Rapid PCR confirmation of E. coli O157:H7 after evanescent wave fiber optic biosensor detection

A simple and integrated fiber-optic real-time qPCR platform for remote and distributed detection of epidemic virus infection

Quantitative polymerase chain reaction (qPCR) is a well-recognized technique for amplifying and quantifying nuclear acid, and its real-time monitoring capability, ultrahigh sensitivity, and accuracy make it a "golden-standard" tool in both molecular biology research and clinical diagnostics. However, current qPCR tests rely on bulky instrumentation and skilled laboratorians in centralized laboratories, which spatially and temporally separate the sample collection and test, leading to longer sample turnaround times (TATs) and limited working conditions. Herein, we propose an integrated optical fiber real-time polymerase chain reaction (iF-PCR) system that successfully allows convenient sample collection, rapid thermocycling, closed-loop thermal annealing, and real-time fluorescence detection in a tiny capillary reactor. By leveraging the easy-handling capillary-fiber structure and rapid photothermal actuation of the graphene-decorated fiber head, the whole TAT can be shortened, including sampling and 40 thermocycle amplifications, within 23 min, in which an ultrasmall sample volume of ∼15 μL is needed. Furthermore, the thermal amplification and fluorescence detection capability of the optical fiber system was cross-checked by a commercial qPCR instrument. The fiber-optic qPCR strategy can correctly distinguish between positive and negative samples of clinical respiratory syncytial virus (RSV) without the need for laboratory professional skills. Taking advantage of the distance signal transmission nature of optical fibers, the proposed strategy enables remote testing, which can eliminate the necessity of instrument deployment in crowded biosafety laboratories and facilitate potential distributed pathogen testing for coping with a new round of pandemics.

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

Selective and sensitive Escherichia coli detection based on a T4 bacteriophage-immobilized multimode microfiber

Escherichia coli bacteria have been found to be responsible for various health outbreaks caused by contaminated food and water. Accurate and rapid test of E. coli is thus crucial for protecting the public health. A fast-response, label-free bacteriophage-based detection of E. coli using multimode microfiber probe is proposed and demonstrated in this article. Due to the abrupt taper and subwavelength diameter, different modes are excited and guided in the microfiber as evanescent field that can interact with surrounding E. coli directly. The change of E. coli concentration and corresponding binding of E. coli bacteria on microfiber surface will lead to the shift of optical spectrum, which can be exploited for the application of biosensing. The proposed method is capable of reliable detection of E. coli concentration as low as 10³ cfu/mL within the range of 10³ to 10⁷  cfu/mL. Owing to the advantages of high sensitivity and fast response, the microfiber probe has great potential application in the fields of environment monitoring and food safety.

Immobilized optical fiber microprobe for selective and sensitive Escherichia coli detection

Escherichia coli (E. coli) bacteria have been found to be responsible for various health outbreaks caused by contaminated food and water. Accurate and rapid test of E. coli is thus crucial for protecting the public health. A fast-response, label-free bacteriophage-based detection of E. coli using multimode microfiber probe is proposed and demonstrated in this paper. Due to the abrupt taper and subwavelength diameter, different modes are excited and guided in the microfiber as evanescent field that can interact with surrounding E. coli directly. The change of E. coli concentration and corresponding binding of E. coli bacteria on microfiber surface will lead to the shift of optical spectrum, which can be exploited for the application of biosensing. The proposed method is capable of reliable detection of E. coli concentration as low as 103 cfu/mL within the range of 103 to 107  cfu/mL. Owing to the advantages of high sensitivity and fast response, the microfiber probe has great potential application in the fields of environment monitoring and food safety.

Bifunctional linker-based immunosensing for rapid and visible detection of bacteria in real matrices

Detection of pathogens present in food and water is essential to help ensure food safety. Among the popular methods for pathogen detection are those based on culture and colony-counting and polymerase chain reaction (PCR). However, the time-consuming nature and/or the need for sophisticated instrumentation of those methods limit their on-site applications. We have developed a rapid and highly sensitive immunosensing method for visible detection of bacteria in real matrices based on the aggregation of AuNPs without requiring any readout device. We use biotinylated anti-bacteria antibodies as bifunctional linkers (BLs) to mediate the aggregation of streptavidin-functionalized gold nanoparticles (st-AuNPs) to produce visually recognizable color change, due to surface plasmon resonance (SPR), which occurs in about 30min of total assay time when the sample is mildly agitated or within three hours in quiescent conditions. The aggregation of st-AuNPs, which produces the indication signal, is achieved very differently than in visual detection methods reported previously and hence affords ultrahigh sensitivity. While BLs can both bind to the target and crosslink st-AuNPs, their latter function is essentially disabled when they bind to the target bacteria. By varying the amount of st-AuNPs used, we can tailor the assay effectiveness improving limit of detection (LOD) down to 10CFUmL^-1 of E. coli and Salmonella. Test results obtained with tap water, lake water and milk samples show that assay performance is unaffected by matrix effects. Further, in a mixture of live and autoclaved E. coli cells our assay could detect only live cells. Therefore, our BL-based immunosensor is suitable for highly sensitive, rapid, and on-site detection of bacteria in real matrices.

Paper-based magnetic nanoparticle-peptide probe for rapid and quantitative colorimetric detection of Escherichia coli O157:H7

There is a critical and urgent demand for a simple, rapid and specific qualitative and quantitative colorimetric biosensor for the detection of the food contaminant Escherichia coli O157:H7 (E. coli O157:H7) in complex food products due to the recent outbreaks of food-borne diseases. Traditional detection techniques are time-consuming, require expensive instrumentation and are labour-intensive. To overcome these limitations, a novel, ultra-rapid visual biosensor was developed based on the ability of E. coli O157:H7 proteases to change the optical response of a surface-modified, magnetic nanoparticle-specific (MNP-specific) peptide probe. Upon proteolysis, a gradual increase in the golden color of the sensor surface was visually observed. The intensification of color was correlated with the E. coli O157:H7 concentration. The color change resulting from the dissociation of the self-assembled monolayer (SAM) was detected by the naked eye and analysed using an image analysis software (ImageJ) for the purpose of quantitative detection. This biosensor demonstrated high sensitivity and applicability, with lower limits of detection of 12CFUmL-1 in broth samples and 30-300CFUmL-1 in spiked complex food matrices. In conclusion, this approach permits the use of a disposable biosensor chip that can be mass-produced at low cost and can be used not only by food manufacturers but also by regulatory agencies for better control of potential health risks associated with the consumption of contaminated foods.

Enhanced detection sensitivity of Escherichia coli O157:H7 using surface-modified gold nanorods

Escherichia coli O157:H7 (O157) is a Gram negative and highly virulent bacteria found in food and water sources, and is a leading cause of chronic diseases worldwide. Diagnosis and prevention from the infection require simple and rapid analysis methods for the detection of pathogens, including O157. Endogenous membrane peroxidase, an enzyme present on the surface of O157, was used for the colorimetric detection of bacteria by catalytic oxidation of the peroxidase substrate. In this study, we have analyzed the impact of the synthesized bare gold nanorods (AuNRs) and silica-coated AuNRs on the growth of E. coli O157. Along with the membrane peroxidase activity of O157, other bacteria strains were analyzed. Different concentrations of nanorods were used to analyze the growth responses, enzymatic changes, and morphological alterations of bacteria by measuring optical density, 3,3',5,5'-tetramethylbenzidine assay, flow cytometry analysis, and microscopy studies. The results revealed that O157 showed higher and continuous membrane peroxidase activity than other bacteria. Furthermore, O157 treated with bare AuNRs showed a decreased growth rate in comparison with the bacteria with surface modified AuNRs. Interestingly, silica-coated AuNRs favored the growth of bacteria and also increased membrane peroxidase activity. This result can be particularly important for the enzymatic analysis of surface treated AuNRs in various microbiological applicants.

Highly sensitive detection of pathogen Escherichia coli O157:H7 by electrochemical impedance spectroscopy

The presence of enterohemorrhagic Escherichia coli bacteria in food can cause serious foodborne disease outbreaks. Early detection and identification of these pathogens is extremely important for public health and safety. Here we present a highly sensitive label-free immunosensor for the detection of pathogenic E. coli O157:H7. Anti-E. coli antibodies were covalently immobilised onto gold electrodes via a self-assembled monolayer (SAM) of mercaptohexadecanoic acid and the pathogenic bacteria were detected by electrochemical impedance spectroscopy (EIS). Surface Plasmon Resonance (SPR) was used to monitor the antibody immobilisation protocol and antibody patterned surfaces were used to demonstrate the specificity of the antibody coated surfaces against the pathogenic bacteria. The immunosensor showed a very low limit of detection (2CFU/mL) and a large linear range (3 × 10-3 × 10(4)CFU/mL). Finally, the selectivity of the sensor was demonstrated and no significant adsorption of Salmonella typhimurium was observed.

Fe2O3@Au core/shell nanoparticle-based electrochemical DNA biosensor for Escherichia coli detection

A Fe(2)O(3)@Au core/shell nanoparticle-based electrochemical DNA biosensor was developed for the amperometric detection of Escherichia coli (E. coli). Magnetic Fe(2)O(3)@Au nanoparticles were prepared by reducing HAuCl(4) on the surfaces of Fe(2)O(3) nanoparticles. This DNA biosensor is based on a sandwich detection strategy, which involves capture probe immobilized on magnetic nanoparticles (MNPs), target and reporter probe labeled with horseradish peroxidase (HRP). Once magnetic field was added, these sandwich complexes were magnetically separated and HRP confined at the surfaces of MNPs could catalyze the enzyme substrate and generate electrochemical signals. The biosensor could detect the concentrations upper than 0.01 pM DNA target and upper than 500 cfu/mL of E. coli without any nucleic acid amplification steps. The detection limit could be lowered to 5 cfu/mL of E. coli after 4.0 h of incubation.

Label-free capacitive immunosensor based on quartz crystal Au electrode for rapid and sensitive detection of Escherichia coli O157:H7

A label-free capacitive immunosensor based on quartz crystal Au electrode was developed for rapid and sensitive detection of Escherichia coli O157:H7. The immunosensor was fabricated by immobilizing affinity-purified anti-E. coli O157:H7 antibodies onto self-assembled monolayers (SAMs) of 3-mercaptopropionic acid (MPA) on the surface of a quartz crystal Au electrode. Bacteria suspended in solution became attached to the immobilized antibodies when the immunosensor was tested in liquid samples. The change in capacitance caused by the bacteria was directly measured by an electrochemical detector. An equivalent circuit was introduced to simulate the capacitive immunosensor. The immunosensor was evaluated for E. coli O157:H7 detection in pure culture and inoculated food samples. The experimental results indicated that the capacitance change was linearly correlated with the cell concentration of E. coli O157:H7. The immunosensor was able to discriminate between cellular concentrations of 10(2)-10(5) cfu mL(-1) and has applications in detecting pathogens in food samples. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were also employed to characterize the stepwise assembly of the immunosensor.

A Novel Label-Free Optical Biosensor Using Synthetic Oligonucleotides from E. coli O157:H7: Elementary Sensitivity Tests

SiO₂-TiO₂ thin films for use as fiber optic guiding layers of optical DNA biosensors were fabricated by the sol-gel dip coating technique. The chemical structure and the surface morphology of the films were characterized before immobilization. Single probe DNA strands were immobilized on the surface and the porosity of the films before the hybridization process was measured. Refractive index values of the films were measured using a Metricon 2010 prism coupler. On the surface of each film, 12 different spots were taken for measurement and calculation of the mean refractive index values with their standard deviations. The increased refractive index values after the immobilization of single DNA strands indicated that immobilization was successfully achieved. A further refractive index increase after the hybridization with target single DNA strands showed the possibility of detection of the E. coli O157:H7 EDL933 species using strands of 20-mers (5′-TAATATCGGTTGCGGAGGTG -3′) sequence.

Monitoring biosensor capture efficiencies: development of a model using GFP-expressing Escherichia coli O157:H7

One of the known limitations for biosensor assays is the high limit of detection for target cells within complex samples (e.g., Escherichia coli at 10(4) to 10(5) CFU/mL) due to poor capture efficiencies. Currently, researchers can only estimate the cell capture efficiency necessary to produce a positive signal for any type of biosensor using either cumbersome techniques or regression modeling. To solve this problem, green fluorescent protein (GFP) transformed E. coli O157:H7 was used to develop a novel method for directly and easily measuring the cell capture efficiency of any given biosensor platform. For demonstration purposes, E. coli-GFP was assayed on both fiber optic and planar waveguide biosensor platforms. Cells were enumerated using an epifluorescent microscope and digital camera to determine the number of cells captured on the surfaces. Conversion algorithms were used with these digital images to determine the cell density of entire waveguide surface areas. For E. coli-GFP, the range of cell capture efficiency was between 0.4 and 1.2%. This indicates that although the developed model works for calculating cell capture, there is still need for significant improvements in capture methods themselves, to increase the capture efficiency and thereby lower detection limits. The use of GFP-transformed target cells and cell capture efficiency calculations can facilitate the development and optimization processes by allowing direct enumeration of new biosensor design configurations and sample processing strategies.

Combination of immunosensor detection with viability testing and confirmation using the polymerase chain reaction and culture

Rapid and accurate differential determination of viable versus nonviable microbes is critical for formulation of an appropriate response after pathogen detection. Sensors for rapid bacterial identification can be used for applications ranging from environmental monitoring and homeland defense to food process monitoring, but few provide viability information. This study combines the rapid screening capability of the array biosensor using an immunoassay format with methods for determination of viability. Additionally, cells captured by the immobilized antibodies can be cultured following fluorescence imaging to further confirm viability and for cell population expansion for further characterization, e.g., strain identification or antibiotic susceptibility testing. Finally, we demonstrate analysis of captured bacteria using the polymerase chain reaction (PCR). PCR results for waveguide-captured cells were 3 orders of magnitude more sensitive than the fluorescence immunoassay and can also provide additional genetic information on the captured microbes. These approaches can be used to rapidly detect and distinguish viable versus nonviable and pathogenic versus nonpathogenic captured organisms, provide culture materials for further analysis on a shorter time scale, and assess the efficacy of decontamination or sterilization procedures.

Pathogen detection: A perspective of traditional methods and biosensors

The detection of pathogenic bacteria is key to the prevention and identification of problems related to health and safety. Legislation is particularly tough in areas such as the food industry, where failure to detect an infection may have terrible consequences. In spite of the real need for obtaining analytical results in the shortest time possible, traditional and standard bacterial detection methods may take up to 7 or 8 days to yield an answer. This is clearly insufficient, and many researchers have recently geared their efforts towards the development of rapid methods. The advent of new technologies, namely biosensors, has brought in new and promising approaches. However, much research and development work is still needed before biosensors become a real and trustworthy alternative. This review not only offers an overview of trends in the area of pathogen detection but it also describes main techniques, traditional methods, and recent developments in the field of pathogen bacteria biosensors.

Real-time detection of Escherichia coli O157:H7 sequences using a circulating-flow system of quartz crystal microbalance

A DNA piezoelectric biosensing method for real-time detection of Escherichia coli O157:H7 in a circulating-flow system was developed in this study. Specific probes [a 30-mer oligonucleotide with or without additional 12 deoxythymidine 5'-monophosphate (12-dT)] for the detection of E. coli O157:H7 gene eaeA, synthetic oligonucleotide targets (30 and 104 mer) and PCR-amplified DNA fragments from the E. coli O157:H7 eaeA gene (104 bp), were used to evaluate the efficiency of the probe immobilization and hybridization with target DNA in the circulating-flow quartz crystal microbalance (QCM) device. It was found that thiol modification on the 5'-end of the probes was essential for probe immobilization on the gold surface of the QCM device. The addition of 12-dT to the probes as a spacer, significantly enhanced (P<0.05) the hybridization efficiency (H%). The results indicate that the spacer enhanced the H% by 1.4- and 2-fold when the probes were hybridized with 30- and 104-mer targets, respectively. The spacer reduced steric interference of the support on the hybridization behavior of immobilized oligonucleotides, especially when the probes hybridized with relatively long oligonucleotide targets. The QCM system was also applied in the detection of PCR-amplified DNA from real samples of E. coli O157:H7. The resultant H% of the PCR-amplified double-strand DNA was comparable to that of the synthetic target T-104AS, a single-strand DNA. The piezoelectric biosensing system has potential for further applications. This approach lays the groundwork for incorporating the method into an integrated system for rapid PCR-based DNA analysis.

Rapid chromatic detection of bacteria by use of a new biomimetic polymer sensor

We present a new platform for visual and spectroscopic detection of bacteria. The detection scheme is based on the interaction of membrane-active compounds secreted by bacteria with agar-embedded nanoparticles comprising phospholipids and the chromatic polymer polydiacetylene (PDA). We demonstrate that PDA undergoes dramatic visible blue-to-red transformations together with an intense fluorescence emission that are induced by molecules released by multiplying bacteria. The chromatic transitions are easily identified by the naked eye and can also be recorded by conventional high-throughput screening instruments. Furthermore, the color and fluorescence changes generally occur in shorter times than the visual appearance of bacterial colonies on the agar. The chromatic technology is generic and simple, does not require identification a priori of specific bacterial recognition elements, and can be applied for detection of both gram-negative and gram-positive bacteria. We demonstrate applications of the new platform for reporting on bacterial contaminations in foods and for screening for bacterial antibiotic resistance.