Use of electrochemical DNA biosensors for rapid molecular identification of uropathogens in clinical urine specimens

Bridging oral and systemic health: exploring pathogenesis, biomarkers, and diagnostic innovations in periodontal disease

PURPOSE

This narrative review explores the multifaceted links between periodontal diseases (gingivitis and periodontitis) and systemic health conditions, including cardiovascular disease, diabetes, adverse pregnancy outcomes, Alzheimer's disease, cancers, rheumatoid arthritis, and respiratory infections. It aims to synthesize evidence on how local oral infections exert systemic effects and evaluate the potential of diagnostic technologies to monitor these interactions.

METHODS

This narrative review synthesizes current scientific literature on periodontal disease pathogenesis, focusing on key pathogens (e.g., Porphyromonas gingivalis, Fusobacterium nucleatum) and their roles in driving local and systemic inflammation via virulence factors and microbial dysbiosis. It examines biomarker-based diagnostic approaches (e.g., IL-1β, TNF-α, microbial DNA) in saliva, blood, and gingival crevicular fluid (GCF) and evaluates current and emerging diagnostic tools (e.g., ELISA, PCR, lateral flow assays, biosensors, microfluidics).

RESULTS

The review highlights that periodontal pathogens contribute to systemic disease through complex mechanisms including persistent inflammation (driven by cytokines like IL-1β, TNF-α), endotoxemia (via LPS, noting pathogen-specific structural variations impacting immune response), molecular mimicry, and immune modulation. Current diagnostic methods provide valuable information but often face limitations in speed, portability, and multiplexing capability needed for comprehensive point-of-care assessment. Emerging technologies, particularly multiplex platforms integrating biosensors or microfluidics, demonstrate significant potential for rapid, user-friendly analysis of multiple biomarkers, facilitating earlier detection and personalized risk stratification, especially in high-risk populations.

CONCLUSION

Periodontal diseases significantly impact systemic health via intricate microbial and inflammatory pathways. The complexity of these interactions necessitates moving beyond conventional diagnostics towards integrated, advanced technologies. Implementing rapid, multiplex biomarker detection platforms within a multidisciplinary healthcare framework holds the potential to revolutionize early detection of linked conditions, improve personalized management strategies, and ultimately reduce the systemic burden of periodontal disease.

Optical Biosensor for Bacteremia detection from human blood samples at a label-free Liquid Crystal-Aqueous Interface: A Rapid and Point-of-Care approach

Detection of bacteremia requires recognizing bloodstream bacteria. Early identification of bacteremia is imperative for treatment and prevents the escalation to systemic infections like septicaemia. This paper introduces a novel, label-free biosensor based on liquid crystals (LCs), designed to offer rapid and reliable optical detection of blood pathogens without using traditional PCR methods. The biosensor utilizes 16S rRNA, a key structural component of the bacterial genome, as a molecular recognition probe. For accurate detection of target DNA, a nematic LC is positioned within a transmission electron microscopy (TEM) grid cell on a DMOAP-coated glass surface and treated with a cationic surfactant, cetyl trimethyl ammonium bromide (CTAB), to facilitate probe adhesion at the LC-aqueous interface. Initially, the CTAB-coated LC displays a homeotropic orientation, but it shifts to a planar/tilted orientation when the primer is added. Upon exposure to the target DNA, the LC returns to its homeotropic configuration, which can be observed using a polarizing optical microscope (POM) fitted with crossed polarizers. An optimal primer adsorption density of 100 nM allows detection of target DNA at concentrations as low as 0.02 nM. The biosensor has been verified for real-time, point-of-care utility by successfully detecting the genomic DNA of the bacterium E. coli cultured in human blood. The operational mechanism of this biosensor has also been confirmed using Circular Dichroism and Synchrotron X-ray Solution Scattering Measurements. Due to its high sensitivity and label-free nature, this biosensor provides a faster, more practical and user-friendly alternative to traditional pathogen detection methods from blood samples of bacteremia patients.

"Urinary tract infection: Conventional testing to developing Technologies"

Urinary tract infections (UTIs) present an escalating global health concern, precipitating increased hospitalizations and antibiotic utilization, thereby fostering the emergence of antimicrobial resistance. Current diagnostic modalities exhibit protracted timelines and substantial financial burdens, necessitating specialized infrastructures. Addressing these impediments mandates the development of a precise diagnostic paradigm to expedite identification and augment antibiotic stewardship. The application of biosensors, recognized for their transformative efficacy, emerges as a promising resolution. Recent strides in biosensor technologies have introduced pioneering methodologies, yielding pertinent biosensors and integrated systems with significant implications for point-of-care applications. This review delves into historical perspectives, furnishing a comprehensive delineation of advancements in UTI diagnostics, disease etiology, and biomarkers, underscoring the potential merits of these innovations for optimizing patient care.

Emerging Biomimetic Sensor Technologies for the Detection of Pathogenic Bacteria: A Commercial Viability Study

Ensuring a rapid and accurate identification of harmful bacteria is crucial in various fields including environmental monitoring, food safety, and clinical diagnostics. Conventional detection methods often suffer from limitations such as long analysis time, complexity, and the need for qualified personnel. Therefore, a lot of research effort is devoted to developing technologies with the potential to revolutionize the detection of pathogenic bacteria by offering rapid, sensitive, and user-friendly platforms for point-of-care analysis. In this light, biosensors have gained significant commercial attention in recent years due to their simplicity, portability, and rapid analysis capabilities. The purpose of this review is to identify a trend by analyzing which biosensor technologies have become commercially successful in the field of bacteria detection. Moreover, we highlight the characteristics that a biosensor must possess to finally arrive in the market and therefore in the hands of the end-user, and we present critical examples of the market applications of various technologies. The aim is to investigate the reason why certain technologies have achieved commercial success and extrapolate these trends to the future economic viability of a new subfield in the world of biosensing: the development of biomimetic sensor platforms. Therefore, an overview of recent advances in the field of biomimetic bacteria detection will be presented, after which the challenges that need to be addressed in the coming years to improve market penetration will be critically evaluated. We will zoom into the current shortcomings of biomimetic sensors based on imprinting technology and aptamers and try to come up with a recommendation for further development based on the trends observed from previous commercial success stories in biosensing.

Nanobiosensors: Concepts and Emerging Clinical Applications

Biosensors have been one of the most fascinating topics for scientists for a long time. This is because biological moieties are multifaceted and are unswervingly related to the presence of a healthy atmosphere. The biosensor approach has also endured profound changes in recent years. Biosensors have been emphasized for various applications, including food quality estimation, surveillance systems, and health and metabolic abnormality diagnostics. The advances in nanotechnology have led to a considerable potential to enhance biosensors' sensitivity, robustness, and anti-interference capabilities. Several new nanomaterials (such as nanoparticles, nanotubes, nanorods, and nanowires) have been fabricated due to the evolution of nanotechnology, and their unique features are gradually being identified, allowing for much faster detection and reproducibility. Biosensor performance has also been enhanced substantially as a result of their use. Because of their capacity to detect a wide range of compounds at deficient concentrations, nanobiosensors have sparked much interest. This article discusses biosensors based on various nanomaterials, their evolution, accompanying features, and their applications in multiple fields.

Liquid NanoBiosensors Enable One-Pot Electrochemical Detection of Bacteria in Complex Matrices

There is a need for point-of-care bacterial sensing and identification technologies that are rapid and simple to operate. Technologies that do not rely on growth cultures, nucleic acid amplification, step-wise reagent addition, and complex sample processing are the key for meeting this need. Herein, multiple materials technologies are integrated for overcoming the obstacles in creating rapid and one-pot bacterial sensing platforms. Liquid-infused nanoelectrodes are developed for reducing nonspecific binding on the transducer surface; bacterium-specific RNA-cleaving DNAzymes are used for bacterial identification; and redox DNA barcodes embedded into DNAzymes are used for binding-induced electrochemical signal transduction. The resultant single-step and one-pot assay demonstrates a limit-of-detection of 10² CFU mL^-1 , with high specificity in identifying Escherichia coli amongst other Gram positive and negative bacteria including Klebsiella pneumoniae, Staphylococcus aureus, and Bacillus subtilis. Additionally, this assay is evaluated for analyzing 31 clinically obtained urine samples, demonstrating a clinical sensitivity of 100% and specify of 100%. When challenging this assay with nine clinical blood cultures, E. coli-positive and E. coli-negative samples can be distinguished with a probability of p < 0.001.

Salivary biomarkers of neurodegenerative and demyelinating diseases and biosensors for their detection

Salivary analysis is gaining increasing interest as a novel and promising field of research for the diagnosis of neurodegenerative and demyelinating diseases related to aging. The collection of saliva offers several advantages, being noninvasive, stress-free, and repeatable. Moreover, the detection of biomarkers directly in saliva could allow an early diagnosis of the disease, leading to timely treatments. The aim of this manuscript is to highlight the most relevant researchers' findings relatively to salivary biomarkers of neurodegenerative and demyelinating diseases, and to describe innovative and advanced biosensing strategies for the detection of salivary biomarkers. This review is focused on five relevant aging-related neurodegenerative disorders (Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, Multiple Sclerosis) and the salivary biomarkers most commonly associated with them. Advanced biosensors enabling molecular diagnostics for the detection of salivary biomarkers are presented, in order to stimulate future research in this direction and pave the way for their clinical application.

Direct-from-specimen microbial growth inhibition spectrums under antibiotic exposure and comparison to conventional antimicrobial susceptibility testing

Increasing global travel and changes in the environment may escalate the frequency of contact with a natural host carrying an infection and, therefore, increase our chances of encountering microorganisms previously unknown to humans. During an emergency, the etiology of infection may be unknown at the time of patient treatment. The existing local or global Antimicrobial Stewardship Programs may not be fully prepared for emerging/re-emerging infectious disease outbreaks, especially if they are caused by an unknown organism, engineered bioterrorist attack, or rapidly evolving superbug. We demonstrate an antimicrobial efficacy profiling method that can be performed in hours directly from clinical urine specimens. The antimicrobial potency was determined by the level of microbial growth inhibition and compared to conventional antimicrobial susceptibility testing results. The oligonucleotide probe pairs on the sensors were designed to target Gram-negative bacteria, specifically Enterobacterales and Pseudomonas aeruginosa. A pilot study of 10 remnant clinical specimens from the Clinical Laboratory Improvement Amendments-certified labs of New York-Presbyterian Queens was conducted, and only one sample was not detected by the probes. The remaining nine samples agreed with reference AST methods (Vitek and broth microdilution), resulting in 100% categorical agreement. In a separate feasibility study, we evaluated a dual-kinetic response approach, in which we inoculated two antibiotic stripwells containing the same antimicrobial concentrations with clinical specimens at the original concentration (1x) and at a 10-fold dilution (0.1x) to cover a broader range of microbiological responses. The combined categorical susceptibility reporting of 12 contrived urine specimens was 100% for ciprofloxacin, gentamicin, and meropenem over a range of microbial loads from 10⁵ to 10⁸ CFU/mL.

A disposable, wearable, flexible, stitched textile electrochemical biosensing platform

Wearable sensors are a fast growing and exciting research area, the success of smart watches are a great example of the utility and demand for wearable sensing systems. The current state of the art routinely uses expensive and bulky equipment designed for long term use. There is a need for cheap and disposable wearable sensors to make single use measurements, primarily in the area of biomarker detection. Herein we report the ability to make cheap (0.22 USD/sensor), disposable, wearable sensors by stitching conductive gold coated threads into fabrics. These threads are easily functionalised with thiolate self-assembled monolayers which can be designed for the detection of a broad range of different biomarkers. This all textile sensing platform is ideally suited to be scaled up and has the added advantage of being stretchable with insignificant effect on the electrochemistry of the devices. As a proof of principle, the devices have been functionalised with a continuous glucose sensing system which was able to detect glucose in human sweat across the clinically relevant range (0.1-0.6 mM). The sensors have a sensitivity of 126 ± 14 nA/mM of glucose and a limit of detection of 301 ± 2 nM. This makes them ideally suited for biomarker detection in point-of-care sensing applications.

Advances in Antimicrobial Resistance Monitoring Using Sensors and Biosensors: A Review

The indiscriminate use and mismanagement of antibiotics over the last eight decades have led to one of the main challenges humanity will have to face in the next twenty years in terms of public health and economy, i.e., antimicrobial resistance. One of the key approaches to tackling antimicrobial resistance is clinical, livestock, and environmental surveillance applying methods capable of effectively identifying antimicrobial non-susceptibility as well as genes that promote resistance. Current clinical laboratory practices involve conventional culture-based antibiotic susceptibility testing (AST) methods, taking over 24 h to find out which medication should be prescribed to treat the infection. Although there are techniques that provide rapid resistance detection, it is necessary to have new tools that are easy to operate, are robust, sensitive, specific, and inexpensive. Chemical sensors and biosensors are devices that could have the necessary characteristics for the rapid diagnosis of resistant microorganisms and could provide crucial information on the choice of antibiotic (or other antimicrobial medicines) to be administered. This review provides an overview on novel biosensing strategies for the phenotypic and genotypic determination of antimicrobial resistance and a perspective on the use of these tools in modern health-care and environmental surveillance.

Transportation protocols for accurate assessment of microbial burden classification using molecular methods

Point-of-care testing is cost-effective, rapid, and could assist in avoiding hospital visits during a pandemic. However, they present some significant risks that current technologies cannot fully address. Skin flora contamination and insufficient specimen volume are two major limitations preventing self-collection microbiological testing outside of hospital settings. We are developing a hybrid testing procedure to bridge the laboratory test with patient-side specimen collection and transportation for molecular microbial classification of causative bacterial infection and early identification of microbial susceptibility profiles directly from whole blood or urine specimens collected patient-side by health care workers such as phlebotomists in nursing homes or family clinics. This feasibility study presents our initial development efforts, in which we tested various transportation conditions (tubes, temperature, duration) for direct-from-specimen viable pathogen detection to determine the ideal conditions that allowed for differentiation between contaminant and causative bacteria in urine specimens and optimal growth for low-concentration blood specimens after transportation. For direct-from-urine assays, the viable pathogen at the clinical cutoff of 10⁵ CFU/mL was detected after transportation with molecular assays while contaminants (≤ 10⁴ CFU/mL) were not. For direct-from-blood assays, contrived blood samples as low as 0.8 CFU/mL were reported positive after transportation without the need for blood culture.

Highly Sensitive Electrochemical Sensor for Diagnosis of Diabetic Ketoacidosis (DKA) by Measuring Ketone Bodies in Urine

In this report, we present an enzyme deposited Au electrode for an electrochemical measurement of acetylacetic acid (AcAc) in urine. The electrode has an immobilized layer of a mixture of D-β-hydroxybutyrate dehydrogenase (HBDH) and nicotinamide adenine dinucleotide (NADH) as sensing material to investigate its electroanalytical properties by means of cyclic voltammetry (CV). The modified electrodes are used for the detection of AcAc and present a linear current increase when the AcAc concentration increases. The electrode presents a limit of detection (LOD) of 6.25 mg/dL in the range of 6.25-100 mg/dL for investigation of clinical relevance. Finally, the electrode was evaluated using 20 patient samples. The measured results of urine ketone by the developed electrode were compared with the clinical results from a commercial kit, and the analysis showed good agreement. The proposed electrode was demonstrated to be a very promising platform as a miniaturized electrochemical analyzer for point-of-care monitoring of the critical biochemical parameters such as urine ketone.

Cranberry Proanthocyanidins-PANI Nanocomposite for the Detection of Bacteria Associated with Urinary Tract Infections

Consumption of cranberries is associated with the putative effects of preventing urinary tract infections (UTIs). Cranberry proanthocyanidins (PAC) contain unusual double A-type linkages, which are associated with strong interactions with surface virulence factors found on UTI-causing bacteria such as extra-intestinal pathogenic Escherichia coli (ExPEC), depicting in bacterial agglutination processes. In this work, we demonstrated the efficacy of cranberry PAC (200 μg/mL) to agglutinate ExPEC (5.0 × 108 CFU/mL) in vitro as a selective interaction for the design of functionalized biosensors for potential detection of UTIs. We fabricated functionalized screen-printed electrodes (SPEs) by modifying with PAC-polyaniline (PANI) nanocomposites and tested the effectiveness of the PAC-PANI/SPE biosensor for detecting the presence of ExPEC in aqueous suspensions. Results indicated that the PAC-PANI/SPE was highly sensitive (limit of quantification of 1 CFU/mL of ExPEC), and its response was linear over the concentration range of 1-70,000 CFU/mL, suggesting cranberry PAC-functionalized biosensors are an innovative alternative for the detection and diagnosis of ExPEC-associated UTIs. The biosensor was also highly selective, reproducible, and stable.

Feasibility and potential significance of rapid in vitro qualitative phenotypic antimicrobial susceptibility testing of gram-negative bacilli with the ProMax system

The emergence and evolution of antibiotic resistance has been accelerated due to the widespread use of antibiotics and a lack of timely diagnostic tests that guide therapeutic treatment with adequate sensitivity, specificity, and antimicrobial susceptibility testing (AST) accuracy. Automated AST instruments are extensively used in clinical microbiology labs and provide a streamlined workflow, simplifying susceptibility testing for pathogenic bacteria isolated from clinical samples. Although currently used commercial systems such as the Vitek2 and BD Phoenix can deliver results in substantially less time than conventional methods, their dependence on traditional AST inoculum concentrations and optical detection limit their speed somewhat. Herein, we describe the GeneFluidics ProMax lab automation system intended for a rapid 3.5-hour molecular AST from clinical isolates. The detection method described utilizes a higher starting inoculum concentration and automated molecular quantification of species-specific 16S rRNA through the use of an electrochemical sensor to assess microbiological responses to antibiotic exposure. A panel of clinical isolates consisting of species of gram-negative rods from the CDC AR bank and two hospitals, New York-Presbyterian Queens and Medical College of Wisconsin, were evaluated against ciprofloxacin, gentamicin, and meropenem in a series of reproducibility and clinical studies. The categorical agreement and reproducibility for Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Klebsiella aerogenes, Klebsiella oxytoca, Klebsiella pneumoniae, and Pseudomonas aeruginosa were 100% and 100% for ciprofloxacin, 98.7% and 100% for gentamicin and 98.5% and 98.5% for meropenem, respectively.

Towards Easy-to-Use Bacteria Sensing: Modeling and Simulation of a New Environmental Impedimetric Biosensor in Fluids

Conventional pathogenic bacteria-detection methods are lab-bound, time-consuming and need trained personnel. Microelectrodes can be used to recognize harmful microorganisms by dielectric impedance spectroscopy. However, crucial for this spectroscopy method are the spatial dimensions and layout of the electrodes, as the corresponding distribution of the electric field defines the sensor system parameters such as sensitivity, SNR, and dynamic range. Therefore, a variety of sensor models are created and evaluated. FEM simulations in 2D and 3D are conducted for this impedimetric sensor. The authors tested differently shaped structures, verified the linear influence of the excitation amplitude and developed a mathematical concept for a quality factor that practically allows us to distinguish arbitrary sensor designs and layouts. The effect of guard electrodes blocking outer influences on the electric field are investigated, and essential configurations are explored. The results lead to optimized electronic sensors in terms of geometrical dimensions. Possible material choices for real sensors as well as design and layout recommendations are presented.

Integration of FISH and Microfluidics

Suitable molecular methods for a faster microbial identification in food and clinical samples have been explored and optimized during the last decades. However, most molecular methods still rely on time-consuming enrichment steps prior to detection, so that the microbial load can be increased and reach the detection limit of the techniques.In this chapter, we describe an integrated methodology that combines a microfluidic (lab-on-a-chip) platform, designed to concentrate cell suspensions and speed up the identification process in Saccharomyces cerevisiae , and a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) protocol optimized and adapted to microfluidics. Microfluidic devices with different geometries were designed, based on computational fluid dynamics simulations, and subsequently fabricated in polydimethylsiloxane by soft lithography. The microfluidic designs and PNA-FISH procedure described here are easily adaptable for the detection of other microorganisms of similar size.

Non-Invasive Electrochemical Biosensors Operating in Human Physiological Fluids

Non-invasive healthcare technologies are an important part of research and development nowadays due to the low cost and convenience offered to both healthcare receivers and providers. This work overviews the recent advances in the field of non-invasive electrochemical biosensors operating in secreted human physiological fluids, viz. tears, sweat, saliva, and urine. Described electrochemical devices are based on different electrochemical techniques, viz. amperometry, coulometry, cyclic voltammetry, and impedance spectroscopy. Challenges that confront researchers in this exciting area and key requirements for biodevices are discussed. It is concluded that the field of non-invasive sensing of biomarkers in bodily fluid is highly convoluted. Nonetheless, if the drawbacks are appropriately addressed, and the pitfalls are adroitly circumvented, the approach will most certainly disrupt current clinical and self-monitoring practices.

DNA Microsystems for Biodiagnosis

Researchers are continuously making progress towards diagnosis and treatment of numerous diseases. However, there are still major issues that are presenting many challenges for current medical diagnosis. On the other hand, DNA nanotechnology has evolved significantly over the last three decades and is highly interdisciplinary. With many potential technologies derived from the field, it is natural to begin exploring and incorporating its knowledge to develop DNA microsystems for biodiagnosis in order to help address current obstacles, such as disease detection and drug resistance. Here, current challenges in disease detection are presented along with standard methods for diagnosis. Then, a brief overview of DNA nanotechnology is introduced along with its main attractive features for constructing biodiagnostic microsystems. Lastly, suggested DNA-based microsystems are discussed through proof-of-concept demonstrations with improvement strategies for standard diagnostic approaches.

Rapid bacterial detection and antibiotic susceptibility testing in whole blood using one-step, high throughput blood digital PCR

Sepsis due to antimicrobial resistant pathogens is a major health problem worldwide. The inability to rapidly detect and thus treat bacteria with appropriate agents in the early stages of infections leads to excess morbidity, mortality, and healthcare costs. Here we report a rapid diagnostic platform that integrates a novel one-step blood droplet digital PCR assay and a high throughput 3D particle counter system with potential to perform bacterial identification and antibiotic susceptibility profiling directly from whole blood specimens, without requiring culture and sample processing steps. Using CTX-M-9 family ESBLs as a model system, we demonstrated that our technology can simultaneously achieve unprecedented high sensitivity (10 CFU per ml) and rapid sample-to-answer assay time (one hour). In head-to-head studies, by contrast, real time PCR and BioRad ddPCR only exhibited a limit of detection of 1000 CFU per ml and 50-100 CFU per ml, respectively. In a blinded test inoculating clinical isolates into whole blood, we demonstrated 100% sensitivity and specificity in identifying pathogens carrying a particular resistance gene. We further demonstrated that our technology can be broadly applicable for targeted detection of a wide range of antibiotic resistant genes found in both Gram-positive (vanA, nuc, and mecA) and Gram-negative bacteria, including ESBLs (bla_CTX-M-1 and bla_CTX-M-2 families) and CREs (bla_OXA-48 and bla_KPC), as well as bacterial speciation (E. coli and Klebsiella spp.) and pan-bacterial detection, without requiring blood culture or sample processing. Our rapid diagnostic technology holds great potential in directing early, appropriate therapy and improved antibiotic stewardship in combating bloodstream infections and antibiotic resistance.

Laser-patterned paper-based sensors for rapid point-of-care detection and antibiotic-resistance testing of bacterial infections

Antimicrobial resistance (AMR) has been identified by the World Health Organisation as a global threat that currently claims at least 25,000 deaths each year in Europe and 700,000 globally; the number is projected to reach 10 million per year between 2015 and 2050. Therefore, there is an urgent need for low-cost but reliable point-of-care diagnostics for early screening of infections especially in developing countries lacking in basic infrastructure and trained personnel. This work is aimed at developing such a device, a paper-based microfluidic device for infection testing by an unskilled user in a low resource setting. Here, we present our work relating to the use of our laser-patterned paper-based devices for detection and susceptibility testing of Escherichia coli, via a simple visually observable colour change. The results indicate the suitability of our integrated paper devices for timely identification of bacterial infections at the point-of-care and their usefulness in providing a hugely beneficial pathway for accurate antibiotic prescribing and thus a novel route to tackling the global challenge of AMR.

Multifunctional Paper-Based Analytical Device for In Situ Cultivation and Screening of Escherichia coli Infections

Point-of-care testing (POCT) for uropathogen detection and chemical screening has great benefits for the diagnosis of urinary tract infections (UTIs). The goal of this study was to develop a portable and inexpensive paper-based analytical device (PAD) for cultivating bacteria in situ and rapidly testing for nitrite on the same device. The PAD was fabricated using a wax printing technique to create a pattern on Whatman No. 1 filter paper, which was then combined with a cotton sheet to support bacterial growth. Nitrite detection was based on the principle of the Griess reaction, and a linear detection range of 0-1.6 mg/dL (R² = 0.989) was obtained. Scanning electron microscopy (SEM) analysis demonstrated that the bacteria were able to grow and formed a cluster on the cellulose fibres within 2 hours. The enzyme β-glucuronidase, which is specifically produced by Escherichia coli, was able to convert the pre-immobilized 5-bromo-4-chloro-3-indolyl-β-D-glucuronide sodium salt (X-GlcA), a colourless substrate, generating a blue colour. Under optimum conditions, the proposed device allowed bacterial concentrations in the range of 10⁴-10⁷ colony forming units (CFU)/mL to be quantified within 6 hours. Moreover, the use of this device enables the identification of E. coli pathogens with selectivity in real urine samples. In conclusion, the PAD developed in this study for UTI screening provides a rapid, cost-effective diagnostic method for use in remote areas.

An electrochemical biosensor for prostate cancer biomarker detection using graphene oxide-gold nanostructures

In this paper, a most sensitive electrochemical biosensor for detection of prostate-specific antigen (PSA) was designed. To reach the goal, a sandwich type electrode composed of reduced graphene oxide/ gold nanoparticles (GO/AuNPs), Anti-Total PSA monoclonal antibody, and anti-Free PSA antibody was assembled. The functionalized materials were thoroughly characterized by atomic force microscope spectroscopy, transmission electron microscopy, and X-ray diffraction techniques. The electrochemical properties of each of the modification step were evaluated by cyclic voltammetry and electrochemical impedance spectroscopy. The results presented that the proposed biosensor possesses high sensitivity toward total and free PSA. Furthermore, the fabricated biosensor revealed an excellent selectivity for PSA in comparison to the other tumor markers such as BHCG, Alb, CEA, CA125, and CA19-9. The limit of detection for the proposed electrochemical biosensor was estimated to be around 0.2 and 0.07 ng/mL for total and free PSA antigen, respectively.

Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends

Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.

Designing a new biosensor "DNA ELISA" to detect Escherichia coli using genomic DNA and comparison of this method to PCR-ELISA

In this experiment, DNA-ELISA biosensor was introduced, bearing the ability to detect specific bacteria in about 4 h. This is a more rapid system in comparison to conventional methods, like colony counting method. Moreover, this method does not require any amplification and directly detects genomic DNA of bacteria, giving a lower limit to the sensitivity of 40,000 bacteria. In this study, two specific probes capture (biotin labelled) and detector (dig labelled), were used against special regions of 16s rRNA gene of Escherichia coli ATCC 25922. The capture probe has the ability to trap the target bacterial DNA from a pool of other kinds of bacteria under specific conditions. The detector probe then was used to hybridize to the genome of trapped bacteria. The detection proceeds by adding HRP-anti dig enzyme and its substrate, ABTS to emit light. Light absorbance is measured for verifying the detection.

Electrochemical Methodologies for the Detection of Pathogens

Bacterial infections remain one of the principal causes of morbidity and mortality worldwide. The number of deaths due to infections is declining every year by only 1% with a forecast of 13 million deaths in 2050. Among the 1400 recognized human pathogens, the majority of infectious diseases is caused by just a few, about 20 pathogens only. While the development of vaccinations and novel antibacterial drugs and treatments are at the forefront of research, and strongly financially supported by policy makers, another manner to limit and control infectious outbreaks is targeting the development and implementation of early warning systems, which indicate qualitatively and quantitatively the presence of a pathogen. As toxin contaminated food and drink are a potential threat to human health and consequently have a significant socioeconomic impact worldwide, the detection of pathogenic bacteria remains not only a big scientific challenge but also a practical problem of enormous significance. Numerous analytical methods, including conventional culturing and staining techniques as well as molecular methods based on polymerase chain reaction amplification and immunological assays, have emerged over the years and are used to identify and quantify pathogenic agents. While being highly sensitive in most cases, these approaches are highly time, labor, and cost consuming, requiring trained personnel to perform the frequently complex assays. A great challenge in this field is therefore to develop rapid, sensitive, specific, and if possible miniaturized devices to validate the presence of pathogens in cost and time efficient manners. Electrochemical sensors are well accepted powerful tools for the detection of disease-related biomarkers and environmental and organic hazards. They have also found widespread interest in the last years for the detection of waterborne and foodborne pathogens due to their label free character and high sensitivity. This Review is focused on the current electrochemical-based microorganism recognition approaches and putting them into context of other sensing devices for pathogens such as culturing the microorganism on agar plates and the polymer chain reaction (PCR) method, able to identify the DNA of the microorganism. Recent breakthroughs will be highlighted, including the utilization of microfluidic devices and immunomagnetic separation for multiple pathogen analysis in a single device. We will conclude with some perspectives and outlooks to better understand shortcomings. Indeed, there is currently no adequate solution that allows the selective and sensitive binding to a specific microorganism, that is fast in detection and screening, cheap to implement, and able to be conceptualized for a wide range of biologically relevant targets.

Detection of PCR-Amplified Tuberculosis DNA Fragments with Polyelectrolyte-Modified Field-Effect Sensors

Field-effect-based electrolyte-insulator-semiconductor (EIS) sensors were modified with a bilayer of positively charged weak polyelectrolyte (poly(allylamine hydrochloride) (PAH)) and probe single-stranded DNA (ssDNA) and are used for the detection of complementary single-stranded target DNA (cDNA) in different test solutions. The sensing mechanism is based on the detection of the intrinsic molecular charge of target cDNA molecules after the hybridization event between cDNA and immobilized probe ssDNA. The test solutions contain synthetic cDNA oligonucleotides (with a sequence of tuberculosis mycobacteria genome) or PCR-amplified DNA (which origins from a template DNA strand that has been extracted from Mycobacterium avium paratuberculosis-spiked human sputum samples), respectively. Sensor responses up to 41 mV have been measured for the test solutions with DNA, while only small signals of ∼5 mV were detected for solutions without DNA. The lower detection limit of the EIS sensors was ∼0.3 nM, and the sensitivity was ∼7.2 mV/decade. Fluorescence experiments using SybrGreen I fluorescence dye support the electrochemical results.

Voltammetric determination of the Escherichia coli DNA using a screen-printed carbon electrode modified with polyaniline and gold nanoparticles

The authors describe an electrochemical assay for fast detection of Escherichia coli (E. coli). It is based on a dual signal amplification strategy and the use of a screen-printed carbon electrode (SPCE) whose surface was modified with a polyaniline (PANI) film and gold nanoparticles (AuNPs) via cyclic voltammetry (CV). In the next step, avidin was covalently immobilized on the PANI/AuNP composite on the SPCE surface. Subsequently, the biotinylated DNA capture probe was immobilized onto the PANI/AuNP/avidin-modified SPCE by biotin-avidin interaction. Then, DNA of E.coli, digoxigenin-labeled DNA detector probe and anti-digoxigenin-labeled horseradish peroxidase (HRP) were placed on the electrode. 3,3',5,5'-Tetramethylbenzidine (TMB) and H₂O₂ solution were added and the CV electrochemical signal was generated at a potential of -0.1 V (vs. Ag/AgCl) and a scan rate 50 mV.s^-1. The assay can detect 4 × 10⁶ to 4 CFU of E. coli without DNA amplification. The biosensor is highly specific over other pathogens including Klebsiella pneumoniae, Proteus mirabilis, Enterococcus faecalis, Staphylococcus haemolyticus and Pseudomonas aeruginosa. It can be concluded that this genosensor has an excellent potential for rapid and accurate diagnosis of E.coli inflicted infections. Graphical Abstract Schematic of an electrochemical E. coli genosensor based on sandwich assay on a polyaniline/gold nanoparticle-modified screen printed carbon electrode (SPCE). The biosensor can detect 4 × 10⁶ to 4 CFU of E. coli without DNA amplification.

Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens

AIMS

To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens.

METHODS AND RESULTS

The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection.

CONCLUSIONS

The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.

Narrow-Spectrum Antibacterial Agents

While broad spectrum antibiotics play an invaluable role in the treatment of bacterial infections, there are some drawbacks to their use, namely selection for and spread of resistance across multiple bacterial species, and the detrimental effect they can have upon the host microbiome. If the causitive agent of the infection is known, the use of narrow-spectrum antibacterial agents has the potential to mitigate some of these issues. This review outlines the advantages and challenges of narrow-spectrum antibacterial agents, discusses the progress that has been made toward developing diagnostics to enable their use, and describes some of the narrow-spectrum antibacterial agents currently being investigated against some of the most clinically important bacteria including Clostridium difficile, Mycobacterium tuberculosis and several ESKAPE pathogens.

Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.

Steric Hindrance Assay for Secreted Factors in Stem Cell Culture

The ex vivo expansion of hematopoietic stem cells is significantly inhibited by secreted proteins that induce negative feedback loops. The ability to effectively monitor these factors is critical for their real-time regulation and control and, by extension, enhancing stem cell expansion. Here, we describe a novel monitoring strategy for the detection of soluble signaling factors in stem cell cultures using a DNA-based sensing mechanism on a chip-based nanostructured microelectrode platform. We combine DNA hybridization engineering with antibody-capturing chemistry in an amplified steric hindrance hybridization assay. This method enables the quantification of important secreted proteins, showcased by the detection of 10 pg·mL^-1 level concentrations of three proteins in stem cell culture samples. This approach is the first universal nonsandwich technique that permits pg·mL^-1 level quantification of small proteins in stem cell culture media without signal loss.

Gonorrhoea diagnostics: An update

Diagnosis of gonorrhoea is an ongoing challenge. The organism is fastidious requiring meticulous collection and transport for successful cultivation. Asymptomatic infections are common which go undetected by conventional methods thereby leading to continued transmission and the risk of complications. The nucleic acid amplification tests, now increasingly used in developed countries, offer improved sensitivity compared to bacterial culture. However, these continue to suffer sequence related problems leading to false positive and false negative results. Further, these cannot be used for generation of data on antibiotic susceptibility because genetic markers of antibiotic resistance to recommended therapies have not been fully characterised. They are unaffordable in a setting like ours where reliance is placed on syndromic approach for sexually transmitted infection (STI) management. The use of syndromic approach has resulted in a considerable decline in the number of Neisseria gonorrhoeae isolates that have been cultured for diagnostic purposes. Many laboratories formerly doing so are no longer performing culture for gonococci, and the basic skills have been lost. There is a need to not only revive this skill but also adopt newer technologies that can aid in accurate diagnosis in a cost-effective manner. There is room for innovation that can facilitate the development of a point-of-care test for this bacterial STI.

PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli) 16S rRNA at 10 fM, which corresponds to ~100-1000 colony forming units/mL (CFU/mL) depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD) of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids.

Label-free electrochemical genosensor based on mesoporous silica thin film

A novel label-free electrochemical strategy for nucleic acid detection was developed by using gold electrodes coated with mesoporous silica thin films as sensing interface. The biosensing approach relies on the covalent attachment of a capture DNA probe on the surface of the silica nanopores and further hybridization with its complementary target oligonucleotide sequence, causing a diffusion hindering of an Fe(CN)6 (3-/4-) electrochemical probe through the nanochannels of the mesoporous film. This DNA-mesoporous silica thin film-modified electrodes allowed sensitive (91.7 A/M) and rapid (45 min) detection of low nanomolar levels of synthetic target DNA (25 fmol) and were successfully employed to quantify the endogenous content of Escherichia coli 16S ribosomal RNA (rRNA) directly in raw bacterial lysate samples without isolation or purification steps. Moreover, the 1-month stability demonstrated by these biosensing devices enables their advanced preparation and storage, as desired for practical real-life applications. Graphical abstract Mesoporous silica thin films as scaffolds for the development of novel label-free electrochemical genosensors to perform selective, sensitive and rapid detection of target oligonucleotide sequences. Application towards E. coli determination.

A Multiplex Electrochemical Biosensor for Bloodstream Infection Diagnosis

Accurate and timely detection of bacterial pathogens will improve the clinical management of infections. Herein, we demonstrate an electrochemical biosensor that directly detects bacteria in human blood samples, resulting in the rapid diagnosis of a bloodstream infection. The multiplex biosensor detects the species-specific sequences of the 16S ribosomal RNA of bacteria for pathogen identification in physiological samples without preamplification. The analytical performance characteristics of the biosensor, including the limit of detection and probe cross-reactivity, are evaluated systematically. The feasibility of the biosensor for a diagnosis of a bloodstream infection is demonstrated by identifying bacterial clinical isolates spiked in whole blood and blood culture samples that were tested positive for bacteria. The electrochemical biosensor correctly identifies all the species in the samples with 100% concordance to microbiological analysis.

An electrochemical immunosensor for efficient detection of uropathogenic E. coli based on thionine dye immobilized chitosan/functionalized-MWCNT modified electrode

Uropathogenic Escherichia coli (UPEC) is the major cause of 150 million Urinary Tract Infections (UTI) reported annually world-wide. High prevalence of multi-drug-resistance makes it dangerous and difficult to cure. Therefore simple, quick and early diagnostic tools are essential for effective treatment and control. We report an electrochemical immunosensor based on thionine dye (Th) immobilized on functionalized-multiwalled carbon nanotube+chitosan composite coated on glassy carbon electrode (GCE/f-MWCNT-Chit@Th) for quick and sensitive detection of UPEC in aqueous solution. This immunosensor was constructed by sequential immobilization of UPEC, bovine serum albumin, primary antibody and Horse Radish Peroxidase (HRP) tagged secondary antibody on the surface of GCE/f-MWCNT-Chit@Th. When analyzed using 2.5mM of hydrogen peroxide reduction reaction using cyclic voltammetry in phosphate buffer, pH 7.0, the immunosensor showed excellent linearity in a range of 10(2)-10(9)cfu of UPEC mL(-1) with a current sensitivity of 7.162μA {log(cfumL(-1))}(-1). The specificity of this immunosensor was tested using other UTI and non-UTI bacteria, Staphylococcus, Klebsiella, Proteus and Shigella. The clinical applicability of the immunosensor was also successfully tested directly in UPEC spiked urine samples (simulated sample).

Label- and amplification-free electrochemical detection of bacterial ribosomal RNA

Current approaches to molecular diagnostics rely heavily on PCR amplification and optical detection methods which have restrictions when applied to point of care (POC) applications. Herein we describe the development of a label-free and amplification-free method of pathogen detection applied to Escherichia coli which overcomes the bottleneck of complex sample preparation and has the potential to be implemented as a rapid, cost effective test suitable for point of care use. Ribosomal RNA is naturally amplified in bacterial cells, which makes it a promising target for sensitive detection without the necessity for prior in vitro amplification. Using fluorescent microarray methods with rRNA targets from a range of pathogens, an optimal probe was selected from a pool of probe candidates identified in silico. The specificity of probes was investigated on DNA microarray using fluorescently labeled 16S rRNA target. The probe yielding highest specificity performance was evaluated in terms of sensitivity and a LOD of 20 pM was achieved on fluorescent glass microarray. This probe was transferred to an EIS end point format and specificity which correlated to microarray data was demonstrated. Excellent sensitivity was facilitated by the use of uncharged PNA probes and large 16S rRNA target and investigations resulted in an LOD of 50 pM. An alternative kinetic EIS assay format was demonstrated with which rRNA could be detected in a species specific manner within 10-40min at room temperature without wash steps.

Aryl Diazonium Chemistry for the Surface Functionalization of Glassy Biosensors

Nanostring resonator and fiber-optics-based biosensors are of interest as they offer high sensitivity, real-time measurements and the ability to integrate with electronics. However, these devices are somewhat impaired by issues related to surface modification. Both nanostring resonators and photonic sensors employ glassy materials, which are incompatible with electrochemistry. A surface chemistry approach providing strong and stable adhesion to glassy surfaces is thus required. In this work, a diazonium salt induced aryl film grafting process is employed to modify a novel SiCN glassy material. Sandwich rabbit IgG binding assays are performed on the diazonium treated SiCN surfaces. Fluorescently labelled anti-rabbit IgG and anti-rabbit IgG conjugated gold nanoparticles were used as markers to demonstrate the absorption of anti-rabbit IgG and therefore verify the successful grafting of the aryl film. The results of the experiments support the effectiveness of diazonium chemistry for the surface functionalization of SiCN surfaces. This method is applicable to other types of glassy materials and potentially can be expanded to various nanomechanical and optical biosensors.

Integrated Biosensor Assay for Rapid Uropathogen Identification and Phenotypic Antimicrobial Susceptibility Testing

BACKGROUND

Standard diagnosis of urinary tract infection (UTI) via urine culture for pathogen identification (ID) and antimicrobial susceptibility testing (AST) takes 2-3 d. This delay results in empiric treatment and contributes to the misuse of antibiotics and the rise of resistant pathogens. A rapid diagnostic test for UTI may improve patient care and antibiotic stewardship.

OBJECTIVE

To develop and validate an integrated biosensor assay for UTI diagnosis, including pathogen ID and AST, with determination of the minimum inhibitory concentration (MIC) for ciprofloxacin.

DESIGN, SETTING, AND PARTICIPANTS

Urine samples positive for Enterobacteriaceae (n=84) or culture-negative (n=23) were obtained from the Stanford Clinical Microbiology Laboratory between November 2013 and September 2014. Each sample was diluted and cultured for 5h with and without ciprofloxacin, followed by quantitative detection of bacterial 16S rRNA using a single electrochemical biosensor array functionalized with a panel of complementary DNA probes. Pathogen ID was determined using universal bacterial, Enterobacteriaceae (EB), and pathogen-specific probes. Phenotypic AST with ciprofloxacin MIC was determined using an EB probe to measure 16S rRNA levels as a function of bacterial growth.

MEASUREMENTS

Electrochemical signals for pathogen ID at 6 SD over background were considered positive. An MIC signal of 0.4 log units lower than the no-antibiotic control indicated sensitivity. Results were compared to clinical microbiology reports.

RESULTS AND LIMITATIONS

For pathogen ID, the assay had 98.5% sensitivity, 96.6% specificity, 93.0% positive predictive value, and 99.3% negative predictive value. For ciprofloxacin MIC the categorical and essential agreement was 97.6%. Further automation, testing of additional pathogens and antibiotics, and a full prospective study will be necessary for translation to clinical use.

CONCLUSIONS

The integrated biosensor platform achieved microbiological results including MIC comparable to standard culture in a significantly shorter assay time. Further assay automation will allow clinical translation for rapid molecular diagnosis of UTI.

PATIENT SUMMARY

We have developed and validated a biosensor test for rapid diagnosis of urinary tract infections. Clinical translation of this device has the potential to significantly expedite and improve treatment of urinary tract infections.