A new approach to identifying pathogens, with particular regard to viruses, based on capillary electrophoresis and other analytical techniques

Differentiation of Escherichia coli and Shigella flexneri by Metabolite Profiles Obtained Using Gold Nanoparticles-Based Surface-Assisted Laser Desorption/Ionization Mass Spectrometry

Escherichia coli and Shigella flexneri are challenging to differentiate using methods such as phenotyping, 16S rRNA sequencing, or protein profiling through matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) due to their close relatedness. This study explores the potential for identifying E. coli and S. flexneri by incorporating reference spectra of metabolite profiles, obtained via surface-assisted laser desorption/ionization mass spectrometry (SALDI MS) employing gold nanoparticles (AuNPs), into the Bruker Biotyper database. Metabolite extracts from E. coli and S. flexneri cells were prepared using liquid-liquid extraction in a chloroform-methanol-water system. The extracts were analyzed using Au-SALDI MS in positive ion mode, and reference spectra, compiled from 30 spectra for each bacterium, were added to the database. Identification of bacteria based on metabolite fingerprints in the Biotyper database produced correct results with scores exceeding 2.75. The results of Partial Least Squares-Discriminant Analysis (PLS-DA) demonstrated that the metabolomic approach could accurately differentiate the microorganisms under study. A panel of nine m/z values was also identified, each with an area under the ROC curve of above 0.8, enabling accurate identification of E. coli and S. flexneri. A search of metabolite databases allowed the following compounds to be assigned to the selected m/z values: N-acetylputrescine, arginine, 2-maleylacetate, benzoyl phosphate, N8-acetylspermidine, alanyl-glutamate, 4-hydroxy-2,3,4,5-tetrahydrodipicolinate, and sucrose. The analyses showed that identification of bacteria based on metabolite profiles obtained by the Au-SALDI MS method is feasible and can be useful for distinguishing closely related microorganisms that are difficult to differentiate by other techniques.

Lipidomic approach to identify Escherichia coli and Shigella spp. by matrix-assisted laser desorption/ionization mass spectrometry

PURPOSE

Escherichia coli (E. coli) and Shigella species, being highly similar, present a challenge for differentiation using classical methods such as phenotyping, 16S rRNA sequencing, or protein profiling using matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The paper proposes a method for identifying E. coli, S. flexneri, S. sonnei, and S. boydii by augmenting the Bruker Biotyper database with reference spectra of lipid profiles obtained using MALDI MS in the positive mode.

MATERIALS/METHODS

Lipid extracts were made from cultured E. coli, S. flexneri, S. sonnei and S. boydii using the Bligh & Dyer protocol. MALDI MS spectra in positive ion mode were performed for the extracts. Reference spectra were created from 30 spectra for each bacterium and added to the Bruker Biotyper database.

RESULTS

Identification of bacteria based on lipid profiles in the Biotyper database gave correct results with scores above 2.49. Statistical analysis of the results by Partial Least Squares-Discriminant Analysis (PLS-DA) showed that it is possible to correctly differentiate the microorganisms studied using the lipidomic approach. A panel of six m/z values was proposed for which the value of the area under the ROC curve is 1, thus enabling the identification of E. coli and S. flexneri with 100 ​% accuracy.

CONCLUSIONS

Identification of bacteria from lipid fingerprints obtained by the MALDI MS technique is possible and may become a useful tool in the future, especially for microorganisms that are difficult to distinguish by other methods.

Development of a DC-Biased AC-Stimulated Microfluidic Device for the Electrokinetic Separation of Bacterial and Yeast Cells

Electrokinetic (EK) microsystems, which are capable of performing separations without the need for labeling analytes, are a rapidly growing area in microfluidics. The present work demonstrated three distinct binary microbial separations, computationally modeled and experimentally performed, in an insulator-based EK (iEK) system stimulated by DC-biased AC potentials. The separations had an increasing order of difficulty. First, a separation between cells of two distinct domains (Escherichia coli and Saccharomyces cerevisiae) was demonstrated. The second separation was for cells from the same domain but different species (Bacillus subtilis and Bacillus cereus). The last separation included cells from two closely related microbial strains of the same domain and the same species (two distinct S. cerevisiae strains). For each separation, a novel computational model, employing a continuous spatial and temporal function for predicting the particle velocity, was used to predict the retention time (tR,p) of each cell type, which aided the experimentation. All three cases resulted in separation resolution values Rs>1.5, indicating complete separation between the two cell species, with good reproducibility between the experimental repetitions (deviations < 6%) and good agreement (deviations < 18%) between the predicted tR,p and experimental (tR,e) retention time values. This study demonstrated the potential of DC-biased AC iEK systems for performing challenging microbial separations.

Glucose-metabolism-triggered colorimetric sensor array for point-of-care differentiation and antibiotic susceptibility testing of bacteria

Simple and sensitive discrimination of multiple bacteria and antimicrobial susceptibility test (AST) are significant for food safety, clinical diagnosis and treatment. Herein, based on different metabolic ability of bacteria on glucose, we presented a colorimetric sensor array for point-of-care testing (POCT) of multiple bacteria with methyl red (MER), bromothymol blue (BTB) and bromocresol green (BCG) as probes. Different bacteria resulted in different color changes of three probes, which was converted to RGB (Red (R)/Green (G)/Blue (B)) signals by the color recognizer APP loaded on smartphone. The sensor array performed differentiation of eleven species of bacteria, achieving the quantitative analysis of individual bacteria in tap water and differentiation of bacterial mixtures. Interestingly, the sensor array can be used for AST and evaluating minimal inhibitory concentration (MIC) of antibiotics to bacteria. The research provided meaningful guidance for distinguishing multiple bacteria and evaluating MIC, presenting great potential in practical application.

Sorting and simultaneous quantitation of intact mixed-cell samples via capillary isotachophoresis

A great need currently exists for rapid, inexpensive, and accurate methods for microbial analysis in the medical, food, industrial, and water quality fields. Here, a novel capillary isotachophoresis (CITP) method is presented for the focusing, sorting, and quantitation of intact cells in mixed samples based on their electrophoretic mobility ranges. Using a series of ion spacers dissolved in the sample, this technique results in several efficient cell peaks in the electropherogram corresponding to specific cell electrophoretic mobility ranges. The concentrations of different species in mixed-cell samples are determined from the cell peak areas and the known peak response factors for the cell species using a series of linear equations. Method design and optimization are discussed, including the choice of running buffer, pH, and ion spacers. Mixed-cell samples of up to four different species were focused and quantified as a proof-of-principle of the method. When sample cell concentrations were toward the middle of the linear response range, accuracies between 1% and 11% and relative standard deviations of 1%-14% were obtained, depending on the number of cell species in the mixture. This work provides a useful basis for future studies of cell quantitation using CITP, which could be potentially applied to a variety of fields including cell growth studies, microbial contamination testing, and sterility testing.

Comparison of the Bruker Microflex LT and Zybio EXS2600 MALDI TOF MS systems for the identification of clinical microorganisms

The emergence of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI TOF MS) technology has expanded the capabilities for identifying microorganisms in clinical labs, replacing traditional biochemical testing with a proteomic approach. In the present study, we compared results between the two commercial MALDI TOF MS systems, Bruker Microflex LT Biotyper and Zybio EXS2600 Ex-Accuspec, for the identification of 1979 urinary isolates by direct extraction method. Current study found that both systems identified a high percentage of isolates to at least the genus level - Bruker 95.6 % of isolates, Zybio 92.4 %. In the case of 89.5 % of all analyzed spectra, the identification results were consistent between the used devices. The highest score values and the highest percentage of spectra identified to species were obtained for gram-negative bacteria. The results show that both systems are equally good choices in terms of analytical performance for routine microbiological diagnostic procedures.

Assessing the Discriminatory Capabilities of iEK Devices under DC and DC-Biased AC Stimulation Potentials

There is a rising need for rapid and reliable analytical methods for separating microorganisms in clinical and biomedical applications. Microscale-insulator-based electrokinetic (iEK) systems have proven to be robust platforms for assessing a wide variety of microorganisms. Traditionally, iEK systems are usually stimulated with direct-current (DC) potentials. This work presents a comparison between using DC potentials and using DC-biased alternating-current (AC) potentials in iEK systems for the separation of microorganisms. The present study, which includes mathematical modeling and experimentation, compares the separation of bacterial and yeast cells in two distinct modes by using DC and DC-biased AC potentials. The quality of both separations, assessed in terms of separation resolution (Rs), showed a complete separation (Rs = 1.51) with the application of a DC-biased low-frequency AC signal but an incomplete separation (Rs = 0.55) with the application of an RMS-equivalent DC signal. Good reproducibility between experimental repetitions (<10%) was obtained, and good agreement (~18% deviation) was observed between modeling and experimental retention times. The present study demonstrates the potential of extending the limits of iEK systems by employing DC-biased AC potentials to perform discriminatory separations of microorganisms that are difficult to separate with the application of DC potentials.

The Rapid Detection of Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus via Polymerase Chain Reaction Combined with Magnetic Beads and Capillary Electrophoresis

Food safety concerns regarding foodborne pathogen contamination have gained global attention due to its significant implications. In this study, we developed a detection system utilizing a PCR array combined with an automated magnetic bead-based system and CE technology to enable the detection of three foodborne pathogens, namely Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus. The results showed that our developed method could detect these pathogens at concentrations as low as 7.3 × 101, 6.7 × 102, and 6.9 × 102 cfu/mL, respectively, in the broth samples. In chicken samples, the limit of detection for these pathogens was 3.1 × 104, 3.5 × 103, and 3.9 × 102 cfu/g, respectively. The detection of these pathogens was accomplished without the necessity for sample enrichment, and the entire protocols, from sample preparation to amplicon analysis, were completed in approximately 3.5 h. Regarding the impact of the extraction method on detection capability, our study observed that an automated DNA extraction system based on the magnetic bead method demonstrated a 10-fold improvement or, at the very least, yielded similar results compared to the column-based method. These findings demonstrated that our developed model is effective in detecting low levels of these pathogens in the samples analyzed in this study. The PCR-CE method developed in this study may help monitor food safety in the future. It may also be extended to identify other foodborne pathogens across a wide range of food samples.

Multi-Instrumental Analysis Toward Exploring the Diabetic Foot Infection Microbiota

The polymicrobial nature of diabetic foot infection (DFI) makes accurate identification of the DFI microbiota, including rapid detection of drug resistance, challenging. Therefore, the main objective of this study was to apply matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS) technique accompanied by multiply culture conditions to determine the microbial patterns of DFIs, as well as to assess the occurrence of drug resistance among Gram-negative bacterial isolates considered a significant cause of the multidrug resistance spread. Furthermore, the results were compared with those obtained using molecular techniques (16S rDNA sequencing, multiplex PCR targeting drug resistance genes) and conventional antibiotic resistance detection methods (Etest strips). The applied MALDI-based method revealed that, by far, most of the infections were polymicrobial (97%) and involved many Gram-positive and -negative bacterial species-19 genera and 16 families in total, mostly Enterobacteriaceae (24.3%), Staphylococcaceae (20.7%), and Enterococcaceae (19.8%). MALDI drug-resistance assay was characterized by higher rate of extended-spectrum beta-lactamases (ESBLs) and carbapenemases producers compared to the reference methods (respectively 31% and 10% compared to 21% and 2%) and revealed that both the incidence of drug resistance and the species composition of DFI were dependent on the antibiotic therapy used. MALDI approach included antibiotic resistance assay and multiply culture conditions provides microbial identification at the level of DNA sequencing, allow isolation of both common (eg. Enterococcus faecalis) and rare (such as Myroides odoratimimus) bacterial species, and is effective in detecting antibiotic-resistance, especially those of particular interest-ESBLs and carbapenemases.

Determination of Pathogens by Electrophoretic and Spectrometric Techniques

In modern medical diagnostics, where analytical chemistry plays a key role, fast and accurate identification of pathogens is becoming increasingly important. Infectious diseases pose a growing threat to public health due to population growth, international air travel, bacterial resistance to antibiotics, and other factors. For instance, the detection of SARS-CoV-2 in patient samples is a key tool to monitor the spread of the disease. While there are several techniques for identifying pathogens by their genetic code, most of these methods are too expensive or slow to effectively analyze clinical and environmental samples that may contain hundreds or even thousands of different microbes. Standard approaches (e.g., culture media and biochemical assays) are known to be very time- and labor-intensive. The purpose of this review paper is to highlight the problems associated with the analysis and identification of pathogens that cause many serious infections. Special attention was paid to the description of mechanisms and the explanation of the phenomena and processes occurring on the surface of pathogens as biocolloids (charge distribution). This review also highlights the importance of electromigration techniques and demonstrates their potential for pathogen pre-separation and fractionation and demonstrates the use of spectrometric methods, such as MALDI-TOF MS, for their detection and identification.

The engineered CRISPR-Mb2Cas12a variant enables sensitive and fast nucleic acid-based pathogens diagnostics in the field

Existing CRISPR/Cas12a-based diagnostic platforms offer accurate and vigorous monitoring of nucleic acid targets, but have the potential to be further optimized for more efficient detection. Here, we profiled 16 Cas12a orthologs, focusing on their trans-cleavage activity and their potential as diagnostic enzymes. We observed the Mb2Cas12a has more robust trans-cleavage activity than other orthologs, especially at lower temperatures. An engineered Mb2Cas12a-RRVRR variant presented robust trans-cleavage activity and looser PAM constraints. Moreover, we found the existing one-pot assay, which simultaneously performed Recombinase Polymerase Amplification (RPA) and Cas12a reaction in one system, resulted in the loss of single-base discrimination during diagnosis. Therefore, we designed a reaction vessel that physically separated the RPA and Cas12a steps while maintaining a closed system. This isolated but closed system made diagnostics more sensitive and specific and effectively prevented contamination. This shelved Mb2Cas12a-RRVRR variant-mediated assay detected various targets in less than 15 min and exhibited equal or greater sensitivity than qPCR when detecting bacterial pathogens, plant RNA viruses and genetically modified crops. Overall, our findings further improved the efficiency of the current CRISPR-based diagnostic system and undoubtedly have great potential for highly sensitive and specific detection of multiple sample types.

Separation of Cells and Microparticles in Insulator-Based Electrokinetic Systems

Presented here is the first continuous separation of microparticles and cells of similar characteristics employing linear and nonlinear electrokinetic phenomena in an insulator-based electrokinetic (iEK) system. By utilizing devices with insulating features, which distort the electric field distribution, it is possible to combine linear and nonlinear EK phenomena, resulting in highly effective separation schemes that leverage the new advancements in nonlinear electrophoresis. This work combines mathematical modeling and experimentation to separate four distinct binary mixtures of particles and cells. A computational model with COMSOL Multiphysics was used to predict the retention times (t_R,p) of the particles and cells in iEK devices. Then, the experimental separations were carried out using the conditions identified with the model, where the experimental retention time (t_R,e) of the particles and cells was measured. A total of four distinct separations of binary mixtures were performed by increasing the level of difficulty. For the first separation, two types of polystyrene microparticles, selected to mimic Escherichia coli and Saccharomyces cerevisiae cells, were separated. By leveraging the knowledge gathered from the first separation, a mixture of cells of distinct domains and significant size differences, E. coli and S. cerevisiae, was successfully separated. The third separation also featured cells of different domains but closer in size: Bacillus cereus versus S. cerevisiae. The last separation included cells in the same domain and genus, B. cereus versus Bacillus subtilis. Separation results were evaluated in terms of number of plates (N) and separation resolution (R_s), where R_s values for all separations were above 1.5, illustrating complete separations. Experimental results were in agreement with modeling results in terms of retention times, with deviations in the 6-27% range, while the variation between repetitions was between 2 and 18%, demonstrating good reproducibility. This report is the first prediction of the retention time of cells in iEK systems.

Recent advances in microchip electrophoresis for analysis of pathogenic bacteria and viruses

Life-threatening diseases, such as hepatitis B, pneumonia, tuberculosis, and COVID-19, are widespread due to pathogenic bacteria and viruses. Therefore, the development of highly sensitive, rapid, portable, cost-effective, and selective methods for the analysis of such microorganisms is a great challenge. Microchip electrophoresis (ME) has been widely used in recent years for the analysis of bacterial and viral pathogens in biological and environmental samples owing to its portability, simplicity, cost-effectiveness, and rapid analysis. However, microbial enrichment and purification are critical steps for accurate and sensitive analysis of pathogenic bacteria and viruses in complex matrices. Therefore, we first discussed the advances in the sample preparation technologies associated with the accurate analysis of such microorganisms, especially the on-chip microfluidic-based sample preparations such as dielectrophoresis and microfluidic membrane filtration. Thereafter, we focused on the recent advances in the lab-on-a-chip electrophoretic analysis of pathogenic bacteria and viruses in different complex matrices. As the microbial analysis is mainly based on the analysis of nucleic acid of the microorganism, the integration of nucleic acid-based amplification techniques such as polymerase chain reaction (PCR), quantitative PCR, and multiplex PCR with ME will result in an accurate and sensitive analysis of microbial pathogens. Such analyses are very important for the point-of-care diagnosis of various infectious diseases.

[Annual review of capillary electrophoresis technology in 2021]

This paper provides an annual review of capillary electrophoresis (CE) technology in 2021. A total of 291 research papers related to CE technology published in 2021 were retrieved from the ISI Web of Science using the keywords, "capillary electrophoresis-mass spectrometry" "capillary isoelectric focusing" "micellar electrokinetic chromatography", or "capillary electrophoresis" (not "capillary electrochromatography" "microchip" and "capillary monolithic column"). In addition, nine research papers related to CE technology in Chinese journals were reviewed: Chinese Journal of Chromatography and Chinese Journal of Analytical Chemistry. This review focused on seven papers published in Coordination Chemistry Reviews, Angewandte Chemie-International Edition, Nature Protocols, TrAC-Trends in Analytical Chemistry, and Signal Transduction and Targeted Therapy with impact factors (IFs) greater than 10.0, as well as 42 papers reported in Analytical Chemistry, Analytica Chimica Acta, Talanta, and Food Chemistry with IFs between 5.0 and 10.0. This review also provides a comprehensive overview of representative CE works in Journal of Chromatography A and Electrophoresis with IFs<5.0, as well as important Chinese journals, Chinese Journal of Chromatography and Chinese Journal of Analytical Chemistry. According to the IF, this paper introduces the representative work of CE-related papers to allow readers to quickly understand the important research progress of CE technology in the past year.

The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics

Phages have certain features, such as their ability to form protein-protein interactions, that make them good candidates for use in a variety of beneficial applications, such as in human or animal health, industry, food science, food safety, and agriculture. It is essential to identify and characterize the proteins produced by particular phages in order to use these viruses in a variety of functional processes, such as bacterial detection, as vehicles for drug delivery, in vaccine development, and to combat multidrug resistant bacterial infections. Furthermore, phages can also play a major role in the design of a variety of cheap and stable sensors as well as in diagnostic assays that can either specifically identify specific compounds or detect bacteria. This article reviews recently developed phage-based techniques, such as the use of recombinant tempered phages, phage display and phage amplification-based detection. It also encompasses the application of phages as capture elements, biosensors and bioreceptors, with a special emphasis on novel bacteriophage-based mass spectrometry (MS) applications.

Identification, Structure and Characterization of Bacillus tequilensis Biofilm with the Use of Electrophoresis and Complementary Approaches

Biofilm is a complex structure formed as a result of the accumulation of bacterial cell clusters on a surface, surrounded by extracellular polysaccharide substances (EPSs). Biofilm-related bacterial infections are a significant challenge for clinical treatment. Therefore, the main goal of our study was to design a complementary approach in biofilm characterization before and after the antibiotic treatment. The 16S rRNA gene sequencing allowed for the identification of Bacillus tequilensis, as a microbial model of the biofilm formation. Capillary electrophoresis demonstrates the capability to characterize and show the differences of the electrophoretic mobility between biofilms untreated and treated with antibiotics: amoxicillin, gentamicin and metronidazole. Electrophoretic results show the clumping phenomenon (amoxicillin and gentamicin) as a result of a significant change on the surface electric charge of the cells. The stability of the dispersion study, the molecular profile analysis, the viability of bacterial cells and the scanning morphology imaging were also investigated. The microscopic and spectrometry study pointed out the degradation/remodeling of the EPSs matrix, the inhibition of the cell wall synthesis and blocking the ribosomal protein synthesis by amoxicillin and gentamicin. However, untreated and treated bacterial cells show a high stability for the biofilm formation system. Moreover, on the basis of the type of the antibiotic treatment, the mechanism of used antibiotics in cell clumping and degradation were proposed.

Use of MALDI-TOF mass spectrometry for virus identification: a review

The possibilities of virus identification, including SARS-CoV-2, by MALDI-TOF mass spectrometry are discussed in this review.

Sensitivity enhancement in capillary electrophoresis and their applications for analyses of pharmaceutical and related biochemical substances

This review aims to illustrate sensitivity enhancement methods in capillary electrophoresis (CE) and their applications for pharmaceutical and related biochemical substance analyses. The first two parts of the article describe the introduction and principle of CE. The main part focuses on strategies for sensitivity improvement in CE including detector and capillary technologies and pre-concentration techniques. Applications of these techniques for pharmaceutical and biomedical substance analyses are surveyed during the years 2018-2021. This article is protected by copyright. All rights reserved.

Microscale electrokinetic-based analysis of intact cells and viruses

Miniaturized electrokinetic methods have proven to be robust platforms for the analysis and assessment of intact microorganisms, offering short response times and higher integration than their bench-scale counterparts. The present review article discusses three types of electrokinetic-based methodologies: electromigration or motion-based techniques, electrode-based electrokinetics, and insulator-based electrokinetics. The fundamentals of each type of methodology are discussed and relevant examples from recent reports are examined, to provide the reader with an overview of the state-of-the-art on the latest advancements on the analysis of intact cells and viruses with microscale electrokinetic techniques. The concluding remarks discuss the potential applications and future directions.