Application of ATP-based bioluminescence technology in bacterial detection: a review

Vancomycin-bacterial imprinted polymer hybrid for viable Staphylococcus aureus highly efficient capture, photothermal inactivation, and sensitive detection

To facilitate the capture, inactivation, and detection of viable Staphylococcus aureus (SA) in food, a vancomycin (Van)-bacterial imprinted polymers (BIPs) hybrid receptor was fabricated by introducing Van into SA-imprinted polydopamine (PDA) via oriented surface imprinting. Taking advantage of the dual recognition arising from Van's affinity for peptidoglycan and BIPs' imprinting effect on SA, the Van-BIPs hybrid exhibited better capture performance than Van or BIPs alone. Leveraging the photothermal effect of PDA, the captured SA could be in situ lysed within 5 min under near-infrared irradiation, causing the release of adenosine triphosphate (ATP) from SA. Using ATP as biomarker, as low as 13.7 CFU/mL of viable SA was able to be detected within 38 min by integrating Van-BIPs hybrid with ATP-bioluminescence assay. Spiked food samples were also successfully analyzed with the recoveries of 85.71 %-106.11 %. The Van-BIPs hybrid might offer a promising tool to control SA in food industries.

Nanopore Detection of Small Molecules Based on Replacement and Complexation Chemical Interactions

Small molecules play important roles in a variety of biological processes such as metabolism, cell signaling and enzyme regulation, and can serve as valuable biomarkers for human diseases. Moreover, they are essential to drug discovery and development, and are important targets for environmental monitoring and food safety. Due to the size incompatibility, small molecule transport is difficult to be monitored with a nanopore. A popular strategy for nanopore detection of small molecules is to introduce a molecular probe as a ligand (or recognition element) and rely on their effect on the ligand transport. One limitation for this sensing strategy is that the probe molecule needs to have a slightly smaller size than the nanopore constriction or can be easily unfolded or unzipped through the pore. Herein, by taking advantage of replacement and complexation chemical interactions, a generic approach is reported for detection of small molecules by using large biomolecules with well-defined stable 3D structures such as aptamers as recognition elements. Given the versatile use of aptamers as capture agents for a wide variety of species, the developed nanopore sensing strategy should find applications in many fields.

Spectroscopic characterization of bacterial colonies through UV hyperspectral imaging techniques

Introduction

Plate culturing and visual inspection are the gold standard methods for bacterial identification. Despite the growing attention on molecular biology techniques, colony identification using agar plates remains manual, interpretative, and heavily reliant on human experience, making it prone to errors. Advanced imaging techniques, like hyperspectral imaging, offer potential alternatives. However, the use of hyperspectral imaging in the VIS-NIR region has been hindered by sensitivity to various components and culture medium changes, leading to inaccurate results. The application of hyperspectral imaging in the ultraviolet (UV) region has not been explored, despite the presence of specific absorption and emission peaks in bacterial components.

Methods

To address this gap, we developed a predictive model for bacterial colony detection and identification using UV hyperspectral imaging. The model utilizes hyperspectral images acquired in the UV wavelength range of 225-400 nm, processed with principal component analysis (PCA) and discriminant analysis (DA). The measurement setup includes a hyperspectral imager, a PC for automated data analysis, and a conveyor belt system to transport agar plates for automated analysis. Four bacterial species (Escherichia coli, Staphylococcus, Pseudomonas, and Shewanella) were cultured on two different media, Luria Bertani and Tryptic Soy, to train and validate the model.

Results

The PCA-DA-based model demonstrated high accuracy (90%) in differentiating bacterial species based on the first three principal components, highlighting the potential of UV hyperspectral imaging for bacterial identification.

Discussion

This study shows that UV hyperspectral imaging, coupled with advanced data analysis techniques, offers a robust and automated alternative to traditional methods for bacterial identification. The model's high accuracy emphasizes the untapped potential of UV hyperspectral imaging in microbiological analysis, reducing human error and improving reliability in bacterial species differentiation.

A phage amplification-assisted SEA-CRISPR/Cas12a system for viable bacteria detection

Rapid and accurate detection of viable bacteria is essential for the clinical diagnosis of urinary tract infections (UTIs) and for making effective therapeutic decisions. However, most current molecular diagnostic techniques are unable to differentiate between viable and non-viable bacteria. In this study, we introduce a novel isothermal platform that integrates strand exchange amplification (SEA) with the CRISPR/Cas12a system, thereby enhancing both the sensitivity and specificity of the assay and achieving detection of phage DNA at concentrations as low as 4 × 102 copies per μL. Moreover, the incorporation of phages facilitates the specific recognition of viable bacteria and amplifies the initial signal through the inherent specificity and propagation properties of these phages. By employing the phage-assisted SEA-Cas12a approach, we successfully detected viable bacteria in human urine samples without the necessity of DNA extraction within 3.5 hours, achieving a detection limit of 103 CFU per mL. Considering its speed, accuracy, and independence from specialized equipment, this platform demonstrates significant potential as a robust tool for the rapid detection of various pathogens in resource-limited settings, thereby facilitating timely clinical management of UTI patients.

Portable foodborne pathogen detection via ratiometric fluorescence nanoprobe for adenosine triphosphate quantification based on DNA-functionalized metal-organic framework

The increasing incidence of foodborne illnesses highlights the need for rapid, sensitive, and portable methods to detect pathogenic bacteria in food. In this work, we develop a portable method that utilizes a ratiometric fluorescence nanoprobe for adenosine triphosphate (ATP) quantification. The nanoprobe is constructed by encapsulating Ru(bpy)32+ within a zirconium-based metal-organic framework, followed by functionalization of double-stranded DNA (dsDNA). This design permits SYBR Green I (SGI) to intercalate into dsDNA, conferring the nanoprobe with dual-emission property. The presence of ATP disrupts dsDNA structure, quenching SGI fluorescence while maintaining Ru(bpy)32+ fluorescence, providing a stable reference signal. This differential response enables the nanoprobe to achieve ratiometric ATP detection with high precision and sensitivity, with a detection limit of 0.63 μM. Since ATP is a reliable biomarker for viable bacterial cells, a portable hydrogel kit was further developed by integrating the ratiometric fluorescence nanoprobe into an agarose hydrogel matrix. The validation of the kit was conducted using a smartphone application for color recognition, enabling the rapid and on-site detection of pathogens in milk samples. The kit exhibits exceptional sensitivity with a detection limit of 10 CFU/mL, making it a promising tool for real-time bacteria detection in food safety monitoring.

Effectiveness of Differentiating Mold Levels in Soybeans with Electronic Nose Detection Technology

This study employed electronic nose technology to assess the mold levels in soybeans, conducting analyses on artificially inoculated soybeans with five strains of fungi and distinguishing them from naturally moldy soybeans. Principal component analysis (PCA) and linear discriminant analysis (LDA) were used to evaluate inoculated and naturally moldy samples. The results revealed that the most influential sensor was W2W, which is sensitive to organic sulfur compounds, followed by W1W (primarily responsive to inorganic sulfur compounds), W5S (sensitive to small molecular nitrogen oxides), W1S (responsive to short-chain alkanes such as methane), and W2S (sensitive to alcohols, ethers, aldehydes, and ketones). These findings highlight that variations in volatile substances among the moldy soybean samples were predominantly attributed to organic sulfur compounds, with significant distinctions noted in inorganic sulfur, nitrogen compounds, short-chain alkanes, and alcohols/ethers/aldehydes/ketones. The results of the PCA and LDA analyses indicated that while both methods demonstrated moderate effectiveness in distinguishing between different dominant fungal inoculations and naturally moldy soybeans, they were more successful in differentiating various levels of moldiness, achieving a discriminative accuracy rate of 82.72% in LDA. Overall, the findings suggest that electronic nose detection technology can effectively identify mold levels in soybeans.

Simultaneous determination of somatic cell count and total plate count in raw milk based on ATP bioluminescence assay

The somatic cell count (SCC) and total plate count (TPC) are essential quality indicators for raw milk. Traditional detection methods require separate measurements and rely on complex, large-scale instruments or cultivation techniques, which are both time-consuming and laborious. To address these challenges, this study developed a novel method for the simultaneous detection of SCC and TPC in the same raw milk sample using the ATP bioluminescence assay. This method utilizes oxy-ethylated iso-nonyl phenol (Neonol-10) and cetyltrimethylammonium bromide (CTAB) to selectively lyse somatic cells and microorganisms, respectively. This technique is straightforward to operate and can be completed within 2.5 h, with detection ranges of 1 × 10⁴ to 3 × 10⁶ cells/mL for SCC and 1 × 10⁵ to 5 × 10⁷ CFU/mL for TPC. Importantly, this technique meets the requirements of detection standards in China, European Union, Canada, United States, etc. For SCC or TPC in raw milk. Overall, this innovative approach does not rely on expensive equipment or facilities and the stepwise reagent addition procedure can be easily developed into an automated high-throughput system for rapid on-site testing of SCC and TPC in raw milk.

Phage-Modified Clear Hydrogel for Simultaneous Detection of Multiple Bacteria

The proliferation speed of live foodborne pathogens is fast. A small number of pathogens will have a great impact on food and the environment if positive samples are not detected timely. In this study, transparent porous hydrogel stir bars, modified by two different phages (corresponding to two different bacteria (Escherichia coli and Hafnia sp)), have been developed for rapid detection of foodborne bacteria. A large number of samples can be analyzed simultaneously with a small animal live imager device to screen out the positive samples, while an adenosine triphosphate (ATP) bioluminescence sensor can be used to quantify the number of bacteria in the positive samples. The phage has good specificity and capture ability to bacteria, which makes the method highly sensitive. In addition, the use of multiple phages also enables the method to detect multiple bacteria simultaneously. The three-dimensional structure of the hydrogel allows it to modify more phages, and its transparent nature also allows the inside bioluminescence to be detected. Both can enhance the sensitivity of the detection. Finally, the reagents needed for bioluminescence, such as d-luciferin, can also be preencapsulated in the hydrogel, thus simplifying the detection step. Under the best conditions, the detection range of the method is 102-108 CFU·mL-1, and the limit of detection is 30 CFU·mL-1 within 11 min. The test results of actual samples show that there is no difference between using the method developed through this study and the traditional plate counting method, but the detection time is greatly shortened.

Air sampling and ATP bioluminescence for quantitative detection of airborne microbes

Exposure to bioaerosol contamination has detrimental effects on human health. Recent advances in ATP bioluminescence provide more opportunities for the quantitative detection of bioaerosols. Since almost all active organisms can produce ATP, the amount of airborne microbes can be easily measured by detecting ATP-driven bioluminescence. The accurate evaluation of microorganisms mainly relies on following the four key steps: sampling and enrichment of airborne microbes, lysis for ATP extraction, enzymatic reaction, and measurement of luminescence intensity. To enhance the effectiveness of ATP bioluminescence, each step requires innovative strategies and continuous improvement. In this review, we summarized the recent advances in the quantitative detection of airborne microbes based on ATP bioluminescence, which focuses on the advanced strategies for improving sampling devices combined with ATP bioluminescence. Meanwhile, the optimized and innovative strategies for the remaining three key steps of the ATP bioluminescence assay are highlighted. The aim is to reawaken the prosperity of ATP bioluminescence and promote its wider utilization for efficient, real-time, and accurate detection of airborne microbes.

Recent advancements in physical and chemical MEMS sensors

Microelectromechanical systems (MEMSs) are microdevices fabricated using semiconductor-fabrication technology, especially those with moving components. This technology has become more widely used in daily life, e.g., in mobile phones, printers, and cars. In this review, MEMS sensors are largely classified as physical or chemical ones. Physical sensors include pressure, inertial force, acoustic, flow, temperature, optical, and magnetic ones. Chemical sensors include gas, odorant, ion, and biological ones. The fundamental principle of sensing is reading out either the movement or electrical-property change of microstructures caused by external stimuli. Here, sensing mechanisms of the sensors are explained using diagrams with equivalent circuits to show the similarity. Examples of multiple parameter measurement with single sensors (e.g. quantum sensors or resonant pressure and temperature sensors) and parallel sensor integration are also introduced.

Electroactive polymer tag modified nanosensors for enhanced intracellular ATP detection

ATP plays a crucial role in cell energy supply, so the quantification of intracellular ATP levels is particularly important for understanding many physio-pathological processes. The intracellular quantification of this non-electroactive molecule can be realized using aptamer-modified nanoelectrodes, but is hindered by the limited quantity of modification and electroactive tags on the nanosized electrodes. Herein, we developed a simple but effective electrochemical signal amplification strategy for intracellular ATP detection, which replaces the regular ATP aptamer-linked ferrocene monomer with a polymer, thus greatly magnifying the amounts of electrochemical reporters linked to one chain of the aptamer and enhancing the signals. This ferrocene polymer-ATP aptamer was further immobilized onto Au nanowire electrodes (SiC@C@Au NWEs) to achieve accurate quantification of intracellular ATP in single cells, presenting high electrochemical signal output and high specificity. This work not only provides a powerful tool for quantifying intracellular ATP but also offers a simple and versatile strategy for electrochemical signal amplification in the detection of broader non-electroactive molecules involved in different kinds of intracellular physiological processes.

Miniaturizable Chemiluminescence System for ATP Detection in Water

We present the design, fabrication, and testing of a low-cost, miniaturized detection system that utilizes chemiluminescence to measure the presence of adenosine triphosphate (ATP), the energy unit in biological systems, in water samples. The ATP-luciferin chemiluminescent solution was faced to a silicon photomultiplier (SiPM) for highly sensitive real-time detection. This system can detect ATP concentrations as low as 0.2 nM, with a sensitivity of 79.5 A/M. Additionally, it offers rapid response times and can measure the characteristic time required for reactant diffusion and mixing within the reaction volume, determined to be 0.3 ± 0.1 s. This corresponds to a diffusion velocity of approximately 44 ± 14 mm2/s.

On-chip bioluminescence biosensor for the detection of microbial surface contamination

Detection of microbial pathogens is important for food safety reasons, and for monitoring sanitation in laboratory environments and health care settings. Traditional detection methods such as culture-based and nucleic acid-based methods are time-consuming, laborious, and require expensive laboratory equipment. Recently, ATP-based bioluminescence methods were developed to assess surface contamination, with commercial products available. In this study, we introduce a biosensor based on a CMOS image sensor for ATP-mediated chemiluminescence detection. The original lens and IR filter were removed from the CMOS sensor revealing a 12 MP periodic microlens/pixel array on an area of 6.5 mm × 3.6 mm. UltraSnap swabs are used to collect samples from solid surfaces including personal electronic devices, and office and laboratory equipment. Samples mixed with chemiluminescence reagents were placed directly on the surface of the image sensor. Close proximity of the sample to the photodiode array leads to high photon collection efficiency. The population of microorganisms can be assessed and quantified by analyzing the intensity of measured chemiluminescence. We report a linear range and limit of detection for measuring ATP in UltraSnap buffer of 10-1000 nM and 225 fmol, respectively. The performance of the CMOS-based device was compared to a commercial luminometer, and a high correlation with a Pearson's correlation coefficient of 0.98589 was obtained. The Bland-Altman plot showed no significant bias between the results of the two methods. Finally, microbial contamination of different surfaces was analyzed with both methods, and the CMOS biosensor exhibited the same trend as the commercial luminometer.

Possibilities of an Electronic Nose on Piezoelectric Sensors with Polycomposite Coatings to Investigate the Microbiological Indicators of Milk

Milk and dairy products are included in the list of the Food Security Doctrine and are of paramount importance in the diet of the human population. At the same time, the presence of many macro- and microcomponents in milk, as available sources of carbon and energy, as well as the high activity of water, cause the rapid development of native and pathogen microorganisms in it. The goal of the work was to assess the possibility of using an array of gas chemical sensors based on piezoquartz microbalances with polycomposite coatings to assess the microbiological indicators of milk quality and to compare the microflora of milk samples. Piezosensors with polycomposite coatings with high sensitivity to volatile compounds were obtained. The gas phase of raw milk was analyzed using the sensors; in parallel, the physicochemical and microbiological parameters were determined for these samples, and species identification of the microorganisms was carried out for the isolated microorganisms in milk. The most informative output data of the sensor array for the assessment of microbiological indicators were established. Regression models were constructed to predict the quantity of microorganisms in milk samples based on the informative sensors' data with an error of no more than 17%. The limit of determination of QMAFAnM in milk was 243 ± 174 CFU/cm3. Ways to improve the accuracy and specificity of the determination of microorganisms in milk samples were proposed.

Online monitoring system for qualitative and quantitative analysis of bioaerosols by combined ATP bioluminescence assay with loop-mediated isothermal amplification

Rapid detection of airborne pathogens is crucial in preventing respiratory infections and allergies. However, technologies aiming to real-time analysis of microorganisms in air remain limited due to the sparse and complex nature of bioaerosols. Here, we introduced an online bioaerosol monitoring system (OBMS) comprised of integrated units including a rotatable stainless-steel sintered filter-based sampler, a lysis unit for extracting adenosine triphosphate (ATP), and a single photon detector-based fluorescence unit. Through optimization of the ATP bioluminescence method and establishment of standard curves between relative luminescence units (RLUs) and ATP as well as microbial concentration, we achieved simultaneous detection of bioaerosols' concentration and activity. Testing OBMS with four bacterial and two fungal aerosols at a sampling flow rate of 10 to 50 L/min revealed an outstanding collection efficiency of 95 % at 30 L/min. A single OBMS measurement takes only 8 min (sampling: 5 min; lysis and detection: 3 min) with detection limits of 3 Pcs/ms photons (2.9 × 103 and 292 CFU/m3 for Staphylococcus aureus and Candida albicans aerosol). In both laboratory and field tests, OBMS detected higher concentrations of bioaerosol compared to the traditional Andersen impactor and liquid biosampler. When combined OBMS with loop-mediated isothermal amplification (LAMP), the bioaerosol can be qualitative and quantitative analyzed within 40 min without the cumbersome procedures of sample pretreatment and DNA extraction. These results offer a high compressive and humidity resistance membrane filtration sampler and validate the potential of OBMS for online measurement of bioaerosol concentration and composition.