected aptamers were determined by nonlinear regression analysis. The selected DNA aptamer was successfully used for the quantification of paramylon, and the results were compared to those obtained by the standard methods. The new approach was also used for quantification of paramylon from E. gracilis cells cultured to different cell stages and physiologies. It can be concluded that the aptamer-based protocol for the measurement of paramylon proposed in this study is highly accurate and comparatively less time-consuming.

Isolation ssDNA aptamers specific for both live and viable but nonculturable stateVibrio vulnificususing whole bacteria-SEILEX technology

Vibrio vulnificus is a ubiquitous marine bacterium that may cause rapid and deadly infection, threatening lives of people living around natural bodies of water, especially in coastal regions. However, traditional culture-based methods are time-consuming and unable to detect Viable But Non-Culturable (VBNC) V. vulnificus cells. In this work, we isolated a batch of detection aptamers specifically binding to V. vulnificus in all culture status. With traditional whole bacteria-SELEX (Systematic Evolution of Ligands by EXponential enrichment), flow cytometer analysis and imaging, we identify 18 candidates and validated two of them (V8 and V13) as applicable aptamers. Their truncated sequences also showed comparable performance. The dissociation constant (KD) value of V8 is shown to be as low as 11.22 ± 1.32 nM. Optimal aptamers V8 and V13 are also validated to be effective to detect different Vibrio vulnificus strains under different binding environments using flow cytometry. As for detection parameters, the LOD of the V8 from cytometry is 29.96 CFU mL⁻¹, and the linear range is 10²–5 × 10⁵ CFU mL⁻¹. This is the first case demonstrating that aptamers can detect the existence of VBNC bacteria as well as live bacteria.

With whole-bacteria SELEX, we got aptamers that can bind to V. vulnificus in VBNC Status for the first time.

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.

Development of novel aptamer-based enzyme-linked apta-sorbent assay (ELASA) for rapid detection of mariculture pathogen Vibrio alginolyticus

As the major opportunistic pathogen to both marine animals and humans, Vibrio alginolyticus (V. alginolyticus) has caused heavy economic losses to mariculture. ssDNA aptamer VA2 targeting live V. alginolyticus was generated by systematic evolution of ligands by exponential enrichment (SELEX) technology in our previous study. In this study, we first developed aptamer (VA2)-based enzyme-linked apta-sorbent assay (VA2-ELASA) for rapid detection of mariculture pathogen V. alginolyticus. The VA2-ELASA could achieve the rapid detection for V. alginolyticus infection with high specificity and sensitivity. The VA2-ELASA could specifically identify V. alginolyticus, but not other non-target bacterial strains. VA2-ELASA could detect V. alginolyticus at the concentration of 5 × 10⁴ /ml, the incubation time short to 1 min and the incubation temperature as high as 45°C, which proved sensitivity and stability of the novel VA2-ELASA in this study. It took less than one hour to accomplish the detection process by VA2-ELASA. The characteristics of specificity, sensitivity and easy operation make VA2-ELASA a novel useful technology for the rapid diagnosis of pathogen V. alginolyticus in mariculture.

Surface-enhanced Raman spectroscopic single step detection of Vibrio parahaemolyticus using gold coated polydimethylsiloxane as the active substrate and aptamer modified gold nanoparticles

A method is described for single-step detection of V. parahaemolyticus in seafood via aptamer-based SERS. A gold-coated polydimethylsiloxane (PDMS) film was used for the enhancement of Raman scattering. The Raman reporter 4-mercaptobenzoic acid was linked to aptamer modified gold nanoparticles (AuNPs) served as a signalling probe. The negatively charged signalling probe was assembled onto the cysteamine-modified Au-PDMS film through electrostatic adsorption. On addition of V. parahaemolyticus, it will be bound by the aptamer as a biorecognition element, and this leads to the dissociation of the signalling probe from the Au-PDMS film. Hence, the Raman signal (at 1592 cm^-1) decreases. The assay has a wide linear response that covers the 1.2 × 10² to 1.2 × 10⁶ cfu·mL^-1 V. parahaemolyticus concentration range. The detection limit is 12 cfu·mL^-1. The method was successfully applied to the determination of V. parahaemolyticus in oyster and salmon samples. Graphical abstract Schematic presentation of a surface-enhanced Raman spectroscopic method for single step detection of Vibrio parahaemolyticus using gold coated polydimethylsiloxane as the active substrate and aptamer modified gold nanoparticles. This solid substrate simplified the analysis procedures and enhanced the sensitivity.

Selection and characterization of ssDNA aptamers specifically recognizing pathogenic Vibrio alginolyticus

Vibrio alginolyticus (V. alginolyticus) is a major opportunistic pathogen to both marine animals and humans, which has also caused heavy economic losses to mariculture. The aim of this study was to develop highly specific aptamers for V. alginolyticus. Single-stranded DNA (ssDNA) aptamers with high binding affinity to viable V. alginolyticus were generated by Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and identified by flow cytometric analysis in this study. The selected aptamers showed high specificity for V. alginolyticus and low apparent binding for other bacteria. The aptamers formed distinct stem-loop structures, which could form the basis of aptamers' specific binding to the target V. alginolyticus. Aptamer VA2 and VA8 showed particularly high binding affinity constant (Kd) of 14.31 ± 4.26 and 90.00 ± 13.51 nM, respectively. The aptamers produced no cytotoxic effects in vitro and in vivo. ssDNA aptamers were successfully selected against the viable bacteria pathogen V. alginolyticus by SELEX. The aptamers selected in this study could be not only applied as specific chemical molecular probes for studying V. alginolyticus pathogenesis to Trachinotus ovatus, but also developing rapid convenient diagnosis assay for V. alginolyticus infection, even when applied to the complex sample matrix, such as food and environment samples.