In vitro selection of DNA aptamers and their integration in a competitive voltammetric biosensor for azlocillin determination in waste water

Selection of a new aptamer targeting amoxicillin for utilization in a label-free electrochemical biosensor

Pharmaceutical pollution has received considerable attention because of the harmful effects of pharmaceutical compounds on human health, even in trace amounts. Amoxicillin is one of the frequently used antibiotics that was included in the list of emerging water pollutants. Therefore, a highly selective and rapid technique for amoxicillin detection is required. In this work, a new aptamer was selected for amoxicillin and utilized for the development of a label-free electrochemical aptasensor. Aptamer selection was performed using the systematic evolution of ligands by exponential enrichment. The selected aptamer showed good specificity against other antibiotics, including the structurally related antibiotics: ampicillin and ciprofloxacin. Among the selected aptamers, Amx3 exhibited the lowest dissociation constant value of 112.9 nM. An aptasensor was developed by immobilization of thiolated Amx3 aptamer onto gold screen-printed electrodes via self-assembly, which was characterized using cyclic voltammetry and electrochemical impedance spectroscopy. The detection was realized by monitoring the change in the differential pulse voltammetry peak current in the ferro/ferricyanide redox couple upon binding of the aptasensor to amoxicillin. The aptasensor showed very good sensitivity with an ultralow limit of detection of 0.097 nM. When the aptasensor was tested using actual spiked milk samples, excellent recovery percentages were observed. The label-free electrochemical aptasensor developed herein is a promising tool for the selective and sensitive detection of amoxicillin in environmental samples.

Aptamer-based biosensors for the detection of neonicotinoid insecticides in environmental samples: A systematic review

Neonicotinoids, sometimes abbreviated as neonics, represent a class of neuro-active insecticides with chemical similarities to nicotine. Neonicotinoids are the most widely adopted group of insecticides globally since their discovery in the late 1980s. Their physiochemical properties surpass those of previously established insecticides, contributing to their popularity in various sectors such as agriculture and wood treatment. The environmental impact of neonicotinoids, often overlooked, underscores the urgency to develop tools for their detection and understanding of their behavior. Conventional methods for pesticide detection have limitations. Chromatographic techniques are sensitive but expensive, generate waste, and require complex sample preparation. Bioassays lack specificity and accuracy, making them suitable as preliminary tests in conjunction with instrumental methods. Aptamer-based biosensor is recognized as an advantageous tool for neonicotinoids detection due to its rapid response, user-friendly nature, cost-effectiveness, and suitability for on-site detection. This comprehensive review represents the inaugural in-depth analysis of advancements in aptamer-based biosensors targeting neonicotinoids such as imidacloprid, thiamethoxam, clothianidin, acetamiprid, thiacloprid, nitenpyram, and dinotefuran. Additionally, the review offers valuable insights into the critical challenges requiring prompt attention for the successful transition from research to practical field applications.

Cell-SELEX for aptamer discovery and its utilization in constructing electrochemical biosensor for rapid and highly sensitive detection of Legionella pneumophila serogroup 1

This study introduces an innovative electrochemical aptasensor designed for the highly sensitive and rapid detection of Legionella pneumophila serogroup 1 (L. pneumophila SG1), a particularly virulent strain associated with Legionellosis. Employing a rigorous selection process utilizing cell-based systematic evolution of ligands by exponential enrichment (cell-SELEX), we identified new high-affinity aptamers specifically tailored for L. pneumophila SG1. The selection process encompassed ten rounds of cell-SELEX cycles with live L. pneumophila, including multiple counter-selection steps against the closely related Legionella sub-species. The dissociation constant (Kd) of the highest affinity sequence to L. pneumophila SG1 was measured at 14.2 nM, representing a ten-fold increase in affinity in comparison with the previously reported aptamers. For the development of electrochemical aptasensor, a gold electrode was modified with the selected aptamer through the formation of self-assembled monolayers (SAMs). The newly developed aptasensor exhibited exceptional sensitivity, and specificity in detecting and differentiating various Legionella sp., with a detection limit of 5 colony forming units (CFU)/mL and an insignificant/negligible cross-reactivity with closely related sub-species. Furthermore, the aptasensor effectively detected L. pneumophila SG1 in spiked water samples, demonstrating an appreciable recovery percentage. This study shows the potential of our aptamer-based electrochemical biosensor as a promising approach for detecting L. pneumophila SG1 in diverse environments.

A simple aptamer-dye fluorescence sensor for detecting Δ9-tetrahydrocannabinol and its metabolite in urban sewage

This work developed an aptamer-dye complex as a label-free ratiometric fluorescence sensor for rapid analysis of THC and its metabolite in sewage samples. Integrated with a portable fluorescence capture device, this sensor exhibited excellent sensitivity with visualization of as low as 0.6 μM THC via naked-eye observation, and THC analysis can be accomplished within 4 min, which would be a complementary tool for quantifying THC in sewage samples to estimate cannabis consumption.

A whole-cell hypersensitive biosensor for beta-lactams based on the AmpR-AmpC regulatory circuit from the Antarctic Pseudomonas sp. IB20

Detecting antibiotic residues is vital to minimize their impact. Yet, existing methods are complex and costly. Biosensors offer an alternative. While many biosensors detect various antibiotics, specific ones for beta-lactams are lacking. To address this gap, a biosensor based on the AmpC beta-lactamase regulation system (ampR-ampC) from Pseudomonas sp. IB20, an Antarctic isolate, was developed in this study. The AmpR-AmpC system is well-conserved in the genus Pseudomonas and has been extensively studied for its involvement in peptidoglycan recycling and beta-lactam resistance. To create the biosensor, the ampC coding sequence was replaced with the mCherry fluorescent protein as a reporter, resulting in a transcriptional fusion. This construct was then inserted into Escherichia coli SN0301, a beta-lactam hypersensitive strain, generating a whole-cell biosensor. The biosensor demonstrated dose-dependent detection of penicillins, cephalosporins and carbapenems. However, the most interesting aspect of this work is the high sensitivity presented by the biosensor in the detection of carbapenems, as it was able to detect 8 pg/mL of meropenem and 40 pg/mL of imipenem and reach levels of 1-10 ng/mL for penicillins and cephalosporins. This makes the biosensor a powerful tool for the detection of beta-lactam antibiotics, specifically carbapenems, in different matrices.

New approaches in antibiotics detection: The use of square wave voltammetry

Antibiotics belongs to a class of pharmaceutical compounds widely used due to their effectiveness against bacterial infections. However, if consumed or inappropriately disposed of in the environment can results in environmental and public health problems, because they are considered emerging contaminants and their residues represent damage, whether in the long or short term, to different terrestrial ecosystems, in addition to bringing potential risks to agricultural sectors, such as livestock and fish farming. For this, the development of analytical methods for low-concentration detection and identification of antibiotics in natural waters, wastewaters, soil, foods, and biological fluids is necessary. This review shows the applicability of square wave voltammetry for the analytical determination of antibiotics from different chemical classes and covers a variety of samples and working electrodes that are used as voltammetric sensors. The review involved the analysis of scientific publications from the Science Direct® and Scopus® databases, with scientific manuscripts covering the period between January 2012 and May 2023. Various manuscripts were discussed indicating the applicability of square wave voltammetry in antibiotics detection in urine, blood, natural waters, milk, among other complex samples.

Updates on developing and applying biosensors for the detection of microorganisms, antimicrobial resistance genes and antibiotics: a scoping review

Background

The inappropriate use of antibiotics in clinical and non-clinical settings contributes to the increasing prevalence of multidrug-resistant microorganisms. Contemporary endeavours are focused on exploring novel technological methodologies, striving to create cost-effective and valuable alternatives for detecting microorganisms, antimicrobial resistance genes (ARGs), and/or antibiotics across diverse matrices. Within this context, there exists an increasingly pressing demand to consolidate insights into potential biosensors and their implications for public health in the battle against antimicrobial resistance (AMR).

Methods

A scoping review was carried out to map the research conducted on biosensors for the detection of microorganisms, ARGs and/or antibiotics in clinical and environmental samples. The Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist was used. Articles published from 1999 to November 2022 and indexed in the following databases were included: MEDLINE, EMBASE, Web of Science, BIOSIS Citation index, Derwent Innovations index, and KCI-Korean Journal.

Results

The 48 studies included in the scoping review described the development and/or validation of biosensors for the detection of microorganisms, ARGs and/or antibiotics. At its current stage, the detection of microorganisms and/or ARGs has focused primarily on the development and validation of biosensors in clinical and bacterial samples. By contrast, the detection of antibiotics has focused primarily on the development and validation of biosensors in environmental samples. Asides from target and samples, the intrinsic characteristics of biosensors described in the scoping review were heterogenous. Nonetheless, the number of studies assessing the efficacy and validation of the aforementioned biosensor remained limited, and there was also a lack of comparative analyses against conventional molecular techniques.

Conclusion

Promoting high-quality research is essential to facilitate the integration of biosensors as innovative technologies within the realm of public health challenges, such as antimicrobial resistance AMR. Adopting a One-Health approach, it becomes imperative to delve deeper into these promising and feasible technologies, exploring their potential across diverse sample sets and matrices.

Aptamer Sensors for the Detection of Antibiotic Residues- A Mini-Review

Food security is a global issue, since it is closely related to human health. Antibiotics play a significant role in animal husbandry owing to their desirable broad-spectrum antibacterial activity. However, irrational use of antibiotics has caused serious environmental pollution and food safety problems; thus, the on-site detection of antibiotics is in high demand in environmental analysis and food safety assessment. Aptamer-based sensors are simple to use, accurate, inexpensive, selective, and are suitable for detecting antibiotics for environmental and food safety analysis. This review summarizes the recent advances in aptamer-based electrochemical, fluorescent, and colorimetric sensors for antibiotics detection. The review focuses on the detection principles of different aptamer sensors and recent achievements in developing electrochemical, fluorescent, and colorimetric aptamer sensors. The advantages and disadvantages of different sensors, current challenges, and future trends of aptamer-based sensors are also discussed.

Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application

Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule-aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.

Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety

Antibiotics are often used in human and veterinary medicine for the treatment of bacterial diseases. However, extensive use of antibiotics in agriculture can result in the contamination of common food staples such as milk. Consumption of contaminated products can cause serious illness and a rise in antibiotic resistance. Conventional methods of antibiotics detection such are microbiological assays chromatographic and mass spectroscopy methods are sensitive; however, they require qualified personnel, expensive instruments, and sample pretreatment. Biosensor technology can overcome these drawbacks. This review is focused on the recent achievements in the electrochemical biosensors based on nucleic acid aptamers for antibiotic detection. A brief explanation of conventional methods of antibiotic detection is also provided. The methods of the aptamer selection are explained, together with the approach used for the improvement of aptamer affinity by post-SELEX modification and computer modeling. The substantial focus of this review is on the explanation of the principles of the electrochemical detection of antibiotics by aptasensors and on recent achievements in the development of electrochemical aptasensors. The current trends and problems in practical applications of aptasensors are also discussed.

A simple and sensitive AuNPs-based colorimetric aptasensor for specific detection of azlocillin

A new colorimetric biosensor for specific detection of azlocillin was developed by using DNA aptamer as recognition element and unmodified gold nanoparticles (AuNPs) as colorimetric indicator. In the absence of azlocillin, the AuNPs were protected by the aptamer and stabilized at high NaCl concentrations, displaying a red solution. In the presence of azlocillin, the aptamer reacts specifically with azlocillin, resulting in the aggregation of AuNPs and an apparent red to blue color change. The characteristic change can be easily observed by the naked eye and quantitatively detected by an ultraviolet-visible (UV-Vis) spectrometer. Under the optimal conditions, the absorbance variation at 522 nm (ΔA₅₂₂) of AuNPs changed proportionally with increasing concentration of azlocillin, which exhibited a linear relationship in the concentration range of 50 nM to 500 nM, with a detection limit of 11.6 nM. Furthermore, the aptasensor was successfully used to detect azlocillin in milk and tap water samples, with recoveries ranging from 97.64% to 102.21% and a relative standard deviation (RSD) less than 3.81%.

Aptamer-based diagnostic and therapeutic approaches in animals: Current potential and challenges

Fast and precise diagnosis of infectious and non-infectious animal diseases and their targeted treatments are of utmost importance for their clinical management. The existing biochemical, serological and molecular methods of disease diagnosis need improvement in their specificity, sensitivity and cost and, are generally not amenable for being used as points-of-care (POC) device. Further, with dramatic changes in environment and farm management practices, one should also arm ourselves and prepare for emerging and re-emerging animal diseases such as cancer, prion diseases, COVID-19, influenza etc. Aptamer – oligonucleotide or short peptides that can specifically bind to target molecules – have increasingly become popular in developing biosensors for sensitive detection of analytes, pathogens (bacteria, virus, fungus, prions), drug residues, toxins and, cancerous cells. They have also been proven successful in the cellular delivery of drugs and targeted therapy of infectious diseases and physiological disorders. However, the in vivo application of aptamer-mediated biosensing and therapy in animals has been limited. This paper reviews the existing reports on the application of aptamer-based biosensors and targeted therapy in animals. It also dissects the various modifications to aptamers that were found to be successful in in vivo application of the aptamers in diagnostics and therapeutics. Finally, it also highlights major challenges and future directions in the application of aptamers in the field of veterinary medicine.

Screening Aptamers that Are Specific for Beclomethasone and the Development of Quantum Dot-Based Assay

We developed an aptamer that was specific for beclomethasone (BEC) via systematic evolution of ligands by exponential enrichment (SELEX). Development was monitored by real-time quantitative PCR (Q-PCR) and the enriched library was sequenced by high-throughput sequencing. Forty-seven aptamer candidates were obtained; of these, BEC-6 showed the highest affinity (K_d = 0.15 ± 0.02 μM) and did not cross-react with other BEC analogs. We also developed a quantum dot-based assay (QDA) for the detection of BEC that was based upon a quantum dot (QD) composite probe. Under optimized reaction conditions, the linear range of this method for BEC was 0.1 to 10 μM with a low detection limit (LOD) of 0.1 μM. Subsequently, the method was used to detect BEC in Traditional Chinese Medicine (TCM) with a mean recovery of 81.72-91.84%. This is the first report to describe the development of an aptamer against BEC; BEC-6 can also be engineered into QDA for the detection of BEC.

Advances in aptamer screening and aptasensors' detection of heavy metal ions

Heavy metal pollution has become more and more serious with industrial development and resource exploitation. Because heavy metal ions are difficult to be biodegraded, they accumulate in the human body and cause serious threat to human health. However, the conventional methods to detect heavy metal ions are more strictly to the requirements by detection equipment, sample pretreatment, experimental environment, etc. Aptasensor has the advantages of strong specificity, high sensitivity and simple preparation to detect small molecules, which provides a new direction platform in the detection of heavy metal ions. This paper reviews the selection of aptamers as target for heavy metal ions since the 21th century and aptasensors application for detection of heavy metal ions that were reported in the past five years. Firstly, the selection methods for aptamers with high specificity and high affinity are introduced. Construction methods and research progress on sensor based aptamers as recognition element are also introduced systematically. Finally, the challenges and future opportunities of aptasensors in detecting heavy metal ions are discussed.

Recent advances in biosensors for antibiotic detection: Selectivity and signal amplification with nanomaterials

Antibiotics are widely used in the prevention and treatment of infectious diseases in animals due to its bactericidal or bacteriostatic action. Residual antibiotics and their metabolites pose great threats to human and animal health, such as potential carcinogenic and mutagenic effects, and bacterial resistances. Therefore, it is necessary and urgent to accurately monitor trace amounts of antibiotics in food samples. Up to now, many analytical methods have been reported for the determination of antibiotics. Biosensors with the advantages of high sensitivity, rapid response, easy miniaturization, and low price have been widely applied to the detection of antibiotics residues in past decades. This review offered an in-depth evaluation of recognition elements for antibiotic residues in diverse food matrices. In addition, it presented a systematical and critical review on signal amplification via various materials, focusing on recently developed nanomaterials. Finally, the review provided an outlook on the future concepts to help upgrade the sensing techniques for antibiotics in food.

Recent development of antibiotic detection in food and environment: the combination of sensors and nanomaterials

In recent years, the abuse of antibiotics has led to the pollution of soil and water environment, not only poultry husbandry and food manufacturing will be influenced to different degree, but also the human body will produce antibody. The detection of antibiotic content in production and life is imperative. In this review, we provide comprehensive information about chemical sensors and biosensors for antibiotic detection. We classify the currently reported antibiotic detection technologies into chromatography, mass spectrometry, capillary electrophoresis, optical detection, and electrochemistry, introduce some representative examples for each technology, and conclude the advantages and limitations. In particular, the optical and electrochemical methods based on nanomaterials are discussed and evaluated in detail. In addition, the latest research in the detection of antibiotics by photosensitive materials is discussed. Finally, we summarize the pros and cons of various antibiotic detection methods and present a discussion and outlook on the expansion of cross-scientific areas. The synthesis and application of optoelectronic nanomaterials and aptamer screening are discussed and prospected, and the future trends and potential impact of biosensors in antibiotic detection are outlined.Graphical abstract.

Target-initiated autonomous synthesis of metal-ion dependent DNAzymes for label-free and amplified fluorescence detection of kanamycin in milk samples

Accurate and sensitive monitoring of the abused antibiotics is vital because excessive antibiotics in human body can cause toxicity to kidney or lead to potential loss of hearing. In this work, we described a label-free and highly sensitive fluorescent aptasensing platform for detecting kanamycin in milk samples based on the synchronization signal amplification of primer exchange reaction (PER) and metal-ion dependent DNAzyme. The target kanamycin binds the aptamer sequence hybridized on a hairpin template and initiates PER for autonomous synthesis of Mg²⁺-dependent DNAzyme sequences with aid of Bst-DNA polymerase at isothermal conditions. Such a synthesis process can be repeated many times to produce lots of DNAzymes to cyclically cleave the rA site in the signal hairpin substrates under the assistance of Mg²⁺ cofactor to liberate numerous free G-quadruplex fragments. The organic dye thioflavin T (ThT) further associates with these G-quadruplex fragments to yield substantially intensified fluorescence for sensitive detection of kanamycin with a low detection limit of 0.36 nM. In addition, the developed aptamer sensing method also shows a good selectivity for kanamycin against other interfering antibiotics, and can realize the monitoring of kanamycin added in milk samples, highlighting its potential for sensitive monitoring of trace amount of kanamycin for food safety applications.

Aptamer selection and aptasensor construction for bone density biomarkers

Osteoporosis (OP) is a bone disease involved in dysregulation of one of the bone metabolism arms, formation, or desorption cause a porous bone. Osteocalcin (OC) and beta-crosslap (BC), are the well-known markers for OP, which are connected to bone formation and desorption, respectively. In addition to the OP biomarker, BC is also used as an estrogen replacement therapeutic monitoring. ELISA and other antibody-based detection methods are routinely used for measuring OC and BC. These methods have limitations that include thermostability, sensitivity, sacrificing animals, and cost of production. However, aptamer-based-assays are of interest to overcome these drawbacks and achieve the most specific and robust application. Herein, specific aptamers for OC and BC were selected by the systematic evolution of ligands by exponential enrichment (SELEX) method from the pool of ssDNA library with 60 random sequences. The binding affinity (K_d) of the selected aptamers were evaluated against the respective biomarkers. The high-affinity aptamers of OC and BC showed the K_d values of 59 and 55 nM respectively. A graphene oxide-based aptasensors were fabricated from the high-affinity aptamers, and the detection limits of OC and BC were found to be 0.4 pg/ml and 0.21 pg/ml, respectively. These aptasensors have been tested with OC and BC spiked buffer samples and validated using serum samples collected from osteoporotic rats.

Probing high-affinity aptamer binding region and development of aptasensor platform for the detection of cylindrospermopsin

Cylindrospermopsin (CYN) is one of the most concerning cyanotoxins due to its potential toxicity and spreading to various environments including drinking water. CYN has potential interferences with human and animal metabolic pathways, which influence the functions of organs including liver, kidneys, lungs, etc. CYN is involved in the inhibition of protein synthesis and detachment of ribosomes from the endoplasmic reticulum membrane. It also interacts with soluble proteins, which are associated with protein translations. It is believed that cytochrome 450 is responsible for the rapid toxicity of CYN. Researchers are urged to develop a high-throughput screening method for the detection of CYN in water. Construction of low cost, rapid, and sensitive analytical methods for the detection of CYN is challenging. Here, we used graphene oxide (GO) as the fluorescence sensing platform for probing the high affinity of the short aptamer derived from the wild-type long aptamer-CYN sensing. The biosensor construction involved two steps: first, quenching the fluorescence of fluorescent-labelled truncated aptamer using GO as a quencher and, second, fluorescence recovery in the presence of CYN by competitive binding between the target and GO. One of the truncate aptamers has a 12-fold higher affinity and enhances sensitivity compared to the long aptamer sequence. The limit of detection of the high affinity truncated aptamer is 17 pM which is 6-fold lower than the long aptamer (100 pM). The sensor specifically detects CYN in the presence of other potential interfering toxins. The performance of the sensor was validated using CYN spiked tap water with very good recovery percentage. A rapid and highly sensitive detection of CYN from water resources has been achieved using this method.

Integrated Electrochemical Biosensors for Detection of Waterborne Pathogens in Low-Resource Settings

More than 783 million people worldwide are currently without access to clean and safe water. Approximately 1 in 5 cases of mortality due to waterborne diseases involve children, and over 1.5 million cases of waterborne disease occur every year. In the developing world, this makes waterborne diseases the second highest cause of mortality. Such cases of waterborne disease are thought to be caused by poor sanitation, water infrastructure, public knowledge, and lack of suitable water monitoring systems. Conventional laboratory-based techniques are inadequate for effective on-site water quality monitoring purposes. This is due to their need for excessive equipment, operational complexity, lack of affordability, and long sample collection to data analysis times. In this review, we discuss the conventional techniques used in modern-day water quality testing. We discuss the future challenges of water quality testing in the developing world and how conventional techniques fall short of these challenges. Finally, we discuss the development of electrochemical biosensors and current research on the integration of these devices with microfluidic components to develop truly integrated, portable, simple to use and cost-effective devices for use by local environmental agencies, NGOs, and local communities in low-resource settings.

Selection, characterization, and electrochemical biosensing application of DNA aptamers for sepiapterin

Sepiapterin reductase deficiency (SR) is a rare inborn disorder of neurotransmitter metabolism. The early diagnosis of SR disease should be achieved through the determination of the sepiapterin level in body fluids of suspected patients. Here, we report the selection, identification, and characterization of DNA aptamers against sepiapterin. The aptamer selection was achieved via the systematic evolution of ligand by the exponential enrichment technique. After ten rounds of selection, high-affinity aptamers were identified. The binding affinities of the selected aptamers were evaluated using fluorescence binding assays showing dissociation constants ranging from 37.3 to 79.0 nM. The highest affinity aptamer was then integrated into a competitive electrochemical biosensor. The biosensor achieved outstanding sensitivity with a detection limit of 0.8 pg/ml which was much lower than the reported chromatographic method for sepiapterin quantification. The aptasensor has also shown a high degree of selectivity against the closely-related compound. The aptasensor was then challenged by detecting the sepiapterin in spiked serum samples where a good recovery percentage was achieved.