A Comprehensive Review of Innovative Paradigms in Microbial Detection and Antimicrobial Resistance: Beyond Traditional Cultural Methods

Microbial detection and antimicrobial resistance (AMR) surveillance are critical components of public health efforts to combat infectious diseases and preserve the efficacy of antimicrobial agents. While foundational in microbial identification, traditional cultural methods are often laborious, time-consuming, and limited in their ability to detect AMR markers. In response to these challenges, innovative paradigms have emerged, leveraging advances in molecular biology, genomics, proteomics, nanotechnology, and bioinformatics. This comprehensive review provides an overview of innovative approaches beyond traditional cultural methods for microbial detection and AMR surveillance. Molecular-based techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer enhanced sensitivity and specificity, enabling the rapid identification of microbial pathogens and AMR determinants. Mass spectrometry-based methods provide rapid and accurate detection of microbial biomarkers, including matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and biosensor technologies. Nanotechnology approaches, such as nanoparticle-based assays and nanopore sequencing, offer novel platforms for sensitive and label-free detection of pathogens and AMR markers. Embracing these innovative paradigms holds immense promise for improving disease diagnosis, antibiotic stewardship, and AMR containment efforts. However, challenges such as cost, standardization, and integration with existing healthcare systems must be addressed to realize the full potential of these technologies. By fostering interdisciplinary collaboration and innovation, we can strengthen our ability to detect, monitor, and combat AMR, safeguarding public health for generations.

Recent advances in the analytical strategies of microbial biosensor for detection of pollutants

Microbial biosensor which integrates different types of microorganisms, such as bacteria, microalgae, fungi, and virus have become suitable technologies to address limitations of conventional analytical methods. The main applications of biosensors include the detection of environmental pollutants, pathogenic bacteria and compounds related to illness, and food quality. Each type of microorganisms possesses advantages and disadvantages with different mechanisms to detect the analytes of interest. Furthermore, there is an increasing trend in genetic modifications for the development of microbial biosensors due to potential for high-throughput analysis and portability. Many review articles have discussed the applications of microbial biosensor, but many of them focusing only about bacterial-based biosensor although other microbes also possess many advantages. Additionally, reviews on the applications of all microbes as biosensor especially viral and microbial fuel cell biosensors are also still limited. Therefore, this review summarizes all the current applications of bacterial-, microalgal-, fungal-, viral-based biosensor in regard to environmental, food, and medical-related applications. The underlying mechanism of each microbes to detect the analytes are also discussed. Additionally, microbial fuel cell biosensors which have great potential in the future are also discussed. Although many advantageous microbial-based biosensors have been discovered, other areas such as forensic detection, early detection of bacteria or virus species that can lead to pandemics, and others still need further investigation. With that said, microbial-based biosensors have promising potential for vast applications where the biosensing performance of various microorganisms are presented in this review along with future perspectives to resolve problems related on microbial biosensors.

Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

Luminescence Nanomaterials for Biosensing Applications

Due to their capabilities of immobilizing more bioreceptor parts with reduced volumes, nanomaterials have emerged as potential tools for increasing sensitivity to specific molecules. Furthermore, carbon nanotube, gold nanoparticles, polymer nanoparticles, semiconductor quantum dots, graphene, nano-diamonds and graphene are among the nanomaterials that are under investigation. Due to the fast development of such a field of research, review summarises the classification of biosensors using main receptors, and designing biosensors. Numerous studies have concentrated on the manipulation of Persistent luminescence nanoparticles (PLNPs) in biosensing, cell tracking, bioimaging, and cancer therapy due to the effective removal of the autofluorescence interferences from tissues and the ultra-long near-infrared afterglow emission. As luminescence has a unique optical property, it can be detected without constant external illumination, preventing autofluorescence and light dispersion through tissues. These successes sparked an increasing curiosity in creating novel PLNP kinds with desired superior properties and multiple purposes. In this review, we emphasize the most recent developments in biosensing, imaging, and image-guided therapy while summarizing the research on synthesis methods, bio applications, bio membrane modification and bio-safety of PLNPs. Finally, the remaining issues and difficulties are examined together with prospective future developments in the field of biomedical applications.

Restoration of the Indicator Properties of Whole-cell Luminescent Biosensors

Whole-cell biosensors are widely used to produce medical diagnostic tests, but in the long term, they tend to lose their indicator properties. Consequently, it is crucial to find ways to restore these properties and prolong the shelf life of the tests. Here, we propose to use electromagnetic radiation with optimally selected parameters of frequency, power, and exposure time. The impact of radiation parameters on biosensor luminescence was studied as well as the effects of different types of radiation coming from laser sources (λ = 875 nm), a LED source (λ = 850 ÷ 890 nm), and microwave units (at frequencies 42.22, 53.53, 61.18 и 34 ÷ 38 GHz). IR treatment resulted in dose-dependent suppression of biosensor luminescence. The luminescence level when exposed to microwave radiation depends on the radiation time and frequency. Also, it has been found that optimal selection of the main radiation parameters enables to restore indicator properties partially lost by biosensors during storage. We explain the mechanism responsible for the sensitizing effect of radiation, which implies the polarization of solvent dipoles and changes in mobility of acceptor molecules. This, in turn, leads to a shift in the chemical equilibrium states and triggers a cascade of biochemical reactions that lead to restoration of the lost indicator properties of biosensors. The study of antagonistic activity has revealed that restored biosensors provide reliable test results after the expiration of their warranty period.

Highly Sensitive Luminescent Bioassay Using Recombinant Escherichia coli Biosensor for Rapid Detection of Low Cr(VI) Concentration in Environmental Water

In this study, we constructed a recombinant Escherichia coli strain with different promoters inserted between the chromate-sensing regulator chrB and the reporter gene luxAB to sense low hexavalent chromium (Cr(VI)) concentrations (<0.05 mg/L); subsequently, its biosensor characteristics (sensitivity, selectivity, and specificity) for measuring Cr(VI) in various water bodies were evaluated. The luminescence intensity of each biosensor depended on pH, temperature, detection time, coexisting carbon source, coexisting ion, Cr(VI) oxyanion form, Cr(VI) concentration, cell type, and type of medium. Recombinant lux-expressing E. coli with the T7 promoter (T7-lux-E. coli, limit of detection (LOD) = 0.0005 mg/L) had the highest luminescence intensity or was the most sensitive for Cr(VI) detection, followed by E. coli with the T3 promoter (T3-lux-E. coli, LOD = 0.001 mg/L) and that with the SP6 promoter (SP6-lux-E. coli, LOD = 0.005 mg/L). All biosensors could be used to determine whether the Cr(VI) standard was met in terms of water quality, even when using thawing frozen cells as biosensors after 90-day cryogenic storage. The SP6-lux-E. coli biosensor had the shortest detection time (0.5 h) and the highest adaptability to environmental interference. The T7-lux-E. coli biosensor—with the optimal LOD, a wide measurement range (0.0005–0.5 mg/L), and low deviation (−5.0–7.9%) in detecting Cr(VI) from industrial effluents, domestic effluents, and surface water—is an efficient Cr(VI) biosensor. This unprecedented study is to evaluate recombinant lux E. coli with dissimilar promoters for their possible practice in Cr(VI) measurement in water bodies, and the biosensor performance is clearly superior to that of past systems in terms of detection time, LOD, and detection deviation for real water samples.

Recent Advances in Nanotechnology-Based Biosensors Development for Detection of Arsenic, Lead, Mercury, and Cadmium

Heavy metals cause considerable environmental pollution due to their extent and non-degradability in the environment. Analysis and trace levels of arsenic, lead, mercury, and cadmium as the most toxic heavy metals show that they can cause various hazards in humans' health. To achieve rapid, high-sensitivity methods for analyzing ultra-trace amounts of heavy metals in different environmental and biological samples, novel biosensors have been designed with the participation of strategies applied in nanotechnology. This review attempted to investigate the novel, sensitive, efficient, cost-benefit, point of care, and user-friendly biosensors designed to detect these heavy metals based on functional mechanisms. The study's search strategies included examining the primary databases from 2015 onwards and various keywords focusing on heavy metal biosensors' performance and toxicity mechanisms. The use of aptamers and whole cells as two important bio-functional nanomaterials is remarkable in heavy metal diagnostic biosensors' bioreceptor design. The application of hybridized nanomaterials containing a specific physicochemical function in the presence of a suitable transducer can improve the sensing performance to achieve an integrated detection system. Our study showed that in addition to both labeled and label-free detection strategies, a wide range of nanoparticles and nanocomposites were used to modify the biosensor surface platform in the detection of heavy metals. The detection limit and linear dynamic range as an essential characteristic of superior biosensors for the primary toxic metals are studied. Furthermore, the perspectives and challenges facing the design of heavy metal biosensors are outlined. The development of novel biosensors and the application of nanotechnology, especially in real samples, face challenges such as the capability to simultaneously detect multiple heavy metals, the interference process in complex matrices, the efficiency and stability of nanomaterials implemented in various laboratory conditions.

Impedimetric transducers based on interdigitated electrode arrays for bacterial detection - A review

Application of the impedance spectroscopy technique to detection of bacteria has advanced considerably over the last decade. This is reflected by the large amount of publications focused on basic research and applications of impedance biosensors. Employment of modern technologies to significantly reduce dimension of impedimetric devices enable on-chip integration of interdigitated electrode arrays for low-cost and easy-to-use sensors. This review is focused on publications dealing with interdigitated electrodes as a transducer unit and different bacteria detection systems using these devices. The first part of the review deals with the impedance technique principles, paying special attention to the use of interdigitated electrodes, while the main part of this work is focused on applications ranging from bacterial growth monitoring to label-free specific bacteria detection.

Extracellular electron transfer features of Gram-positive bacteria

Electroactive microorganisms possess the unique ability to transfer electrons to or from solid phase electron conductors, e.g., electrodes or minerals, through various physiological mechanisms. The processes are commonly known as extracellular electron transfer and broadly harnessed in microbial electrochemical systems, such as microbial biosensors, microbial electrosynthesis, or microbial fuel cells. Apart from a few model microorganisms, the nature of the microbe-electrode conductive interaction is poorly understood for most of the electroactive species. The interaction determines the efficiency and a potential scaling up of bioelectrochemical systems. Gram-positive bacteria generally have a thick electron non-conductive cell wall and are believed to exhibit weak extracellular electron shuttling activity. This review highlights reported research accomplishments on electroactive Gram-positive bacteria. The use of electron-conducting polymers as mediators is considered as one promising strategy to enhance the electron transfer efficiency up to application scale. In view of the recent progress in understanding the molecular aspects of the extracellular electron transfer mechanisms of Enterococcus faecalis, the electron transfer properties of this bacterium are especially focused on. Fundamental knowledge on the nature of microbial extracellular electron transfer and its possibilities can provide insight in interspecies electron transfer and biogeochemical cycling of elements in nature. Additionally, a comprehensive understanding of cell-electrode interactions may help in overcoming insufficient electron transfer and restricted operational performance of various bioelectrochemical systems and facilitate their practical applications.

Recent progress on cell-based biosensors for analysis of food safety and quality control

Food quality and safety has become a subject of major concern for authorities and professionals in the food supply chain. Rapid methods, particularly biosensors, have exceptional specificity and sensitivity, rapid response times, low cost, relatively compact size, and are user friendly to operate. Cell-based biosensors are portable, and provide the biological activity of the analyte suitable for an initial screening of food. In this overview, the utilization of cell-based biosensors for food safety and quality analyses, such as detecting toxins, foodborne pathogens, allergens, and evaluating toxicity and function are summarized. Our results will promote the future development of cell-based biosensors in the food field.

The fabrication and the use of immobilized cells as test organisms in a ferricyanide-based toxicity biosensor

Cell immobilization is an effective method to prolong the lifetime of a microorganism and has proven feasibility in some other biosensors. Thus, we studied the use of Escherichia coli immobilized by agar, gelatin, an agar/gelatin mixture, chitosan, and polyvinyl alcohol (PVA) to screen toxicity electrochemically. The E. coli immobilized by PVA gel showed the highest apparent bioactivity and the longest storage time in pH 7.0 phosphate-buffered saline solution. Furthermore, the E. coli immobilized by different gels was applied in the toxicity determination via a reported ferricyanide-mediated electrochemical method, where 3,5-dichlorophenol (DCP) was used as a model toxin. The E. coli immobilized by PVA showed the highest sensitivity to DCP, and the corresponding value of 50% inhibition concentration was 9.62 mg L^-1 . Inhibition concentrations were in the range of 6.32 to 13.75% when the E. coli immobilized by PVA was challenged by wastewater, which were comparable with values obtained with the standard luminescent bacteria method (effective inhibition were in the range 7.96-25.42% for the same samples). Given the apparent bioactivity, storage ability, and sensitivity to toxin, PVA was the best polymer to confine cells among the polymers used in the present study. Environ Toxicol Chem 2018;37:329-335. © 2017 SETAC.

Biosensors for the Detection of Environmental and Urban Pollutions

Release of harmful pollutants such as heavy metals, pesticides, and pharmaceuticals to the environment is a global concern. Rapid and reproducible detection of these pollutants is thus necessary. Biosensors are the sensitive and high specific tools for detection of environmental pollutants. Broad range various types of biosensors have been fabricated for this purpose. This review focuses on the feature and application of biosensors developed for environmental and urban pollutants detection. J. Cell. Biochem. 119: 207-212, 2018. © 2017 Wiley Periodicals, Inc.

Utility of Ochrobactrum anthropi YC152 in a Microbial Fuel Cell as an Early Warning Device for Hexavalent Chromium Determination

Fast hexavalent chromium (Cr(VI)) determination is important for environmental risk and health-related considerations. We used a microbial fuel cell-based biosensor inoculated with a facultatively anaerobic, Cr(VI)-reducing, and exoelectrogenic Ochrobactrum anthropi YC152 to determine the Cr(VI) concentration in water. The results indicated that O. anthropi YC152 exhibited high adaptability to pH, temperature, salinity, and water quality under anaerobic conditions. The stable performance of the microbial fuel cell (MFC)-based biosensor indicated its potential as a reliable biosensor system. The MFC voltage decreased as the Cr(VI) concentration in the MFC increased. Two satisfactory linear relationships were observed between the Cr(VI) concentration and voltage output for various Cr(VI) concentration ranges (0.0125-0.3 mg/L and 0.3-5 mg/L). The MFC biosensor is a simple device that can accurately measure Cr(VI) concentrations in drinking water, groundwater, and electroplating wastewater in 45 min with low deviations (<10%). The use of the biosensor can help in preventing the violation of effluent regulations and the maximum allowable concentration of Cr(VI) in water. Thus, the developed MFC biosensor has potential as an early warning detection device for Cr(VI) determination even if O. anthropi YC152 is a possible opportunistic pathogen.

Nanomaterials for biocatalyst immobilization – state of the art and future trends

Advantages, drawbacks and trends in nanomaterials for enzyme immobilization.

Fiber-Optic Chemical Sensors and Fiber-Optic Bio-Sensors

This review summarizes principles and current stage of development of fiber-optic chemical sensors (FOCS) and biosensors (FOBS). Fiber optic sensor (FOS) systems use the ability of optical fibers (OF) to guide the light in the spectral range from ultraviolet (UV) (180 nm) up to middle infrared (IR) (10 μm) and modulation of guided light by the parameters of the surrounding environment of the OF core. The introduction of OF in the sensor systems has brought advantages such as measurement in flammable and explosive environments, immunity to electrical noises, miniaturization, geometrical flexibility, measurement of small sample volumes, remote sensing in inaccessible sites or harsh environments and multi-sensing. The review comprises briefly the theory of OF elaborated for sensors, techniques of fabrications and analytical results reached with fiber-optic chemical and biological sensors.