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

The Potential Clinical Applications of a Microfluidic Lab-on-a-Chip for the Identification and Antibiotic Susceptibility Testing of Enterococcus faecalis-Associated Endodontic Infections: A Systematic Review

This systematic review evaluated the potential clinical use of microfluidic lab-on-a-chip (LOC) technology in the identification and antibiotic susceptibility testing of E. faecalis in endodontic infections. The search methodology employed in this review adhered to the PRISMA guidelines. Multiple scientific databases, including PubMed/MEDLINE, SCOPUS, and SCIELO, were utilized, along with exploration of grey literature sources. Up to September 2023, these resources were searched using specific keywords and MeSH terms. An initial comprehensive search yielded 202 articles. Ultimately, this systematic review incorporated 12 studies. Out of these, seven aimed to identify E. faecalis, while the remaining five evaluated its susceptibility to different antibiotics. All studies observed that the newly developed microfluidic chip significantly reduces detection time compared to traditional methods. This enhanced speed is accompanied by a high degree of accuracy, efficiency, and sensitivity. Most research findings indicated that the entire process took anywhere from less than an hour to five hours. It is important to note that this approach bypasses the need for minimum inhibitory concentration measurements, as it does not rely on traditional methodologies. Microfluidic devices enable the rapid identification and accurate antimicrobial susceptibility testing of E. faecalis, which are crucial for timely diagnosis and treatment in endodontic infections.

Direct, ultrafast, and sensitive detection of environmental pathogenic microorganisms based on a graphene biosensor

Pathogenic microorganisms in the environment pose a serious threat to global human health. This study developed a reduced graphene oxide (rGO)-field effect transistor (FET) biosensor to realize the rapid and sensitive detection of pathogenic microorganisms. The rGO-FET sensors were prepared by in-situ thermal reduction method, and biorecognition elements were immobilized using a crosslinking agent to realize the surface functionalization of rGO. The rGO-FET biosensors can detect Escherichia coli O157:H7 as low as 1.4 CFU mL-1 within 46 s. The normalized current response was linearly correlated with E. coli concentration in the range of 1.4-1.4 × 107 CFU mL-1. The normalized current response of E. coli O157:H7 was about an order of magnitude higher than those of other microorganisms, indicating that the biosensor has good specificity. The current loss rates of the unmodified rGO-FET sensors and the biosensors modified with anti-E. coli O157:H7 after 30 days of storage at 4 °C were approximately 8% and 15%, respectively. Most importantly, the rGO-FET biosensors can directly detect real samples without pretreatment. Compared with other technologies, the rGO-FET biosensors can detect pathogenic microorganisms with a wider linear range in a shorter time, which is of great importance for the rapid warning and control of pathogenic microorganisms in the environment.

Rapid identification of bacteria by the pattern of redox reactions rate using 2',7'-dichlorodihydrofluorescein diacetate

Bacterial infection is a life-threatening situation, and its rapid diagnosis is essential for treatment. Apart from medical applications, rapid identification of bacteria is vital in the food industry or the public health system. There are various bacterial identification techniques, including molecular-based methods, immunological approaches, and biosensor-based procedures. The most commonly used methods are culture-based methods, which are time-consuming. The objective of this study is to find a fingerprint of bacteria to identify them. Three strains of bacteria were selected, and seven different concentrations of each bacterium were prepared. The bacteria were then treated with two different molar concentrations of the fluorescent fluorophore, dichlorodihydrofluorescein diacetate for 30 minutes. Then, using the fluorescence mode of a multimode reader, the fluorescence emission of each bacterium is scanned twice during 60 minutes. Plotting the difference between two scans versus the bacteria concentration results in a unique fluorescence pattern for each bacterium. Observation of the redox state of bacteria, during 90 minutes, results in a fluorescence pattern that is clearly a fingerprint of different bacteria. This pattern is independent of fluorophore concentration. Mean Squares Errors (MSE) between the fluorescence patterns of similar bacteria is less than that of different bacteria, which shows the method can properly identify the bacteria. In this study, a new label-free method is developed to detect and identify different species of bacteria by measuring the redox activity and using the fluorescence fluorophore, dichlorodihydrofluorescein diacetate. This robust and low-cost method can properly identify the bacteria, uses only one excitation and emission wavelength, and can be simply implemented with current multimode plate readers.

Tools to Enumerate and Predict Distribution Patterns of Environmental Vibrio vulnificus and Vibrio parahaemolyticus

Vibrio vulnificus (Vv) and Vibrio parahaemolyticus (Vp) are water- and foodborne bacteria that can cause several distinct human diseases, collectively called vibriosis. The success of oyster aquaculture is negatively impacted by high Vibrio abundances. Myriad environmental factors affect the distribution of pathogenic Vibrio, including temperature, salinity, eutrophication, extreme weather events, and plankton loads, including harmful algal blooms. In this paper, we synthesize the current understanding of ecological drivers of Vv and Vp and provide a summary of various tools used to enumerate Vv and Vp in a variety of environments and environmental samples. We also highlight the limitations and benefits of each of the measurement tools and propose example alternative tools for more specific enumeration of pathogenic Vv and Vp. Improvement of molecular methods can tighten better predictive models that are potentially important for mitigation in more controlled environments such as aquaculture.

CPA-Cas12a-based lateral flow strip for portable assay of Methicillin-resistant Staphylococcus aureus in clinical sample

The rapid and accurate identification of methicillin-resistant Staphylococcus aureus at an early antibiotic therapy stage would be benefit to disease diagnosis and antibiotic selection. Herein, we integrated cross-priming amplification (CPA) and CRISPR/Cas 12a (designated as CPA-Cas 12a) systems to establish a sensitive and efficient lateral flow assay to detect methicillin-resistant Staphylococcus aureus. This assay relies on the CPA isothermal nucleic acid amplification strategy which can amplify the DNA extracted from Staphylococcus aureus and accompanying the indiscriminately trans-cleavage process of Cas 12a/CrRNA duplex after recognizing specific sequence. Taking the advantage of reporter and high turnover Cas 12a activity, a dramatic change in response was achieved to produce a significant increase in the analytical sensitivity. The signal conversion and output were realized using a lateral flow strip to achieve field-deployable detection. Furthermore, this bioassay was accommodated with a microfluidic device to realize automatically portable detection. This proposed assay completed within 30 min with the detection limit of 5 CFU mL^-1, was verified by testing bacterial suspension and 202 clinical samples. Given the high sensitivity, specificity and efficiency, this colorimetric readout assay through strip could be further promoted to the clinical diagnosis, clinical medication of multidrug-resistant bacteria.

Advances in paper based isothermal nucleic acid amplification tests for water-related infectious diseases

Water-associated or water-related infectious disease outbreaks are caused by pathogens such as bacteria, viruses, and protozoa, which can be transmitted through contaminated water sources, poor sanitation practices, or insect vectors. Low- and middle-income countries bear the major burden of these infections due to inadequate hygiene and subpar laboratory facilities, making it challenging to monitor and detect infections in a timely manner. However, even developed countries are not immune to these diseases, as inadequate wastewater management and contaminated drinking water supplies can also contribute to disease outbreaks. Nucleic acid amplification tests have proven to be effective for early disease intervention and surveillance of both new and existing diseases. In recent years, paper-based diagnostic devices have made significant progress and become an essential tool in detecting and managing water-associated diseases. In this review, we highlight the importance of paper and its variants as a diagnostic tool and discuss the properties, design modifications, and various paper-based device formats developed and used for detecting water-associated pathogens.

Current and emerging trends in techniques for plant pathogen detection

Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.

Conventional and advanced detection techniques of foodborne pathogens: A comprehensive review

Foodborne pathogens are a major public health concern and have a significant economic impact globally. From harvesting to consumption stages, food is generally contaminated by viruses, parasites, and bacteria, which causes foodborne diseases such as hemorrhagic colitis, hemolytic uremic syndrome (HUS), typhoid, acute, gastroenteritis, diarrhea, and thrombotic thrombocytopenic purpura (TTP). Hence, early detection of foodborne pathogenic microbes is essential to ensure a safe food supply and to prevent foodborne diseases. The identification of foodborne pathogens is associated with conventional (e.g., culture-based, biochemical test-based, immunological-based, and nucleic acid-based methods) and advances (e.g., hybridization-based, array-based, spectroscopy-based, and biosensor-based process) techniques. For industrial food applications, detection methods could meet parameters such as accuracy level, efficiency, quickness, specificity, sensitivity, and non-labor intensive. This review provides an overview of conventional and advanced techniques used to detect foodborne pathogens over the years. Therefore, the scientific community, policymakers, and food and agriculture industries can choose an appropriate method for better results.

Searching pathogenic bacteria in the rare biosphere of the ocean

Harmful marine bacteria, such as Vibrio or Aeromonas species, typically exist at low abundance in ocean environments but represent a reservoir from which epidemics can arise. Particularly, Vibrio strains and their associated infections are on the rise globally due to increasing sea surface temperature representing an emergent threat for human and animal health also being responsible for large economic losses in the aquaculture industry worldwide. New technological approaches are needed to improve strategies targeting these pathogens. This review discusses new approaches based on improved sampling strategies and novel analytical methods offering increased accuracy, high throughput, and informativeness to study and detect microbial pathogens in the marine environment. Detecting and characterizing ultra-low-abundance pathogenic strains can serve as a critical tool in risk management and outbreak prevention of diseases caused by emerging marine pathogens.

Rapid Reverse Purification DNA Extraction Approaches to Identify Microbial Pathogens in Wastewater

Wastewater monitoring became a promising solution in the early detection of outbreaks. Despite the achievements in the identification of pathogens in wastewater using real-time PCR, there is still a lack of reliable rapid nucleic acid extraction protocols. Therefore, in this study, samples were subjected to alkali, proteinase K and/or bead-beating followed by reverse purification magnetic beads-based separation. Wastewater samples spiked with S. aureus, E. coli and C. parvum were used as examples for Gram-positive and -negative bacteria and protozoa, respectively. All results were compared with a spin column technology as a reference method. Proteinase K with bead beating (vortexing with 0.1 mm glass beads for three minutes) was particularly successful for bacterial DNA extraction (three- to five-fold increase). The most useful extraction protocol for protozoa was pre-treatment with proteinase K (eight-fold increase). The selected methods were sensitive as far as detecting one bacterial cell per reaction for S. aureus, ten bacterial cells for E. coli and two oocysts for C. parvum. The extraction reagents are cold chain independent and no centrifuge or other large laboratory equipment is required to perform DNA extraction. A controlled validation trial is needed to test the effectiveness at field levels.

Engineering a sustainable future for point-of-care diagnostics and single-use microfluidic devices

Single-use, disposable, point-of-care diagnostic devices carry great promise for global health, including meeting urgent needs for testing and diagnosis in places with limited laboratory facilities. Unfortunately, the production and disposal of single-use devices, whether in lateral flow assay, cartridges, cassettes, or lab-on-chip microfluidic format, also poses significant challenges for environmental and human health. Point-of-care devices are commonly manufactured from unsustainable polymeric materials derived from fossil sources. Their disposal often necessitates incineration to reduce infection risk, thereby creating additional release of CO2. Many devices also contain toxic chemicals, such as cyanide derivatives, that are damaging to environmental and human health if not disposed of safely. Yet, in the absence of government regulatory frameworks, safe and sustainable waste management for these novel medical devices is often left unaddressed. There is an urgent need to find novel solutions to avert environmental and human harm from these devices, especially in low- and middle-income countries where waste management infrastructure is often weak and where the use of point-of-care tests is projected to rise in coming years. We review here common materials used in the manufacture of single-use point-of-care diagnostic tests, examine the risks they pose to environmental and human health, and investigate replacement materials that can potentially reduce the impact of microfluidic devices on the production of harmful waste. We propose solutions available to point-of-care test developers to start embedding sustainability at an early stage in their design, and to reduce their non-renewable plastic consumption in research and product development.

An Overview of Healthcare Associated Infections and Their Detection Methods Caused by Pathogen Bacteria in Romania and Europe

Healthcare-associated infections can occur in different care units and can affect both patients and healthcare professionals. Bacteria represent the most common cause of nosocomial infections and, due to the excessive and irrational use of antibiotics, resistant organisms have appeared. The most important healthcare-associated infections are central line-associated bloodstream infections, catheter-associated urinary tract infections, surgical site, soft tissue infections, ventilator-associated pneumonia, hospital acquired pneumonia, and Clostridioides difficile colitis. In Europe, some hospitalized patients develop nosocomial infections that lead to increased costs and prolonged hospitalizations. Healthcare-associated infection prevalence in developed countries is lower than in low-income and middle-income countries such as Romania, an Eastern European country, where several factors contribute to the occurrence of many nosocomial infections, but official data show a low reporting rate. For the rapid identification of bacteria that can cause these infections, fast, sensitive, and specific methods are needed, and they should be cost-effective. Therefore, this review focuses on the current situation regarding healthcare-associated infections in Europe and Romania, with discussions regarding the causes and possible solutions. As a possible weapon in the fight against the healthcare-associated infections, the diagnosis methods and tests used to determine the bacteria involved in healthcare-associated infections are evaluated.

The status of potable water reuse implementation

A review of the current status of direct and indirect potable water reuse (DPR/IPR) implementation has been conducted, focusing on the regulatory and practical aspects and with reference to the most recent published literature. The review encompasses (a) the principal contaminant types, their required removal and the methods by which their concentration is monitored, (b) regulatory approaches and stipulations in assessing/ratifying treatment schemes and maintaining treated water quality, and (c) existing full-scale installations. Analytical methods discussed include established in-line monitoring tools, such as turbidity measurement, to more recent polymerase chain reaction (PCR)-based assay methods for microbial detection. The key risk assessment tools of quantitative microbial risk assessment (QMRA) and water safety plans (WSPs) are considered in relation to their use in selecting/ratifying treatment schemes, and the components of the treatment schemes from 40 existing IPR/DPR installations summarised. Five specific schemes are considered in more detail. The review reveals:Whilst there are a number of ongoing projects where RO is not used because of the challenge imposed by disposal of RO concentrate, the prevalence of the sequential RO-UV combination implies the importance of quantifying the impact of process upsets on these unit operations.

Applications of Nanozymology in the Detection and Identification of Viral, Bacterial and Fungal Pathogens

Nanozymes are synthetic nanoparticulate materials that mimic the biological activities of enzymes by virtue of their surface chemistry. Enzymes catalyze biological reactions with a very high degree of specificity. Examples include the horseradish peroxidase, lactate, glucose, and cholesterol oxidases. For this reason, many industrial uses of enzymes outside their natural environments have been developed. Similar to enzymes, many industrial applications of nanozymes have been developed and used. Unlike the enzymes, however, nanozymes are cost-effectively prepared, purified, stored, and reproducibly and repeatedly used for long periods of time. The detection and identification of pathogens is among some of the reported applications of nanozymes. Three of the methodologic milestones in the evolution of pathogen detection and identification include the incubation and growth, immunoassays and the polymerase chain reaction (PCR) strategies. Although advances in the history of pathogen detection and identification have given rise to novel methods and devices, these are still short of the response speed, accuracy and cost required for point-of-care use. Debuting recently, nanozymology offers significant improvements in the six methodological indicators that are proposed as being key in this review, including simplicity, sensitivity, speed of response, cost, reliability, and durability of the immunoassays and PCR strategies. This review will focus on the applications of nanozymes in the detection and identification of pathogens in samples obtained from foods, natural, and clinical sources. It will highlight the impact of nanozymes in the enzyme-linked immunosorbent and PCR strategies by discussing the mechanistic improvements and the role of the design and architecture of the nanozyme nanoconjugates. Because of their contribution to world health burden, the three most important pathogens that will be considered include viruses, bacteria and fungi. Although not quite seen as pathogens, the review will also consider the detection of cancer cells and helminth parasites. The review leaves very little doubt that nanozymology has introduced remarkable advances in enzyme-linked immunosorbent assays and PCR strategies for detecting these five classes of pathogens. However, a gap still exists in the application of nanozymes to detect and identify fungal pathogens directly, although indirect strategies in which nanozymes are used have been reported. From a mechanistic point of view, the nanozyme technology transfer to laboratory research methods in PCR and enzyme-linked immunosorbent assay studies, and the point-of-care devices such as electronic biosensors and lateral flow detection strips, that is currently taking place, is most likely to give rise to no small revolution in each of the six methodological indicators for pathogen detection and identification. While the evidence of widespread research reports, clinical trials and point-of-care device patents support this view, the gaps that still exist point to a need for more basic research studies to be conducted on the applications of nanozymology in pathogen detection and identification. The multidisciplinary nature of the research on the application of nanozymes in the detection and identification of pathogens requires chemists and physicists for the design, fabrication, and characterization of nanozymes; microbiologists for the design, testing and analysis of the methodologies, and clinicians or clinical researchers for the evaluation of the methodologies and devices in the clinic. Many reports have also implicated required skills in mathematical modelling, and electronic engineering. While the review will conclude with a synopsis of the impact of nanozymology on the detection and identification of viruses, bacteria, fungi, cancer cells, and helminths, it will also point out opportunities that exist in basic research as well as opportunities for innovation aimed at novel laboratory methodologies and devices. In this regard there is no doubt that there are numerous unexplored research areas in the application of nanozymes for the detection of pathogens. For example, most research on the applications of nanozymes for the detection and identification of fungi is so far limited only to the detection of mycotoxins and other chemical compounds associated with fungal infection. Therefore, there is scope for exploration of the application of nanozymes in the direct detection of fungi in foods, especially in the agricultural production thereof. Many fungal species found in seeds severely compromise their use by inactivating the germination thereof. Fungi also produce mycotoxins that can severely compromise the health of humans if consumed.

Development of a proof-of-concept microfluidic portable pathogen analysis system for water quality monitoring

Waterborne diseases cause millions of deaths worldwide, especially in developing communities. The monitoring and rapid detection of microbial pathogens in water is critical for public health protection. This study reports the development of a proof-of-concept portable pathogen analysis system (PPAS) that can detect bacteria in water with the potential application in a point-of-sample collection setting. A centrifugal microfluidic platform is adopted to integrate bacterial cell lysis in water samples, nucleic acid extraction, and reagent mixing with a droplet digital loop mediated isothermal amplification assay for bacteria quantification onto a single centrifugal disc (CD). Coupled with a portable "CD Driver" capable of automating the assay steps, the CD functions as a single step bacterial detection "lab" without the need to transfer samples from vial-to-vial as in a traditional laboratory. The prototype system can detect Enterococcus faecalis, a common fecal indicator bacterium, in water samples with a single touch of a start button within 1 h and having total hands-on-time being less than 5 min. An add-on bacterial concentration cup prefilled with absorbent polymer beads was designed to integrate with the pathogen CD to improve the downstream quantification sensitivity. All reagents and amplified products are contained within the single-use disc, reducing the opportunity of cross contamination of other samples by the amplification products. This proof-of-concept PPAS lays the foundation for field testing devices in areas needing more accessible water quality monitoring tools and are at higher risk for being exposed to contaminated waters.

African fermented foods: overview, emerging benefits, and novel approaches to microbiome profiling

Traditional fermented foods are of major importance with respect to the socio-economic growth, food security, nutrition, and health of African consumers. In several African countries, traditional fermentation processes provide a means of food preservation, improving the shelf life and adding to the nutrients in the food products. As with any fermented foods, the associated food microbiota is of great importance and interest. Recent studies on the microbiome of African fermented foods using high-throughput DNA sequencing techniques have revealed the presence of diverse microbial populations of fundamental, technological, and commercial interest that could be harnessed to further improve health, food safety, and quality. This review provides an overview of African fermented foods, their microbiota, and the health-promoting potential of these foods and microbes.

Quantifying Circulating IgY Antibody Responses against Select Opportunistic Bacterial Pathogens and Correlations with Body Condition Factors in Wild American Alligators, Alligator mississippiensis

Simple Summary

Immunoglobulin Y (IgY) was purified from American alligator, Alligator mississippiensis, serum and used to develop a monoclonal antibody (mAb AMY-9) specific for the heavy chains of IgY. This antibody tool was then used to develop an ELISA for quantifying serum antibody responses against whole bacterial pathogens in alligators sampled in Florida, USA and South Carolina, USA. Antibody responses against some of the bacteria were very robust and varied by location and year, and in general these antibody responses correlated well with body condition factors, such as body-mass-indices (BMI). A novel mAb is now available to the scientific community interested in disease ecology of alligators.

Abstract

Little is known about the disease ecology of American alligators (Alligator mississippiensis), and especially how they respond immunologically to emerging infectious diseases and zoonotic pathogens. In this study, we examined serum samples collected from wild alligators in Florida (2010–2011) and South Carolina (2011–2012, 2014–2017) for antibody responses to multiple bacteria. Immunoglobulin Y (IgY) was purified from serum to generate a mouse monoclonal antibody (mAb AMY-9) specific to the IgY heavy chain. An indirect ELISA was then developed for quantifying antibody responses against whole cell Escherichia coli,Vibrio parahaemolyticus, Vibrio vulnificus, Mycobacterium fortuitum, Erysipelothrix rhusiopthiae, and Streptococcus agalactiae. In Florida samples the primary differences in antibody levels were between January–March and late spring through summer and early fall (May-October), most likely reflecting seasonal influences in immune responses. Of note, differences over the months in antibody responses were confined to M. fortuitum, E. rhusiopthiae, V. vulnificus, and E. coli. Robust antibody responses in SC samples were observed in 2011, 2014, and 2015 against each bacterium except E. coli. All antibody responses were low in 2016 and 2017. Some of the highest antibody responses were against V. parahaemolyticus, M. fortuitum, and E. rhusiopthiae. One SC alligator estimated to be 70+ years old exhibited the highest measured antibody response against V. parahaemolyticus and M. fortuitum. By combining data from both sites, we show a clear correlation between body-mass-indices (BMI) and antibody titers in all six of the bacteria examined. Our study provides a critical antibody reagent and a proof-of-concept approach for studying the disease ecology of alligators in both the wild and in captivity.

Membrane-Based In-Gel Loop-Mediated Isothermal Amplification (mgLAMP) System for SARS-CoV-2 Quantification in Environmental Waters

Since the COVID-19 pandemic is expected to become endemic, quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambient waters is critical for environmental surveillance and for early detection of outbreaks. Herein, we report the development of a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system that is designed for the rapid point-of-use quantification of SARS-CoV-2 particles in environmental waters. The mgLAMP system integrates the viral concentration, in-assay viral lysis, and on-membrane hydrogel-based RT-LAMP quantification using enhanced fluorescence detection with a target-specific probe. With a sample-to-result time of less than 1 h, mgLAMP successfully detected SARS-CoV-2 below 0.96 copies/mL in Milli-Q water. In surface water, the lowest detected SARS-CoV-2 concentration was 93 copies/mL for mgLAMP, while the reverse transcription quantitative polymerase chain reaction (RT-qPCR) with optimal pretreatment was inhibited at 930 copies/mL. A 3D-printed portable device is designed to integrate heated incubation and fluorescence illumination for the simultaneous analysis of nine mgLAMP assays. Smartphone-based imaging and machine learning-based image processing are used for the interpretation of results. In this report, we demonstrate that mgLAMP is a promising method for large-scale environmental surveillance of SARS-CoV-2 without the need for specialized equipment, highly trained personnel, and labor-intensive procedures.

Microbiological survey and occurrence of bacterial foodborne pathogens in raw and ready-to-eat green leafy vegetables marketed in Tehran, Iran

Fresh leafy (FL) and ready-to-eat (RTE) vegetables are recognized as an important source of foodborne disease outbreaks worldwide. Currently, there are no data available for the prevalnce of bacterial foodborne pathogens (FBPs) in raw vegetables consumed in Iran. Here, we evalated the presence of common bacterial FBPs among 366 samples of raw vegetables including 274 FL and 92 RTE collected from 21 districts of Tehran. The presence of FBPs were screened using conventional microbiological culture methods and real-time PCR assays. Overall, a higher rate of bacterial contamination was detected in FL compared to RTE samples using both detection methods. The results obtained by microbiological methods showed that Staphylococcus aureus (134/366, 36.6%), followed by Escherichia coli (85/366, 23.2%) and Clostridium perfringens (66/366, 18%) were detetcted as the most prevalent pathogens in this study. Vibrio cholerae was not detected in any of the samples either by microbiological methods or by the real-time PCR assays. There was a noticeable reduction in the proportion of Campylobacter positive samples using conventional microbiological methods (3.5%) compared to the real-time PCR assay (20.7%). The proportion of FL and RTE positive samples obtained by conventional microbiological methods was significantly different (P < 0.05) for C. perfringens, Campylobacter spp. and S. aureus. The proportion of positive samples in FL and RTE vegetables obtained by the real-time PCR assays was significantly different (P < 0.05) for C. perfringens, S. aureus, Helicobacter pylori and STEC/EHEC, the last one was found more frequently in RTE than in FL samples. Our findings indicated a contamination of FL and RTE vegetables in Iran with a range of well-known and emerging FBPs. Positivity and the distribution of bacterial species from the current data indicated different contamination sources, and overall a lack of effective decontamination steps during the production chain. Moreover, further information about the quality of the water, the hygiene measures implemented during the processing, storage and marketing are required to better identify the critical points and define the proper measures.

Nanotechnology-based Colorimetric Approaches for Pathogenic Virus Sensing: A review

Fast and inexpensive virus identification protocols are paramount to hinder the further extent of pandemic diseases, minimize economic and social damages, and expedite proper clinical rehabilitation. Until now, various biosensors have been fabricated for the identification of pathogenic particles. But, they offer many difficulties. Nanotechnology resolves these difficulties and offers direct identification of pathogenic species in real-time. Among them, nanomaterial based-colorimetric sensing approach of pathogenic viruses by the naked eye has attracted much awareness because of their simplicity, speed, and low cost. In this review, the latest tendencies and advancements are overviewed in detecting pathogenic viruses using colorimetric concepts. We focus on and reconsider the use of distinctive nanomaterials such as metal nanoparticles, carbon nanotubes, graphene oxide, and conducting polymer to form colorimetric pathogenic virus sensors.

Rapid quantification of fecal indicator bacteria in water using the most probable number - loop-mediated isothermal amplification (MPN-LAMP) approach on a polymethyl methacrylate (PMMA) microchip

Fecal contamination of water and its associated pathogens are a major public health concern in both developing and industrialized areas. Fecal indicator bacteria (FIB) are commonly used to assess microbial water quality, but they require a relatively long period of incubation time. Currently, molecular techniques have been applied to rapidly detect FIB. However, these molecular techniques require expensive and sophisticated equipment. In this study, we developed a rapid on-chip gene quantification method based on loop-mediated isothermal amplification (LAMP) PCR. The LAMP assays can measure the target genes of the fecal indicator bacteria (FIB), including E. coli and Enterococcus spp, using the most probable number (MPN) approach. The colorimetric LAMP assay allows for naked-eye observation of the PCR reaction as few as 4 gene copies / well. When the reaction ends, MPN measurement of positive outcomes on the white-based PMMA (polymethacrylic acid) microchips provides the concentrations of the target genes of FIB with a confidence interval. We validated the feasibility of the MPN-LAMP approach by obtaining a strong correlation between the results of the MPN estimations and the qPCR analysis. Moreover, the MPN-LAMP approach was used to quantify the FIB in different environmental water collected from the freshwater reservoirs, beach, agriculture farm, and sewage. Our research demonstrates that the MPN- LAMP method enables us to easily and quickly quantifying FIB genes isolated from the environment without expensive qPCR instruments.

Three-Way Junction-Induced Isothermal Amplification with High Signal-to-Background Ratio for Detection of Pathogenic Bacteria

The consumption of water and food contaminated by pathogens is a major cause of numerous diseases and deaths globally. To control pathogen contamination and reduce the risk of illness, a system is required that can quickly detect and monitor target pathogens. We developed a simple and reproducible strategy, termed three-way junction (3WJ)-induced transcription amplification, to detect target nucleic acids by rationally combining 3WJ-induced isothermal amplification with a light-up RNA aptamer. In principle, the presence of the target nucleic acid generates a large number of light-up RNA aptamers (Spinach aptamers) through strand displacement and transcription amplification for 2 h at 37 °C. The resulting Spinach RNA aptamers specifically bind to fluorogens such as 3,5-difluoro-4-hydroxybenzylidene imidazolinone and emit a highly enhanced fluorescence signal, which is clearly distinguished from the signal emitted in the absence of the target nucleic acid. With the proposed strategy, concentrations of target nucleic acids selected from the genome of Salmonellaenterica serovar Typhi (S. Typhi) were quantitatively determined with high selectivity. In addition, the practical applicability of the method was demonstrated by performing spike-and-recovery experiments with S. Typhi in human serum.

Covalent capture and electrochemical quantification of pathogenic E. coli

Pathogenic E. coli pose a significant threat to public health, as strains of this species cause both foodborne illnesses and urinary tract infections. Using a rapid bioconjugation reaction, we selectively capture E. coli at a disposable gold electrode from complex solutions and accurately quantify the pathogenic microbes using electrochemical impedance spectroscopy.

Field grand challenge with emerging superbugs and the novel coronavirus (SARS-CoV-2) on plastics and in water

This opinion paper reports field grand challenges associated with plastic and water contaminated with the novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) and superbugs, given the emergency of public health and environmental protection from the presence of lethal viruses and bacteria. Two primary focuses of detection and treatment methods for superbugs and the novel coronavirus (SARS-CoV-2) are investigated, and the future outlook is provided based on grand challenges identified in the water field. Applying conventional treatment technologies to treat superbugs or the novel coronavirus (SARS-CoV-2) has brought negative results, including ineffective treatment, formation of toxic byproducts, and limitation of long-term performance. Existing detection methods are not feasible to apply in terms of sensitivity, difficulty of applications in field samples, speed, and accuracy at the time of sample collection. Few studies are found on superbugs or adsorption of the novel coronavirus (SARS-CoV-2) on plastic, as well as effects of superbugs or the novel coronavirus (SARS-CoV-2) on treatment of plastic waste and wastewater. With the need for and directions of further research and challenges discussed in this paper, we believe that this opinion paper offers information useful to a wide audience, including scientists, policy makers, consultants, public health workers, and field engineers in the water sector.