Continuous and Real-Time Detection of Drinking-Water Pathogens with a Low-Cost Fluorescent Optofluidic Sensor

Fluorescence Spectroscopy Based Identification of Pseudomonas Aeruginosa and Escherichia Coli Suspensions

In this article, Fluorescence spectroscopy has been employed for the identification of Pseudomonas aeruginosa (PA) and Escherichia coli (E. coli) in water suspension. Emission spectra of PA and E. coli suspensions have been acquired by using excitation wavelengths from 270 to 420 nm with steps of 10 nm to explore their spectral features. It has been found that the emission spectra of tryptophan, tyrosine, NADH and FAD, being the intracellular biomolecules present in both bacteria, can be used as fingerprints for their identification, differentiation and quantification. Both bacterial strains can clearly be differentiated from water and from each other by using λex 270-290 nm through spectral analysis and from λex: 300-500 nm by applying statistical analysis. Furthermore, calibration curves for different bacterial loads of PA and E. coli suspensions have been produced between colonies forming units per ml (CFUs/ml) the integrated intensities of their emission spectra. CFUs/ml of both bacterial suspensions have been determined through plate count method which was used as cross-reference for the analysis of emission spectra of both bacterial suspensions. These curves may be used to estimate CFU/ml of both PA and E. coli in unknown water suspensions by determining the integrating intensity of their emission spectra.

Fluorescence Spectroscopy Based Characterization of Pseudomonas Aeruginosa Suspension

In this article, optical characterization of Pseudomonas aeruginosa (PA) suspension has been performed by using Fluorescence spectroscopy. Optical density (OD) and plate count methods have been employed as a reference for the analysis of emission spectra of Pseudomonas aeruginosa in water suspension. Emission spectra of PA suspension has been acquired by using excitation wavelengths from 270 to 420 nm with step of 10 nm to explore its spectral behavior. It has been found that emission spectra of tryptophan, tyrosine, NADH and FAD, the intracellular biomolecules of bacteria, can be used as finger prints for the detection of Pseudomonas aeruginosa. Furthermore, the effect of water matrix on the spectral emission of Pseudomonas aeruginosa has been investigated that might be one of the limitation of Fluorescence spectroscopy for complex water matrices. Moreover, a calibration curve has been produced between ODs600 of Pseudomonas aeruginosa suspensions of different bacterial load and integrated intensities of the emission spectra of same samples. These ODs600 and integrating intensities have been further vetted through plate count method by determining their corresponding colony forming units per ml (CFU/ml). This calibration curve may be used to determine CFU/ml of Pseudomonas aeruginosa in water sample by determining integrating intensity of its emission spectrum.

Antimicrobial photodynamic therapy against Escherichia coli by exploiting endogenously produced Protoporphyrin IX- In vitro study

Due to antimicrobial drug resistance, there is a growing interest in the development of light based alternative antibacterial therapies. This research work is focused on the inactivation of Escherichia coli (E. coli) by exploiting the absorption bands 405, 505, 542, 580 and 631 nm of its indigenously produced Protoporphyrin IX (PpIX) excited by three LEDs with broad emission bands at 418, 522 and 630 nm and two laser diodes with narrow emission bands at 405 and 635 nm. Fluorescence spectroscopy and plate count method have been employed for studying the inactivation rate of E. coli strain in autoclaved water suspension. It has been found that LEDs at 418, 522 and 630 nm produced pronounced antimicrobial photodynamic effect on E. coli strain comparing laser diodes at 405 and 635 nm, which might be attributed to the overlapping of broad emission bands of LEDs with the absorption bands of PpIX than narrow emission bands of laser diodes. Particular effect of LED at 522 nm has been noticed because its broad emission band overlaps three absorption bands 505, 542 and 580 nm of PpIX. The gold standard plate count method strongly correlates with Fluorescence spectroscopy, making it an innovative tool to administer bacterial inactivation. The experimental results suggested the development of a light source that entirely overlap absorption bands of PpIx to produce a pronounced antimicrobial photodynamic effect, which might become an effective modality for in vivo disinfection of antibiotic resistant microbes in wounds and lesions.

A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens

Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.

A continuous, in-situ, near-time fluorescence sensor coupled with a machine learning model for detection of fecal contamination risk in drinking water: Design, characterization and field validation

We designed and validated a sensitive, continuous, in-situ, remotely reporting tryptophan-like fluorescence sensor and coupled it with a machine learning model to predict high-risk fecal contamination in water (>10 colony forming units (CFU)/100mL E. coli). We characterized the sensor's response to multiple fluorescence interferents with benchtop analysis. The sensor's minimum detection limit (MDL) of tryptophan dissolved in deionized water was 0.05 ppb (p <0.01) and its MDL of the correlation to E. coli present in wastewater effluent was 10 CFU/100 mL (p <0.01). Fluorescence response declined exponentially with increased water temperature and a correction factor was calculated. Inner filter effects, which cause signal attenuation at high concentrations, were shown to have negligible impact in an operational context. Biofouling was demonstrated to increase the fluorescence signal by approximately 82% in a certain context, while mineral scaling reduced the sensitivity of the sensor by approximately 5% after 24 hours with a scaling solution containing 8 times the mineral concentration of the Colorado River. A machine learning model was developed, with TLF measurements as the primary feature, to output fecal contamination risk levels established by the World Health Organization. A training and validation data set for the model was built by installing four sensors on Boulder Creek, Colorado for 88 days and enumerating 298 grab samples for E. coli with membrane filtration. The machine learning model incorporated a proxy feature for fouling (time since last cleaning) which improved model performance. A binary classification model was able to predict high risk fecal contamination with 83% accuracy (95% CI: 78% - 87%), sensitivity of 80%, and specificity of 86%. A model distinguishing between all World Health Organization established risk categories performed with an overall accuracy of 64%. Integrating TLF measurements into an ML model allows for anomaly detection and noise reduction, permitting contamination prediction despite biofilm or mineral scaling formation on the sensor's lenses. Real-time detection of high risk fecal contamination could contribute to a major step forward in terms of microbial water quality monitoring for human health.

A Comprehensive Review on Water Quality Monitoring Devices: Materials Advances, Current Status, and Future Perspective

Water quality monitoring has become more critical in recent years to ensure the availability of clean and safe water from natural aquifers and to understand the evolution of water contaminants across time and space. The conventional water monitoring techniques comprise of sample collection, preservation, preparation, tailed by laboratory testing and analysis with cumbersome wet chemical routes and expensive instrumentation. Despite the high accuracy of these methods, the high testing costs, laborious procedures, and maintenance associated with them don't make them lucrative for end end-users and field testing. As the participation of ultimate stakeholders, that is, common man for water quality and quantity can play a pivotal role in ensuring the sustainability of our aquifers, thus it is essential to develop and deploy portable and user-friendly technical systems for monitoring water sources in real-time or on-site. The present review emphasizes here on possible approaches including optical (absorbance, fluorescence, colorimetric, X-ray fluorescence, chemiluminescence), electrochemical (ASV, CSV, CV, EIS, and chronoamperometry), electrical, biological, and surface-sensing (SPR and SERS), as candidates for developing such platforms. The existing developments, their success, and bottlenecks are discussed in terms of various attributes of water to escalate the essentiality of water quality devices development meeting ASSURED criterion for societal usage. These platforms are also analyzed in terms of their market potential, advancements required from material science aspects, and possible integration with IoT solutions in alignment with Industry 4.0 for environmental application.

Advances in Technological Research for Online and In Situ Water Quality Monitoring—A Review

Monitoring water quality is an essential tool for the control of pollutants and pathogens that can cause damage to the environment and human health. However, water quality analysis is usually performed in laboratory environments, often with the use of high-cost equipment and qualified professionals. With the progress of nanotechnology and the advance in engineering materials, several studies have shown, in recent years, the development of technologies aimed at monitoring water quality, with the ability to reduce the costs of analysis and accelerate the achievement of results for management and decision-making. In this work, a review was carried out on several low-cost developed technologies and applied in situ for water quality monitoring. Thus, new alternative technologies for the main physical (color, temperature, and turbidity), chemical (chlorine, fluorine, phosphorus, metals, nitrogen, dissolved oxygen, pH, and oxidation–reduction potential), and biological (total coliforms, Escherichia coli, algae, and cyanobacteria) water quality parameters were described. It was observed that there has been an increase in the number of publications related to the topic in recent years, mainly since 2012, with 641 studies being published in 2021. The main new technologies developed are based on optical or electrochemical sensors, however, due to the recent development of these technologies, more robust analyses and evaluations in real conditions are essential to guarantee the precision and repeatability of the methods, especially when it is desirable to compare the values with government regulatory standards.

Rapid Detection of Three Common Bacteria Based on Fluorescence Spectroscopy

As an important part of environmental water quality monitoring, efficient bacterial detection has attracted widespread attention. Among them, LIF (laser-induced fluorescence) technology has the characteristics of high efficiency and sensitivity for bacterial detection. To simplify the experimental process of bacterial detection, fluorescence emission spectra of E. coli (Escherichia coli) and its deactivated controls, K. pneumoniae (Klebsiella pneumoniae) and S. aureus (Staphylococcus aureus), were analyzed with fluorescence excitation by a 266 nm laser. By analyzing the results, it was found that the dominant fluorescence peaks of bacterial solutions at 335~350 nm were contributed by tryptophan, and the subfluorescence peaks at 515.9 nm were contributed by flavin; besides, K. pneumoniae and S. aureus had their own fluoresces characteristics, such as tyrosine contributing to sub-fluorescence peaks at 300 nm. The three species of bacteria can be differentiated with whole fluorescence spectrum by statistically analysis (p < 0.05), for various concentrations of aromatic amino acids and flavin in different bacteria. The experimental results also proved that the inactivation operation did not alter the spectral properties of E. coli. The indexes of fluorescence intensity and FIR (fluorescence intensity ratio, I_335~350/I_515.9) can be used to retrieve the bacteria concentration as well as for bacteria differentiation using the index of slopes. The detection limit of bacteria is less than ~10⁵ cell/mL using laser induced fluorescence methods in the paper. The study demonstrated the rapid detection capability of the LIF bacterial detection system and its great potential for rapid quantitative analysis of bacteria. This may bring new insight into the detection of common bacteria in water in situ.

Low-cost portable bioluminescence detector based on silicon photomultiplier for on-site colony detection

A low-cost, portable bioluminescence detector based on a silicon photomultiplier (SiPM) was developed for on-site colony detection, the main components of which are a low-noise photoelectric signal detection and processing circuit, power management module, and high-performance embedded microcontroller subsystem with peripheral circuits. Balanced chopper modulation and lock-in amplification techniques were adopted to improve the signal-to-noise ratio, and a zero-adjustment technique was used to eliminate the dark current of the SiPM to expand the dynamic range. Using this bioluminescence detector, adenosine triphosphate could be determined in the range of 3.6 × 10^-6 to 3.6 × 10^-11 mol/L, and bacterial colonies could be determined in the range of 1.0 × 10³ to 1.0 × 10⁹ CFU/mL, with a limit of quantitation of 1.0 × 10³ CFU/mL. Satisfactory recoveries and precision were obtained. Actual samples were accurately tested and the data were verified by comparison with those from the national standard method. The manufacturing cost of the bioluminescence detector was only $30, which is only approximately 1% of the price of current commercial instruments. This study provides a tool for rapid on-site detection of bacterial colonies, as well as a new concept for the development of low-cost portable detection equipment.

3D microfluidic gradient generator for combination antimicrobial susceptibility testing

Microfluidic concentration gradient generators (µ-CGGs) have been utilized to identify optimal drug compositions through antimicrobial susceptibility testing (AST) for the treatment of antimicrobial-resistant (AMR) infections. Conventional µ-CGGs fabricated via photolithography-based micromachining processes, however, are fundamentally limited to two-dimensional fluidic routing, such that only two distinct antimicrobial drugs can be tested at once. This work addresses this limitation by employing Multijet-3D-printed microchannel networks capable of fluidic routing in three dimensions to generate symmetric multidrug concentration gradients. The three-fluid gradient generation characteristics of the fabricated 3D µ-CGG prototype were quantified through both theoretical simulations and experimental validations. Furthermore, the antimicrobial effects of three highly clinically relevant antibiotic drugs, tetracycline, ciprofloxacin, and amikacin, were evaluated via experimental single-antibiotic minimum inhibitory concentration (MIC) and pairwise and three-way antibiotic combination drug screening (CDS) studies against model antibiotic-resistant Escherichia coli bacteria. As such, this 3D µ-CGG platform has great potential to enable expedited combination AST screening for various biomedical and diagnostic applications.

Monitoring Approaches for Faecal Indicator Bacteria in Water: Visioning a Remote Real-Time Sensor for E. coli and Enterococci

A comprehensive review was conducted to assess the current state of monitoring approaches for primary faecal indicator bacteria (FIB) E. coli and enterococci. Approaches were identified and examined in relation to their accuracy, ability to provide continuous data and instantaneous detection results, cost, environmental awareness regarding necessary reagent release or other pollution sources, in situ monitoring capability, and portability. Findings showed that several methods are precise and sophisticated but cannot be performed in real-time or remotely. This is mainly due to their laboratory testing requirements, such as lengthy sample preparations, the requirement for expensive reagents, and fluorescent tags. This study determined that portable fluorescence sensing, combined with advanced modelling methods to compensate readings for environmental interferences and false positives, can lay the foundations for a hybrid FIB sensing approach, allowing remote field deployment of a fleet of networked FIB sensors that can collect high-frequency data in near real-time. Such sensors will support proactive responses to sudden harmful faecal contamination events. A method is proposed to enable the development of the visioned FIB monitoring tool.

Quick assessment of influenza a virus infectivity with a long-range reverse-transcription quantitative polymerase chain reaction assay

BACKGROUND

The polymerase chain reaction (PCR) is commonly used to detect viral pathogens because of its high sensitivity and specificity. However, conventional PCR methods cannot determine virus infectivity. Virus infectivity is conventionally examined with methods such as the plaque assay, even though such assays require several days. Long-range reverse-transcription quantitative PCR (RT-qPCR) has previously been suggested for the rapid assessment of RNA virus infectivity where the loss of infectivity is attributable to genomic fragmentation.

METHODS

IAV was irradiated with 253.7 nm ultraviolet (UV) rays to induce genomic strand breaks that were confirmed by a full-length RT-PCR assay. The IAV was then subjected to plaque assay, conventional RT-qPCR and long-range RT-qPCR to examine the relationship between infectious titer and copy number. A simple linear regression analysis was performed to examine the correlation between the results of these assays.

RESULTS

A long-range RT-qPCR assay was developed and validated for influenza A virus (IAV). Although only a few minutes of UV irradiation was required to completely inactivate IAV, genomic RNA remained detectable by the conventional RT-qPCR and the full-length RT-PCR for NS of viral genome following inactivation. A long-range RT-qPCR assay was then designed using RT-priming at the 3' termini of each genomic segment and subsequent qPCR of the 5' regions. UV-mediated IAV inactivation was successfully analyzed by the long-range RT-qPCR assay especially when targeting PA of the viral genome. This was also supported by the regression analysis that the long-range RT-qPCR is highly correlated with plaque assay (Adjusted R² = 0.931, P = 0.000066).

CONCLUSIONS

This study suggests that IAV infectivity can be predicted without the infectivity assays. The rapid detection of pathogenic IAV has, therefore, been achieved with this sensing technology.

Rapid Detection Methods for Bacterial Pathogens in Ambient Waters at the Point of Sample Collection: A Brief Review

The world is currently facing a serious health burden of waterborne diseases, including diarrhea, gastrointestinal diseases, and systemic illnesses. The control of these infectious diseases ultimately depends on the access to safe drinking water, properly managed sanitation, and hygiene practices. Therefore, ultrasensitive, rapid, and specific monitoring platforms for bacterial pathogens in ambient waters at the point of sample collection are urgently needed. We conducted a literature review on state-of-the-art research of rapid in-field aquatic bacteria detection methods, including cell-based methods, nucleic acid amplification detection methods, and biosensors. The detection performance, the advantages, and the disadvantages of the technologies are critically discussed. We envision that promising monitoring approaches should be automated, real-time, and target-multiplexed, thus allowing comprehensive evaluation of exposure risks attributable to waterborne pathogens and even emerging microbial contaminants such as antibiotic resistance genes, which leads to better protection of public health.

Recent methods and biosensors for foodborne pathogen detection in fish: progress and future prospects to sustainable aquaculture systems

The aquaculture industry has advanced toward sustainable recirculating systems, in where parameters of food quality are strictly monitored. Despite that, as in the case of conventional aquaculture practices, the recirculating systems also suffer threats from Aeromonas spp., Vibrio spp., Streptococcus spp., among other foodborne pathogens infecting farmed fish. The aquaculture pathogens are routinely detected by conventional PCR methods or antibody-based tests, with the detection protocols confined to laboratory use. Emerging assay technologies and biosensors recently reported in the literature open new opportunities to the development of sensitive, specific, and portable analytical devices to use in the field. Techniques of DNA/RNA analysis, immunoassays and other nanomolecular technologies have been facing important advances in response time, sensitivity, and enhanced power of discrimination among and within species. Moreover, the recent developments of electrochemical and optical signal transduction have facilitated the incorporation of the innovative assays to practical miniaturized devices. In this work, it is provided a critical review over foodborne pathogen detection by existing and promising methods and biosensors applied to fish samples and extended to other food matrices. While isothermal DNA/RNA amplification methods can be highlighted among the assay methods for their promising analytical performance and suitability for point-of-care testing, the electrochemical transduction provides a way to achieve cost-effective biosensors amenable to use in the aquaculture field. The adoption of new methods and biosensors would constitute a step forward in securing sustainable aquaculture systems.

Processing Fluorescence Spectra for Pollutants Detection Systems in Inland Waters

Development of contaminant detection systems in various natural and industrial environments has been favored in recent years thanks to the evolution of processors and sensors. Our group works specifically on contaminant detection systems in inland waters: immediate and continuous detection is a fundamental requirement in this type of sensing. Regarding the sensors, the proposed system is based on fluorescence, since it offers a method in which there is no contact with water, which means less wear on the components and a great saving in cleaning and maintenance. On the other hand, the spectrum processing is of great importance, since it is used both in the generation of a library of fluorescence spectra taken in the laboratory and in the continuous analysis of the samples and in the comparison algorithm for identification. The validity of the system is based on the last process that is carried out in a very short time. This article describes a system to process spectra in a more accelerated way.

Demonstration of Tryptophan-Like Fluorescence Sensor Concepts for Fecal Exposure Detection in Drinking Water in Remote and Resource Constrained Settings

Low-cost, field-deployable, near-time methods for assessing water quality are not available when and where waterborne infection risks are greatest. We describe the development and testing of a novel device for the measurement of tryptophan-like fluorescence (TLF), making use of recent advances in deep-ultraviolet light emitting diodes (UV-LEDs) and sensitive semiconductor photodiodes and photomultipliers. TLF is an emerging indicator of water quality that is associated with members of the coliform group of bacteria and therefore potential fecal contamination. Following the demonstration of close correlation between TLF and E. coli in model waters and proof of principle with sensitivity of 4 CFU/mL for E. coli, we further developed a two-LED flow-through configuration capable of detecting TLF levels corresponding to “high risk” fecal contamination levels (>10 CFU/100 mL). Findings to date suggest that this device represents a scalable solution for remote monitoring of drinking water supplies to identify high-risk drinking water in near-time. Such information can be immediately actionable to reduce risks.

Trends in fabrication, data gathering, validation, and application of molecular fluorometer and spectrofluorometer

Technological advances have widely improved the field of research as spectroscopic methods are now flexible in analyzing different sample matrix. There have been various methods used in applications of spectrofluorometer, but some were costly, time consuming or complicated for routine analysis, creating barrier for students to understand the basic concepts of fluorescence. This review focuses on the different fluorometer designs and techniques which promote cost efficiency and/or having modifications without compromise in data gathering, and its applications to various scientific fields. The usage of pesticides has a wide range of effects when it comes to the environment and to human health especially when it enters the food chain. The characteristic of having a low-cost, user-friendly and efficient device can occur in different variations as materials and technology are employed to fluorescence detection which primarily contributes to the different applications of the device such as in food safety and security.

Monitoring of drinking water quality using automated ATP quantification

A microfluidic based system was developed for automated online method for the rapid detection and monitoring of drinking water contamination utilising microbial Adrenosine-5'-Triphosphate (ATP) as a bacterial indicator. The system comprises a polymethyl methacrylate based microfluidic cartridge inserted into an enclosure incorporating the functions of fluid storage and delivery, lysis steps and real-time detection. Design, integration and operation of the resulting automated system are reported, including the lysis method, the design of the mixing circuit, the choices of flow rate, temperature and reagent amount. Calibration curves of both total and free ATP were demonstrated to be highly linear over a range from 2.5-5000 pg/mL with the limit of detection being lower than 2.5 pg/mL of total ATP. The system was trialled in a lab study with different types of water, with lysis efficiency being found to be strongly dependent upon water type. Further development is required before online implementation.

A fluorimetric nitrite biosensor with polythienothiophene-fullerene thin film detectors for on-site water monitoring

A novel fluorimetric sensor for highly sensitive nitrite detection on the site is presented in this study. The proposed on-chip approach comprises the use of integrated polymer photodetectors to detect light from fluorescence reactions with a diaminofluorescein probe. The detectors were prepared with a heterostructured nanofilm of polythieno[3,4-b]thiophene/benzodithiophene and (6,6)-phenyl-C₇₁-butyric-acid methyl-ester as a photoactive layer. Prior to fluorimetric detection, the quality of the spin-coated photoactive layer was characterized via nano-morphology and current-density measurements. Nitrite assays were conducted on a poly(methyl methacrylate) microchannel chip, to which polythienothiophene-C₇₁ based detectors were aligned. Results of signal-to-noise ratio determination have indicated a detection limit below 0.55 μM, lower than the 0.1 mg L^-1 maximum limit of operation in recirculating aquaculture systems for farming Atlantic salmon Salmo salar. An increase of the nitrite concentration to toxic levels may therefore be possible to detect. The fluorimetric sensor exhibited good linearity over three orders of magnitude and acceptable detection reproducibility, which confirmed its analytical value. Further tests revealed great promise of the integrated biosensor device for detecting nitrite in aquaculture-relevant samples with high precision. The approach reported hereby may provide impetus to in situ analytical tools for monitoring water quality at aquaculture facilities, the food industries or water monitoring stations.