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In this work, a microfluidic prototype based on polymeric materials was developed to monitor surface processes using surface-enhanced Raman spectroscopy (SERS), keeping the reagents free of environmental contamination. The prototype was fabricated on poly(methyl methacrylic acid) (PMMA). A micrometric membrane of a functional organic polymer (FOP) based on p-terphenyl and bromopyruvic acid monomers was formed on the PMMA surface to promote the formation of metal nanoclusters. Au nanosized film was deposited on the FOP membrane to give rise to the SERS effect. A microchannel was formed on another piece of PMMA using micromachining. A representative 3D model of the prototype layer arrangement was built and simulated in COMSOL Multiphysics® to approximate the electric field distribution and calculate the power enhancement factor as the Au film changes over time. The fabrication process was characterized using UV–visible and Raman spectroscopies and XPS. The prototype was tested using a Raman microscope and liquid solutions of cysteamine and Escherichia coli (E. coli). The simulation results demonstrated that the morphological characteristics of the Au layer give rise to the SERS effect, and the power enhancement factor reaches values as high as 8.8 × 105 on the FOP surface. The characterization results showed the formation of the FOP and the Au film on PMMA and the surface functionalization with amine groups. The Raman spectra of the prototype showed temporal evolution as different compounds were deposited on the upper wall of the microchannel. Characteristic peaks associated with these compounds were detected with continuous monitoring over time. This prototype offers many benefits for applications like monitoring biological processes. Some advantages include timely surface evaluation while avoiding environmental harm, decreased use of reagents and samples, minimal interference with the process by measuring, and detecting microorganisms in just 1 h, as demonstrated with the E. coli sample. [ABSTRACT FROM AUTHOR]

Contamination of cell cultures can result in a significant loss of precious biological material, particularly in long-term processes including amplification of chimeric antigen receptors (CAR)-T cells and differentiation of patient-derived stem cells, for therapeutic purposes. Bacterial contamination can also lead to more complex conditions such as sepsis which can cause morbidity and mortality, despite strict controls and good laboratory/manufacturing practices in the manipulation of complex biological samples such as blood used in autologous and allogeneic stem cells transplantation.The current standard method to identify biological risk is the set-up of microbial cultures, which can be time consuming with the likelihood of wasting large amounts of reagents in the event of contamination.Real-Time Polymerase Chain Reaction (qPCR) is a molecular method able to detect biological agents in a highly sensitive and specific way and in a short time. However, qPCR assays require complex DNA/RNA purification steps and expensive benchtop instruments, which may not always be available.This paper reports an extraction-free and low-volume protocol for qPCR in a standard instrument, which has been demonstrated to be effective on both Gram-positive (Gram+) and Gram-negative (Gram-) bacteria. Detection has been obtained from spiked cell culture samples, reaching a limit of detection (LOD) of 1 colony forming unit (CFU)/ml. To demonstrate the high potential of this optimized procedure, the same samples were also tested on a Point-Of-Care platform, which includes a cartridge with micro-chambers and a compact instrument, capable of performing qPCR with the same efficiency. Staphylococcus aureus (Gram+) was selected as the target for a proof of concept, achieving a LOD of 1 CFU/ml also on the portable device. The availability of these results paves the way for a simplified protocol for DNA extraction and amplification.

To ensure clean drinking water, viable pathogens in water must be rapidly and efficiently screened. The traditional culture or spread-plate process—the conventional standard for bacterial detection—is laborious, time-consuming, and unsuitable for rapid detection. Therefore, we developed a colorimetric assay for rapid microorganism detection using a metabolism-based approach. The reaction between a viable microorganism and the combination of 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium sodium salt (WST-8) and 1-methoxy-5-methylphenazinium methyl sulfate (mPMS) results in a color change. In combination with a microplate reader, WST-8-mPMS reactivity was leveraged to develop a colorimetric assay for the rapid detection of various bacteria. The detection limit of the WST-8-mPMS assay for both gram-negative and gram-positive bacteria was evaluated. This WST-8-mPMS assay can be used to perform colorimetrical semi-quantitative detection of various bacterial strains in buffers or culture media within 1 h without incubation before the reaction. The easy-to-use, robust, rapid, and sensitive nature of this novel assay demonstrates its potential for practical and medical use for microorganism detection. [ABSTRACT FROM AUTHOR]

In this work, a microfluidic prototype based on polymeric materials was developed to monitor surface processes using surface-enhanced Raman spectroscopy (SERS), keeping the reagents free of environmental contamination. The prototype was fabricated on poly(methyl methacrylic acid) (PMMA). A micrometric membrane of a functional organic polymer (FOP) based on p-terphenyl and bromopyruvic acid monomers was formed on the PMMA surface to promote the formation of metal nanoclusters. Au nanosized film was deposited on the FOP membrane to give rise to the SERS effect. A microchannel was formed on another piece of PMMA using micromachining. A representative 3D model of the prototype layer arrangement was built and simulated in COMSOL Multiphysics® to approximate the electric field distribution and calculate the power enhancement factor as the Au film changes over time. The fabrication process was characterized using UV–visible and Raman spectroscopies and XPS. The prototype was tested using a Raman microscope and liquid solutions of cysteamine and Escherichia coli (E. coli). The simulation results demonstrated that the morphological characteristics of the Au layer give rise to the SERS effect, and the power enhancement factor reaches values as high as 8.8 × 105 on the FOP surface. The characterization results showed the formation of the FOP and the Au film on PMMA and the surface functionalization with amine groups. The Raman spectra of the prototype showed temporal evolution as different compounds were deposited on the upper wall of the microchannel. Characteristic peaks associated with these compounds were detected with continuous monitoring over time. This prototype offers many benefits for applications like monitoring biological processes. Some advantages include timely surface evaluation while avoiding environmental harm, decreased use of reagents and samples, minimal interference with the process by measuring, and detecting microorganisms in just 1 h, as demonstrated with the E. coli sample.

Corrosion is a key common science and technologies problem for oil and gas field pipelines. Microbiologically influenced corrosion(MIC) is one of the main types of corrosion in oil and gas fields, and how to control MIC is also a challenge in the oil and gas field exploitation. This paper reviews the research status, progress and the current main control methods and technologies of MIC in oil and gas fields. Corrosion microbial community, MIC mechanisms and corrosive microorganism detection and MIC control technologies are introduced, respectively. The future MIC research and corrosion control technologies are suggested as the conclusion. [ABSTRACT FROM AUTHOR]

Having an insight into graphene and graphene derivatives such as graphene oxide, reduced graphene oxide and graphene quantum dots is necessary since it can help scientists to detect possible properties and features that could be useful when using these carbon materials in preparation of a nanocomposites. In recent years, graphene and its derivatives have attracted a lot of attention and been extensively applied in biosensors due to fascinating properties, such as large surface area, optical and magnetic properties, and high elasticity for the detection of microorganisms as they can be modified with some other materials such as macromolecules, oxide metals and metals to improve the electrochemical behaviour of the biosensor. In this review paper, biosensor design strategies based on graphene and its derivatives (graphene-based nanocomposites in biosensors) are described. Then their application for the detection of microorganisms including prions, viroids, viral and bacterial cells as well as fungi, protozoa, microbial toxins and even microbial sources of antibiotics is reviewed.

To ensure clean drinking water, viable pathogens in water must be rapidly and efficiently screened. The traditional culture or spread-plate process—the conventional standard for bacterial detection—is laborious, time-consuming, and unsuitable for rapid detection. Therefore, we developed a colorimetric assay for rapid microorganism detection using a metabolism-based approach. The reaction between a viable microorganism and the combination of 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium sodium salt (WST-8) and 1-methoxy-5-methylphenazinium methyl sulfate (mPMS) results in a color change. In combination with a microplate reader, WST-8-mPMS reactivity was leveraged to develop a colorimetric assay for the rapid detection of various bacteria. The detection limit of the WST-8-mPMS assay for both gram-negative and gram-positive bacteria was evaluated. This WST-8-mPMS assay can be used to perform colorimetrical semi-quantitative detection of various bacterial strains in buffers or culture media within 1 h without incubation before the reaction. The easy-to-use, robust, rapid, and sensitive nature of this novel assay demonstrates its potential for practical and medical use for microorganism detection.

Having an insight into graphene and graphene derivatives such as graphene oxide, reduced graphene oxide and graphene quantum dots is necessary since it can help scientists to detect possible properties and features that could be useful when using these carbon materials in preparation of a nanocomposites. In recent years, graphene and its derivatives have attracted a lot of attention and been extensively applied in biosensors due to fascinating properties, such as large surface area, optical and magnetic properties, and high elasticity for the detection of microorganisms as they can be modified with some other materials such as macromolecules, oxide metals and metals to improve the electrochemical behaviour of the biosensor. In this review paper, biosensor design strategies based on graphene and its derivatives (graphene-based nanocomposites in biosensors) are described. Then their application for the detection of microorganisms including prions, viroids, viral and bacterial cells as well as fungi, protozoa, microbial toxins and even microbial sources of antibiotics is reviewed. [ABSTRACT FROM AUTHOR]

A series of fluorogenic heterocyclic azides were prepared and assessed as reductase substrates across a selection of Gram-negative and Gram-positive microorganisms. The majority of these azides showed similar activity profiles to nitroreductase substrates. Microorganisms that do not produce hydrogen sulfide reduced the azides, indicating reductase activity was not linked to hydrogen sulfide production. [ABSTRACT FROM AUTHOR]

Graphical abstract Abstract Six novel fluorogenic enzyme substrates for detecting l -alanylaminopeptidase activity in microorganisms have been prepared and evaluated in Columbia agar media. The substrates are l -alanyl derivatives of 6-amino-2-hetarylquinolines and 7-amino-3-hetarylcoumarins. Both the quinoline and coumarin series of substrates produced fluorescence in the presence of Gram-negative microorganisms. In contrast, fluorescence generation in the presence of the Gram-positive microorganisms and yeasts was limited or absent. [ABSTRACT FROM AUTHOR]

The early detection of Legionella in water reservoirs, and the prevention of their often fatal diseases, requires the development of rapid and reliable detection processes. A method for the magnetic separation (MS) of Legionella pneumophila by superparamagnetic iron oxide nanoparticles is developed, which represents the basis for future bacteria detection kits. The focus lies on the separation process and the simplicity of using magnetic nanomaterials. Iron oxide nanoparticles are functionalized with epoxy groups and Legionella-specific antibodies are immobilized. The resulting complexes are characterized with infrared spectroscopy and tested for the specific separation and enrichment of the selected microorganisms. The cell-particle complexes can be isolated in a magnetic field and detected with conventional methods such as fluorescence detection. A nonspecific enrichment of bacteria is also possible by using bare iron oxide nanoparticles (BIONs), which we used as a reference to the nanoparticles with immobilized antibodies. Furthermore, the immunomagnetic separation can be applied for the detection of multiple other microorganisms and thus might pave the way for simpler bacterial diagnosis.

The safety in agriculture, food and medicine production and processing is of grave importance to global economic and social stability. Efficient techniques for microorganism detection are essential to control health risks during product circulation. Rapid development in functional nucleic acids (FNAs) and molecular amplification technologies with improvements in the operation time, sensitivity and high throughput analysis have brought about a qualitative leap in microorganism detection. This review gives an investigative summary of many novel microorganism detection methods driven by nucleic acid-aided molecular amplification techniques (NAAMAT) in three aspects: direct to indirect methods, simple to integrated strategies, and representative applications. This paper will provide a useful reference and guide for future development of more advanced nucleic acid-aided molecular amplification techniques. • Nucleic acid aided-molecular amplification techniques (NAAMAT) are divided into 3 aspects from direct to indirect, simple to comprehensive. • The functional nucleic acids from multidimensional driven high performance amplification technology is reviewed. • A gradual in-depth participation of NAAMAT in the process of microorganism detection is analyzed comprehensively. • The application status and promising of NAAMAT in microbial detection is systematically expounded. [ABSTRACT FROM AUTHOR]

Pathogenic bacteria cause serious harm to human health, which calls for the development of advanced detection methods. Herein, we developed a novel detection platform based on fluorescence resonance energy transfer (FRET) for rapid, ultrasensitive and specific bacteria detection, where gold nanoparticles (AuNPs, acceptor) were conjugated with aptamers while upconversion nanoparticles (UCNPs, donor) were functionalized with corresponding complementary DNA (cDNA). The spectral overlap between UCNPs fluorescence emission and AuNPs absorption enables the occurrence of FRET when hybridizing the targeted aptamer and cDNA, causing upconversion fluorescence quenching. In the presence of target bacteria, the aptamers preferentially bind to bacteria forming a three-dimensional structure and thereby dissociate UCNPs-cDNA from AuNPs-aptamers, resulting in the recovery of upconversion fluorescence. Using the UCNPs based FRET aptasensor, we successfully detected Escherichia coli ATCC 8739 (as a model analyte) with a detection range of 5–10 6 cfu/mL and detection limit of 3 cfu/mL. The aptasensor was further used to detect E. coli in real food and water samples (e.g., tap/pond water, milk) within 20 min. The novel UCNPs based FRET aptasensor could be used to detect a broad range of targets from whole cells to metal ions by using different aptamer sequences, holding great potential in environmental monitoring, medical diagnostics and food safety analysis. [ABSTRACT FROM AUTHOR]

Contamination of cell cultures can result in a significant loss of precious biological material, particularly in long-term processes including amplification of chimeric antigen receptors (CAR)-T cells and differentiation of patient-derived stem cells, for therapeutic purposes. Bacterial contamination can also lead to more complex conditions such as sepsis which can cause morbidity and mortality, despite strict controls and good laboratory/manufacturing practices in the manipulation of complex biological samples such as blood used in autologous and allogeneic stem cells transplantation. The current standard method to identify biological risk is the set-up of microbial cultures, which can be time consuming with the likelihood of wasting large amounts of reagents in the event of contamination. Real-Time Polymerase Chain Reaction (qPCR) is a molecular method able to detect biological agents in a highly sensitive and specific way and in a short time. However, qPCR assays require complex DNA/RNA purification steps and expensive benchtop instruments, which may not always be available. This paper reports an extraction-free and low-volume protocol for qPCR in a standard instrument, which has been demonstrated to be effective on both Gram-positive (Gram+) and Gram-negative (Gram-) bacteria. Detection has been obtained from spiked cell culture samples, reaching a limit of detection (LOD) of 1 colony forming unit (CFU)/ml. To demonstrate the high potential of this optimized procedure, the same samples were also tested on a Point-Of-Care platform, which includes a cartridge with micro-chambers and a compact instrument, capable of performing qPCR with the same efficiency. Staphylococcus aureus (Gram+) was selected as the target for a proof of concept, achieving a LOD of 1 CFU/ml also on the portable device. The availability of these results paves the way for a simplified protocol for DNA extraction and amplification., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

A series of carboxy-substituted 2-(nitroaryl)benzothiazole derivatives and carboxy-substituted 2-(nitroaryl)benzoxazole derivatives were prepared and evaluated as potential nitroreductase substrates for the purpose of detecting clinically important microorganisms. Several of the substrates produced highly fluorescent colonies with the majority of a panel of 10 Gram-negative bacteria and also with two of a panel of 8 Gram-positive bacteria. [ABSTRACT FROM AUTHOR]

The early detection of Legionella in water reservoirs, and the prevention of their often fatal diseases, requires the development of rapid and reliable detection processes. A method for the magnetic separation (MS) of Legionella pneumophila by superparamagnetic iron oxide nanoparticles is developed, which represents the basis for future bacteria detection kits. The focus lies on the separation process and the simplicity of using magnetic nanomaterials. Iron oxide nanoparticles are functionalized with epoxy groups and Legionella-specific antibodies are immobilized. The resulting complexes are characterized with infrared spectroscopy and tested for the specific separation and enrichment of the selected microorganisms. The cell-particle complexes can be isolated in a magnetic field and detected with conventional methods such as fluorescence detection. A nonspecific enrichment of bacteria is also possible by using bare iron oxide nanoparticles (BIONs), which we used as a reference to the nanoparticles with immobilized antibodies. Furthermore, the immunomagnetic separation can be applied for the detection of multiple other microorganisms and thus might pave the way for simpler bacterial diagnosis. [ABSTRACT FROM AUTHOR]

Classical and culture-based methods for the identification and characterization of the biochemical properties of microorganisms are slow and labor-intensive. Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) has been used for the analysis of bacterial pathogen strain-specific diagnostic peptides allowing the characterization of bacterial strains.Here, we describe the analysis of tryptic digestion peptides by LC-ESI-MS/MS to search for specific biomarkers useful for the rapid identification of, on the one hand, the bacterial species and, on the other hand, the physiological and biochemical characteristics such as the expression of virulence factors, including toxins, immune-modulatory factors, and exoenzymes.