Biosensing for rapid detection of MDR, XDR and PDR bacteria

The emergence of multidrug-resistant (MDR), extensively drug-resistant (XDR), and pandrug-resistant (PDR) bacteria poses a significant threat to global public health, complicating the management of infectious diseases and increasing morbidity and mortality rates. Rapid and sensitive detection of these resistant pathogens is crucial for effective treatment and infection control. This manuscript provides a comprehensive overview of various biosensor technologies developed for the rapid identification and quantification of MDR and XDR bacteria. We discuss the principles of operation, sensitivity, specificity, and practical applications of different biosensing platforms, including electrochemical, optical, and piezoelectric sensors. Additionally, we explore recent advancements in nanomaterials and microfluidics that enhance biosensor performance and enable point-of-care testing. The manuscript also addresses the challenges faced in the implementation of these technologies in clinical settings, such as regulatory hurdles and the need for standardization. A systematic literature review was conducted to identify relevant studies. Databases utilized include PubMed and Scopus, covering the time frame from 2015 to 2024. The literature screening criteria focused on the inclusion of only clinically validated studies to ensure the reliability and applicability of the findings. By highlighting the potential of biosensors to revolutionize the detection of drug-resistant bacteria, this work aims to inform researchers, clinicians, and policymakers about the critical role of innovative diagnostic tools in combating antibiotic resistance and improving patient outcomes.

Multipedal DNA Walker: Engineering Strategy, Biosensing Application and Future Perspectives

With the continuous development of DNA nanotechnology, DNA walkers have attracted increased attention because of their autonomous and progressive walking along predesigned tracks. Compared with the traditional DNA walkers, the emerged multipedal DNA walkers showed their special charm with sustainable walking capability, higher reaction efficiency, expanded walking region, and improved amplification capability. Consequently, multipedal DNA walkers have developed rapidly and shown potential in biosensing applications. Hence, in this review, we make a comprehensive representation of the engineering strategy of multipedal DNA walkers, which focused on the design of multiple walking strands as well as the construction of tracks and driving forces. Meanwhile, the application of multipedal DNA walkers in biosensors has been thoroughly described according to the type of biosensing signal readout. By illustrating some representative works, we also summarized the merits and challenges of multipedal DNA walker-based biosensors and offered a deep discussion of the latest progress and future.

Advances in Bioreceptor Layer Engineering in Nanomaterial-based Sensing of Pseudomonas Aeruginosa and its Metabolites

Pseudomonas aeruginosa is a pathogen that infects wounds and burns and causes severe infections in immunocompromised humans. The high virulence, the rise of antibiotic-resistant strains, and the easy transmissibility of P. aeruginosa necessitate its fast detection and control. The gold standard for detecting P. aeruginosa, the plate culture method, though reliable, takes several days to complete. Therefore, developing accurate, rapid, and easy-to-use diagnostic tools for P. aeruginosa is highly desirable. Nanomaterial-based biosensors are at the forefront of detecting P. aeruginosa and its secondary metabolites. This review summarises the biorecognition elements, biomarkers, immobilisation strategies, and current state-of-the-art biosensors for P. aeruginosa. The review highlights the underlying principles of bioreceptor layer engineering and the design of optical, electrochemical, mass-based, and thermal biosensors based on nanomaterials. The advantages and disadvantages of these biosensors and their future point-of-care applications are also discussed. This review outlines significant advancements in biosensors and sensors for detecting P. aeruginosa and its metabolites. Research efforts have identified biorecognition elements specific and selective towards P. aeruginosa. The stability, ease of preparation, cost-effectiveness, and integration of these biorecognition elements onto transducers are pivotal for their application in biosensors and sensors. At the same time, when developing sensors for clinically significant analytes such as P. aeruginosa, virulence factors need to be addressed, such as the sensor's sensitivity, reliability, and response time in samples obtained from patients. The point-of-care applicability of the developed sensor may be an added advantage since it enables onsite determination. In this context, optical methods developed for P. aeruginosa offer promising potential.

Electrochemical nucleic acid sensors: Competent pathways for mobile molecular diagnostics

Electrochemical nucleic acid biosensor has demonstrated great promise in clinical diagnostic tests, mainly because of its flexibility, high efficiency, low cost, and easy integration for analytical applications. Numerous nucleic acid hybridization-based strategies have been developed for the design and construction of novel electrochemical biosensors for diagnosing genetic-related diseases. This review describes the advances, challenges, and prospects of electrochemical nucleic acid biosensors for mobile molecular diagnosis. Specifically, the basic principles, sensing elements, applications in diagnosis of cancer and infectious diseases, integration with microfluidic technology and commercialization are mainly included in this review, aiming to provide new insights and directions for the future development of electrochemical nucleic acid biosensors.

Highly Sensitive β-Lactoglobulin Fluorescent Aptamer Biosensors Based on Tungsten Disulfide Nanosheets and DNase I-Assisted Signal Amplification

β-lactoglobulin (β-Lg) is a protein found in milk that can cause severe allergic reactions, including rash, vomiting, and diarrhea. Thus, it is crucial to develop a sensitive β-Lg detection method to protect people who are susceptible to allergies. Here, we introduce a novel and highly sensitive fluorescent aptamer biosensor for detecting β-Lg. First, a fluorescein-based dye (FAM)-labeled β-lactoglobulin aptamer (β-Lg aptamer) is adsorbed on the surface of tungsten disulfide (WS₂) nanosheets via van der Waals forces, resulting in fluorescence quenching. When β-Lg is present, the β-Lg aptamer selectively binds to β-Lg, causing a conformational change in the β-Lg aptamer and releasing it from the surface of WS₂ nanosheets, which restores the fluorescence signal. Simultaneously, DNase I in the system cleaves the aptamer bound to the target, producing a short oligonucleotide fragment and releasing β-Lg. The released β-Lg then binds to another β-Lg aptamer adsorbed on WS₂, initiating the next round of cleavage, resulting in significant amplification of the fluorescence signal. This method has a linear detection range of 1-100 ng mL^-1, and the limit of detection is 0.344 ng mL^-1. Furthermore, this approach has been successfully used for detecting β-Lg in milk samples with satisfactory results, providing new opportunities for food analysis and quality control.

Ratiometrically homogeneous electrochemical biosensor based on the signal amplified strategy of dual DNA nanomachines for microRNA analysis

Precise and sensitive microRNA (miRNA) analysis is very significant for early disease diagnosis. In this work, a dual DNA nanomachines-based homogeneous electrochemical biosensor was constructed for the sensitively ratiometric detection of miRNA by a nicking enzyme (Nt.AlwI)-assisted cycling signal amplification strategy. The Co-based metal organic frameworks (Co-MOFs) and toluidine blue (TB) were employed as signal probes and internal reference probes, respectively. The introduction of internal reference probes can actually calibrate the interferent factors of the analytical system to improve the stability in detection procedure. In addition, with the help of the magnetic separation technique, the homogeneous electrochemical biosensor provides a more simpler way for the development of immobilization-free electrochemical miRNA biosensors, avoiding the complex modification procedure of traditional electrochemical biosensing interfaces. Consequently, taking advantages of this proposed dual DNA nanomachines-based homogeneous electrochemical biosensor, the highly sensitive and selective detection of miRNA-141 as model could be accomplished in ranging from 1 fM to 10 nM with detection limit of 0.46 fM. This strategy exhited good sensitivity and stability to integrate the nicking enzyme-powered dual DNA nanomachines with the ratiometric electrochemical output modes, which open new opportunities for the sensitive and reliable diagnosis of miRNA-related diseases.

Nucleic acid isothermal amplification-based soft nanoarchitectonics as an emerging electrochemical biosensing platform

The emergence of nucleic acid isothermal amplification strategies based on soft nanoarchitectonics offers a new dimension to the traditional electrochemical technique, particularly because of its flexibility, high efficiency, and increased sensitivity for analytical applications. Various DNA/RNA isothermal amplification strategies have been developed for the design and fabrication of new electrochemical biosensors for efficient and important biomolecular detection. Herein, we provide an overview of recent efforts in this research field and the strategies for signal-amplified sensing systems, with their biological applications, current challenges and prospects in this promising new area.

Multiregion Linear DNA Walker-Mediated Ultrasensitive Electrochemical Biosensor for miRNA Detection

In this work, an intelligent multiregion linear DNA walker (MLDW) with a high walking rate and a high amplification efficiency was explored for ultrasensitive detection of miRNA. Significantly, amounts of functional domain could be concentrated in a long linear DNA obtained by the target miRNA-mediated rolling-circle amplification to simultaneously increase the local concentration and collision probability, resulting in an obviously improved reaction rate. Impressively, the MLDW can accomplish the reaction within 30 min, which is at least 4 times beyond that of traditional single-leg and multiple-leg DNA walkers. As a proof of concept, the high-efficiency MLDW was used to develop an electrochemical biosensing platform for ultrasensitive detection of target miRNA-21 with a low detection limit down to 36 aM. Therefore, the MLDW we designed puts forward an innovative insight to construct a functional DNA nanodevice and promote the investigation of the inherent performance of nucleic acid signal amplification for ultimate application in the detection of biomolecules and clinical disease diagnosis.

A cascade amplification strategy for ultrasensitive Salmonella typhimurium detection based on DNA walker coupling with CRISPR-Cas12a

Salmonella typhimurium (S. typhimurium) infection is one of leading causes of severe foodborne illness, which poses grievous threats to public health. Thus, the detection with ultra-sensitivity is highly demanded for timely prevention and diagnosis of S. typhimurium. In this study, we developed a novel detection machinery based on DNA walker and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas12a technologies. Mechanistically, the S. typhimurium specific sequence triggers Nt.AlwI nicking endonuclease and produces particular signaling nucleotide, which further activates Cas12a for strong fluorescence signal output. This cascade amplification strategy exhibits excellent specificity and successfully decreases the limit of detection (LOD) of DNA walker by 2,000 folds to 5 CFU/mL. Collectively, this combinatorial approach offers great promises to effectively reduce foodborne diseases by ultrasensitive detection of S. typhimurium. As a proof of concept, this innovative design also shows prominent potential in detections of other biomolecules, cells and pathogens.

An in situ quenching electrochemiluminescence biosensor amplified with aptamer recognition-induced multi-DNA release for sensitive detection of pathogenic bacteria

An in situ quenching electrochemiluminescence (ECL) biosensor sensitized with the aptamer recognition-induced multi-DNA release was designed for pathogenic bacterial detection. Benefitting from the high binding ability of the aptamer to targets and large enrichment capacity of magnetic bead separation, the proposed sensing system not only exhibited outstanding identification to Staphylococcus aureus (S. aureus) among various bacteria, but also released abundant signal transduction DNAs. One S. aureus initiated the dissociation of four kinds of DNA sequences, achieving a one-to-multiple amplification effect. These multi-DNA strands were further hybridized with capture DNA, which were assembled to an electrode modified with Ru(bpy)₃²⁺-conjugated silica nanoparticles (RuSi NPs). Then, glucose oxidase (GOD) was introduced via the functional conjugation of GOD-multi-DNA, leading to the presence of H₂O₂ by in situ catalysis of GOD on glucose. Relying on the ECL quenching of H₂O₂ in the Ru(bpy)₃²⁺ system, S. aureus was quantified with a linear range from 10 to 10⁷ CFU/mL. In addition, the negative results of non-target bacteria and good recovery efficiency in real samples revealed the system's remarkable selectivity and potential application in infectious food tests.

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.

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.

Nucleic acid-based electrochemical biosensor: Recent advances in probe immobilization and signal amplification strategies

With the increasing importance of accurate and early disease diagnosis and the development of personalized medicine, DNA-based electrochemical biosensor has attracted broad scientific and clinical interests in the past decades due to its unique hybridization specificity, fast response time, and potential for miniaturization. In order to achieve high detection sensitivity, the design of DNA electrochemical biosensors depends critically on the improvement of the accessibility of target molecules and the enhancement of signal readout. Here, we summarize the recent advances in DNA probe immobilization and signal amplification strategies with a special focus on DNA nanostructure-supported DNA probe immobilization method, which provides the opportunity to rationally control the distance between probes and keep them in upright confirmation, as well as the contribution of functional nanomaterials in enhancing the signal amplification. The next challenge of biosensors will be the fabrication of point-of-care devices for clinical testing. The advancement of multidisciplinary areas, including nanofabrication, material science, and biochemistry, has exhibited profound promise in achieving such portable sensing devices. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.

Graphene-based fluorometric determination of agrD gene transcription in methicillin-resistant Staphylococcus aureus using exonuclease III-aided target recycling and DNA walker cascade amplification

A graphene-based bioassay is described for the fluorometric determination of agrD gene transcription (mRNA) in methicillin-resistant Staphylococcus aureus (MRSA). This method includes exonuclease III (Exo III)-assisted target recycling and DNA walker cascade amplification. Hairpin1 (HP1) consists of a capture probe (CP) and DNA walker sequence. In the absence of the target, 5'-amino modified hairpin2 (HP2) labeled with carboxyfluorescein (FAM) at its 3' terminus is covalently linked to graphene via 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS) catalysis, resulting in the quenching of the FAM signal. The stem-loop structure of HP1 opens when the target is added to form partially complementary DNA/RNA hybrids. Exo III then initiates the target recycling process by cleaving the CP and DNA walker cascade reaction by automatic walking. This iterative reaction causes the FAM to dissociate from the graphene, and the fluorescence can be measured at excitation/emission wavelengths of 480/514 nm. Therefore, the target can be assayed by fluorescence. This method has a linear relationship with the concentration of target within the range 1 fM to 100 pM with a detection limit of 1 fM. The developed bioassay was used to monitor biofilm formation and investigate the mechanism of drug action with satisfactory results. Schematic representation of the graphene-based fluorescent bioassay for agrD gene transcription in methicillin-resistant Staphylococcus aureus by using exonuclease III-aided target recycling and DNA walker cascade amplification.

Recent advances in DNA walker machines and their applications coupled with signal amplification strategies: A critical review

DNA walkers, a type of dynamic nanomachines, have become the subject of burgeoning research in the field of biology. These walkers are powered by driving forces based on strand displacement reactions, protein enzyme/DNAzyme reactions and conformational transitions. With the unique properties of high directionality, flexibility and efficiency, DNA walkers move progressively and autonomously along multiple dimensional tracks, offering abundant and promising applications in biosensing, material assembly and synthesis, and early cancer diagnosis. Notably, DNA walkers identified as signal amplifiers can be combined with various amplification approaches to enhance signal transduction and amplify biosensor sensing signals. Herein, we systematically and comprehensively review the walking principles of various DNA walkers and the recent progress on multiple dimensional tracks by presenting representative examples and an insightful discussion. We also summarized and categorized the diverse signal amplification strategies with which DNA walkers have coupled. Finally, we outline the challenges and future trends of DNA walker machines in emerging analytical fields.

Electrochemical sensing technology for liquid biopsy of circulating tumor cells-a review

In recent years, a lot of new detection techniques for circulating tumor cells (CTCs) have been developed. Among them, electrochemical sensing technology has gradually developed because of its advantages of good selectivity, high sensitivity, low cost and rapid detection. Especially in the latest decade, the field of electrochemical biosensing has witnessed great progress, thanks to the merging of biosensing research area with nanotechnology, immunotechnology, nucleic acid technology, and microfluidic technology. In this review, the recent progress for the detection of CTCs according to the principle of detection was summarized and how they can contribute to the enhanced performance of such biosensors was explained. The latest electrode construction strategies such as rolling circle amplification reaction, DNA walker and microfluidic technology and their advantages were also introduced emphatically. Moreover, the main reasonswhy the existing biosensors have not been widely used clinically and the next research points were clearly put forward.

Dual-readout proximity hybridization-regulated and photothermally amplified protein analysis based on MXene nanosheets

Herein, an ingenious dual-readout sensing platform based on a proximity hybridization-regulated strategy is proposed for protein detection. For the first time, Ti₃C₂ MXene@thionine composites (MXene@Thi) with an excellent photothermal effect not only acted as an amplifier to enhance the electrochemical signal, but were also used as a converter to achieve the temperature readout.

Three-Dimensional DNA Nanomachine Biosensor by Integrating DNA Walker and Rolling Machine Cascade Amplification for Ultrasensitive Detection of Cancer-Related Gene

Stochastic DNA walkers capable of traversing on three-dimensional (3D) tracks have received great deal of attention. However, DNA walker-based biosensors exhibit limited amplification efficiency because of their slow walking kinetics and low processivity. Herein, by taking advantage of the high processivity of a DNA rolling machine, a sensitive ratiometric DNA nanomachine biosensor is designed. The biosensor is constructed with hairpin-loaded Au nanoparticles (NPs) (hpDNA@AuNPs) as a DNA walker and AgNCs-decorated magnetic NPs (AgNCs@MNPs) as a DNA rolling machine. In the presence of target DNA, exonuclease III (Exo III)-powered DNA walker is activated to accomplish first-stage amplification via a burnt-bridge mechanism, generating a great deal of toehold-loaded AuNPs (Toehold@AuNPs) to hybridize with magnetic nanoparticles loaded with silver-nanoclusters-labeled DNA (AgNCs@MNPs) with the assistance of Exo III. These trigger rapid rolling of AuNPs on the AgNCs@MNPs surface and release free AgNCs, converting the biological signal into a mass spectrometric signal ratio (¹⁰⁷Ag/¹⁹⁷Au) with detection by ICP-MS. A linear range of 0.5-500 fmol L^-1 is achieved with a detection limit of 119 amol L^-1 for the p53 gene. The practical applicability of the biosensor has been demonstrated in the accurate assay of the p53 gene in the human blood.