Comprehensive shotgun proteomic characterization and virulence factors of seafood spoilage bacteria

This article summarizes the characterization, by shotgun proteomics, of 11 bacterial strains identified as responsible for seafood spoilage. A total of 4455 peptide spectrum matches, corresponding to 4299 peptides and 3817 proteins were identified. Analyses of data determined the functional pathways they are involved in. The proteins identified were integrated into a protein-protein network that involves 371 nodes and 3016 edges. Those proteins are implicated in energy pathways, peptidoglycan biosynthesis, spermidine/putrescine metabolism. An additional 773 peptides were characterized as virulence factors, that participates in bacterial pathogenesis; while 14 peptides were defined as biomarkers, as they can be used to differentiate the bacterial species present. This report represents the most extensive proteomic repository available in the field of seafood spoilage bacteria; the data substantially advances the understanding of seafood decay, as well as provides fundamental bases for the recognition of the bacteria existent in seafood that cause spoilage during food processing/storage.

Bacterial detection based on Förster resonance energy transfer

The huge economic loss and threat to human health caused by bacterial infection have attracted the public's concern, and there is an urgent need to relieve and improve the tough problem. Therefore, it is significant to establish a facile, rapid, and sensitive method for bacterial detection considering the shortcomings of existing methods. Förster resonance energy transfer (FRET)-based sensors have exhibited immense potential and applicability for bacterial detection given their high signal-to-noise ratio and high sensitivity. This review focuses on the development of FRET-based fluorescence assays for bacterial detection. We summarize the principle of FRET-based assays, discuss the commonly used recognition molecules and further introduce three frequent construction strategies. Based on the strategies and materials, relevant applications are presented. Moreover, some restrictions of FRET fluorescence sensors and development prospects are discussed. Suitable donor-acceptor pairs and stable recognition molecules are the essential conditions for sensors to play their roles, and there is still some room for development. Besides, applying FRET fluorescence sensors to point-of-care detection is still difficult. Future developments could focus on near-infrared fluorescent dyes and simultaneous detection of multiple analytes.

Evaluating smartphone-based optical readouts for immunoassays in human and veterinary healthcare: A comparative study

Recent advances have significantly enhanced the use of smartphone devices for medical diagnostics. This study uses high-resolution cameras in mobile devices to capture and process bioassay images, enabling the quantification of diverse biomarkers across a range of diagnostic tests conducted on 96-well microplates. The study evaluates the effectiveness of this technology through protein quantification techniques and immunoassays that generate colorimetric responses at specific wavelengths. It includes the assessment of bicinchoninic acid and Bradford protein quantification methods, alongside a conventional immunoassay for detecting mare antibodies in colostrum to monitor foal immunodeficiencies. Further application involves the readout of magneto-actuated immunoassays aimed at quantifying bacteria. The results obtained from benchtop spectrophotometry at 595, 562, and 450 nm are compared with those acquired using a smartphone, which identified color intensities in shades of blue, purple, and yellow. This comparison yields promising correlations for the samples tested, suggesting a high degree of accuracy in the smartphone capability to analyze bioassay outcomes. The analysis via smartphone is facilitated by a specific app, which processes the images captured by the phone camera to quantify color intensities corresponding to different biomarker concentrations. Detection limits of 12.3 and 22.8 μg mL-1 for the bicinchoninic acid assay and 36.7 and 45.4 μg mL-1 for the Bradford are obtained for protein quantification using the spectrophotometer and the smartphone app, respectively. For mare's antibodies in colostrum, the values are 1.14 and 1.72 ng mL-1, while the detection of E. coli is performed at 2.0 x 104 and 2.9 × 104 CFU mL-1, respectively. This approach offers further advantages, including wide availability, cost-effectiveness, portability, compared to traditional and expensive benchtop instruments.

Electrocatalytic aptasensor for bacterial detection exploiting ferricyanide reduction by methylene blue on mixed PEG/aptamer monolayers

Pathogen-triggered infections are the most severe global threat to human health, and to provide their timely treatment and prevention, robust methods for rapid and reliable identification of pathogenic microorganisms are required. Here, we have developed a fast and inexpensive electrocatalytic aptamer assay enabling specific and ultrasensitive detection of E. coli. E. coli, a biomarker of environmental contamination and infections, was captured on the mixed aptamer/thiolated PEG self-assembled monolayers formed on electrochemically pre-treated gold screen-printed electrodes (SPE). Signals from aptamer - E. coli binding were amplified by electrocatalytic reduction of ferricyanide mediated by methylene blue (MB) adsorbed on bacterial and aptamer surfaces. PEG operated as an antifouling agent and inhibited direct (not MB-mediated) discharge of ferricyanide. The assay allowed from 10 to 1000 CFU mL-1E. coli detection in 30 min, with no interference from B. subtilis, in buffer and artificial urine samples. This electrocatalytic approach is fast, specific, sensitive, and can be used directly in in-field and point-of-care applications for analysis of bacteria in human environment.

Highly sensitive SERS platform for pathogen analysis by cyclic DNA nanostructure@AuNP tags and cascade primer exchange reaction

The capacity to identify small amounts of pathogens in real samples is extremely useful. Herein, we proposed a sensitive platform for detecting pathogens using cyclic DNA nanostructure@AuNP tags (CDNA) and a cascade primer exchange reaction (cPER). This platform employs wheat germ agglutinin-modified Fe3O4@Au magnetic nanoparticles (WMRs) to bind the E. coli O157:H7, and then triggers the cPER to generate branched DNA products for CDNA tag hybridization with high stability and amplified SERS signals. It can identify target pathogens as low as 1.91 CFU/mL and discriminate E. coli O157:H7 in complex samples such as water, milk, and serum, demonstrating comparable or greater sensitivity and accuracy than traditional qPCR. Moreover, the developed platform can detect low levels of E. coli O157:H7 in mouse serum, allowing the discrimination of mice with early-stage infection. Thus, this platform holds promise for food analysis and early infection diagnosis.

Rapid detection of nucleic acid sequences of pathogenic bacteria based on a series piezoelectric quartz crystal sensor with transcription activator-like effectors

Accurate and rapid detection of pathogenic bacteria is of great importance in the field of clinical diagnosis and food safety. Current methods for pathogenic bacteria detection have some problems in accurate, rapid and universal application. Here we proposed a pathogenic bacteria series piezoelectric quartz crystal (SPQC) sensor for achieving highly specific and sensitive detection of pathogenic bacteria. The universal sequences of common clinical pathogens screened by our group were used as detection targets. A new TALEs nuclease was synthesized as a recognition element, which recognizes double-stranded DNA at the level of a single base mismatch in the range of 17-19 bases. Targets could be specifically recognized by TALEs, resulting in the change of electrode surface, which would be further amplified by hybridization chain reaction and silver staining technique. Finally, the changes would be detected by SPQC system. This strategy was demonstrated to have excellent performance, enabling sensitive detection of targets with a detection limit of 25 cfu/mL in less than 3 h. What's more, the identification of single base mismatch could be achieved when the target ranging in length between 17 and 19 bases. The proposed method is rapid, accurate and easy universal application and expected to be applied in clinical diagnosis and food safety.

A portable smartphone-based colorimetric sensor that utilizes dual amplification for the on-site detection of airborne bacteria

Over the past few years, infections caused by airborne pathogens have spread worldwide, infecting several people and becoming an increasingly severe threat to public health. Therefore, there is an urgent need for developing airborne pathogen monitoring technology for use in confined environments to enable epidemic prevention. In this study, we designed a colorimetry-based bacterial detection platform that uses a clustered regularly interspaced short palindromic repeat-associated protein 12a system to amplify signals and a urease enzyme to induce color changes. Furthermore, we have developed a smartphone application that can distinguish colors under different illumination conditions based on the HSV model and detect three types of disease-causing bacteria. Even synthetic oligomers of a few picomoles of concentration and genomic DNA of airborne bacteria smaller than several nanograms can be detected with the naked eye and using color analysis systems. Furthermore, in the air capture model system, the bacterial sample generated approximately a 2-fold signal difference compared with that in the control group. This colorimetric detection method can be widely applied for public safety because it is easy to use and does not require complex equipment.

Bioinspired hot-spot engineering strategy towards ultrasensitive SERS sandwich biosensor for bacterial detection

Surface-enhanced Raman spectroscopy (SERS) sandwich biosensors have received tremendous attention in early diagnosis of bacterial infections. However, efficiently engineering nanoscale plasmonic hots pots (HS) towards ultrasensitive SERS detection still remains challenging. Herein, we propose a bioinspired synergistic HS engineering strategy to construct ultrasensitive SERS sandwich bacterial sensor (named USSB), by coupling bioinspired signal module and plasmonic enrichment module to synergistically boost the number and intensity of HS. The bioinspired signal module is based on dendritic mesoporous silica nanocarrier (DMSN) loaded with plasmonic nanoparticles and SERS tag, while magnetic Fe3O4 nanoparticles coated with Au shell are employed in plasmonic enrichment module. We demonstrate that DMSN effectively shrank nanogaps between plasmonic nanoparticles to improve HS intensity. Meanwhile, plasmonic enrichment module contributed to plenty of additional HS inside and outside individual "sandwich". Ascribing to the boosted number and intensity of HS, the constructed USSB sensor exhibits ultrahigh detection sensitivity (7 CFU/mL) and selectivity towards model pathogenic bacteria of Staphylococcus aureus. Remarkably, the USSB sensor enables fast and accurate bacterial detection in real blood samples of septic mice, achieving early diagnosis of bacterial sepsis. The proposed bioinspired synergistic HS engineering strategy opens up a new direction for constructing ultrasensitive SERS sandwich biosensors, and may promote their advancing applications in the early diagnosis and prognosis of devastating diseases.

Detection and discrimination of pathogenic bacteria with nanomaterials-based optical biosensors: A review

Pathogenic bacteria can pose a great threat to food safety and human health. It is therefore imperative to develop a rapid, portable, and sensitive determination and discrimination method for pathogenic bacteria. Over the past few years, various nanomaterials (NMs) have been employed as desirable nanoprobes because they possess extraordinary properties that can be used for optical signal enabled detection and identification of bacteria. By means of modification, NMs can, depending on different mechanisms, sense targets directly or indirectly, which then provides an essential support for the detection and differentiation of pathogenic bacteria. In this review, recent application of NMs-based optical biosensors for food safety bacterial detection and discrimination is performed, mainly in but not limited to noble metal NMs, fluorescent NMs, and point-of-care testing (POCT). This review also focuses on future trends in bacterial detection and discrimination, and machine learning in performing intelligent rapid detection and multiple accurate identification of bacteria.

Construction of chitosan-based thermosensitive composite hydrogels for recognizing and combined chemo-photodynamic elimination of Gram-negative bacterial infections

Recently, rapid acquisition of bacterial resistance and consequent slow healing of infected wounds threaten human life and health. In this study, chitosan-based hydrogels and nanocomplexes ZnPc(COOH)₈:PMB composed of photosensitizer ZnPc(COOH)₈ and antibiotic polymyxin B (PMB) were integrated into a thermosensitive antibacterial platform ZnPc(COOH)₈:PMB@gel. Interestingly, fluorescence and reactive oxygen species (ROS) of ZnPc(COOH)₈:PMB@gel can be triggered by E. coli bacteria at 37 °C, but not by S. aureus bacteria, which gave the potential to simultaneously detect and treat Gram-negative bacteria. The survival rate for a certain amount of E. coli bacteria treated with ZnPc(COOH)₈:PMB (ZnPc(COOH)₈ 2 μM) was decreased by approximately fivefold than that with either ZnPc(COOH)₈ or PMB alone, indicating combined antibacterial efficacy. ZnPc(COOH)₈:PMB@gel facilitated the complete healing of wounds infected with E. coli bacteria in about seven days, while over 10 % wounds treated with ZnPc(COOH)₈ or PMB remained unhealed on the 9th day. ZnPc(COOH)₈:PMB resulted in a threefold increase of ZnPc(COOH)₈ fluorescence in E. coli bacteria suggesting enhanced uptake of ZnPc(COOH)₈ for the intervention of PMB on membrane permeability. The construction principle of the thermosensitive antibacterial platform and the combined antimicrobial strategy can be applied to other photosensitizers and antibiotics for detection and treatment of wound infections.

Rapid detection of live bacteria in water using nylon filter membrane-integrated centrifugal microfluidics

Water is one of the most indispensable elements for human beings. People can live without food for a couple of weeks but cannot live without water for a couple of days. Unfortunately, drinking water is not always safe around the world; in many areas, the water for drinking could be contaminated with various microbes. However, the total viable microbe count in water still relies on culture-based methods in laboratories. Therefore, in this work, we report a novel, simple, and highly efficient strategy to detect live bacteria in water via a nylon membrane-integrated centrifugal microfluidic device. A handheld fan and a rechargeable hand warmer were utilized as the centrifugal rotor and the heat resource for reactions, respectively. The bacteria in water can be rapidly concentrated >500-fold by our centrifugation system. After incubation with water-soluble tetrazolium-8 (WST-8), the color change of the nylon membranes can be visually interpreted directly by the naked eye or recorded with a smartphone camera. The whole process can be finished in 3 h, and the detection limit can reach 10² CFU/mL. The detection range ranges from 10² CFU/mL to 10⁵ CFU/mL. The cell counting results of our platform are highly positively correlated with the results of cell counting by the conventional lysogeny broth (LB) agar plate approach or the commercial 3 M Petrifilm™ cell counting plate. Our platform provides a convenient and sensitive strategy for rapid monitoring. We highly anticipate that this platform can improve water quality monitoring in resource-poor countries in the near future.

Genetic engineering of bacteriophages: Key concepts, strategies, and applications

Bacteriophages are the most abundant biological entity in the world and hold a tremendous amount of unexplored genetic information. Since their discovery, phages have drawn a great deal of attention from researchers despite their small size. The development of advanced strategies to modify their genomes and produce engineered phages with desired traits has opened new avenues for their applications. This review presents advanced strategies for developing engineered phages and their potential antibacterial applications in phage therapy, disruption of biofilm, delivery of antimicrobials, use of endolysin as an antibacterial agent, and altering the phage host range. Similarly, engineered phages find applications in eukaryotes as a shuttle for delivering genes and drugs to the targeted cells, and are used in the development of vaccines and facilitating tissue engineering. The use of phage display-based specific peptides for vaccine development, diagnostic tools, and targeted drug delivery is also discussed in this review. The engineered phage-mediated industrial food processing and biocontrol, advanced wastewater treatment, phage-based nano-medicines, and their use as a bio-recognition element for the detection of bacterial pathogens are also part of this review. The genetic engineering approaches hold great potential to accelerate translational phages and research. Overall, this review provides a deep understanding of the ingenious knowledge of phage engineering to move them beyond their innate ability for potential applications.

Development of a phage-based electrochemical biosensor for detection of Escherichia coli O157: H7 GXEC-N07

Escherichia coli (E. coli) O157:H7 is one of the most important foodborne pathogens that causing severe foodborne diseases. With the development of foodborne diseases, there is an urgent need to seek new methods for early detection and monitoring of E. coli O157:H7. In this study, an electrochemical biosensor using phage EP01 as the recognition agent for detection of E. coli O157:H7 GXEC-N07 was established due to the specificity and high efficiency of phage EP01 in recognizing GXEC-N07. The biosensor was developed by depositing phages conjugated carboxyl graphene oxide (CFGO) and conductive carbon black (CB) onto the surface of glass carbon electrodes (GCEs). When detecting GXEC-N07 in the concentration range of 10² ∼ 10⁷ CFU/mL, the biosensor showed good linearity with a low detection limit of 11.8 CFU/mL, and the whole progress was in less than 30 min. The biosensor was successfully applied to the quantitative detection of GXEC-N07 in fresh milk and raw pork. The recovery values ranged from 60.8 % to 114.2 %. The biosensor provides a rapid, specific, low cost, and label free tool for E. coli O157:H7 GXEC-N07 detection. It is expected to become a powerful method for the detection of bacteria that threatening food safety and public health security.

Deep-learning model AIBISI predicts bacterial infection across cancer types based on pathological images

Microorganisms play an important role in many physiological functions. Many studies have found that bacteria also regulate cancer susceptibility and tumor progression by affecting some metabolic or immune system signaling pathways. However, current bacterial detection methods are inaccurate or inefficient. Thus, we constructed a deep neural network (AIBISI) based on hematoxylin and eosin (H&E)-stained pathology slides to predict and visualize bacterial infection. Our model performance achieved as high as 0.81 of AUC (area under the ROC curve) within cancer type. We also built a pan-cancer model to predict bacterial infection across cancer types. To facilitate clinical usage, AIBISI visualized image areas affected by possible infection. Importantly, we successfully validated our model (AUC = 0.755) in pathological images from an independent patient cohort of stomach cancer (n = 32). To our best knowledge, this is the first artificial intelligence (AI)-based model to investigate bacterial infection in pathology images and has the potential to enable fast clinical decision related to pathogens in tumors.

Semi-circle magnetophoretic separation under rotated magnetic field for colorimetric biosensing of Salmonella

Magnetic separation was often applied to isolate and concentrate foodborne bacteria using immunomagnetic nanobeads before downstream bacterial detection. However, nanobead-bacteria conjugates (magnetic bacteria) were coexisting with excessive unbound nanobeads, limiting these nanobeads on magnetic bacteria to further act as signal probes for bacterial detection. Here, a new microfluidic magnetophoretic biosensor was elaboratively developed using a rotated high gradient magnetic field and platinum modified immunomagnetic nanobeads for continuous-flow isolation of magnetic bacteria from free nanobeads, and combined with nanozyme signal amplification for colorimetric biosensing of Salmonella. First, the platinum modified immunomagnetic nanobeads were mixed with the bacterial sample to form the magnetic bacteria, and magnetically separated to eliminate non-magnetic background. Then, the mixture of free immunomagnetic nanobeads and magnetic bacteria was injected with sheath flow (PBS) at higher flowrate into the semi-circle magnetophoretic separation channel under rotated magnetic field, which was generated by two repulsive cylindric magnets and their in-between ring iron gear, leading to continuous-flow isolation of magnetic bacteria from free immunomagnetic nanobeads because they suffered from different magnetic forces and thus had different deviating positions at the outlet. Finally, the separated magnetic bacteria and unbound magnetic nanobeads were respectively collected and used to catalyze coreless substrate into blue product, which was further analyzed using the microplate reader to obtain bacterial amount. This biosensor could determinate Salmonella as low as 41 CFU/mL in 40 min.

Ionic crosslinking of alginate/carboxymethyl chitosan fluorescent hydrogel for bacterial detection and sterilization

Herein, a polysaccharide-based fluorescent hydrogel with multi-responsiveness simply implemented by concurrent effects of ionic crosslinking/rehydration processes is presented. Specifically, the alginate and carboxymethyl chitosan are chosen to prepare the interpenetrating polymer matrix while a pair of metal cations has been selectively sequentially integrated to alter hydrogel mechanical and fluorescent properties. Experimental results indicate the hydrogels show tunable fluorescent emission in response to multiple cations and pH conditions, and display a reversible "ON/OFF" fluorescent response to Mⁿ⁺/ethylenediaminetetraacetic acid. Moreover, this synergistic ionic crosslinking strategy is proved to be highly effective in preparing multifunctional metallohydrogels possessing robust/anisotropic mechanical properties, typical shape memory and cation/pH-responsive fluorescence performance, and a proof-of-application for bacterial detection and sterilization has also been demonstrated. Therefore, we believe this study would provide new insights into multifunctional luminescent hydrogels for advanced biomedical systems.

Systematic review and critical reflection on the isolation and identification methods for spoilage associated bacteria in fresh marine fish

Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.

Multifunctional Au nano-bridged nanogap probes as ICP-MS/SERS dual-signal tags and signal amplifiers for bacteria discriminating, quantitative detecting and photothermal bactericidal activity

Ultra-sensitive detection of pathogenic bacteria is of great significance in the early stage of bacterial infections and treatment. In this work, we report a novel strategy using multifunctional Au nano-bridged nanogap nanoparticles (Au NNPs)-based sandwich nanocomposites, that made of Concanavalin A-conjugated Fe₃O₄@SiO₂ NPs (ConA-Fe₃O₄@SiO₂ NPs)/bacteria/aptamer-modified Au NNPs (apt-Au NNPs), for bacteria discrimination and quantitative detection by surface-enhanced Raman scattering (SERS) and inductively coupled plasma mass spectrometry (ICP-MS), and subsequently photothermal antibacterial assay. The sandwich nanocomposite consists of ConA-Fe₃O₄@SiO₂ NPs to magnetically enrich and photothermal killing bacteria, and dual-signal tags of apt-Au NNPs for both SERS sensing and ICP-MS quantification. This strategy can specifically distinguish different kinds of pathogenic bacteria, and provided a good linear relationship of Staphylococcus aureus (S. aureus) in the range from 50 to 10⁴ CFU/mL with a detection limit of 11 CFU/mL, as well as realized ultralow amounts of bacterial detection in serum sample with high accuracy. Based on the quantitative detection, high antibacterial efficiency was monitored by ICP-MS. Overall, the established method combines bacteria discrimination, quantitative detection, and photothermal elimination with a simple and rapid process, which provides a novel way for the early diagnosis and treatment of bacterial infection.

A novel portable label-free electrochemical immunosensor for ultrasensitive detection of Aeromonas salmonicida in aquaculture seawater

Infectious diseases caused by Aeromonas salmonicida (A. salmonicida) have a huge impact and produce significant losses in aquaculture and fish farming. Fish pathogen early detection is a critical step for the rapid identification and prevention of these problems. This work presents a novel portable label-free ultrasensitive electrochemical immunosensor for A. salmonicida detection in seawater. It consists of a fluidic integrated electrochemical-cell-chip (ECC) with independent chambers enclosing three electrochemical cells (ECs). Anti-A. salmonicida (AbSalm) antibodies were covalently attached to the gold surface of the microfabricated electrodes and were used for the sensitive detection of A. salmonicida. The antibody-antigen immunoreaction was studied by enzyme-linked immunosorbent assay (ELISA), and the surface functionalization was characterized by using quartz crystal microbalance (QCM), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The performance of the developed immunosensor, in terms of sensitivity, repeatability, and specificity, was also studied. The linear working range varied between 1 and 10⁷ CFU mL^-1, with a limit of detection (LOD) as low as 1 CFU mL^-1. The suitability of the immunosensor for real sample detection was successfully demonstrated via recovery studies performed in spiked seawater samples. The proposed technology supports the use of low-cost and portable instrumentation that concedes the ultrasensitive, simple, and fast quantification of the A. salmonicida. To the best of our knowledge, this is the first portable sensing system for the detection of A. salmonicida in seawater samples, which provides a promising online monitoring platform for the detection of this bacterium in aquaculture facilities.

Potential of bacteriophage proteins as recognition molecules for pathogen detection

Bacterial pathogens are leading causes of infections with high mortality worldwide having a great impact on healthcare systems and the food industry. Gold standard methods for bacterial detection mainly rely on culture-based technologies and biochemical tests which are laborious and time-consuming. Regardless of several developments in existing methods, the goal of achieving high sensitivity and specificity, as well as a low detection limit, remains unaccomplished. In past years, various biorecognition elements, such as antibodies, enzymes, aptamers, or nucleic acids, have been widely used, being crucial for the pathogens detection in different complex matrices. However, these molecules are usually associated with high detection limits, demand laborious and costly production, and usually present cross-reactivity. (Bacterio)phage-encoded proteins, especially the receptor binding proteins (RBPs) and cell-wall binding domains (CBDs) of endolysins, are responsible for the phage binding to the bacterial surface receptors in different stages of the phage lytic cycle. Due to their remarkable properties, such as high specificity, sensitivity, stability, and ability to be easily engineered, they are appointed as excellent candidates to replace conventional recognition molecules, thereby contributing to the improvement of the detection methods. Moreover, they offer several possibilities of application in a variety of detection systems, such as magnetic, optical, and electrochemical. Herein we provide a review of phage-derived bacterial binding proteins, namely the RBPs and CBDs, with the prospect to be employed as recognition elements for bacteria. Moreover, we summarize and discuss the various existing methods based on these proteins for the detection of nosocomial and foodborne pathogens.

Advances, limitations, and prospects of biosensing technology for detecting phytopathogenic bacteria

Phytopathogenic bacteria cause severe economic losses in agricultural production worldwide. The spread rates, severity, and emerging plant bacterial diseases have become serious threat to the sustainability of food sources and the fruit industry. Detection and diagnosis of plant diseases are imperative in order to manage plant diseases in field conditions, greenhouses, and food storage conditions as well as to maximize agricultural productivity and sustainability. To date, various techniques including, serological, observation-based, and molecular methods have been employed for plant disease detection. These methods are sensitive and specific for genetic identification of bacteria. However, these methods are specific for genetic identification of bacteria. Currently, the innovative biosensor-based disease detection technique is an attractive and promising alternative. A biosensor system involves biological recognition and transducer active receptors based on sensors used in plant-bacteria diagnosis. This system has been broadly used for the rapid diagnosis of plant bacterial pathogens. In the present review, we have discussed the conventional methods of bacterial-disease detection, however, the present review mainly focuses on the applications of different biosensor-based techniques along with point-of-care (POC), robotics, and cell phone-based systems. In addition, we have also discussed the challenges and limitations of these techniques.

Rhodol-derived turn-on fluorescent chemosensor for ultrasensitive detection of nitroreductase activity in bacteria and bioimaging in oral cancer cells

The detection of intracellular nitroreductase (NTR) activity is important for the study of hypoxia in organisms. In the present study, a Rhodol-derived fluorescent chemosensor (Rhod-NO₂) was synthesized in a one-step procedure. Rhod-NO₂ exhibits 110-fold fluorescence enhancement in the presence of NTR. Moreover, Rhod-NO₂ demonstrates high NTR selectivity and sensitivity (LOD, 0.6 ng/mL). The mode of Rhod-NO₂ binding to NTR was also revealed by molecular docking. In addition, the reaction and luminescence mechanisms were evaluated by MS and TDDFT theoretical calculations, respectively. Finally, Rhod-NO₂ was successfully applied to monitor NTR production during Escherichia coli (E. coli) growth, and to visually analyze NTR production in malignant oral cancer cells under hypoxia. Thus, Rhod-NO₂ represents a new molecular tool to further understanding of the biological function of NTR.

Structural Properties Dictating Selective Optotracer Detection of S. aureus

Optotracers are conformation‐sensitive fluorescent tracer molecules that detect peptide‐ and carbohydrate‐based biopolymers. Their binding to bacterial cell walls allows selective detection and visualisation of Staphylococcus aureus (S. aureus). Here, we investigated the structural properties providing optimal detection of S. aureus. We quantified spectral shifts and fluorescence intensity in mixes of bacteria and optotracers, using automatic peak analysis, cross‐correlation, and area‐under‐curve analysis. We found that the length of the conjugated backbone and the number of charged groups, but not their distribution, are important factors for selective detection of S. aureus. The photophysical properties of optotracers were greatly improved by incorporating a donor‐acceptor‐donor (D‐A‐D)‐type motif in the conjugated backbone. With significantly reduced background and binding‐induced on‐switch of fluorescence, these optotracers enabled real‐time recordings of S. aureus growth. Collectively, this demonstrates that chemical structure and photophysics are key tunable characteristics in the development of optotracers for selective detection of bacterial species.

SERS-based CRISPR/Cas assay on microfluidic paper analytical devices for supersensitive detection of pathogenic bacteria in foods

Rapid and point-of-need (PON) detection of bacteria is crucial to directly provide rapid and reliable diagnostics information during on-site tests, allowing more room for taking proactive measures. By taking the multifaceted advantages of CRISPR/Cas12a and surface-enhanced Raman scattering (SERS), for the first time, we designed a recombinase polymerase amplification (RPA)-integrated microfluidic paper-based analytical device (μPAD), coined RPA-Cas12a-μPAD for supersensitive SERS detection. Single-stranded DNAs were designed to "pull down" SERS nanoprobes. The amplicons of the invA gene triggered the trans-cleavage of Cas12a, resulting in the indiscriminate shredding of linker ssDNA. Thus, the degree of aggregation of SERS nanoprobes was dependent on the concentration of Salmonella typhimurium (S. typhi), which was determined on a μPAD and monitored by a Raman spectrometer. The limit of detection for S. typhi was approximately 3-4 CFU/mL for spiked milk and meat samples with a dynamic detection range from 1 to 10⁸ CFU/mL. The RPA-Cas12a-μPAD secured accurate tests for food samples in 45 min. This work expands the reach of CRISPR-based diagnostics (CRISPR-Dx) and provides a novel and robust bacterial PON detection platform.

Sandwich method-based sensitivity enhancement of Ω-shaped fiber optic LSPR for time-flexible bacterial detection

The development of rapid and sensitive detection methods for pathogenic bacteria is crucial for the therapy and prevention of related diseases. However, the rapid and ultrasensitive assays are difficult to be realized simultaneously. To solve the problem, a sandwich method based on Ω-shaped fiber optic localized surface resonance (Ω-FOLSPR) was constructed, where poly adenine-tailed aptamer (PolyA-apt) and SH modified gold nanoparticles tags (AuNPs tags) were chosen as the capturing aptamer and amplifying tags, respectively. The small AuNPs were modified on the surface of fiber-optic (FO) rapidly, which saved the preparation time. Then, the PolyA-apt was modified on the AuNPs surface to capture the bacteria effectively due to its ability to adjust the density and conformation of aptamer on the AuNPs surface. Finally, the large AuNPs tags were used to generate intense signal enhancement. It is found that the sandwich method enables the unique characteristic of a time-dependent sensitivity enhancement. Specifically, the LOD of 108.0 CFU/mL and 7.4 CFU/mL was achieved with the analysis time of 10 min and 100 min, respectively. Besides, the Ω-FOLSPR sensor exhibits excellent selectivity against the other bacteria and good performance for detecting the spiked and natural samples. This sandwich method provides a time-flexible strategy due to the combination of effective signal amplification and real-time analysis for bacterial detection, displaying great potential for practical bacterial detection.

Gold nanorod arrays enable highly sensitive bacterial detection via surface-enhanced infrared absorption (SEIRA) spectroscopy

Infrared (IR) spectroscopy is a unique and powerful method in the identification, characterization, and classification of chemical and biological molecules. However, the low absorbance of biological molecules has arisen as a major bottleneck and inhibits the application of IR in practical applications. To overcome this limitation, in the last four decades, surface-enhanced IR absorption (SEIRA) spectroscopy has been proposed and has become the focus of interest in various applications. In this study, for the first time, we proposed the employment of 3D anisotropic gold nanorod arrays (GNAs) as a highly active SEIRA platform in bacterial detection. For this, GNA platforms were fabricated through an oblique angle deposition (OAD) approach by using a physical vapor deposition (PVD) system. OAD of gold at proper deposition angle (10°) created closely-packed and columnar gold nanorod structures onto the glass slides in a well-controlled manner. GNA platform was tested as a SEIRA system in three different species of bacteria (Escherichia coli, Staphylococcus aureus, and Bacillus subtilis) by collecting IR spectra of each bacteria from different parts of GNA. The employment of GNA provided robust IR spectra with high reproducibility and signal-to-noise ratio. For the comparison, IR spectra of each bacteria were collected from aluminum foil and a smooth gold surface (SGS). No or very low IR spectra were observed in comparison to the GNA platform for these substrates. Unsupervised (PCA, HCA) and supervised (SIMCA, LDA, and SVM classification) machine learning analysis of bacteria spectra obtained from GNA substrate indicated that all bacteria samples can be detected and identified without using a label-containing biosensor, in a fast and simple manner.

Fluorescence characteristics of E. faecalis in dentine following treatment with oxidizing endodontic irrigants

INTRODUCTION

This study aimed to assess changes in the fluorescence characteristics of Enterococcus faecalis in human dentine over a period of 24 h following treatment with endodontic irrigants.

METHOD

Sterilised, non-functional extracted third molars were embedded in acrylic resin and uniformly sectioned into 2 mm thick dentine sections. After the removal of smear layer, the dentine sections were inoculated with E. faecalis and cultured for 7 days. The infected dentine sections were subsequently treated with different concentrations of sodium hypochlorite (NaOCl) and hydrogen peroxide (H₂O₂). Bacterial fluorescence readings were assessed at different time points using a calibrated laser device. All data were assessed for normality (Kolmogorov Smirnoff test) and analysed using ANOVA with Bonferroni post-hoc tests.

RESULTS

Fluorescence readings were quenched when E. faecalis infected human dentine sections were treated with oxidizing irrigants in vitro. Throughout a 24-hour period, fluorescence recovered in part but did not return to baseline level.

CONCLUSION

The fluorescence quenching effect of these oxidizing agents needs to be considered when using laser fluorescence in assessing the quality of root canal debridement or disinfection.

Sniffing Bacteria with a Carbon-Dot Artificial Nose

Novel artificial nose based upon electrode-deposited carbon dots (C-dots). Significant selectivity and sensitivity determined by "polarity matching" between the C-dots and gas molecules. The C-dot artificial nose facilitates, for the first time, real-time, continuous monitoring of bacterial proliferation and discrimination among bacterial species, both between Gram-positive and Gram-negative bacteria and between specific strains. Machine learning algorithm furnishes excellent predictability both in the case of individual gases and for complex gas mixtures. Continuous, real-time monitoring and identification of bacteria through detection of microbially emitted volatile molecules are highly sought albeit elusive goals. We introduce an artificial nose for sensing and distinguishing vapor molecules, based upon recording the capacitance of interdigitated electrodes (IDEs) coated with carbon dots (C-dots) exhibiting different polarities. Exposure of the C-dot-IDEs to volatile molecules induced rapid capacitance changes that were intimately dependent upon the polarities of both gas molecules and the electrode-deposited C-dots. We deciphered the mechanism of capacitance transformations, specifically substitution of electrode-adsorbed water by gas molecules, with concomitant changes in capacitance related to both the polarity and dielectric constants of the vapor molecules tested. The C-dot-IDE gas sensor exhibited excellent selectivity, aided by application of machine learning algorithms. The capacitive C-dot-IDE sensor was employed to continuously monitor microbial proliferation, discriminating among bacteria through detection of distinctive "volatile compound fingerprint" for each bacterial species. The C-dot-IDE platform is robust, reusable, readily assembled from inexpensive building blocks and constitutes a versatile and powerful vehicle for gas sensing in general, bacterial monitoring in particular.

Sonochemical coating of Prussian Blue for the production of smart bacterial-sensing hospital textiles

In healthcare facilities, environmental microbes are responsible for numerous infections leading to patient's health complications and even death. The detection of the pathogens present on contaminated surfaces is crucial, although not always possible with current microbial detection technologies requiring sample collection and transfer to the laboratory. Based on a simple sonochemical coating process, smart hospital fabrics with the capacity to detect live bacteria by a simple change of colour are presented here. Prussian Blue nanoparticles (PB-NPs) are sonochemically coated on polyester-cotton textiles in a single-step requiring 15 min. The presence of PB-NPs confers the textile with an intensive blue colour and with bacterial-sensing capacity. Live bacteria in the textile metabolize PB-NPs and reduce them to colourless Prussian White (PW), enabling in situ detection of bacterial presence in less than 6 h with the bare eye (complete colour change requires 40 h). The smart textile is sensitive to both Gram-positive and Gram-negative bacteria, responsible for most nosocomial infections. The redox reaction is completely reversible and the textile recovers its initial blue colour by re-oxidation with environmental oxygen, enabling its re-use. Due to its simplicity and versatility, the current technology can be employed in different types of materials for control and prevention of microbial infections in hospitals, industries, schools and at home.

Microbial biosensor for Salmonella using anti-bacterial antibodies isolated from human serum

In this work, we present a novel microbial biosensor for Salmonella based on impedance spectrometry by using isolated antibodies against a specific bacterial strain from human serum. Anti-Salmonella (or BL21(DE3)) antibodies were isolated from human serum using S. enteritidis (or BL21(DE3)) and the mutant strain ClearColi. After the purification steps, the purification yield of the antibodies was calculated to be 0.2 %. From the FACS analysis, the isolated anti-Salmonella antibodies were estimated to have more than 6-fold higher binding affinity for S. enteritidis compared to antibodies against other kinds of Gram-negative bacterial strains, including HB101, ClearColi, JM110, DH5α, and BL21(DE3). Finally, the anti-Salmonella antibodies isolated herein were used for bacterial detection using electrochemical biosensors based on impedance spectrometry and the R_ct value of the antibodies was estimated for S. enteritidis from the Nyquist plot. The limit of detection of the isolated anti-Salmonella antibodies was estimated to be 1.0 × 10³ cells/mL for S. enteritidis and 1.0 × 10⁶ cells/mL for BL21(DE3), respectively.

One step synthesis of red-emitting fluorescence turn-on probe for nitroreductase and its application to bacterial detection and oral cancer cell imaging

Nitroreductase (NTR) belongs to a class of flavin mononucleotide-dependent and flavin adenine dinucleotide-dependent cytoplasmic enzymes; its contents in tumor cells increase during hypoxia. The development of fluorescent probes for detection of NTR activity is of great significance for the study of the state of hypoxia in living organisms. In this paper, a red-emitting fluorescence turn-on probe EBI-NO₂ was synthesized using a one-step method. The fluorescence of the probe was enhanced by 60 folds in the presence of NTR. The probe also had high selectivity towards NTR, and its detection limit was as low as 1 ng/mL. The reaction mechanism was verified using MS, molecular docking and theoretical calculations. In addition, it was successfully applied in real-time monitoring of NTR produced during growth of Escherichia coli (BL21) and in visualization of NTR in oral cancer cells (Cal-27) under hypoxia. This work provides a new imaging tool that can be applied to investigate the physiological and pathological changes in hypoxia oral cells.

Self-assembled nanogels of luminescent thiolated silver nanoclusters and chitosan as bactericidal agent and bacterial sensor

Multifunctional theranostic agents with the features of good biocompatibility, long-term antibacterial efficacy, and rapid bacterial detection are the desired future medicine for infectious diseases, but which poses huge challenges on the design of such multifunctional nanocomposites in a single entity. Herein, self-assembled nanogels of thiolated silver nanoclusters (Ag NCs) and chitosan was designed and synthesized, which combines the desirable biocompatible, targeting specific, luminescent properties. This nanogel displays an amplified luminescence via strong matrix-ligand coordination between thiolate ligands and chitosan matrix to rigidify the molecular structure on the surface of Ag NCs. Concomitantly, this nanogel exhibits exceptional bactericidal activity, with approximately >10-fold stronger activity compared to its counterpart Ag NCs. Furthermore, a bacterial detection system was developed based on the bacterial binding on the fluorescent nanogels. This work provides a new strategy in designing multifunctional theranostic agents and this new composite Ag NC nanogel holds great promise for practical applications as the theranostic nanomedicines.

Development and analytical validation of real-time PCR for the detection of Streptococcus agalactiae in pregnant women

Background

Group B Streptococcus (GBS) is the leading cause of invasive neonatal infection. In this study, we aimed to evaluate the analytical validation of qualitative real-time polymerase chain reaction (qPCR) as a means to detect GBS.

Methods

Genomic DNA (gDNA) was purified from 12 ATCC bacterial strains, two belonging to GBS and the remainder acting as negative controls. Additionally, gDNA was isolated from 21 strains of GBS from various serotypes (Ia, Ib and II-VIII). All gDNA was used to evaluate the analytical validation of the qPCR method employing a specific Taqman probe. Inclusivity, exclusivity, anticipated reportable range, the limit of detection and robustness were evaluated. The methods used are described in international guidelines and other existing reports. The performance of this qPCR method for detecting GBS was compared to other microbiological methods used with vaginal-rectal samples from pregnant women.

Results

Our qPCR method for detecting GBS was analytically validated. It has a limit of detection of 0.7 GE/μL and 100% analytical specificity. It detects all strains of GBS with the same level of performance as microbiological methods.

Conclusion

Data suggest that this qPCR method performs adequately as a means to detect GBS in vaginal-rectal swabs from pregnant women.

Rapid Detection of Proliferative Bacteria by Electrical Stimulation

Detecting live bacteria is an important task for antimicrobial susceptibility testing (AST) in the medical sector and for quality-monitoring in biological industries. Current methods for live-bacteria detection suffer limitations in speed or sensitivity. In a recent paper, we reported that electrical response dynamics in membrane potential enable single-cell rapid detection of live bacteria. The electrical response can be observed within a minute after electrical stimulation. Thus, it has potential in accelerating AST and the monitoring of biological samples. This method also enables experiments for biophysical and microbiological investigations into bacterial electrophysiology. With the hope that more researchers, scientists and engineers will use electrical stimulation for their assays, here we detail each step of the electrical stimulation experiment.

Preparation and characterization of carboxymethyl cashew gum grafted with immobilized antibody for potential biosensor application

This report details the design of carboxymethylated cashew gum (CG) as a platform for antibody (Ab) immobilization, which can then be used as a biosensor for bacteria detection. The CG was isolated and characterized, followed by conversion to carboxymethyl cashew gum (CMCG). The CMCG film was a viable support for antibody immobilization; it was electrodeposited on gold surface using the cyclic voltammetry technique, applying a potential sweep from -1.0 V to 1.3 V with a scan rate of 50 mV s^-1 and 10 scans. The COOH groups on the surface of the film were critical in promoting Ab bonding. The immobilization of the Ab was mediated by protein A (PrA) for recognition of the antigen. Voltammetry studies were used to monitor the antibody immobilization. Finally, the analytical response of the CMCG-PrA-Ab system was evaluated with the chronoamperometry technique and was found to detect Salmonella Typhimurium bacteria rapidly and efficiently.

A composite prepared from carboxymethyl chitosan and aptamer-modified gold nanoparticles for the colorimetric determination of Salmonella typhimurium

An aptamer-based assay is described for the determination of Salmonella typhimurium (S. typh). Carboxymethyl chitosan was loaded with amino-modified aptamer against S. typh, and then adsorbed on gold nanoparticles by electrostatic interaction to form a composite that acts as the molecular recognition element. In the presence of S. typh, it will be bound by the aptamer, and this changes the structure of the recognition element. On addition of salt solution, the gold nanoparticles agglomerate so that the color of the solution changes from red to blue. S. typh can be detected via measurement of the absorbance at 550 nm. Absorbance increases linearly with the logarithm of the S. typh concentration in the range from 100 to 10⁹ cfu·mL^-1. The limit of detection is 16 cfu·mL^-1. The specificity and practicability of the assay were evaluated. The recoveries of S. typh from spiked milk samples are between 92.4 and 97.2%. The analytical results are basically consistent with those of a plate counting method. Graphical abstract Schematic representation of the colorimetric assay for Salmonella typhimuium (S. typh) using carboxymethyl chitosan (CMCS)-aptamer (Apt)-gold nanoparticles (AuNPs) composites.

Aggregation-induced emission-based ionic liquids for bacterial killing, imaging, cell labeling, and bacterial detection in blood cells

A series of aggregation-induced emission (AIE)-based imidazolium-type ionic liquids (ILs) were designed and synthesized for bacterial killing and imaging, cell labeling, and bacterial detection in blood cells. The AIE-based ILs showed antibacterial activities against both Escherichia coli and Staphylococcus aureus. The carbon chain length of substitution at the N3 position of the imidazolium cations highly affects the antibacterial properties of ILs. Owing to their AIE characteristics, the ILs could selectively capture fluorescence image of dead bacteria while killing the bacteria. The fluorescence intensity varied with the concentration of bacteria, indicating that AIE-based ILs has potential as an antibacterial material and an efficient probe for bacterial viability assay. In addition, the synthesized AIE-based ILs exhibit relatively low cytotoxicity and hemolysis rate and therefore potential for cell labeling, as well as bacterial detection in blood cells. STATEMENT OF SIGNIFICANCE: Bacteria are ubiquitous, especially the pathogenic bacteria, which pose a serious threat to human health. There is an urgent need for materials with efficient antibacterial properties and biocompatibility and without causing drug resistance. In this work, we synthesized a series of aggregation-induced emission (AIE)-doped imidazolium type ionic liquids (ILs) with multifunction potential of bacterial killing and imaging, cell labeling, and detection of bacteria from blood cells. The synthesized AIE-based ILs can image dead bacteria at the same time of killing these bacteria, which can avoid the fluorescent dyeing process. Simultaneously, the fluorescent imaging of dead bacteria can be distinguished by the naked eye, and the fluorescence intensity from the AIE-based ILs varied with the concentration of bacteria. In addition, the AIE-based ILs exhibit relatively low cytotoxicity and hemolysis rate and therefore potential for cell labeling as well as detection of bacteria from red blood cell suspension.

Terminal deoxynucleotidyl transferase (TdT)-catalyzed homo-nucleotides-constituted ssDNA: Inducing tunable-size nanogap for core-shell plasmonic metal nanostructure and acting as Raman reporters for detection of Escherichia coli O157:H7

Core-shell plasmonic metal nanoparticles with interior nanogaps are superior nanostructures owing to their large signal enhancement for Surface enhanced Raman spectroscopy (SERS). Herein, we incorporated Terminal deoxynucleotidyl transferase (TdT)-catalyzed DNA in the preparation of core-shell nanostructures for the detection of Escherichia coli O157:H7 (E. coli O157:H7) cells. The elongated products-homo-nucleotides-composed of long single DNA strands (hn-D) are used not only to induce tunable-size nanogaps but also as Raman reporters with consistent and uniform signal enhancement. Using this synthetic process of hn-D-embedded core-shell nanoparticles (hn-DENPs), we found that the length of hn-D strands affects the size of the nanogap. In addition, performances of the specific Raman imaging of E. coli O157:H7, high detection sensitivity of 2 CFU/mL, and the recovery of 98.1%-105.2% measured in the real food samples, make hn-DENP a biosensor that will be widely used in biological detection.

Fluorescent microbeads for point-of-care testing: a review

Microbead-based point-of-care testing (POCT) has demonstrated great promise in translating detection modalities from bench-side to bed-side. This is due to the ease of visualization, high surface area-to-volume ratio of beads for efficient target binding, and efficient encoding capability for simultaneous detection of multiple analytes. This review (with 112 references) summarizes the progress made in the field of fluorescent microbead-based POCT. Following an introduction into the field, a first large section sums up techniques and materials for preparing microbeads, typically of dye-labelled particles, various kinds of quantum dots and upconversion materials. Further subsections cover the encapsulation of nanoparticles into microbeads, decoration of nanoparticles on microbeads, and in situ embedding of nanoparticles during microbead synthesis. A next large section summarizes microbead-based fluorometric POCT, with subsections on detection of nucleic acids, proteins, circulating tumor cells and bacteria. A further section covers emerging POCT based on the use of smartphones or flexible microchips. The last section gives conclusions and an outlook on current challenges and possible solutions. Aside from giving an overview on the state of the art, we expect this article to boost the further development of POCT technology. Graphical Abstract Schematic presentation of the fabrication of microbeads, the detection targets of interest including bacteria, circulating tumor cells (CTCs), protein and nucleic acid, and the emerging point-of-care testing (POCT) platform. The colored wheels of the bus represent the fluorescent materials embedded in (red color) or decorated on the surface of microbeads (green color).

A multiplexed, indirect enzyme-linked immunoassay for the detection and differentiation of E. coli from other Enterobacteriaceae and P. aeruginosa from other glucose non-fermenters

Gram-negative bacteria (GNB) are important causes of community (CA) and hospital (HA)- associated infections. Here we describe the development of an indirect ELISA (I-ELISA), which can be used to detect and differentiate the Enterobacteriaceae Escherichia coli, and glucose non-fermenter Pseudomonas aeruginosa from other GNB species. The I-ELISA utilizes six antibodies for bacterial speciation, which were grouped according to their bacterial targets; Enterobacteriaceae (SL-EntA and CH1810 mAb), Escherichia coli (SL-EcA and 6103-46 mAb), Pseudomonas aeruginosa (SL-PaA and SL-PaB). The six, anti-GNB antibodies were first screened against a panel of well-characterized clinical GNB isolates to optimize assay conditions and to determine individual antibody sensitivity and specificity. When tested against a diverse, blinded panel of 94 GNB clinical isolates, the I-ELISA exhibited the following sensitivity/specificity for each target: Enterobacteriaceae (94.4%/95%), E. coli (82.6%/88.7%), P. aeruginosa (83.3%/96%). An I-ELISA to detect and differentiate the most common GNB pathogens offers advantage in terms of simplicity over diagnostic tests currently used in most clinical settings.

Bacterial contamination of platelets for transfusion: strategies for prevention

Platelet transfusions carry greater risks of infection, sepsis, and death than any other blood product, owing primarily to bacterial contamination. Many patients may be at particular risk, including critically ill patients in the intensive care unit. This narrative review provides an overview of the problem and an update on strategies for the prevention, detection, and reduction/inactivation of bacterial contaminants in platelets. Bacterial contamination and septic transfusion reactions are major sources of morbidity and mortality. Between 1:1000 and 1:2500 platelet units are bacterially contaminated. The skin bacterial microflora is a primary source of contamination, and enteric contaminants are rare but may be clinically devastating, while platelet storage conditions can support bacterial growth. Donor selection, blood diversion, and hemovigilance are effective but have limitations. Biofilm-producing species can adhere to biological and non-biological surfaces and evade detection. Primary bacterial culture testing of apheresis platelets is in routine use in the US. Pathogen reduction/inactivation technologies compatible with platelets use ultraviolet light-based mechanisms to target nucleic acids of contaminating bacteria and other pathogens. These methods have demonstrated safety and efficacy and represent a proactive approach for inactivating contaminants before transfusion to prevent transfusion-transmitted infections. One system, which combines ultraviolet A and amotosalen for broad-spectrum pathogen inactivation, is approved in both the US and Europe. Current US Food and Drug Administration recommendations advocate enhanced bacterial testing or pathogen reduction/inactivation strategies (or both) to further improve platelet safety. Risks of bacterial contamination of platelets and transfusion-transmitted infections have been significantly mitigated, but not eliminated, by improvements in prevention and detection strategies. Regulatory-approved technologies for pathogen reduction/inactivation have further enhanced the safety of platelet transfusions. Ongoing development of these technologies holds great promise.

Coumarin-based, switchable fluorescent substrates for enzymatic bacterial detection

Enzymatically-switchable fluorescent substrates, such as the commercially available 4-methyl umbelliferones (4-MU) are used as standard indicators of enzymatic activity for the detection of various microorganisms and pathogens. However, a major disadvantage of 4-MU is its relatively high pKa leading to only partial dissociation of the fluorescent anion under the conditions where the enzymes are most effective (pH 6-6.5). Here we present a method for new, enzymatically-switchable, fluorescent substrates with improved photo-physico/chemical properties. The lead derivative, 4-AAU, shows excellent solubility in aqueous media (0.81 mg/mL) when compared to 4-MU (0.16 mg/mL), significantly improved quantum yield and wider dynamic range of its fluorescence properties. The corresponding bacterial substrate β-4-AAUG showed superior selectivity in the detection of clinically relevant amounts of E. coli, Enterococcus and K. pneumonia (1 CFU). The fluorescence intensity of β-4-AAUG was almost 5 times higher than that of the standard, the detection was possible in reasonably short time (∼ 2.5 h) and with excellent sensitivity.

The synthesis of novel chromogenic enzyme substrates for detection of bacterial glycosidases and their applications in diagnostic microbiology

The preparation and evaluation of chromogenic substrates for detecting bacterial glycosidase enzymes is reported. These substrates are monoglycoside derivatives of the metal chelators catechol, 2,3-dihydroxynaphthalene (DHN) and 6,7-dibromo-2,3-dihydroxynaphthalene (6,7-dibromo-DHN). When hydrolysed by appropriate bacterial enzymes these substrates produced coloured chelates in the presence of ammonium iron(III) citrate, thus enabling bacterial detection. A β-d-riboside of DHN and a β-d-glucuronide derivative of 6,7-dibromo-DHN were particularly effective for the detection of S. aureus and E. coli respectively.

Bacterial biosensing: Recent advances in phage-based bioassays and biosensors

In nature, different types of bacteria including pathogenic and beneficial ones exist in different habitats including environment, plants, animals, and humans. Among these, the pathogenic bacteria should be detected at earlier stages of infection; however, the conventional bacterial detection procedures are complex and time-consuming. In contrast, the advanced molecular approaches such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) have significantly reduced the detection time; nevertheless, such approaches are not acceptable to a large extent and are mostly laborious and expensive. Therefore, the development of fast, inexpensive, sensitive, and specific approaches for pathogen detection is essential for different applications in food industry, clinical diagnosis, biological defense and counter-terrorism. To this end, the novel sensing approaches involving bacteriophages as recognition elements are receiving immense consideration owing to their high degree of specificity, accuracy, and reduced assay times. Besides, the phages are easily produced and are tolerant to extreme pH, temperature, and organic solvents as compared to antibodies. To date, several phage-based assays and sensors have been developed involving different systems such as quartz crystal microbalance, magnetoelastic platform, surface plasmon resonance, and electrochemical methods. This review highlights different taxonomic species and genera of phages infecting eight common disease-causing bacterial genera. It further overviews the most recent advancements in phage-based sensing assays and sensors. Likewise, it elaborates various whole-phage and phage components-based assays. Overall, this review emphasizes the importance of electrochemical biosensors as simple, reliable, cost-effective, and accurate tools for bacterial detection.

Impedimetric detection of bacteria by using a microfluidic chip and silver nanoparticle based signal enhancement

The authors describe a method that can significantly improve the performance of impedimetric detection of bacteria. A multifunctional microfluidic chip was designed consisting of interdigitated microelectrodes and a micro-mixing zone with a Tesla structure. This maximizes the coating of bacterial surfaces with nanoparticles and results in improved impedimetric detection. The method was applied to the detection of Escherichia coli O157:H7 (E. coli). Silver enhancement was accomplished by coating E.coli with the cationic polymer diallyldimethylammonium chloride (PDDA) to form positively charged E. coli/PDDA complexes. Then, gold nanoparticles (AuNPs) were added, and the resulting E. coli/PDDA/AuNPs complexes were collected at interdigitated electrodes via positive dielectrophoresis (pDEP). A silver adduct was then formed on the E. coli/PDDA/AuNP complexes by using silver enhancement solutions and by using the AuNPs as catalysts. The combination of pDEP based capture and of using silver adducts reduces impedance by increasing the conductivity of the solution and the double layer capacitance around the microelectrodes. Impedance decreases linearly in the 2 × 10³-2 × 10⁵ cfu·mL^-1 E. coli concentration range, with a 500 cfu·mL^-1 detection limit. Egg shell wash samples and tap water spiked with E. coli were successfully used for validation, and this demonstrates the practical application of this method. Graphical abstract Schematic representation of the AuNP@Ag enhancement method integrated with multifunctional microfluidic chip platform for impedimetric quantitation of bacteria. The method significantly improves the performance of impedimetric detection of bacteria.

Dopamine-mediated immunoassay for bacteria detection

Traditional enzyme-linked immunosorbent assay (ELISA) with sufficient sensing specificity is a useful analytical approach for the detection of toxicologically important substances in in vivo systems or complicated biological systems. Increasing worldwide demand for analyses of bacteria by signal amplification and increasing concern regarding their safe development and use require a simple, stable, and sensitive detection assay for target evaluation and clinical diagnosis. A sensitive and selective immunoassay for detection of bacteria is constructed that combines horseradish peroxidase (HRP)-catalyzed signal amplification with the strong linker of the polydopamine-biotin complex on the surface of solid substances or biomolecules. The incorporation of HRP labeling and amplification increases the detection sensitivity by about one to two orders of magnitude compared with conventional ELISA systems. A linear relationship between the response and the logarithm of the bacterial concentration was observed in the range from 1.5 × 10² to 1.5 × 10⁷ colony-forming units per milliliter. This work demonstrates a new signal-amplification-based dopamine-mediated process for the development of a sensitive method. This dopamine-mediated immunoassay may be broadly applied in clinical diagnoses and for the monitoring of water environmental pollution. The approach proposed is distinct with simple protocols and easy processes, which allow it to be applied in a broad area.

Production of recombinant flagellin to develop ELISA-based detection of Salmonella Enteritidis

Food-borne diseases, caused by the pathogenic bacteria, are highly prevalent in the world. Salmonella is one of the most important bacterial genera responsible for this. Salmonella Enteritidis (SE) is one of the non-typhoid Salmonellae that can be transmitted to human from poultry products, water, and contaminated food. In recent years, new and rapid detection methods such as enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) have been developed. In this study, recombinant FliC (rFliC) was produced to be used as an antigen. The immunization was conducted in mice with the purified recombinant FliC (rFliC). The mice were subcutaneously immunized with rFliC and elicited significant rFliC specific serum IgG antibodies. An indirect ELISA system was established for the detection of Salmonella Enteritidis. Our results confirmed that the recombinant flagellin can be one of the excellent indicators for the detection of Salmonella Enteritidis.

[Significance of bacteria detection with filter paper method on diagnosis of diabetic foot wound infection]

Objective: To evaluate the significance of bacteria detection with filter paper method on diagnosis of diabetic foot wound infection. Methods: Eighteen patients with diabetic foot ulcer conforming to the study criteria were hospitalized in Liyuan Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology from July 2014 to July 2015. Diabetic foot ulcer wounds were classified according to the University of Texas diabetic foot classification (hereinafter referred to as Texas grade) system, and general condition of patients with wounds in different Texas grade was compared. Exudate and tissue of wounds were obtained, and filter paper method and biopsy method were adopted to detect the bacteria of wounds of patients respectively. Filter paper method was regarded as the evaluation method, and biopsy method was regarded as the control method. The relevance, difference, and consistency of the detection results of two methods were tested. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of filter paper method in bacteria detection were calculated. Receiver operating characteristic (ROC) curve was drawn based on the specificity and sensitivity of filter paper method in bacteria detection of 18 patients to predict the detection effect of the method. Data were processed with one-way analysis of variance and Fisher's exact test. In patients tested positive for bacteria by biopsy method, the correlation between bacteria number detected by biopsy method and that by filter paper method was analyzed with Pearson correlation analysis. Results: (1) There were no statistically significant differences among patients with wounds in Texas grade 1, 2, and 3 in age, duration of diabetes, duration of wound, wound area, ankle brachial index, glycosylated hemoglobin, fasting blood sugar, blood platelet count, erythrocyte sedimentation rate, C-reactive protein, aspartate aminotransferase, serum creatinine, and urea nitrogen (with F values from 0.029 to 2.916, P values above 0.05), while there were statistically significant differences among patients with wounds in Texas grade 1, 2, and 3 in white blood cell count and alanine aminotransferase (with F values 4.688 and 6.833 respectively, P<0.05 or P<0.01). (2) According to the results of biopsy method, 6 patients were tested negative for bacteria, and 12 patients were tested positive for bacteria, among which 10 patients were with bacterial number above 1×10(5)/g, and 2 patients with bacterial number below 1×10(5)/g. According to the results of filter paper method, 8 patients were tested negative for bacteria, and 10 patients were tested positive for bacteria, among which 7 patients were with bacterial number above 1×10(5)/g, and 3 patients with bacterial number below 1×10(5)/g. There were 7 patients tested positive for bacteria both by biopsy method and filter paper method, 8 patients tested negative for bacteria both by biopsy method and filter paper method, and 3 patients tested positive for bacteria by biopsy method but negative by filter paper method. Patients tested negative for bacteria by biopsy method did not tested positive for bacteria by filter paper method. There was directional association between the detection results of two methods (P=0.004), i. e. if result of biopsy method was positive, result of filter paper method could also be positive. There was no obvious difference in the detection results of two methods (P=0.250). The consistency between the detection results of two methods was ordinary (Kappa=0.68, P=0.002). (3) The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of filter paper method in bacteria detection were 70%, 100%, 1.00, 0.73, and 83.3%, respectively. Total area under ROC curve of bacteria detection by filter paper method in 18 patients was 0.919 (with 95% confidence interval 0-1.000, P=0.030). (4) There were 13 strains of bacteria detected by biopsy method, with 5 strains of Acinetobacter baumannii, 5 strains of Staphylococcus aureus, 1 strain of Pseudomonas aeruginosa, 1 strain of Streptococcus bovis, and 1 strain of bird Enterococcus. There were 11 strains of bacteria detected by filter paper method, with 5 strains of Acinetobacter baumannii, 3 strains of Staphylococcus aureus, 1 strain of Pseudomonas aeruginosa, 1 strain of Streptococcus bovis, and 1 strain of bird Enterococcus. Except for Staphylococcus aureus, the sensitivity and specificity of filter paper method in the detection of the other 4 bacteria were all 100%. The consistency between filter paper method and biopsy method in detecting Acinetobacter baumannii was good (Kappa=1.00, P<0.01), while that in detecting Staphylococcus aureus was ordinary (Kappa=0.68, P<0.05). (5) There was no obvious correlation between the bacteria number of wounds detected by filter paper method and that by biopsy method (r=0.257, P=0.419). There was obvious correlation between the bacteria numbers detected by two methods in wounds with Texas grade 1 and 2 (with r values as 0.999, P values as 0.001). There was no obvious correlation between the bacteria numbers detected by two methods in wounds with Texas grade 3 (r=-0.053, P=0.947). Conclusions: The detection result of filter paper method is in accordance with that of biopsy method in the determination of bacterial infection, and it is of great importance in the diagnosis of local infection of diabetic foot wound.

Extensible multiplex real-time PCR for rapid bacterial identification with carbon nanotube composite microparticles

The early diagnosis of pathogenic bacteria is significant for bacterial identification and antibiotic resistance. Implementing rapid, sensitive, and specific detection, molecular diagnosis has been considered complementary to the conventional bacterial culture. Composite microparticles of a primer-immobilized network (cPIN) are developed for multiplex detection of pathogenic bacteria with real-time polymerase chain reaction (qPCR). A pair of specific primers are incorporated and stably conserved in a cPIN particle. One primer is crosslinked to the polymer network, and the other is bound to carbon nanotubes (CNTs) in the particle. At the initiation of qPCR, the latter primer is released from the CNTs and participates in the amplification. The amplification efficiency of this cPIN qPCR is estimated at more than 90% with suppressed non-specific signals from complex samples. In multiplexing, four infective pathogens are successfully discriminated using this cPIN qPCR. Multiplex qPCR conforms with the corresponding singleplex assays, proving independent amplification in each particle. Four bacterial targets from clinical samples are differentially analyzed in 30min of a single qPCR trial with multiple cPIN particles.

Comparison of methods for identifying causative bacterial microorganisms in presumed acute endophthalmitis: conventional culture, blood culture, and PCR

Background

Identification of bacterial pathogens in endophthalmitis is important to inform antibiotic selection and treatment decisions. Hemoculture bottles and polymerase chain reaction (PCR) analysis have been proposed to offer good detection sensitivity. This study compared the sensitivity and accuracy of a blood culture system, a PCR approach, and conventional culture methods for identification of causative bacteria in cases of acute endophthalmitis.

Methods

Twenty-nine patients with a diagnosis of presumed acute bacterial endophthalmitis who underwent vitreous specimen collection at King Chulalongkorn Memorial Hospital were enrolled in this study. Forty-one specimens were collected. Each specimen was divided into three parts, and each part was analyzed using one of three microbial identification techniques: conventional plate culture, blood culture, and polymerase chain reaction and sequencing. The results of the three methods were then compared.

Results

Bacteria were identified in 15 of the 41 specimens (36.5%). Five (12.2%) specimens were positive by conventional culture methods, 11 (26.8%) were positive by hemoculture, and 11 (26.8%) were positive by PCR. Cohen’s kappa analysis revealed p-values for conventional methods vs. hemoculture, conventional methods vs. PCR, and hemoculture vs. PCR of 0.057, 0.33, and 0.009, respectively. Higher detection rates of Enterococcus faecalis were observed for hemoculture and PCR than for conventional methods.

Conclusions

Blood culture bottles and PCR detection may facilitate bacterial identification in cases of presumed acute endophthalmitis. These techniques should be used in addition to conventional plate culture methods because they provide a greater degree of sensitivity than conventional plate culture alone for the detection of specific microorganisms such as E. faecalis.

Trial registration

Thai Clinical Trial Register No. TCTR20110000024.