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

An ultrasensitive fluorescence nano-biosensor based on RBP 41-quantum dot microspheres for rapid detection of Salmonella in the food matrices

Swift screening of Salmonella-contaminated food is crucial for timely prevention and control of foodborne illness outbreaks. A novel phage receptor binding protein (RBP 41) was previously identified and characterized from phage T102. This study functionalized RBP 41 onto magnetic beads (MBs) and quantum dot microspheres (QDMs) to form magnetic separation and fluorescent probes, respectively. The bacteria were captured by RBP 41-MBs and labelled with RBP 41-QDMs to form MBs-RBP 41-bacteria-RBP 41-QDMs complexes, then the fluorescence intensity of complexes was detected for determination of Salmonella. This proposed biosensor was demonstrated to detect Salmonella as low as 0.1245 Log10 CFU/mL (∼2 CFU/mL) within ∼1.5 h. The recovery yield of Salmonella in the spiked food samples ranged from 87 % to 119 %, indicating that it could detect Salmonella in real samples. This novel magnetic fluorescence nano-biosensor has potential to detect the bacteria in the different sample to reduce the detection time and increase sensitivity.

High sensitive Ratiometric fluorescent Aptasensor with AIE properties for Deoxynivalenol (DON) detection

An emerging fluorescent ratiometric aptasensor based on gold nanoclusters (AuNCs) with aggregation-induced emission (AIE) properties was prepared and studied for deoxynivalenol (DON) detection. The ratiometric aptasensor used red fluorescent AuNCs620 labelled with DON aptamer (Apt-AuNCs620) as an indicator and green fluorescent AuNCs519 modified by complementary DNA (cDNA) and magnetic beads (MBs) as internal reference, namely MBs-cDNA-AuNCs519. Under the optimal conditions, the aptasensor exhibited two good linear ranges of 0.1-50 and 50-5000 pg/mL for DON detection with coefficient of determination (R2) of 0.9937 and 0.9928, respectively, and the low detection limit (LOD) of 4.09 pg/mL was achieved. Furthermore, this aptasensor was feasible to detect DON in positive wheat samples, and the results were in line with those from HPLC and ELISA, thus providing a promising route to detect DON with high sensitivity in cereals, even for other mycotoxins by replacing the suitable aptamer and cDNA.

Unlocking precision in aptamer engineering: a case study of the thrombin binding aptamer illustrates why modification size, quantity, and position matter

The thrombin binding aptamer (TBA) is a prototypical platform used to understand the impact of chemically-modified nucleotides on aptamer stability and target affinity. To provide structural insight into the experimentally-observed effects of modification size, location, and number on aptamer performance, long time-scale molecular dynamics (MD) simulations were performed on multiple binding orientations of TBA-thrombin complexes that contain a large, flexible tryptophan thymine derivative (T-W) or a truncated analogue (T-K). Depending on modification position, T-W alters aptamer-target binding orientations, fine-tunes aptamer-target interactions, strengthens networks of nucleic acid-protein contacts, and/or induces target conformational changes to enhance binding. The proximity and 5'-to-3' directionality of nucleic acid structural motifs also play integral roles in the behavior of the modifications. Modification size can differentially influence target binding by promoting more than one aptamer-target binding pose. Multiple modifications can synergistically strengthen aptamer-target binding by generating novel nucleic acid-protein structural motifs that are unobtainable for single modifications. By studying a diverse set of modified aptamers, our work uncovers design principles that must be considered in the future development of aptamers containing chemically-modified nucleotides for applications in medicine and biotechnology, highlighting the value of computational studies in nucleic acids research.

Advances in Aptamer-Based Biosensors for the Detection of Foodborne Mycotoxins

Foodborne mycotoxins (FBMTs) are toxins produced by food itself or during processing and transportation that pose an enormous threat to public health security. However, traditional instrumental and chemical methods for detecting toxins have shortcomings, such as high operational difficulty, time consumption, and high cost, that limit their large-scale applications. In recent years, aptamer-based biosensors have become a new tool for food safety risk assessment and monitoring due to their high affinity, good specificity, and fast response. In this review, we focus on the progress of single-mode and dual-mode aptasensors in basic research and device applications over recent years. Furthermore, we also point out some problems in the current detection strategies, with the aim of stimulating future toxin detection systems for a transition toward ease of operation and rapid detection.

DNA Meets Protein─Development, Characterization, and Application of Aptamers against Peanut Allergen

Allergen detection methods support food labeling and quality assessment at the allergen component level of allergen preparations used for allergy diagnosis and immunotherapy (AIT). Commonly applied enzyme-linked immunosorbent assay (ELISA) requires animal antibodies but potentially shows batch variations. We developed synthetic aptamers as alternative binders in allergen detection to meet the replacement, reduction, and refinement (3R) principle on animal protection in science. ssDNA aptamers were specifically selected against the major peanut allergen Ara h 1 and identified by next-generation sequencing. Application in various detection systems (ELISA-like assays, western blot, and surface plasmon resonance) was demonstrated. The ELISA-like assay comprised a sensitivity of 10 ng/mL Ara h 1, comparable to published antibody-based ELISA, and allowed Ara h 1 detection in various peanut flours, similar to those used in peanut AIT as well as in processed food. This ELISA-like aptamer-based assay proofs antibody-free allergen detection for food labeling or quality assessment of diagnostic and therapeutic allergen products.

Generating robust aptamers for food analysis by sequence-based configuration optimization

Advanced analytical techniques are emerging in the food industry. Aptamer-based biosensors achieve rapid and highly selective analysis, thus drawing particular attention. Aptamers are oligonucleotide probes screened via in vitro Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which can bind with their specific targets by folding into three-dimensional configurations and accept various modifications to be incorporated into biosensors, showing great potential in food analysis. Unfortunately, aptamers obtained by SELEX may not possess satisfactory affinity. Post-SELEX strategies were proposed to optimize aptamers' configuration and enhance the binding affinity, with specificity confirmed. Sequence-based optimization strategies exhibit great advantages in simple operation, good generalization, low cost, etc. This review summarizes the latest study (2015-2023) on generating robust aptamers for food targets by sequence-based configuration optimization, as well as the generated aptamers and aptasensors, with an expectation to provide inspirations for developing aptamer and aptasensors with high performance for food analysis and to safeguard food quality and safety.

An electrochemical method based on CRISPR-Cas12a and enzymatic reaction for the highly sensitive detection of tumor marker MUC1 mucin

Anti-cancer therapy is crucial in cancer prevention and anti-cancer, and thus, highly sensitive methods for detecting cancer biomarkers are essential for cancer early diagnosis. Herein, an electrochemical aptamer biosensor based on the CRISPR-Cas12a system was constructed for the detection of cancer tumor biomarker MUC1 mucin. The sensitivity was significantly prompted by enzyme-catalyzed signal amplification, and the selectivity was improved by the dual recognition of the aptamer to MUC1 and crRNA-Cas12a system to the aptamer. Glucose oxidase (GOD) was loaded on the surface of magnetic Fe3O4@Au (MGNP) via probe single-stranded DNA (pDNA) with the terminal modification of mercapto (-SH) to form GOD-pDNA/MGNP. The corresponding aptamer of MUC1 (MUC1 Apt) binds to its complementary ssDNA (cDNA) to form the activator Apt/cDNA, which is specifically recognized by crRNA-Cas12a and excites the trans-cleavage function of Cas12a, thus in turn trans-cleaves pDNA and detaches GOD from the magnetic particles. The magnetic beads were separated and transferred into a glucose solution, and the oxidation current of H2O2 produced by the catalytic reaction of GOD was measured on a Pt-modified magnetically-controlled glassy carbon electrode, resulting in an indirect determination of MUC1. The current change was linear with the logarithm of MUC1 concentration in the range from 1.0 × 10-17 g mL-1 to 1.0 × 10-10 g mL-1. The detection limit was as low as 7.01 × 10-18 g mL-1. The method was applied for the detection of MUC1 in medical samples.

UIO66 low background signal and fluorescence synergism strategy for highly sensitive detection of Salmonella typhimurium

Successful construction of a detection method for Salmonella typhimurium (S. typhimurium) based on the synergy of hybridization chain reaction (HCR) and fluorescence was realized in this paper. First, the aptamer modified with the quenching group Black Hole Quencher-1 acid (BHQ1) was immobilized on the magnetic beads in combination with the complementary chain of the aptamer modified with 6-carboxyfluorescein (6-FAM). Second, S. typhimurium and cDNA-6-FAM immobilized on magnetic beads competitively bound to the aptamer. Finally, the cDNA-6-FAM was released after magnetic separation acted as a promoter to trigger HCR amplification when the target presented. The fluorescence signal could be significantly improved by the combination of green SYBR Green I (SGI) and HCR long double-stranded DNA and the fluorescent synergy of 6-FAM and SGI. Because of the separation of target and its aptamer, the trigger strand was abstracted by magnetic separation. There was no HCR to generate long double-stranded DNA, and the fluorescence of excess hairpin/SGI could be adsorbed through UIO66 so that only a very low background signal was detected. This fluorescent sensor was capable of monitoring S. typhimurium in the range of 10-3.2 × 107 CFU mL-1 with a limit of detection as low as 1.5 CFU mL-1. Because of the excellent properties of the aptasensor and the validity of SGI fluorescence synergy, this HCR enzyme-free amplification strategy could be generalized to other areas.

Sensitive and on-Site Detection of Staphylococcus aureus Based on CRISPR/Cas 13a-Assisted Chemiluminescence Resonance Energy Transfer

Developing a specific, sensitive, rapid, and on-site method for detecting pathogenic bacteria in food samples is critical to ensuring public safety. This article demonstrates a CRISPR/Cas13a system and a chemiluminescence resonance energy transfer (CRET) (CRISPR/Cas 13a-assisted CRET)-based strategy for sensitive and on-site detection of pathogenic bacteria in real samples. Once the hybrid double strand of aptamerS. aureus-cRNA recognizes the target model bacteria of Staphylococcus aureus (S. aureus), the released cRNA would bind with CRISPR/Cas 13a to form a complex of cRNA-CRISPR/Cas 13a, which could cleave the RNA molecule in the detecting probe of horseradish peroxidase (HRP) modified-gold nanoparticles (AuNPs) linked by RNA (AuNPs-RNA-HRP), resulting in an enhanced chemiluminescence signal due to the CRET "OFF" phenomenon after introducing the chemiluminescence substrate of luminol. The CRISPR/Cas 13a-assisted CRET strategy successfully detected S. aureus in drinking water and milk with detection limits of 20 and 30 cfu/mL, respectively, within the recovery of 90.07-105.50%. Furthermore, after integrating with an immunochromatographic test strip (ICTS), the CRISPR/Cas 13a-assisted CRET strategy achieved the on-site detection of as low as 102 cfu/mL of S. aureus in drinking water and milk via a smartphone, which is about 10 times lower than that in the previously reported AuNPs-based colorimetric ICTS, demonstrating a convenient and sensitive detection method for S. aureus in real samples.

Dialdehyde cellulose films covalently crosslinked with porphyrin-based covalent organic polymers for photodynamic sterilization

Foodborne pathogens result in a great harm to human, which is an urgent problem to be addressed. Herein, a novel cellulose-based packaging films with excellent anti-bacterial properties under visible light were prepared. A porphyrin-based covalent organic polymer (Por-COPs) was constructed, then covalently grafted onto dialdehyde cellulose (DAC). The addition of Por-COPs enhanced the mechanical, hydrophobicity, and water resistance of the DAC-based composite films. DAC/Por-COP-2.5 film exhibited outstanding properties for the photodynamic inactivation of bacteria under visible light irradiation, delivering inactivation efficiencies of 99.90 % and 99.45 % towards Staphylococcus aureus and Escherichia coli within 20 min. The DAC/Por-COPs films efficiently generated •O2- and 1O2 under visible light, thereby causing oxidative stress to cell membranes for bacterial inactivation. The prepared composite film forms a protective barrier against bacterial contamination. Results guide the development of high performance and more sustainable packaging films for the food sector.

Recent Advances in Aptamer-Based Biosensors for Bacterial Detection

The rapid and sensitive detection of pathogenic bacteria is becoming increasingly important for the timely prevention of contamination and the treatment of infections. Biosensors based on nucleic acid aptamers, integrated with optical, electrochemical, and mass-sensitive analytical techniques, have garnered intense interest because of their versatility, cost-efficiency, and ability to exhibit high affinity and specificity in binding bacterial biomarkers, toxins, and whole cells. This review highlights the development of aptamers, their structural characterization, and the chemical modifications enabling optimized recognition properties and enhanced stability in complex biological matrices. Furthermore, recent examples of aptasensors for the detection of bacterial cells, biomarkers, and toxins are discussed. Finally, we explore the barriers to and discuss perspectives on the application of aptamer-based bacterial detection.

Surface-Activated Ti3C2Tx Adsorption of Acetylene Black Coupled with Polyaniline as a Signal Tag for the Detection of the ESAT-6 Antigen of Mycobacterium tuberculosis

Early secretory antigenic target-6 (ESAT-6) is regarded as the most immunogenic protein produced by Mycobacterium tuberculosis, whose detection is of great clinical significance for tuberculosis diagnosis. However, the detection of the ESAT-6 antigen has been hampered by the expensive cost and complex experimental procedures, resulting in low sensitivity. Herein, we developed a titanium carbide (Ti3C2Tx)-based aptasensor for ESAT-6 detection utilizing a triple-signal amplification strategy. First, acetylene black (AB) was immobilized on Ti3C2Tx through a cross-linking reaction to form the Ti3C2Tx-AB-PAn nanocomposite. Meanwhile, AB served as a conductive bridge, and Ti3C2Tx can synergistically promote the electron transfer of PAn. Ti3C2Tx-AB-PAn exhibited outstanding conductivity, high electrochemical signals, and abundant sites for the loading of ESAT-6 binding aptamer II (EBA II) to form a novel signal tag. Second, N-CNTs were adsorbed on NiMn layered double hydride (NiMn LDH) nanoflowers to obtain NiMn LDH/N-CNTs, exhibiting excellent conductivity and preeminent stability to be used as electrode modification materials. Third, the biotinylated EBA (EBA I) was immobilized onto a streptavidin-coated sensing interface, forming an amplification platform for further signal enhancement. More importantly, as a result of the synergistic effect of the triple-signal amplification platform, the aptasensor exhibited a wide detection linear range from 10 fg mL-1 to 100 ng mL-1 and a detection limit of 4.07 fg mL-1 for ESAT-6. We envision that our aptasensor provides a way for the detection of ESAT-6 to assist in the diagnosis of tuberculosis.

Selection and application of highly specific Salmonella typhimurium aptamers against matrix interference

In practical applications, the structure and performance of aptamers can be influenced by the presence of sample matrices, which interferes with the specific binding between the aptamer and its target. In this work, to obtain aptamer chains resistant to matrix interference, four typical food matrices were introduced as negative selection targets and selection environments in the process of selecting aptamers for Salmonella typhimurium using the systematic evolution of ligands by exponential enrichment (SELEX) technology. As a result, some highly specific candidate aptamers for Salmonella typhimurium (BB-34, BB-37, ROU-8, ROU-9, ROU-14, ROU-24, DAN-3, NAI-12, and NAI-21) were successfully obtained. Based on the characterization results of secondary structure, affinity, and specificity of these candidate aptamers, ROU-24 selected in the pork matrix and BB-34 selected in the binding buffer were chosen to develop label-free fluorescence aptasensors for the sensitive and rapid detection of the Salmonella typhimurium and verify the performance against matrix interference. The ROU-24-based aptasensor demonstrated a larger linear range and better specificity compared to the BB-34-based aptasensor. Meanwhile, the recovery rate of the ROU-24-based aptasensor in real sample detection (ranging from 94.2% to 110.7%) was significantly higher than that of the BB-34-based aptasensor. These results illustrated that the negative selection of food matrices induced in SELEX could enhance specific binding between the aptamer and its target and the performance against matrix interference. Overall, the label-free fluorescence aptasensors were developed and successfully validated in different foodstuffs, demonstrating a theoretical and practical basis for the study of aptamers against matrix interference.

Piezoelectric biosensors: shedding light on principles and applications

The three decades of experience with piezoelectric devices applied in the field of bioanalytical chemistry are shared. After introduction to principles and suitable measuring approaches, active and passive methods based on oscillators and impedance analysis, respectively, the focus is directed towards biosensing approaches. Immunosensing examples are provided, followed by other affinity sensing approaches based on hybridization of nucleic acids, aptamers, monitoring of enzyme activities, and detection of pathogenic microbes. The combination of piezosensors with cell lines and testing of drugs is highlighted, including mechanically active cells. The combination of piezosensors with other measuring techniques providing original hybrid devices is briefly discussed.

High-affinity truncated aptamers for detection of Cronobacter spp with magnetic separation-assisted DNAzyme-driven 3D DNA walker

After optimizing the original aptamer sequence by truncation strategy, a magnetic separation-assisted DNAzyme-driven 3D DNA walker fluorescent aptasensor was developed for detecting the food-borne pathogen Cronobacter species. Iron oxide magnetic nanoparticles (MNPs) modified with a hybrid of truncated aptamer probe and DNAzyme strand (AP-E1) denoted as MNPs@AP-E1, were employed as capture probes. Simultaneously, a DNAzyme-driven 3D-DNA walker was utilized as the signal amplification element. The substrate strand (Sub) was conjugated with the gold nanoparticles (AuNPs), resulting in the formation of AuNPs@Sub, which served as a 3D walking track. In the presence of the target bacteria and Mg2+, E1-DNAzyme was activated and moved along AuNPs@Sub, continuously releasing the signal probe. Under optimized conditions, a strong linear correlation was observed for Cronobacter sakazakii (C. sakazakii) in the concentration range 101 to 106 CFU mL-1, with a low detection limit of 2 CFU mL-1. The fluorescence signal responses for different Cronobacter species exhibited insignificant differences, with a relative standard deviation of 3.6%. Moreover, the aptasensor was successfully applied to determine  C. sakazakii in real samples with recoveries of 92.86%-108.33%. Therefore, the novel method could be a good candidate for ultra-sensitive and selective detection of Cronobacter species without complex manipulation.

One-pot rapid visual detection of E. coli O157:H7 by label-free AuNP-based plasmonic-aptasensor in water sample

Access to clean water for irrigation and drinking has long been a global concern. The need for fast, precise, and cost-effective methods to detect harmful bacteria like Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 is high due to the potential for severe infectious diseases. Fortunately, recent research has led to developing and utilizing rapid bacterial detection methods. The creation of an aptamer-based biosensor (aptasensor) for the detection of E. coli O157:H7 using label-free aptamers and gold nanoparticles (AuNPs) is described in this study. The specific aptamers that can detect target bacteria are adsorbed on the surface of unmodified AuNPs to form the aptasensor. The detection is performed by target bacterium-induced aptasensor aggregation, which is associated with a red-to-purple color change under high-salt circumstances. We devised a quick and easy method for detecting bacteria using an anti-E. coli O157:H7 aptamer without the need for specialized equipment or pretreatment processes like cell lysis. The aptasensor could identify target bacteria with only as few as 250 colony-forming units (CFU)/ml in 15 min or less, and its specificity based on our test was 100%. This method not only provides a fast direct preparation process but also exhibits remarkable proficiency in promptly identifying the intended target with a heightened level of sensitivity and specificity. Therefore, it can serve as an intelligent tool for monitoring water reservoirs and preventing the transmission of infectious diseases associated with EHEC.

Advances in signal amplification strategies applied in pathogenic bacteria apta-sensing analysis-A review

Pathogenic bacteria are primarily kinds of food hazards that provoke serious harm to human health via contaminated or spoiled food. Given that pathogenic bacteria continue to reproduce and expand once they contaminate food, pathogenic bacteria of high concentration triggers more serious losses and detriments. Hence, it is essential to detect low-dose pollution at an early stage with high sensitivity. Aptamers, also known as "chemical antibodies", are oligonucleotide sequences that have attracted much attention owing to their merits of non-toxicity, small size, variable structure as well as easy modification of functional group. Aptamer-based bioanalysis has occupied a critical position in the field of rapid detection of pathogenic bacteria. This is attributed to the unique advantage of using aptamers as recognition elements in signal amplification strategies. The signal amplification strategy is an effective means to improve the detection sensitivity. Some diverse signal amplification strategies emphasize the synthesis and assembly of nanomaterials with signal amplification capabilities, while others introduce various nucleic acid amplification techniques into the detection system. This review focuses on a variety of signal amplification strategies employed in aptamer-based detection approaches to pathogenic bacteria. Meanwhile, we provided a detailed introduction to the design principles and characteristics of signal amplification strategies, as well as the improvement of sensor sensitivity. Ultimately, the existing issues and development trends of applying signal amplification strategies in apta-sensing analysis of pathogenic bacteria are critically proposed and prospected. Overall, this review discusses from a new perspective and is expected to contribute to the further development of this field.

Advances in endotoxin analysis

The outer membrane of gram-negative bacteria is primarily composed of lipopolysaccharide (LPS). In addition to protection, LPS defines the distinct serogroups used to identify bacteria specifically. Furthermore, LPS also act as highly potent stimulators of innate immune cells, a phenomenon essential to understanding pathogen invasion in the body. The complex multi-step process of LPS binding to cells involves several binding partners, including LPS binding protein (LBP), CD14 in both membrane-bound and soluble forms, membrane protein MD-2, and toll-like receptor 4 (TLR4). Once these pathways are activated, pro-inflammatory cytokines are eventually expressed. These binding events are also affected by the presence of monomeric or aggregated LPS. Traditional techniques to detect LPS include the rabbit pyrogen test, the monocyte activation test and Limulus-based tests. Modern approaches are based on protein, antibodies or aptamer binding. Recently, novel techniques including electrochemical methods, HPLC, quartz crystal microbalance (QCM), and molecular imprinting have been developed. These approaches often use nanomaterials such as gold nanoparticles, quantum dots, nanotubes, and magnetic nanoparticles. This chapter reviews current developments in endotoxin detection with a focus on modern novel techniques that use various sensing components, ranging from natural biomolecules to synthetic materials. Highly integrated and miniaturized commercial endotoxin detection devices offer a variety of options as the scientific and technologic revolution proceeds.

Aptamer tuned nanozyme activity of nickel-metal-organic framework for sensitive electrochemical aptasensing of tetracycline residue

It is urgently needed to develop high-performance method for tetracycline (TC) analysis to meet the growing concerns about food safety. Herein, a MOF of Ni2+-2,3,6,7,10,11-hexahydroxytriphenylene (Ni-HHTP) with peroxidase activity has been prepared and coated on a screen printing electrode, followed by non-covalent adsorption of tetracycline aptamer (TC-Apt) through the π-stacking. The spectroscopic and electrochemical assays show that TC-Apt can effectively enhance the nanozyme activity of Ni-HHTP using 3,3',5,5'-tetramethylbenzidine (TMB)/H2O2 as the probe. Upon binding with TC, the configuration of TC-Apt is changed and desorbs from the Ni-HHTP, resulting in the decrease of the nanozyme activity of aptasensor. Based on this principle, the target TC can be analyzed in concentrations ranging from 10 pM to 1.0 μM, with a detection limit of 1.9 pM. The aptsensor is also applicable for TC analysis in fresh Ctenopharyngodon idella meat and milk, which provides a new approach for TC residue monitoring in food.

Porphyrin-based covalent organic polymers with customizable photoresponses for photodynamic inactivation of bacteria

Porphyrin-linked covalent organic polymers (COPs) provide a reliable photocatalytic platform, while photodynamic inactivation (PDI) induced by reliable porphyrin-based COPs is considered to be an effective method to resist microbial contamination. Herein, three tunable porphyrin-based covalent organic polymers (H2-Por-COPs, OH-Por-COPs, and Zn-Por-COPs) are designed and employed for the PDI of Staphylococcus aureus and Escherichia coli under visible light illumination. Interestingly, singlet oxygen (1O2) generation by the Por-COPs can be manipulated via intramolecular regulation with the order Zn-Por-COP > OH-Por-COP > H2-Por-COP. With rationally tune, the Zn-Por-COP demonstrated remarkable antibacterial activity against Staphylococcus aureus (kill percentage 99.65 % ± 0.24 %) and Escherichia coli (kill percentage 97.25 % ± 1.78 %) in only 15 min under visible-light irradiation. Density functional theory (DFT) calculations and photophysical tests showed that the presence of electron-donating -OH groups on the aromatic linkers and Zn2+ ions in porphyrin units narrowed the HOMO-LUMO gap, enhancing both light absorption, intersystem crossing (ISC) and 1O2 generation for more efficient bacteria inactivation. This work can be applied to efficiently screen suitable photosensitizers and provides a rational regulatory strategy for PDI of pathogenic bacteria.

Nanoparticles-assisted aptamer biosensing for the detection of environmental pathogens

Given the importance of public health, it is crucial to develop quick, targeted, highly sensitive, and accurate technologies to monitor pathogenic microbes in response to the growing concerns of food and environmental safety. Although conventional approaches for microbiological detection are available, they are laborious, and often skill demanding. Therefore, such approaches are incompetent in the on-site or high-throughput assessment of pathogenic microbes. Numerous efforts have been made to develop biosensors that use nucleic acid aptamer as the biorecognition element, which would avoid the abovementioned limitations. Incorporating nanomaterials (NMs) into aptamer-based biosensors (aptasensors) improves their sensitivity and specificity, opening exciting possibilities for various applications, such as bioanalysis of food and environmental samples. Over the last decade, nanomaterial-conjugated aptasensors have seen a steadily rising demand. To this end, the main goal of this study is to demonstrate the novelty in the design of nanomaterial-conjugated aptasensors and how they can be used to detect different pathogenic microbes in water and food. The intent of this paper is to evaluate the cutting-edge techniques that have appeared in nano-aptasensors throughout the past few years, such as manufacturing procedures, analytical credibility, and sensing mechanisms. Additionally, the fundamental performance parameters of aptasensing techniques (such as detection limits, and sensing ranges response) were also used to evaluate their practical applicability. Finally, it is anticipated that this study will inspire innovative ideas and techniques for the construction and use of aptasensors for monitoring pathogenic microorganisms in food, drinks, recreational water, and wastewater.

Silver/copper bimetallic nanoclusters integrating with cryonase-assisted target recycling amplification detection of Salmonella typhimurium

An unsophisticated fluorescence-enabled strategy is brought forward to process the highly sensitive fluorescence detection of Salmonella typhimurium (S. typhimurium) which based on polyethyleneimine (PEI)-templated silver/copper nanoclusters (Ag/CuNCs) (λ excitation = 334 nm and λ emission = 466 nm) with cryonase-assisted target recycling amplification. The Ag/CuNCs nanoclusters are synthesized as fluorescent materials due to their strong and stable fluorescence characteristics and are modified with S. typhimurium aptamers to form aptamer-Ag/CuNCs probes. The probes can be adsorbed on the surface of quenching agents-polydopamine nanospheres (PDANSs), thereby inducing fluorescence quenching of the probes. Once the aptamers are bound to the target, the aptamers/targets complexes are separated from the PDANSs surface, and the Ag/CuNCs recover the fluorescence signal. The released complexes will immediately be transformed into a substrate digested by cryonase (an enzyme that can digest all types of nucleic acids), and the released targets are bound to another aptamers to initiate the next round of cleavage. This reaction will be repeated continuously until all relevant aptamers are consumed and all Ag/CuNCs are released, resulting in a significant amplification of the fluorescence signal and improved sensitivity. Using Ag/CuNCs as fluorescent probes combined with cryonase-assisted amplification strategy, the fluorescence aptasensor is constructed with detection limits as low as 3.8 CFU mL-1, which is tenfold better than without the cryonase assistance. The method developed has been applied to milk, orange juice, chicken, and egg white samples with excellent selectivity and accuracy providing an approach for the early and rapid detection of S. typhimurium in food.

A simple and robust aptasensor assembled on surfactant-mediated liquid crystal interface for ultrasensitive detection of mycotoxin

Here, a simple aptasensing approach is represented to sensitively detect ochratoxin A (OTA) as one of the most perilous mycotoxins with carcinogenic, nephrotoxic, teratogenic, and immunosuppressive sequels on human health. The aptasensor is based on the alteration in the orientational order of liquid crystal (LC) molecules at the surfactant-arranged interface. Homeotropic alignment of LCs is achieved by the interaction of the surfactant tail with LCs. By perturbing the alignment of LCs due to the electrostatic interaction of the aptamer strand with the surfactant head, a colorful polarized view of the aptasensor substrate is induced drastically. While OTA causes the re-orientation of LCs to a vertical state by forming an OTA-aptamer complex that induces darkness of the substrate. This study shows that the length of the aptamer strand impacts the efficiency of the aptasensor; longer strand results in the greater disruption of LCs, and therefore, increases the aptasensor sensitivity. Hence, the aptasensor can determine OTA in the linear concentration range of 0.1 fM-1 pM as low as 0.021 fM. The aptasensor is capable to monitor OTA in grape juice, coffee drink, corn, and human serum real samples. The proposed LC-based aptasensor provides a cost-effective, easy-to-carry, operator-independent, and user-friendly array with great potential to develop portable sensing gadgets for food quality control and health care monitoring.

An ultrasensitive aptamer-based fluorescent on/off system for trace amount evaluation of Yersinia enterocolitica in food samples

An innovative aptamer labeled with 5-FAM has been developed with a high affinity for Yersinia enterocolitica (Y. enterocolitica) using graphene oxide (GO) as a quenching platform. The selectivity of the prepared system was evaluated in the presence of common coexisted bacteria like Yersinia pseudotuberculosis, Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, and Salmonella typhimurium. Some experimental factors like pH and stability were investigated. The results showed that in the absence of Y. enterocolitica, aptamer labeled with 5-FAM was bonded with GO, causing fluorescence to be relatively weak. After the addition of Y. enterocolitica, the aptamer is released from the GO surface and binds to the target bacteria, and significantly increases the fluorescence intensity with an excitation wavelength of 410 nm and an emission wavelength of 530 nm. After optimizing all conditions, the system exhibited a wide linear response for Y. enterocolitica in the concentration range 10 to 1.0 × 10⁹ CFU•mL^-1 and the limit of detection (LOD) was 3 CFU•mL^-1. This system demonstrated that GO-designed aptamers can be successful in detecting Y. enterocolitica in whole-cell forms, making them potentially useful for screening and rapid detection.

A review of advances in aptamer-based cell detection technology

Since cells are the basic structural and functional units of organisms, the detection or quantitation of cells is one of the most common basic problems in life science research. The established cell detection techniques mainly include fluorescent dye labeling, colorimetric assay, and lateral flow assay, all of which employ antibodies as cell recognition elements. However, the widespread application of the established methods generally dependent on antibodies is limited, because the preparation of antibodies is complicated and time-consuming, and unrecoverable denaturation is prone to occur with antibodies. By contrast, aptamers that are generally selected through the systematic evolution of ligands by exponential enrichment can avoid the disadvantages of antibodies due to their controllable synthesis, thermostability, and long shelf life, etc. Accordingly, aptamers may serve as novel molecular recognition elements like antibodies in combination with various techniques for cell detection. This paper reviews the developed aptamer-based cell detection methods, mainly including aptamer-fluorescent labeling, aptamer-isothermal amplification assay, electrochemical aptamer sensor, aptamer-based lateral flow analysis, and aptamer-colorimetric assay. The principles, advantages, progress of application in cell detection and future development trend of these methods were specially discussed. Overall, different assays are suitable for different detection purposes, and the development of more accurate, economical, efficient, and rapid aptamer-based cell detection methods is always on the road in the future. This review is expected to provide a reference for achieving efficient and accurate detection of cells as well as improving the usefulness of aptamers in the field of analytical applications.

Separation and colorimetric detection of Escherichia coli by phage tail fiber protein combined with nano-magnetic beads

A colorimetric detection method for Escherichia coli (E. coli) in water was established based on a T7 phage tail fiber protein-magnetic separation. Firstly, the tail fiber protein (TFP) was expressed and purified to specifically recognize E. coli, which was verified by using fusion protein GFP-tagged TFP (GFP-TFP) and fluorescence microscopy. Then TFP conjugated with magnetic beads were applied to capture and separate E. coli. The TFP was covalently immobilized on the surface of magnetic beads and captured E. coli as verified by scanning electron microscopy (SEM). Finally, polymyxin B was used to lyse E. coli in solution and the released intracellular β-galactosidase (β-gal) could hydrolyze the colorimetric substrate chlorophenol red-β-D-galactopyranoside (CPRG), causing color change from yellow to purple. The high capture efficiencies of E. coli ranged from 88.70% to 95.65% and E. coli could be detected at a concentration of 10² CFU/mL by naked eyes. The specificity of the chromogenic substrate was evaluated using five different pathogen strains as competitors and tests with four kinds of real water samples showed recoveries of 86.00% to 92.25%. The colorimetric changes determined by visual inspection can be developed as an efficient platform for point-of-care detection of E. coli in resource-limited regions.

A dual-mode ratiometric aptasensor for accurate detection of pathogenic bacteria based on recycling of DNAzyme activation

Pathogenic bacteria have a significant impact on food safety. Herein, an innovative dual-mode ratiometric aptasensor was constructed for ultrasensitive and accurate detection of Staphylococcus aureus (S. aureus) based on recycling of DNAzyme activation on gold nanoparticles-functionalized MXene nanomaterials (MXene@Au NPs). Electrochemiluminescent (ECL) emitter-labeled probe DNA (probe 2-Ru) containing the blocked DNAzyme was partly hybridized with aptamer and then captured by electrochemical (EC) indicator-labeled probe DNA (probe 1-MB) on electrode surface. When S. aureus presented, the conformation vibration of probe 2-Ru activated the blocked DNAzymes, leading to recycling cleavage of probe 1-MB and ECL tag close to electrode surface. Based on the reverse change tendencies of ECL and EC signals, aptasensor achieved S. aureus quantification from 5 to 10⁸ CFU/mL. Moreover, the self-calibration characteristic of the aptasensor with dual-mode ratiometric readout ensured the reliable measurement of S. aureus in real samples. This work showed useful insight into sensing foodborne pathogenic bacteria.

Selection of spore-specific aptamers for Geobacillus stearothermophilus, a food spoilage bacterium

Due to their ability to form extremely heat resistant spores, anaerobic bacteria are responsible for frequent food spoilage. The development of rapid and specific methods for the detection and quantification of spore contamination is therefore of major interest. In this paper, we describe for the first time the selection of aptamers specific to spores of Geobacillus stearothermophilus (Gbs), which induce flat sour spoilage in vegetable cans. Eighteen Spore-SELEX cycles were performed including 4 counter-selections with 12 bacteria commonly found in cannery. To optimise candidate amplification, PCR in emulsion was performed, and high-throughput sequencing analysis was applied to follow candidate evolution. Sequencing of aptamers from cycle 18 revealed 43 overrepresented sequences whose copy number exceeds 0.15% of the total obtained sequences. Within this group, the A01 aptamer presented a much higher enrichment with a relative abundance of 17.71%. Affinity and specificity for Gbs spores of the 10 most abundant candidates at cycle 18 were confirmed by PCR assay based on aptamer-spore complex formation and filtration step. Obtaining these aptamers is the starting point for the future development of biosensors dedicated to the detection of Gbs spores.

Isolation of Bacteria Aptamers with Non-SELEX for the Development of a Highly Sensitive Colorimetric Assay Based on Dual Signal Amplification

In this work, an aptamer against Escherichia coli is isolated via non-SELEX, which executes efficient selection by employing repetitive cycles of centrifugation-based partitioning, and the binding site of the aptamer on E. coli cell surfaces is inferred to be a membrane protein. Moreover, truncated sequence 2-17-2 with a higher affinity (K_d = 101.76 nM) is employed for highly sensitive colorimetric detection of bacteria based on the dual signal amplification strategy. When targets exist, the release of DNA 1 from the polymer activates a hybridization chain reaction (HCR) between DNA 1 and DNA 2, thereby inducing the aggregation of probe 1. Subsequently, DNA 3 dissociated from probe 1 as a linker DNA further assembles probe 2/3. In this system, two types of DNA@gold nanoparticles (AuNPs) coexist and successively aggregate AuNPs based on divergent triggering mechanisms. Under optimal conditions, the dual signal amplification strategy presents excellent sensitivity (10 CFU mL^-1) and specificity, as well as the realization of real sample analysis.

Current Scenario of Pathogen Detection Techniques in Agro-Food Sector

Over the past-decade, agricultural products (such as vegetables and fruits) have been reported as the major vehicles for foodborne diseases, which are limiting food resources. The spread of infectious diseases due to foodborne pathogens poses a global threat to human health and the economy. The accurate and timely detection of infectious disease and of causative pathogens is crucial in the prevention and treatment of disease. Negligence in the detection of pathogenic substances can be catastrophic and lead to a pandemic. Despite the revolution in health diagnostics, much attention has been paid to the agro-food sector regarding the detection of food contaminants (such as pathogens). The conventional analytical techniques for pathogen detection are reliable and still in operation. However, laborious procedures and time-consuming detection via these approaches emphasize the need for simple, easy-to-use, and affordable detection techniques. The rapid detection of pathogens from food is essential to avoid the morbidity and mortality originating from the suboptimal nature of empiric pathogen treatment. This review critically discusses both the conventional and emerging bio-molecular approaches for pathogen detection in agro-food.

Dual-Target Electrochemical Sensor Based on 3D MoS2-rGO and Aptamer Functionalized Probes for Simultaneous Detection of Mycotoxins

A dual-target aptamer functionalized probes (DTAFP) was applied for the detection of aflatoxin B1 (AFB1) and zearalenone (ZEN) simultaneously, which has not been reported. Meanwhile, two functional materials for signal amplification of the DTAFP were synthesized: 1) a three-dimensional molybdenum disulfide-reduced graphene oxide (MoS₂-rGO) as a favorable loading interface; 2) a double-probes gold nanoparticles (AuNPs) modified by Thionin (Thi) and 6-(Ferrocenyl) hexanethiol (FC6S) as distinguishable and non-interfering signals. Mycotoxins on the electrode surface release into solution under the function of the DTAFP, leading a reduction of the differential peak impulse in signal response. Under the optimum conditions, the aptasensor exhibited a detection range of 1.0 pg mL⁻¹–100 ng mL⁻¹ for AFB1 and ZEN, with no observable cross reactivity. In addition, the aptasensor performed excellent stability, reproducibility, specificity, and favorable recovery in the detection of edible oil. This work demonstrated a novel method for the construction of a simple, rapid, and sensitive aptasensor in the detection of multiple mycotoxins simultaneously.