Characterization and analysis of mycobacteria and Gram-negative bacteria and co-culture mixtures by Raman microspectroscopy, FTIR, and atomic force microscopy

The molecular composition of mycobacteria and Gram-negative bacteria cell walls is structurally different. In this work, Raman microspectroscopy was applied to discriminate mycobacteria and Gram-negative bacteria by assessing specific characteristic spectral features. Analysis of Raman spectra indicated that mycobacteria and Gram-negative bacteria exhibit different spectral patterns under our experimental conditions due to their different biochemical components. Fourier transform infrared (FTIR) spectroscopy, as a supplementary vibrational spectroscopy, was also applied to analyze the biochemical composition of the representative bacterial strains. As for co-cultured bacterial mixtures, the distribution of individual cell types was obtained by quantitative analysis of Raman and FTIR spectral images and the spectral contribution from each cell type was distinguished by direct classical least squares analysis. Coupled atomic force microscopy (AFM) and Raman microspectroscopy realized simultaneous measurements of topography and spectral images for the same sampled surface. This work demonstrated the feasibility of utilizing a combined Raman microspectroscopy, FTIR, and AFM techniques to effectively characterize spectroscopic fingerprints from bacterial Gram types and mixtures.

Synchrotron FTIR microspectroscopy of Escherichia coli at single-cell scale under silver-induced stress conditions

The present work was focused on elucidating biochemical changes in the model bacterium Escherichia coli exposed to ionic silver mediated stress, at a single-cell scale. In order to achieve this, in situ synchrotron Fourier-transform infrared (sFTIR) microspectroscopy was performed, for the first time, on individual cells by attenuated total reflectance (ATR) combined with the use of zinc-selenide hemisphere for high spatial resolution. In a first part, the potential of the method was evaluated on bacteria subjected to a lethal 100 μM AgNO₃ concentration for 2 h compared to untreated 100 % viable cells. Differences in cell composition were assessed for the C–H stretching and protein spectral regions, indicating that the inhibitory action was targeted against both fatty acids and proteins. Transmission electron microscopy (TEM) confirmed morphological damages of the cell ultrastructure. The relevance of ATR-sFTIR microspectroscopy for highlighting the heterogeneity in Ag⁺-mediated effects within a given bacterial population was also pointed out. In a second part, cells were exposed to sub-lethal Ag⁺ concentrations (<10 μM AgNO₃) tested under “dynamic” growth mode: early addition vs. pulse in the mid-exponential phase, and compared to simultaneously batch-grown untreated bacteria or cells sampled just before the pulse, respectively. sFTIR microspectroscopy and TEM imaging were performed in close relation with growth kinetics characterization. No significant effect of the Ag⁺ pulses was detected, in accordance with macrokinetics data. For early-treated cells, effects on fatty acid composition were shown, although no major alteration of protein secondary structure was noticed. These partial effects were consistent with TEM observations and growth kinetics.

Development of polymer-modified magnetic nanoparticles and quantum dots for Escherichia coli binding test

A rapid binding test has been developed for the detection of bacteria using polymer-modified magnetic nanoparticles. Polydopamine (PDA) can effectively act as a sorbent even in water solution, and a PDA coating on magnetic nanoparticles (MNPs) was therefore prepared to bind Escherichia coli (E. coli). Albeit non-selective, PDA-modified magnetic nanoparticles (MNPs@PDA) show nearly 100% efficiency in binding E. coli. If E. coli, grown in tryptic soy broth medium, is analyzed by capillary electrophoresis (CE) using phosphate buffer as the background electrolyte, two peaks are found, while a single peak is found with carbonate buffer containing 0.05% of poly(ethylene glycol). Self-polymerization of dopamine on E. coli at pH 9.5 is also feasible. The detection of E. coli is demonstrated by adding quantum dots (QDs) to form a QDs-PDA-E. coli aggregate for better CE analysis.

Rapid and sensitive detection of bacteria via platinum-labeled antibodies and on-particle ionization and enrichment prior to MALDI-TOF mass spectrometry

We introduce a rapid and sensitive approach to study the interactions of an affinity probe with the bacterial wall. Immunoglobulin was immobilized on platinum nanoparticles, and the resulting probe nanoparticles bind to bacterial walls as confirmed by transmission electron microscopy. A MALDI-MS assay was developed that can detect ~10⁵ cfu mL^?1 of S. marcescens and E. coli. This approach enables simple, rapid and straightforward detection of bacterial proteins, with high resolution and sensitivity, and without the requirement for tedious washing/separation steps.

An efficient electrochemical disinfection of E. coli and S. aureus in drinking water using ferrocene–PAMAM–multiwalled carbon nanotubes–chitosan nanocomposite modified pyrolytic graphite electrode

This work reported an efficient electrochemical treatment for drinking water disinfection using a pyrolytic graphite electrode modified with ferrocenyl tethered poly(amidoamine) dendrimers–multiwalled carbon nanotubes–chitosan nanocomposite. The influence parameters of electrochemical disinfection of Escherichia coli and Staphylococcus aureus, such as applied potential and sterilization time, were investigated. Further investigation indicated that almost all (99.99 %) of the initial bacteria were killed after applying a low potential of 0.4 V for 10 min. During the electrochemical disinfection process, the oxidized form of ferrocene was formed on electrode, which played a key role in the disinfection towards E. coli and S. aureus. Hence, the proposed method may provide potential application for the disinfection of drinking water.

Bacterial Spores Survive Electrospray Charging and Desolvation

The survivability of Bacillus subtilis spores and vegetative Escherichia coli cells after electrospray from aqueous suspension was tested using mobility experiments at atmospheric pressure. E. coli did not survive electrospray charging and desolvation, but B. subtilis did. Experimental conditions ensured that any surviving bacteria were de-agglomerated, desolvated, and electrically charged. Based on mobility measurements, B. subtilis spores survived even with 2,000–20,000 positive charges. B. subtilis was also found to survive introduction into vacuum after either positive or negative electrospray. Attempts to measure the charge distribution of viable B. subtilis spores using electrostatic deflection in vacuum were inconclusive; however, viable spores with low charge states (less than 42 positive or less than 26 negative charges) were observed.

Spectral signatures for the classification of microbial species using Raman spectra

In general, classification-based methods based on confocal Raman microscopy are focused on targeted studies under which the spectral libraries are collected under controlled instrument parameters, which facilitate analyses via standard multivariate data analysis methods and cross-validation. We develop and compare approaches to transform spectra collected at different spectral ranges and varying levels of resolution into a single lower-dimension spectral signature library. This will result in a more robust analysis method able to accommodate spectra accumulated at different times and conditions. We demonstrate these approaches on a relevant test case; the identification of microbial species from a natural environment. The training data were based on samples prepared for three unique species collected at two time points and the test data consisted of blinded unknowns prepared and analyzed at a later date with different instrument parameters. The results indicate that using reduced dimension representations of the spectral signatures improves classification accuracy over basic alignment protocols. In particular, utilizing the microbial species partial least squares discriminant analysis classifier on the blinded samples based on alignment achieved ~78 % accuracy, while both binning and peak selection approaches yielded 100 % accuracy.

Determination of some trace elements by flame atomic absorption spectrometry after preconcentration and separation by Escherichia coli immobilized on multiwalled carbon nanotubes

We have immobilized living and non-living Escherichia coli (E. coli) bacteria on multiwalled carbon nanotubes (MWCNT) and used such materials as a biosorbent for the separation and preconcentration of copper, cobalt, cadmium and nickel prior to their determination by flame atomic absorption spectrometry (FAAS). E. coli bacteria cells were mixed with MWCNTs in a 1:1 ratio, dried and placed at the tip of a 50-mL syringe. The ions were retained on the sorbent and then eluted by drawing and ejecting back the sample (or standard solution) and an eluent, respectively. The effects of various experimental parameters on the sorption and elution were investigated. The analytes were quantitatively retained (at pH values of 7) and eluted (with 0.5 M nitric acid) with high precision, the RSD being <5%. The performances of the new sorbents were compared using certified reference materials. The sorbent modified with living E. coli has a higher adsorption capacity and displays somewhat better recoveries compared to sorbent based on non-living E. coli. Both sorbents were successfully used for the separation and preconcentration of copper, cobalt, cadmium and nickel prior to their determination by flame atomic absorption spectrometry.

UPLC-UV-MSE analysis for quantification and identification of major carotenoid and chlorophyll species in algae

A fast method for quantification and identification of carotenoid and chlorophyll species utilizing liquid chromatography coupled with UV detection and mass spectrometry has been demonstrated and validated for the analysis of algae samples. This method allows quantification of targeted pigments and identification of unexpected compounds, providing isomers separation, UV detection, accurate mass measurements, and study of fragment ions for structural elucidation in a single run. This is possible using parallel alternating low- and high-energy collision spectral acquisition modes, which provide accurate mass full scan chromatograms and accurate mass high-energy chromatograms. Here, it is shown how this approach can be used to confirm carotenoid and chlorophyll species by identification of key diagnostic fragmentations during high-energy mode. The developed method was successfully applied for the analysis of Dunaliella salina samples during defined red LED lighting growth conditions, identifying 37 pigments including 19 carotenoid species and 18 chlorophyll species, and providing quantification of 7 targeted compounds. Limit of detections for targeted pigments ranged from 0.01?ng/mL for lutein to 0.24?ng/mL for chlorophyll a. Inter-run precision ranged for of 3 to 24 (RSD%) while inter-run inaccuracy ranged from ?17 to 11.

MALDI-FTICR MS Imaging as a Powerful Tool to Identify Paenibacillus Antibiotics Involved in the Inhibition of Plant Pathogens

Nowadays, microorganisms are more and more often used as biocontrol agents for crop protection against diseases. Among them, bacteria of Bacillus and Paenibacillus genders are already used as commercial biocontrol agents. Their mode of action is supposed to be related to their production of antibiotics, such as cyclic lipopeptides, which exhibit great antimicrobial activities. We chose to work with a Paenibacillus polymyxa strain (Pp56) very resistant to various microorganisms. The bacteria were grown simultaneously with Fusarium oxysporum and we applied matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance (MALDI-FTICR) mass spectrometry to identify the antibiotics compounds present in the fungus growth inhibition area. We, therefore, identified fusaricidins A, B, and C and numerous members of the LI-F antibiotics family. MALDI-FTICR mass spectrometry imaging was then used to follow the diffusion of lipopeptides involved in the inhibitory activity over time. We analyzed the molecular content of the inhibitory area at different Pp56 and Fusarium incubation durations and concluded that some lipopeptides such as fusaricidin B and a mixture of LI-F05b/06b/08a were mainly involved in the defense mechanism of Pp56. Our study confirms that MALDI imaging may be a powerful tool to quickly determine which molecular species is involved in an antagonism with another microorganism, avoiding time-consuming steps of extraction, purification, and activity tests, which are still commonly used in microbiology.

Rapid separation of four probiotic bacteria in mixed samples using microchip electrophoresis with laser-induced fluorescence detection

Microchip electrophoresis (MCE) coupled to laser-induced fluorescence detection was applied to the rapid separation of Bifidobacterium, Lactobacillus casei, Lactobacillus acidophilus, and Enterococccus faecalis. All bacteria were quickly separated within 150?s using a running buffer of pH 8.5 containing Tris, borate, EDTA, and poly(ethylene oxide). The latter was crucial to reduce the bacterial adsorption on the walls of the microchannels. The pH of 8.5 warrants that bacteria carry a negative charge at their surface and thus display good electrophoretic performance. The method was used to analyze medical samples containing these probiotics, and the results showed that the identification and detection of bacteria by MCE is advantageous in terms of sample consumption, waste production, time of analysis, and instrumental effort.

Laser desorption VUV postionization MS imaging of a cocultured biofilm

Laser desorption postionization mass spectrometry (LDPI-MS) imaging is demonstrated with a 10.5 eV photon energy source for analysis and imaging of small endogenous molecules within intact biofilms. Biofilm consortia comprised of a synthetic Escherichia coli K12 coculture engineered for syntrophic metabolite exchange are grown on membranes and then used to test LDPI-MS analysis and imaging. Both E. coli strains displayed many similar peaks in LDPI-MS up to m/z 650, although some observed differences in peak intensities were consistent with the appearance of byproducts preferentially expressed by one strain. The relatively low mass resolution and accuracy of this specific LDPI-MS instrument prevented definitive assignment of species to peaks, but strategies are discussed to overcome this shortcoming. The results are also discussed in terms of desorption and ionization issues related to the use of 10.5 eV single-photon ionization, with control experiments providing additional mechanistic information. Finally, 10.5 eV LDPI-MS was able to collect ion images from intact, electrically insulating biofilms at ～100 μm spatial resolution. Spatial resolution of ～20 μm was possible, although a relatively long acquisition time resulted from the 10 Hz repetition rate of the single-photon ionization source.

An innovative, easily fabricated, silver nanoparticle-based titanium implant coating: development and analytical characterization

Microbial colonization and biofilm formation on implanted devices represent an important complication in orthopaedic and dental surgery and may result in implant failure. Controlled release of antibacterial agents directly at the implant site may represent an effective approach to treat these chronic complications. Resistance to conventional antibiotics by pathogenic bacteria has emerged in recent years as a major problem of public health. In order to overcome this problem, non-conventional antimicrobial agents have been under investigation. In this study, polyacrylate-based hydrogel thin coatings have been electrosynthesised on titanium substrates starting from poly(ethylene glycol diacrylate)–co–acrylic acid. Silver nanoparticles (AgNPs) with a narrow size distribution have been synthesized using a “green” procedure and immobilized on Ti implant surfaces exploiting hydrogel coatings’ swelling capabilities. The coatings have been characterized by XPS and SEM/EDX, while their silver release performances have been monitored by ICP–MS. The antibacterial activity of these AgNP-modified hydrogel coatings was tested evaluating in vitro inhibition growth of Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli, among the most common pathogens in orthopaedic infections. Moreover, a preliminary investigation of the biocompatibility of silver-loaded coatings versus MG63 human osteoblast-like cells has been performed. An important point of strength of this paper, in fact, is the concern about the effect of silver species on the surrounding cell system in implanted medical devices. Silver ion release has been properly tuned in order to assure antibacterial activity while preserving osteoblasts’ response at the implant interface.

Establishing Drug Resistance in Microorganisms by Mass Spectrometry

A rapid method to determine drug resistance in bacteria based on mass spectrometry is presented. In it, a mass spectrum of an intact microorganism grown in drug-containing stable isotope-labeled media is compared with a mass spectrum of the intact microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting characteristic mass shifts of one or more microorganism biomarkers using bioinformatics algorithms. Observing such characteristic mass shifts indicates that the microorganism is viable even in the presence of the drug, thus incorporating the isotopic label into characteristic biomarker molecules. The performance of the method is illustrated on the example of intact E. coli, grown in control (unlabeled) and ¹³C-labeled media, and analyzed by MALDI TOF MS. Algorithms for data analysis are presented as well.

Spectroscopic analysis of bacterial biological warfare simulants and the effects of environmental conditioning on a bacterial spectrum

The ability to distinguish bacteria from mixed samples is of great interest, especially in the medical and defence arenas. This paper reports a step towards the aim of differentiating pathogenic endospores in situ, to aid any required response for hazard management using infrared spectroscopy combined with multivariate analysis. We describe a proof-of-principle study aimed at discriminating biological warfare simulants from common environmental bacteria. We also report an evaluation of multiple pre-processing techniques and subsequent differences in cross-validation of two pattern recognition models (Support Vector Machines and Principal Component–Linear Discriminant Analysis) for a six-class classification (bacterial classification). These classifications were possible with an average sensitivity of 88.0 and 86.9?%, and an average specificity of 97.6 and 97.5?% for the SVM and the PC-LDA models, respectively. Most spectroscopic models are built upon spectra from bacteria that have been specifically prepared for analysis by a particular method; this paper will comment upon the differences in the bacterial spectrum that occur between specific preparations when the bacteria have spent 30?days in the simulated weather conditions of a hot dry climate.

Oral cancer diagnostics based on infrared spectral markers and wax physisorption kinetics

Infrared microspectroscopy is an emerging approach for disease analysis owing to its capability for in situ chemical characterization of pathological processes. Synchrotron-based infrared microspectroscopy (SR-IMS) provides ultra-high spatial resolution for profiling biochemical events associated with disease progression. Spectral alterations were observed in cultured oral cells derived from healthy, precancerous, primary, and metastatic cancers. An innovative wax-physisorption-based kinetic FTIR imaging method for the detection of oral precancer and cancer was demonstrated successfully. The approach is based on determining the residual amount of paraffin wax (C₂₅H₅₂) or beeswax (C₄₆H₉₂O₂) on a sample surface after xylene washing. This amount is used as a signpost of the degree of physisorption that altered during malignant transformation. The results of linear discriminant analysis (LDA) of oral cell lines indicated that the methylene (CH₂) and methyl group (CH₃) stretching vibrations in the range of 3,000–2,800 cm^?1 have the highest accuracy rate (89.6 %) to discriminate the healthy keratinocytes (NHOK) from cancer cells. The results of wax-physisorption-based FTIR imaging showed a stronger physisorption with beeswax in oral precancerous and cancer cells as compared with that of NHOK, which showed a strong capability with paraffin wax. The infrared kinetic study of oral cavity tissue showed a consistency in the wax physisorption of the cell lines. On the basis of our findings, these results show the potential use of wax-physisorption-based kinetic FTIR imaging for the early screening of oral cancer lesions and the chemical changes during oral carcinogenesis.

Rapid on-site TLC–SERS detection of four antidiabetes drugs used as adulterants in botanical dietary supplements

A novel facile method has been established for rapid on-site detection of antidiabetes chemicals used to adulterate botanical dietary supplements (BDS) for diabetes. Analytes and components of pharmaceutical matrices were separated by thin-layer chromatography (TLC) then surface-enhanced Raman spectroscopy (SERS) was used for qualitative identification of trace substances on the HPTLC plate. Optimization and standardization of the experimental conditions, for example the method used for preparation of silver colloids, the mobile phase, and the concentration of colloidal silver, resulted in a very robust and highly sensitive method which enabled successful detection when the amount of adulteration was as low as 0.001 % (w/w). The method was also highly selective, enabling successful identification of some chemicals in extremely complex herbal matrices. The established TLC–SERS method was used for analysis of real BDS used to treat diabetes, and the results obtained were verified by liquid chromatography–triple quadrupole mass spectrometry (LC–MS–MS). The study showed that TLC–SERS could be used for effective separation and detection of four chemicals used to adulterate BDS, and would have good prospects for on-site qualitative screening of BDS for adulterants.

Capillary liquid chromatographic fingerprint used for discrimination of Zingiber montanum from related species

Fingerprint analysis using capillary liquid chromatography (CLC) has been developed for discrimination of Zingiber montanum (ZM) from related species, for example Z. americans (ZA) and Z. zerumbet (ZZ). By comparing the fingerprint chromatograms of ZM, ZA, and ZZ we could identify ZM samples and discriminate them from ZA and ZZ by using their marker peaks. We also combined CLC fingerprint with multivariate analysis, including principal-component analysis (PCA) and canonical variate analysis (CVA); all three species were discriminated successfully. This result indicates that CLC fingerprint analysis in combination with PCA and CVA can be used for discrimination of ZM samples from samples of related species.

Multidimensional nano-HPLC coupled with tandem mass spectrometry for analyzing biotinylated proteins

Multidimensional high-performance liquid chromatography (HPLC) is a key method in shotgun proteomics approaches for analyzing highly complex protein mixtures by complementary chromatographic separation principles. Here, we describe an integrated 3D-nano-HPLC/nano-electrospray ionization quadrupole time-of-flight mass spectrometry system that allows an enzymatic digestion of proteins followed by an enrichment and subsequent separation of the created peptide mixtures. The online 3D-nano-HPLC system is composed of a monolithic trypsin reactor in the first dimension, a monolithic affinity column with immobilized monomeric avidin in the second dimension, and a reversed phase C18 HPLC-Chip in the third dimension that is coupled to a nano-ESI-Q-TOF mass spectrometer. The 3D-LC/MS setup is exemplified for the identification of biotinylated proteins from a simple protein mixture. Additionally, we describe an online 2D-nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS setup for the enrichment, separation, and identification of cross-linked, biotinylated species from chemical cross-linking of cytochrome c and a calmodulin/peptide complex using a novel trifunctional cross-linker with two amine-reactive groups and a biotin label.

Model system for targeted drug release triggered by immune-specific signals

A new sense-and-act system was realized by integrating a biocatalytic/bioaffinity electrode responding to immune signals represented by an antibody and a polymer-modified electrode loaded with drug-mimicking species. The release of the drug-mimicking species was achieved specifically in response to a signal antibody, thus demonstrating for the first time an immune-induced drug-releasing process. The present approach promises new options for future applications in controlled drug release and personalized medicine.