Sensitive and isothermal electrochemiluminescence gene-sensing of Listeria monocytogenes with hyperbranching rolling circle amplification technology

A novel PCR-free and label-free cloth-based DNA sensor for sensitive and rapid detection of Escherichia coli

BACKGROUND

As is known to all, pathogenic bacteria have a serious impact on human health. The development of sensitive, simple, rapid and low-cost bacterial detection method is necessary. Nowadays, some conventional methods (such as plate count, polymerase chain reaction (PCR) and immunological techniques) can not meet the above needs. This work was aimed at providing a new method for addressing these unmet needs.

RESULT

This study proposed a novel PCR-free and label-free DNA sensor based on multiple linear hybridization chain reaction (ML-HCR) and cloth-based closed bipolar electrochemiluminescence for sensitive and rapid detection of Escherichia coli (E. coli). The target DNA can be obtained from the E. coli genomic DNA by using the restriction enzyme instead of PCR. The auxiliary probe-triggered ML-HCR is carried out with continuous hybridization of two hairpin DNA, and as a result the double stranded DNA is formed to provide a large number of binding sites for Ru(bpy)₃²⁺. The whole detection is PCR-free and label-free, and thus the detection procedure is easier and faster. Under optimized conditions, the linear detection range was from 10² to 10⁷ CFU/mL, and the detection limit was low to 38 CFU/mL. In addition, the proposed DNA sensor has an acceptable selectivity, stability and reproducibility, and is successfully applied to detect E. coli in milk samples with the recoveries from 96.24% to 105.98%.

SIGNIFICANCE

The proposed DNA sensor has broad application prospects in the fields of bacterial detection and gene diagnose. Further, this method has potential to be extended for establishing miniaturized, integrated, and automated detection system.

Biosensors Based on Isothermal DNA Amplification for Bacterial Detection in Food Safety and Environmental Monitoring

The easy and rapid spread of bacterial contamination and the risk it poses to human health makes evident the need for analytical methods alternative to conventional time-consuming laboratory-based techniques for bacterial detection. To tackle this demand, biosensors based on isothermal DNA amplification methods have emerged, which avoid the need for thermal cycling, thus facilitating their integration into small and low-cost devices for in situ monitoring. This review focuses on the breakthroughs made on biosensors based on isothermal amplification methods for the detection of bacteria in the field of food safety and environmental monitoring. Optical and electrochemical biosensors based on loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), strand displacement amplification (SDA), and isothermal strand displacement polymerisation (ISDPR) are described, and an overview of their current advantages and limitations is provided. Although further efforts are required to harness the potential of these emerging analytical techniques, the coalescence of the different isothermal amplification techniques with the wide variety of biosensing detection strategies provides multiple possibilities for the efficient detection of bacteria far beyond the laboratory bench.

Recent Advances in Electrochemiluminescence Sensors for Pathogenic Bacteria Detection

Pathogenic bacterial contamination greatly threats human health and safety. Rapidly biosensing pathogens in the early stage of infection would be helpful to choose the correct drug treatment, prevent transmission of pathogens, as well as decrease mortality and economic losses. Traditional techniques, such as polymerase chain reaction and enzyme-linked immunosorbent assay, are accurate and effective, but are greatly limited because they are complex and time-consuming. Electrochemiluminescence (ECL) biosensors combine the advantages of both electrochemical and photoluminescence analysis and are suitable for high sensitivity and simple pathogenic bacteria detection. In this review, we summarize recent advances in ECL sensors for pathogenic bacteria detection and highlight the development of paper-based ECL platforms in point of care diagnosis of pathogens.

Antimicrobial Activity and Action Approach of the Olive Oil Polyphenol Extract Against Listeria monocytogenes

Olive oil polyphenol extract (OOPE) has been reported to have antibacterial activity; however, its effect on Listeria monocytogenes is less studied so far. This study, thus, aimed to reveal its antimicrobial activity and action approach against L. monocytogenes via evaluating the minimum inhibitory concentration (MIC) as well as the changes of intracellular adenosine 5′-triphosphate (ATP) concentration, cell membrane potential, bacterial protein, DNA, and cell morphology. The results showed that OOPE could inhibit the growth of L. monocytogenes with a measured MIC of 1.25 mg/ml. L. monocytogenes cells treated by OOPE showed significant reduction in intracellular ATP concentrations, bacterial protein, or DNA (p < 0.05), in comparison with those without any treatment. In addition, OOPE was observed to depolarize strain cells and alter cell morphology, resulting in damaged cell membrane and, thereby, leakage of cell fluid. These findings demonstrated that OOPE had inhibition on L. monocytogenes via its action on cells, suggesting its potential as a natural preservative.

Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection

Background:

Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).

Methods:

Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.

Results:

The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.

Discussion:

Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.

Point-of-Need DNA Testing for Detection of Foodborne Pathogenic Bacteria

Foodborne pathogenic bacteria present a crucial food safety issue. Conventional diagnostic methods are time-consuming and can be only performed on previously produced food. The advancing field of point-of-need diagnostic devices integrating molecular methods, biosensors, microfluidics, and nanomaterials offers new avenues for swift, low-cost detection of pathogens with high sensitivity and specificity. These analyses and screening of food items can be performed during all phases of production. This review presents major developments achieved in recent years in point-of-need diagnostics in land-based sector and sheds light on current challenges in achieving wider acceptance of portable devices in the food industry. Particular emphasis is placed on methods for testing nucleic acids, protocols for portable nucleic acid extraction and amplification, as well as on the means for low-cost detection and read-out signal amplification.

Biosensor for the detection of Listeria monocytogenes: emerging trends

The early detection of Listeria monocytogenes (L. monocytogenes) and understanding the disease burden is of paramount interest. The failure to detect pathogenic bacteria in the food industry may have terrible consequences, and poses deleterious effects on human health. Therefore, integration of methods to detect and trace the route of pathogens along the entire food supply network might facilitate elucidation of the main contamination sources. Recent research interest has been oriented towards the development of rapid and affordable pathogen detection tools/techniques. An innovative and new approach like biosensors has been quite promising in revealing the foodborne pathogens. In spite of the existing knowledge, advanced research is still needed to substantiate the expeditious nature and sensitivity of biosensors for rapid and in situ analysis of foodborne pathogens. This review summarizes recent developments in optical, piezoelectric, cell-based, and electrochemical biosensors for Listeria sp. detection in clinical diagnostics, food analysis, and environmental monitoring, and also lists their drawbacks and advantages.

Au nanocluster-embedded chitosan nanocapsules as labels for the ultrasensitive fluorescence immunoassay of Escherichia coli O157:H7

Ultrasensitive fluorescence immunoassay of Escherichia coli O157:H7 is described using Au nanocluster-embedded chitosan nanocapsules as labels.

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.

A review of electrogenerated chemiluminescent biosensors for assays in biological matrices

Electrogenerated chemiluminescence (ECL) is the production of light via electron transfer reactions between electrochemically produced reagents. ECL-based biosensors use specific biological interactions to recognize an analyte and produce a luminescent signal. Biosensors fabricated with novel biorecognition species have increased the number of analytes detected. Some of these analytes include peptides, cells, enzymes and nucleic acids. ECL biosensors are selective, simple, sensitive and have low detection limits. Traditional methods use ruthenium complexes or luminol to generate ECL. Nanomaterials can be incorporated into ECL biosensors to improve efficiency, but also represent a new class of ECL emitters. This article reviews the application of ruthenium complex, luminol and nanomaterial-based ECL biosensors to making measurements in biological matrices over the past 4 years.

A label-free electrochemiluminescence immunosensor based on EuPO4 nanowire for the ultrasensitive detection of Prostate specific antigen

EuPO4 nanowire, which exhibited strong and stable cathodic electrochemiluminescence (ECL) activity, was used for the first time to fabricate an immunosensor for the detection of prostate specific antigen (PSA). EuPO4 has some inherent excellent properties such as long luminescence lifetime, narrow emission band, high quantum yield and low toxicity. Based on these properties, a novel label-free ECL immunosensor was developed using EuPO4 as a sensing matrix. Chitosan solution was used to disperse EuPO4 nanowires and the amino groups on chitosan enabled the covalent attachment of capture antibodies. After the modification of the electrode surface with EuPO4 nanowires, anti-PSA was then immobilized on them, forming a label-free immunosensing interface. The specific binding of PSA on the electrode inhibited the ECL reaction of EuPO4 nanowires with the coreactant due to the steric hindrance effect (Deng et al., 2013). Under the optimum conditions, a good linear relationship between ECL intensity and the logarithm of PSA concentration was obtained in the range of 0.0005-80 ng/mL with a detection limit of 177.33 fg/mL. The proposed ECL immunosensor showed good stability, acceptable selectivity and reproducibility.

Ultrasensitive colorimetric carcinoembryonic antigen biosensor based on hyperbranched rolling circle amplification

In this study, a hyperbranched rolling circle amplification (HRCA)-based colorimetric biosensor for carcinoembryonic antigen (CEA) is developed with high sensitivity and specificity. A CEA aptamer can bind with its target (CEA) to form a complex due to their high affinity, and the introduced CDNA cannot hybridize with the aptamer. Thus, free CDNA can propagate the HRCA reaction to form a large number of single-stranded DNA (ss-DNA). ss-DNA can be easily adsorbed onto AuNPs and prevent salt-induced AuNPs aggregation, which causes the change in the color of the system. It is found that the absorbance intensity ratio (A520/A660) has a linear relationship with the concentration of the target in the range of 5 pM-0.5 nM, and the detection limit is as low as 2 pM (S/N = 3).

A novel ultrasensitive ECL sensor for DNA detection based on nicking endonuclease-assisted target recycling amplification, rolling circle amplification and hemin/G-quadruplex

In this study, we describe a novel universal and highly sensitive strategy for the electrochemiluminescent (ECL) detection of sequence specific DNA at the aM level based on Nt.BbvCI (a nicking endonuclease)-assisted target recycling amplification (TRA), rolling circle amplification (RCA) and hemin/G-quadruplex. The target DNAs can hybridize with self-assembled capture probes and assistant probes to form “Y” junction structures on the electrode surface, thus triggering the execution of a TRA reaction with the aid of Nt.BbvCI. Then, the RCA reaction and the addition of hemin result in the production of numerous hemin/G-quadruplex, which consume the dissolved oxygen in the detection buffer and result in a significant ECL quenching effect toward the O₂/S₂O₈²⁻ system. The proposed strategy combines the amplification ability of TRA, RCA and the inherent high sensitivity of the ECL technique, thus enabling low aM (3.8 aM) detection for sequence-specific DNA and a wide linear range from 10.0 aM to 1.0 pM. At the same time, this novel strategy shows high selectivity against single-base mismatch sequences, which makes our novel universal and highly sensitive method a powerful addition to specific DNA sequence detection.

Real-time detection of H5N1influenza virus through hyperbranched rolling circle amplification

In the HRCA process, by replacing heat shock by pH shock, H₅N₁was detected at 9 fM more easily and safely.

Isothermal amplified detection of DNA and RNA

This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.

Hyperbranched rolling circle amplification based electrochemiluminescence aptasensor for ultrasensitive detection of thrombin

An ultrasensitive electrochemiluminescence (ECL) aptamer sensor for protein (thrombin as an example) detection based on hyperbranched rolling circle amplification (HRCA) had been developed. A complementary single-strand DNA (CDNA) of the thrombin aptamer had been modified on the gold electrode firstly, and then hybridized with thrombin aptamer to make the aptamer immobilized on the electrode surface, in the presence of thrombin, aptamer-thrombin bioaffinity complexes formed and made thrombin aptamer leave the electrode surface. Thus, the linear padlock probe hybridized with the free CDNA on the electrode surface and circularized by Escherichia coli DNA ligase. Subsequently, the linear padlock probe was served as a template for the initiation of HRCA reaction, and a lot of dsDNA modified on the electrode surface. Then Ru(phen)₃²⁺ (acted as the ECL indicator) intercalates specifically into double-stranded DNA (dsDNA) grooves to generate ECL signal. The ECL intensity of the system has a linear relationship with thrombin concentration in the range of 3.0-300 aM with a detection limit of 1.2 aM (S/N=3). The proposed method combines the high sensitivity of ECL, exponential amplification of HRCA for signal enhancement and high selectivity of aptamer.

Quantum dots and graphene oxide fluorescent switch based multivariate testing strategy for reliable detection of Listeria monocytogenes

Graphene oxide (GO) and quantum dots (QDs), as burgeoning types of nanomaterials, have gained tremendous interest in the biosensor field. In this work, we designed a novel multivariate testing strategy that depends on the fluorescence resonance energy transfer (FRET) effect between quantum dots (QDs) and graphene oxide (GO). It integrates the QD-GO FRET principle and QD probes with different emission peaks into a platform, aims at multiplex gene detection of a human infectious and highly pathogenic pathogen, Listeria monocytogenes (L. monocytogenes). With the development of a multiplex linear-after-the-exponential (LATE) polymerase chain reaction (PCR) system, the single-stranded DNA (ssDNA) products of hlyA genes and iap genes are obtained by simultaneous amplification of the target genes. Then with the hybridization of ssDNA products and QD probes, simultaneous homogeneous detection of two gene amplification products can be achieved by using GO as a fluorescence switch and monitoring the relevant emissions excited by a single light source. Distinguishable signals corresponding to target genes are obtained. With this developed approach, genomic DNA from L. monocytogenes can be detected as low as 100 fg/μL. Moreover, this platform has a good dynamic range from 10(2) to 10(6) fg/μL. It is indicated that this platform has potential to be a reliable complement for rapid gene detection technologies and is capable of reducing the false-negative and false-dismissal probabilities in routine tests.

A label-free ultrasensitive electrochemical aptameric recognition system for protein assay based on hyperbranched rolling circle amplification

A label-free ultrasensitive electrochemical aptameric sensor which combined the advantages of an aptamer and hyperbranched rolling circle amplification (HRCA) has been developed for specific recognition of a platelet-derived growth factor B-chain (PDGF-BB).

Visual and sensitive detection of viable pathogenic bacteria by sensing of RNA markers in gold nanoparticles based paper platform

Food-borne pathogens have been recognized as a major cause of human infections worldwide. Their identification needs to be simpler, cheaper and more reliable than the traditional methods. Here, we constructed a low-cost paper platform for viable pathogenic bacteria detection with the naked eye. In this study, an effective isothermal amplification method was used to amplify the hlyA mRNA gene, a specific RNA marker in Listeria monocytogenes. The amplification products were applied to the paper-based platform to perform a visual test using sandwich hybridization assays. When the RNA products migrated along the platform by capillary action, the gold nanoparticles accumulated at the designated area. Under optimized experimental conditions, as little as 0.5 pg/μL genomic RNA from L. monocytogenes could be detected. It could also be used to specifically detect 20 CFU/mL L. monocytogenes from actual samples. The whole assay process, including RNA extraction, amplification, and visualization, can be completed within several hours. This method is suitable for point-of-care applications to detect food-borne pathogens, as it can overcome the false-positive results caused by amplifying nonviable L. monocytogenes. Furthermore, the results can be imaged and transformed into a two-dimensional bar code through an Android-based smart phone for further analysis or in-field food safety tracking.

Sensitive and label-free DNA methylation detection by ligation-mediated hyperbranched rolling circle amplification

Sensitive and specific detection of DNA methylation in CpG sites of genomic DNA is imperative for rapid epigenetic evaluation and early cancer diagnosis. Here, we employ for the first time the thermostable ligation for methylated DNA discrimination and hyperbranched rolling circle amplification (HRCA) for signal enhancement, without the need for restriction enzymes, PCR amplification, or fluorescence-labeled probes. After bisulfite treatment of methylated DNA, the methylation-specific linear padlock probe can be circularized only in the presence of methylated DNA and serves subsequently as a template for HRCA, whose products are easily detected using SYBR Green I and a standard fluorometer. While in the presence of unmethylated DNA, the linear padlock probe cannot be circularized because of the defectively matched substrate, and no HRCA occurs. This ligation-mediated HRCA-based method exhibits excellent specificity and high sensitivity with a detection limit of 0.8 fM and a detection range of 4 orders of magnitude, and it can even distinguish as low as 0.01% methylation level from the mixture, which is superior to most currently used methods for DNA methylation assay. This method can be further applied to analyze genomic DNA in human lung cancer cells.

Diagnostic devices for isothermal nucleic acid amplification

Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development.

Colorimetric nucleic acid testing assay for RNA virus detection based on circle-to-circle amplification of padlock probes

We developed a molecular diagnostic method for detection of RNA virus based on padlock probes and colorimetric readout. The feasibility of our approach was demonstrated by using detection of Crimean-Congo hemorrhagic fever (CCHF) virus as a model. Compared with conventional PCR-based methods, our approach does not require advanced equipment, involves easier assay design, and has a sensitivity of 10(3) viral copies/ml. By using a cocktail of padlock probes, synthetic templates representing different viral strain variants could be detected. We analyzed 34 CCHF patient samples, and all patients were correctly diagnosed when the results were compared to those of the current real-time PCR method. This is the first time that highly specific padlock probes have been applied to detection of a highly variable target sequence typical of RNA viruses.