Rapid detection of Escherichia coli based on 16S rDNA nanogap network electrochemical biosensor

Disposable electrochemical biosensors for the detection of bacteria in the light of antimicrobial resistance

Persistent and inappropriate use of antibiotics is causing rife antimicrobial resistance (AMR) worldwide. Common bacterial infections are thus becoming increasingly difficult to treat without the use of last resort antibiotics. This has necessitated a situation where it is imperative to confirm the infection to be bacterial, before treating it with antimicrobial speculatively. Conventional methods of bacteria detection are either culture based which take anywhere between 24 and 96 hor require sophisticated molecular analysis equipment with libraries and trained operators. These are difficult propositions for resource limited community healthcare setups of developing or less developed countries. Customized, inexpensive, point-of-care (PoC) biosensors are thus being researched and developed for rapid detection of bacterial pathogens. The development and optimization of disposable sensor substrates is the first and crucial step in development of such PoC systems. The substrates should facilitate easy charge transfer, a high surface to volume ratio, be tailorable by the various bio-conjugation chemistries, preserve the integrity of the biorecognition element, yet be inexpensive. Such sensor substrates thus need to be thoroughly investigated. Further, if such systems were made disposable, they would attain immunity to biofouling. This article discusses a few potential disposable electrochemical sensor substrates deployed for detection of bacteria for environmental and healthcare applications. The technologies have significant potential in helping reduce bacterial infections and checking AMR. This could help save lives of people succumbing to bacterial infections, as well as improve the overall quality of lives of people in low- and middle-income countries.

Strand displacement amplification triggered 3D DNA roller assisted CRISPR/Cas12a electrochemiluminescence cascaded signal amplification for sensitive detection of Ec-16S rDNA

BACKGROUND

Escherichia coli can cause gastrointestinal infection, urinary tract infection and other infectious diseases. Accurate detection of Escherichia coli 16S rDNA (Ec-16S rDNA) in clinical practice is of great significance for the identification and treatment of related diseases. At present, there are various types of sensors that can achieve accurate detection of Ec-16S rDNA. Electrochemiluminescence (ECL) has attracted considerable attention from researchers, which causes excellent performance in bioanalysis. Based on the previous research, it is significance to develop a novel, sensitive and efficient ECL biosensor.

RESULTS

In this work, an ECL biosensor for the detection of Ec-16S rDNA was constructed by integrating CRISPR/Cas12a technology with the cascade signal amplification strategy consisting of strand displacement amplification (SDA) and dual-particle three-dimensional (3D) DNA rollers. The amplification products of SDA triggered the operation of the DNA rollers, and the products generated by the DNA rollers activated CRISPR/Cas12a to cleave the signal probe, thereby realizing the change of the ECL signal. The cascade amplification strategy realized the exponential amplification of the target signal and greatly improved the sensitivity. Manganese dioxide nanoflowers (MnO2 NFs) as a co-reaction promoter effectively enhanced the ECL intensity of tin disulfide quantum dots (SnS2 QDs). A new ternary ECL system (SnS2 QDs/S2O82-/MnO2 NFs) was prepared, which made the change of ECL intensity of biosensor more significant. The proposed biosensor had a response range of 100 aM-10 nM and a detection limit of 27.29 aM (S/N = 3).

SIGNIFICANCE AND NOVELTY

Herein, the cascade signal amplification strategy formed by SDA and dual-particle 3D DNA rollers enabled the ECL biosensor to have high sensitivity and low detection limit. At the same time, the cascade signal amplification strategy was integrated with CRISPR/Cas12a to enable the biosensor to efficiently detect the target. It can provide a new idea for the detection of Ec-16S rDNA in disease diagnosis and clinical analysis.

Electrochemical biosensing for E.coli detection based on triple helix DNA inhibition of CRISPR/Cas12a cleavage activity

BACKGROUND

Escherichia coli (E.coli) is both a commensal and a foodborne pathogenic bacterium in the human gastrointestinal tract, posing significant potential risks to human health and food safety. However, one of the major challenges in E.coli detection lies in the preparation and storage of antibodies. In traditional detection methods, antibodies are indispensable, but their instability often leads to experimental complexity and increased false positives. This underscores the need for new technologies and novel sensors. Therefore, the development of a simple and sensitive method for analyzing E.coli would make significant contributions to human health and food safety.

RESULTS

We constructed an electrochemical biosensor based on triple-helical DNA and entropy-driven amplification reaction (EDC) to inhibit the cleavage activity of Cas12a, enabling high-specificity detection of E.coli. Replacing antibodies with nucleic acid aptamers (Apt) as recognition elements, we utilized the triple-helical DNA generated by the binding of DNA2 and DNA5/DNA6 double-helical DNA through the entropy-driven amplification reaction to inhibit the collateral cleavage activity of clustered regularly interspaced short palindromic repeats gene editing system (CRISPR) and its associated proteins (Cas). By converting E.coli into electrical signals and recording signal changes in the form of square wave voltammetry (SWV), rapid detection of E.coli was achieved. Optimization of experimental conditions and data detection under the optimal conditions provided high sensitivity, low detection limits, and high specificity.

SIGNIFICANCE

With a minimal detection limit of 5.02 CFU/mL and a linear range of 1 × 102 - 1 × 107 CFU/mL, the suggested approach was successfully verified to analyze E.coli at various concentrations. Additionally, after examining E.coli samples from pure water and pure milk, the recoveries ranged between 95.76 and 101.20%, demonstrating the method's applicability. Additionally, it provides a feasible research direction for the detection of pathogenic bacteria causing other diseases using the CRISPR/Cas gene editing system.

Recent Advances in Electrochemical Biosensors for the Detection of Foodborne Pathogens: Current Perspective and Challenges

Foodborne pathogens cause many diseases and significantly impact human health and the economy. Foodborne pathogens mainly include Salmonella spp., Escherichia coli, Staphylococcus aureus, Shigella spp., Campylobacter spp. and Listeria monocytogenes, which are present in agricultural products, dairy products, animal-derived foods and the environment. Various pathogens in many different types of food and water can cause potentially life-threatening diseases and develop resistance to various types of antibiotics. The harm of foodborne pathogens is increasing, necessitating effective and efficient methods for early monitoring and detection. Traditional methods, such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA) and culture plate, are time-consuming, labour-intensive and expensive and cannot satisfy the demands of rapid food testing. Therefore, new fast detection methods are urgently needed. Electrochemical biosensors provide consumer-friendly methods to quickly detect foodborne pathogens in food and the environment and achieve extensive accuracy and reproducible results. In this paper, by focusing on various mechanisms of electrochemical transducers, we present a comprehensive overview of electrochemical biosensors for the detection of foodborne pathogens. Furthermore, the review introduces the hazards of foodborne pathogens, risk analysis methods and measures of control. Finally, the review also emphasizes the recent research progress and solutions regarding the use of electrochemical biosensors to detect foodborne pathogens in food and the environment, evaluates limitations and challenges experienced during the development of biosensors to detect foodborne pathogens and discusses future possibilities.

A Label-Free Carbohydrate-Based Electrochemical Sensor to Detect Escherichia coli Pathogenic Bacteria Using D-mannose on a Glassy Carbon Electrode

Controlling water and food contamination by pathogenic organisms requires quick, simple, and low-cost methods. Using the affinity between mannose and type I fimbriae in the cell wall of Escherichia coli (E. coli) bacteria as evaluation elements compared to the conventional plate counting technique enables a reliable sensing platform for the detection of bacteria. In this study, a simple new sensor was developed based on electrochemical impedance spectroscopy (EIS) for rapid and sensitive detection of E. coli. The biorecogniton layer of the sensor was formed by covalent attachment of p-carboxyphenylamino mannose (PCAM) to gold nanoparticles (AuNPs) electrodeposited on the surface of a glassy carbon electrode (GCE). The resultant structure of PCAM was characterized and confirmed using a Fourier Transform Infrared Spectrometer (FTIR). The developed biosensor demonstrated a linear response with a logarithm of bacterial concentration (R² = 0.998) in the range of 1.3 × 10 ¹~1.3 × 10⁶ CFU·mL^-1 with the limit of detection of 2 CFU·mL^-1 within 60 min. The sensor did not generate any significant signals with two non-target strains, demonstrating the high selectivity of the developed biorecognition chemistry. The selectivity of the sensor and its applicability to analysis of the real samples were investigated in tap water and low-fat milk samples. Overall, the developed sensor showed to be promising for the detection of E. coli pathogens in water and low-fat milk due to its high sensitivity, short detection time, low cost, high specificity, and user-friendliness.

Nanostructured biosensing platforms for the detection of food- and water-borne pathogenic Escherichia coli

Pathogenic bacterial infection is one of the principal causes affecting human health and ecosystems. The accurate identification of bacteria in food and water samples is of significant interests to maintain safety and health for humans. Culture-based tests are practically tedious and may produce false-positive results, while viable but non-culturable microorganisms (NCMs) cannot be retrieved. Thus, it requires fast, reliable, and low-cost detection strategies for on-field analysis and point-of-care (POC) monitoring. The standard detection methods such as nucleic acid analysis (RT-PCR) and enzyme-linked immunosorbent assays (ELISA) are still challenging in POC practice due to their time-consuming (several hours to days) and expensive laboratory operations. The optical (surface plasmon resonance (SPR), fluorescence, and surface-enhanced Raman scattering (SERS)) and electrochemical-based detection of microbes (early stage of infective diseases) have been considered as alternative routes in the emerging world of nanostructured biosensing since they can attain a faster and concurrent screening of several pathogens in real samples. Moreover, optical and electrochemical detection strategies are opening a new route for the ability of detecting pathogens through the integration of cellphones, which is well fitted for POC analysis. This review article covers the current state of sensitive mechanistic approaches for the screening and detection of Escherichia coli O157:H7 (E. coli) pathogens in food and water samples, which can be potentially applied in clinical and environmental monitoring.

Rapid Quantitative Detection of Live Escherichia coli Based on Chronoamperometry

The rapid quantitative detection of Escherichia coli (E. coli) is of great significance for evaluating water and food safety. At present, the conventional bacteria detection methods cannot meet the requirements of rapid detection in water environments. Herein, we report a method based on chronoamperometry to rapidly and quantitatively detect live E. coli. In this study, the current indicator i0 and the electricity indicator A were used to record the cumulative effect of bacteria on an unmodified glassy carbon electrode (GCE) surface during chronoamperometric detection. Through the analysis of influencing factors and morphological characterization, it was proved that the changes of the two set electrochemical indicator signals had a good correlation with the concentration of E. coli; detection time was less than 5 min, the detection range of E. coli was 104−108 CFU/mL, and the error range was <30%. The results of parallel experiments and spiking experiments showed that this method had good repeatability, stability, and sensitivity. Humic acid and dead cells did not affect the detection results. This study not only developed a rapid quantitative detection method for E. coli in the laboratory, but also realized a bacterial detection scheme based on the theory of bacterial dissolution and adsorption for the first time, providing a new direction and theoretical basis for the development of electrochemical biosensors in the future.

Rapid 16S rDNA electrochemical sensor for detection of bacteria based on the integration of target-triggered hairpin self-assembly and tripedal DNA walker amplification

Diseases caused by bacteria pose great challenges to human health. The key to reduce disease transmission and mortality is to develop accurate and rapid methods for the detection and identification of bacteria. Herein, a rapid bacteria 16S rDNA electrochemical sensor based on target-triggered hairpin self-assembly and tripedal DNA walker (TD walker) amplification strategy was constructed. Specific variable region of 16S rDNA fragment of bacteria was used as biomarker. The target-triggered hairpin self-assembly strategy was used to prepare a TD walker. The hairpin DNA probes labeled with ferrocene (F_c) were designed and modified on surface of electrode. The "legs" of TD walker hybridized with three hairpin probes and opened their hairpin structures. Exo III enzyme recognised hybrid duplexes and selectively digest hairpin probes. The "legs" of TD walker was released and hybridized with the other three hairpin probes. In this way, the enzyme drived the walkers to walk along electrode interface, until hairpin DNA probes were all removed from the electrode, the F_c was far away from electrode interface. A significantly current reduction signal was obtained and bacteria were detected by recording this response. This strategy was low-cost and scalable, it could continuously recycle low-concentration targets, thus enhanced the detection sensitivity. As the proof-of-concept work, the electrochemical sensor was utilized as detector. The limit of detection (LOD) of detecting Staphylococcus aureus (S. aureus) was 20 CFU mL^-1 and detection time was less than 3 h. It was expected to be widely used in clinical early diagnosis.

A SERS aptasensor based on porous Au-NC nanoballoons for Staphylococcus aureus detection

In this work, we developed a new approach for fabricating hollow and porous nitrogen doped carbon nanoballoons loading AuNPs (Au-NC-NBs) with a large specific surface area, a high N and Au content. The surface-enhanced Raman scattering (SERS) aptasensor based on the resulting Au-NC-NBs possess a wider linear range (10 to 10⁷ cells/mL), a lower detection limit (3 cells/mL), better selectivity for detecting bacteria than previously reported sensors. Importantly, Au-NC-NBs SERS aptasensor also exhibits excellent performance for detecting bacteria in the real food and biological samples. This work provides a facile and versatile designing strategy for controlled construction of SERS biosensor by combination of Au nanoparticles and carbon materials, which has a great applied potential in food safety monitoring and clinical diagnosis.

Nanomaterial application in bio/sensors for the detection of infectious diseases

Infectious diseases are a potential risk for public health and the global economy. Fast and accurate detection of the pathogens that cause these infections is important to avoid the transmission of the diseases. Conventional methods for the detection of these microorganisms are time-consuming, costly, and not applicable for on-site monitoring. Biosensors can provide a fast, reliable, and point of care diagnostic. Nanomaterials, due to their outstanding electrical, chemical, and optical features, have become key players in the area of biosensors. This review will cover different nanomaterials that employed in electrochemical, optical, and instrumental biosensors for infectious disease diagnosis and how these contributed to enhancing the sensitivity and rapidity of the various sensing platforms. Examples of nanomaterial synthesis methods as well as a comprehensive description of their properties are explained. Moreover, when available, comparative data, in the presence and absence of the nanomaterials, have been reported to further highlight how the usage of nanomaterials enhances the performances of the sensor.

Analysis of drug sensitivity of Escherichia Coli O157H7

Sensitive and rapid tests of Escherichia coli drug sensitivity is very important for health of human and animals. An E. coli immunosensor was built based on electrochemical detection and immune detection technologies, through pretreating screen-printed electrodes, and analyzing the optimal reaction concentration of antigen antibody binding with the AC impedance method. Based on the detection system combining the immunosensor and electrochemical workstation, tests were carried out to measure the accuracy of E. coli concentration and drug sensitivity, and error of the detection system was calibrated in accordance with data from the electrochemical workstation. E. coli O157:H7 can be detected in the range of 10³ cfu/ml ~ 10¹² cfu/ml, and the detection error controlled within 5%. Results from the electrochemical workstation and those from the detection device were consistent, and both demonstrated a greater inhibitory effect of antibiotics on E. coli than on Bacillus subtilis. The electrochemical detection system is highly efficient and accurate, and could be widely applied to E. coli drug sensitivity tests in clinical medicine.

Microbial biosensors for recreational and source waters

Biosensors are finding new places in science, and the growth of this technology will lead to dramatic improvements in the ability to detect microorganisms in recreational and source waters for the protection of public health. Much of the improvement in biosensors has followed developments in molecular biology processes and coupling these with advances in engineering. Progress in the fields of nano-engineering and materials science have opened many new avenues for biosensors. The adaptation of these diverse technological fields into sensors has been driven by the need to develop more rapid sensors that are highly accurate, sensitive and specific, and have other desirable properties, such as robust deployment capability, unattended operations, and remote data transfer. The primary challenges to the adoption of biosensors in recreational and source water applications are cost of ownership, particularly operations and maintenance costs, problems caused by false positive rates, and to a lesser extent false negative rates, legacy technologies, policies and practices which will change as biosensors improve to the point of replacing more traditional methods for detecting organisms in environmental samples.

Recent progress and challenges on the bioassay of pathogenic bacteria

The present review (containing 242 references) illustrates the importance and application of optical and electrochemical methods as well as their performance improvement using various methods for the detection of pathogenic bacteria. The application of advanced nanomaterials including hyper branched nanopolymers, carbon-based materials and silver, gold and so on. nanoparticles for biosensing of pathogenic bacteria was also investigated. In addition, a summary of the applications of nanoparticle-based electrochemical biosensors for the identification of pathogenic bacteria has been provided and their advantages, detriments and future development capabilities was argued. Therefore, the main focus in the present review is to investigate the role of nanomaterials in the development of biosensors for the detection of pathogenic bacteria. In addition, type of nanoparticles, analytes, methods of detection and injection, sensitivity, matrix and method of tagging are also argued in detail. As a result, we have collected electrochemical and optical biosensors designed to detect pathogenic bacteria, and argued outstanding features, research opportunities, potential and prospects for their development, according to recently published research articles.

Sensitive electrochemical detection of aflatoxin B1 using DNA tetrahedron-nanostructure as substrate of antibody ordered assembly and template of aniline polymerization

A novel strategy for AFB1 detection in grains was proposed based on DNA tetrahedron-structured probe (DTP) and horseradish peroxidase (HRP) triggered polyaniline (PANI) deposition. Briefly, the DNA tetrahedron nanostructures were assembled on the gold electrode, with carboxylic group designed on top vertex of them. The carboxylic group was conjugated with the AFB1 monoclonal antibody (mAb) to form DTP. The test sample and a known fixed concentration of HRP-labeled AFB1 were mixed and they compete for binding to DTP. The HRP assembled on the gold electrode catalyzed the polymerization of aniline on DTP. AFB1 in grains could be determined by using PANI as electrochemical signal molecules. Interestingly, DNA tetrahedron-structure, which has mechanical rigidity and structural stability, can improve antigen-antibody specific recognition and binding efficiency through the use of mAb ordered assembly. Meanwhile, nucleic acid backbone with a large amount of negative charge is good template for aniline polymerization under mild conditions.

Amperometric genosensor for culture independent bacterial count

Bacterial plate count for general assessment of water quality requires lengthy bacterial culturing. We report here a new DNA induced current genosensor for culture independent total bacteria determination. Since the amount of bacterial DNA is correlated to the number of bacteria, the genosensor measures the amount of bacterial DNA to determine bacterial count. The approach relies on bacteria lysis to release DNA which can react with molybdate to form redox molybdophosphate and measured electrochemically. Analysis of E. coli and S. aureus demonstrated that the DNA generated current is highly correlated with the level of bacteria lysis which was confirmed by spectrometric measurement. Culture independent measurement of S. aureus bacterial load suggests limit of detection is 21.9 CFU/mL, with linear range from 3×10² to 3×10⁷ CFU/mL and correlation coefficient of 0.992. For E. coli analysis, the detection limit is 25.1 CFU/mL with the same linear range. The use of electrochemical microbial DNA quantitation for culture independent bacterial count is a new approach, the genosensor measurement is rapid (within 1 h) and has potential use for analysis of broad-spectrum bacteria for various applications.

CdS quantum dots/Au nanoparticles/ZnO nanowire array for self-powered photoelectrochemical detection of Escherichia coli O157:H7

In this paper, the hydrothermally grown ZnO nanowire array (NWs) was modified by Au nanoparticles (NPs) and CdS quantum dots (QDs) to construct a high-performance photoelectrochemical (PEC) electrode. The aligned ZnO NWs, which decorated Au NPs and CdS QDs have the effective light absorption range from UV to visible region. This hybrid structure provided a self-powered PEC electrode with a favorable energy-band configuration for fast charge separation and transportation. Meanwhile, the Au NPs and CdS QDs also made increase of the surface area to improve the immobilization of the analytes. After assembling aptamer as recognition element, this composite nanoarray was further developed as a self-powered PEC biosensor by synergizing above multiple enhancement factors. The PEC aptasensor exhibited a rapid response in a wide linear range of 10-10⁷ CFU/mL with the detection limit as low as 1.125 CFU/mL to Escherichia coli O157:H7 (E. coli O157:H7). This approach would offer an alternative PEC transduction for fast environment monitoring and clinical diagnosis related to pathogenic bacteria.

Recent Advances in Biosensors for Nucleic Acid and Exosome Detection

Biosensors are analytical devices for biomolecule detection that compromise three essential components: recognition moiety, transducer, and signal processor. The sensor converts biomolecule recognition to detectable signals, which has been applied in diverse fields such as clinical monitoring, in vitro diagnostics, food industry etc. Based on signal transduction mechanisms, biosensors can be categorized into three major types: optical biosensors, electrochemical biosensors, and mass-based biosensors. Recently, the need for faster, more sensitive detection of biomolecules has compeled researchers to develop various sensing techniques. In this review, the basic structure and sensing principles of biosensors are introduced. Additionally, the review discusses multiple recent works about nucleic acid and exosome sensing.