Use of Fourier transform infrared spectroscopy (FTIR) spectroscopy for rapid and accurate identification of Yeasts isolated from human and animals

Effects of endodontic root canal irrigants on tooth dentin revealed by infrared spectroscopy: a systematic literature review

BACKGROUND

Root canal irrigation endodontic solutions have effects on the chemistry of dentin. Infrared spectroscopy is a non-destructive chemical characterization method where the strength of absorption often correlates with mineral or organic composition.

OBJECTIVES

To survey effects of commonly used irrigation solutions on the composition of root dentin as detected by widely-available Fourier transform infrared spectroscopy (FTIR) methods.

METHODS

Electronic databases were searched for articles published between 1983 to 2023. After risk of bias assessments (OHAT), studies were grouped according to effects per irrigation solution. Inclusion criteria comprised in vitro studies that used extracted human or bovine teeth, treated by irrigation solutions characterized using FTIR spectroscopy and presenting spectral data. Publications that did not share FTIR spectra were excluded.

RESULTS

A wide range of concentrations, durations, and methodologies have been tested but only 30 out of 3452 studies met our inclusion criteria. Different FTIR methods were used with the Attenuated Total Reflection (ATR) variant being the most common (21 studies). Investigated solutions included sodium hypochlorite (NaOCl), ethylenediaminetetraacetic-acid (EDTA), 1-hydroxyethylidene-1-1-diphosphonic-acid (HEDP), peracetic-acid (PAA), glycolic-acid (GA), and citric-acid (CA) though most focused on NaOCl and EDTA. All solutions had detectable effects on the FTIR signature of dentin. NaOCl mainly affects the organic signatures, revealing reduced amide/phosphate ratios with increasing concentrations. EDTA mainly effects the inorganic component, increasing with time and concentration, yet glycolic acid has stronger effects than EDTA on dentin. Beyond the type of irrigant and dentin exposure durations, concentration and protocol of application had strong effects. There is a lack of studies comparing similar irrigants under conditions that mimic clinical scenarios analyzing bulk sample because FTIR of powder dentin differs from bulk measurements.

SIGNIFICANCE

The ideal root-canal irrigant should combine local disinfection properties with minimal compositional effects on healthy dentin. FTIR methods appear reliable to identify important changes in root dentin chemical composition. Such information can help understand when endodontic irrigation might lead to root degradation or possibly contribute to long term failures such as vertical fractures. Awareness of chemical damage from irrigation procedures may help clinicians select procedures that reduce deleterious effects on the root canal structures.

A rapid spectroscopic method for the identification of the filamentous fungi isolated from Turkish traditional mold-ripened cheeses

Fourier transform infrared spectroscopy (FTIR) is an alternative microbial identification technique due to its faster analysis times and lower cost compared to molecular methods. In this study, forty-three fungal strains isolated from different Turkish traditional mold-ripened cheeses representing nine different Penicillium species (P. roqueforti, P. corylophilum, P. before, P. crustosum, P. spinulosum, P. rubens, P. brevicompactum, P. paneum, and P. solitum) were analyzed by using FTIR HTS-XT (High Throughput Screening Extension) method in the 4000-400 cm-1 wavenumber range. The spectra of the isolates were evaluated, and the chemical structures corresponding to the fungus-specific spectral regions were determined as fatty acids (3600-2800 cm-1), amide I and amide II of proteins and peptides (1740-1500 cm-1), polysaccharides (1200-900 cm-1) and carbohydrates (900-600 cm-1). The isolates were grouped according to the hierarchical clustering analysis (HCA) by applying chemometrics combined with FTIR spectroscopy. Results showed that FTIR spectroscopy has a high capability for rapid determination of cheese fungi based on their FTIR spectra.

Redox mediators boost NOx reduction via trade-off electron charges using a cube-shaped (cMn@rGO) catalyst; mechanism and electrochemical study

Gaseous pollutants like sulfur dioxide and nitrogen oxide(s) (SO2, NOx) have been increasing exponentially for the last two decades, which have had adverse effects on human health, aquatic life, and the environment. Recently, for air pollution taming, manganese/oxide (Mn/MnO) has become a very promising heterogeneous catalyst due to its environment-friendly, low-price, and remarkable catalytic abilities for toxic gases. In this work, cube-shaped Mn nanoparticles (cMn NPs) were decorated on the surface of reduced graphene oxide (rGO) by the solvothermal method. The resulting cMn@rGO composite was employed for electrochemical NOx reduction. However, the microscopic (TEM/HRTEM) and structural analysis were utilised to investigate the morphology and characteristics of the cMn@rGO composite. This electrochemical-based treatment for NOx reduction is employed by using electron shuttle or redox mediators. Here, four distinct redox mediators are used to address electrochemical obstacles, which effectively facilitate electron transportation and promoted NOx reduction on the electrode surface. These mediators not only significantly enhanced the NOx conversion into valuable products, i.e., N2 and N2O, but also made the process smooth with high performance. Among these mediators, neutral red (N.R) exhibited extraordinary potential in enhancing NOx reduction. The obtained results indicated that the remarkable catalytic performance (∼93%) of the cMn@rGO can be attributed to several factors, including the catalyst's three-dimensional architecture structure and abundant active sites. The designed catalyst (cMn@rGO) is not only cost-effective and sustainable but also exhibits excellent potential in effectively reducing NOx, which could be beneficial for large-scale NOx abatement.

Effective and reproducible biosynthesis of nanogold-composite catalyst for paracetamol oxidation

Pharmaceutical products are some of the most serious emergent pollutants in the environment, especially nowadays of the COVID-19 pandemic. In this study, nanogold-composite was prepared, and its catalytic activity for paracetamol degradation was investigated. Moreover, for the first time, recycled waste diatomite earth (WDE) from beer filtration was used for reproducible gold nanoparticle (Au NPs) preparation. We studied Au NPs by various psychical-chemical and analytical methods. Transmission and scanning electron microscopy were used for nanogold-composite morphology, size and shape characterization. Total element concentrations were determined using inductively coupled plasma mass and X-ray fluorescence spectrometry. X-ray powder diffraction analysis was used for crystal structure characterization of samples. Fourier transform infrared spectrometer was used to study the chemical changes before and after Au NP formation. The results revealed that the WDE served as both a reducing and a stabilizing agent for crystalline spherical 30 nm Au NPs as well as acting as a direct support matrix. The kinetics of paracetamol degradation was studied by high-performance liquid chromatography with a photodiode array detector. The conversion of paracetamol was 62% and 67% after 72 h in the absence or presence of light irradiation, respectively, with 0.0126 h^-1 and 0.0148 h^-1 reaction rate constants. The presented study demonstrates the successful use of waste material from the food industry for nanogold-composite preparation and its application as a promising catalyst in paracetamol removal.

Temperature- and Nutrients-Induced Phenotypic Changes of Antarctic Green Snow Bacteria Probed by High-Throughput FTIR Spectroscopy

Simple Summary

Green snow microorganisms play an important role in biogeochemical cycle and carbon sink processes and they can be a source of biotechnologically interesting cell factories. A wide temperature tolerance is a unique property of bacteria isolated from cold environments, which has received great attention in the last years. The present paper examines the growth and chemical profile flexibility for green snow bacteria exposed to different temperature and nutrient fluctuations. By applying high-throughput chemical phenotyping with FTIR spectroscopy we discovered chemical changes possessed by green snow bacteria when grown at high/low temperature and rich/minimal media.

Abstract

Temperature fluctuations and nutrient composition are the main parameters influencing green snow microbiome. In this study we investigated the influence of temperature and nutrient conditions on the growth and cellular chemical profile of bacteria isolated from green snow. Chemical profiling of the green snow bacteria was done by high-throughput FTIR spectroscopy combined with multivariate data analysis. We showed that temperature and nutrients fluctuations strongly affect growth ability and chemical profile of the green snow bacteria. The size of colonies for green snow bacteria grown at higher (25 °C) and lower (4 °C and 10 °C) than optimal temperature (18 °C) was smaller. All isolates grew on rich medium, and only 19 isolates were able to grow on synthetic minimal media. Lipid and mixed spectral regions showed to be phylogeny related. FTIR fingerprinting indicates that lipids are often affected by the temperature fluctuations. Growth on different media resulted in the change of the whole chemical profile, where lipids showed to be more affected than proteins and polysaccharides. Correlation analysis showed that nutrient composition is clearly strongly influencing chemical changes in the cells, followed by temperature.

Multicenter evaluation of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy-based method for rapid identification of clinically relevant yeasts

Fourier transform infrared (FTIR) spectroscopy has demonstrated applicability as a reagent-free whole-organism fingerprinting technique for both microbial identification and strain typing. For routine application of this technique in microbiology laboratories, acquisition of FTIR spectra in the attenuated total reflectance (ATR) mode simplifies the FTIR spectroscopy workflow, providing results within minutes after initial culture without prior sample preparation. In our previous central work, 99.7% correct species identification of clinically relevant yeasts was achieved by employing an ATR-FTIR-based method and spectral database developed by our group. In this study, ATR-FTIR spectrometers were placed in 6 clinical microbiology laboratories over a 16-month period and were used to collect spectra of routine yeast isolates for on-site identification to the species level. The identification results were compared to those obtained from conventional biochemical tests and/or matrix-assisted laser desorption/ionization time of flight mass spectrometry. Isolates producing discordant results were reanalyzed by routine identification methods, ATR-FTIR spectroscopy and PCR gene sequencing of the D1/D2 and ITS regions. Among the 573 routine clinical yeast isolates collected and identified by the ATR-FTIR-based method, 564 isolates (98.4%) were correctly identified at the species level while the remaining isolates were inconclusive with no misidentifications. Due to the low prevalence of Candida auris in routine isolates, additional randomly selected C. auris (n = 24) isolates were obtained for evaluation and resulted in 100% correct identification. Overall, the data obtained in our multicenter evaluation study using multiple spectrometers and system operators indicate that ATR-FTIR spectroscopy is a reliable, cost-effective yeast identification technique that provides accurate and timely (∼3 minutes/sample) species identification promptly after the initial culture.

Membrane Fouling Phenomena in Microfluidic Systems: From Technical Challenges to Scientific Opportunities

The almost ubiquitous, though undesired, deposition and accumulation of suspended/dissolved matter on solid surfaces, known as fouling, represents a crucial issue strongly affecting the efficiency and sustainability of micro-scale reactors. Fouling becomes even more detrimental for all the applications that require the use of membrane separation units. As a matter of fact, membrane technology is a key route towards process intensification, having the potential to replace conventional separation procedures, with significant energy savings and reduced environmental impact, in a broad range of applications, from water purification to food and pharmaceutical industries. Despite all the research efforts so far, fouling still represents an unsolved problem. The complex interplay of physical and chemical mechanisms governing its evolution is indeed yet to be fully unraveled and the role played by foulants' properties or operating conditions is an area of active research where microfluidics can play a fundamental role. The aim of this review is to explore fouling through microfluidic systems, assessing the fundamental interactions involved and how microfluidics enables the comprehension of the mechanisms characterizing the process. The main mathematical models describing the fouling stages will also be reviewed and their limitations discussed. Finally, the principal dynamic investigation techniques in which microfluidics represents a key tool will be discussed, analyzing their employment to study fouling.

Rapid classification of chromoblastomycosis agents genera by infrared spectroscopy and chemometrics supervised by sequencing of rDNA regions

Chromoblastomycosis (CBM) is a skin and subcutaneous infection caused by species of seven fungal genera. Identification of CBM species is performed by DNA sequencing of one or more genes, which becomes a time-consuming work. Fourier Transform Infrared Spectroscopy (FTIR) has been used for the identification of other microorganisms, however, only one CBM genus was evaluated by FTIR analysis to date. Therefore, the study is aimed to differentiate the CBM agents for identification at genera level using FTIR supervised by Internal Transcribed Spacer (ITS) rDNA region. Seventy-seven isolates of the main five CBM genera were prepared for Attenuated Total Reflection FTIR (ATR-FTIR) with a new methodology using slices of dry fungus in glass fixing-modeling proposed in this study. The algorithm Hierarchical Cluster Analysis (HCA) was used to analyze the differences and similarities between species through the spectra. Orthogonal Partial Least Square Discriminant Analysis (OPLS-DA) allowed to correctly classify all samples of five CBM genera. The ATR-FTIR/OPLS-DA models highlighted important contributions of regions attributed to NH and OH stretching, amide I of proteins, polysaccharides bands and fingerprint region for the complete differentiation of the genera investigated. Thus, FTIR can be a fast and inexpensive alternative for identification of CBM agents.

A review on plant-mediated synthesis of silver nanoparticles, their characterization and applications

For decades, silver has been used as a non-toxic inorganic antimicrobial agent. Silver has a lot of potential in a variety of biological/chemical applications, particularly in the form of nanoparticles (NPs). Eco-friendly synthesis approach for NPs are becoming more common in nanobiotechnology, and the demand for biological synthesis methods is growing, with the goal of eliminating hazardous and polluting agents. Cultures of bacteria, fungi, and algae, plant extracts, and other biomaterials are commonly used for NP synthesis in the ‘green synthesis’ process. Plant-based green synthesis is a simple, fast, dependable, cost-effective, environmentally sustainable, and one-step method that has a significant advantage over microbial synthesis due to the lengthy process of microbial isolation and pure culture maintenance. In this report, we focussed on phytosynthesis of silver nanoparticles (AgNPs) and their characterization using various techniques such as spectroscopy (UV–vis, FTIR), microscopy (TEM, SEM), X-Ray diffraction (XRD), and other particle analysis. The potential applications of AgNPs in a variety of biological and chemical fields are discussed.

Inhibitory Effect of Eugenol and trans-Anethole Alone and in Combination with Antifungal Medicines on Candida albicans Clinical Isolates

One of the most common pathogens among yeasts is Candida albicans, which presents a serious health threat. The study aimed to check the antifungal properties of trans-anethole and eugenol with selected antifungal medicines (AMs) against C. albicans clinical isolates. The checkerboard method was used to tests of interactions between these compounds. Achieved results indicated that eugenol showed synergistic and additive activities with miconazole and econazole against investigated clinical isolates, respectively. Moreover, the combination - trans-anethole - miconazole also showed an additive effect against two clinical isolate. We tried to relate the results to changes in C. albicans cell sheaths under the influence of essential oils compounds (EOCs) performing the Fourier transform infrared spectra analysis to confirm the presence of particular chemical moieties in C. albicans cells. Nevertheless, no strong relationships was observed between synergistic and additive actions of used EOC-AMs combinations and chemical moieties in C. albicans cells.

Differentiation of S. chartarum (Ehrenb.) S. Hughes Chemotypes A and S via FT-IR Spectroscopy

Stachybotrys (S.) chartarum is a cellulolytic mould with the ability to produce highly cytotoxic macrocyclic trichothecenes. Two chemotypes are defined according to their ability to produce either atranones or satratoxins. S. chartarum has been well known as the causative agent of the lethal disease stachybotryotoxicosis in horses. Further investigations revealed that this disease is strictly correlated with the presence of macrocyclic trichothecenes. Furthermore, their occurrence in water-damaged buildings has been linked to adverse health effects such as the sick building syndrome. As the chemotypes cannot be characterized via phenotypic criteria, different methods such as PCR, MALDI–TOF MS, LC–MS/MS, thin-layer chromatography and cytotoxicity assays have been used so far. Fourier-transform-infrared spectroscopy (FT-IR) is commonly used for the differentiation of bacteria and yeasts, but this technique is also applicable to filamentous fungi. Hence, this study aimed at evaluating to which extent a reliable differentiation of S. chartarum chemotypes A and S is possible. Besides, another objective was to verify if the recently introduced third genotype of S. chartarum can be identified. Therefore, 28 strains including the two chemotypes and the third genotype H were cultivated on malt extract agar (MEA) and potato dextrose agar in three biological replicates. Each sample was applied to FT-IR measurements on day 7, 14 and 21 of cultivation. In this study, we achieved a distinction of the chemotypes A and S via FT-IR spectroscopy after incubation for 7 days on MEA. In terms of genotype differentiation, the PCR detecting satratoxin- and atranone-gene clusters remained the only applicable method.

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.

Reagent-Free Identification of Clinical Yeasts by Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy

Invasive fungal infections by opportunistic yeasts have increased concomitantly with the growth of an immunocompromised patient population. Misidentification of yeasts can lead to inappropriate antifungal treatment and complications. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a promising method for rapid and accurate identification of microorganisms. ATR-FTIR spectroscopy is a standalone, inexpensive, reagent-free technique that provides results within minutes after initial culture. In this study, a comprehensive spectral reference database of 65 clinically relevant yeast species was constructed and tested prospectively on spectra recorded (from colonies taken from culture plates) for 318 routine yeasts isolated from various body fluids and specimens received from 38 microbiology laboratories over a 4-month period in our clinical laboratory. ATR-FTIR spectroscopy attained comparable identification performance with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a preliminary validation of the ATR-FTIR method, correct identification rates of 100% and 95.6% at the genus and species levels, respectively, were achieved, with 3.5% unidentified and 0.9% misidentified. By expanding the number of spectra in the spectral reference database for species for which isolates could not be identified or had been misidentified, we were able to improve identification at the species level to 99.7%. Thus, ATR-FTIR spectroscopy provides a new standalone method that can rival MALDI-TOF MS for the accurate identification of a broad range of medically important yeasts. The simplicity of the ATR-FTIR spectroscopy workflow favors its use in clinical laboratories for timely and low-cost identification of life-threatening yeast strains for appropriate treatment.

Biodiversity and technological properties of yeasts from Turkish sourdough

In this study, yeasts were isolated and characterized from twelve traditional sourdough samples which belongs to Black Sea and Aegean regions of Turkey. Twenty six yeast species were isolated and identified by both 26S rDNA sequencing and FTIR spectroscopy. Saccharomyces cerevisiae (50%), Torulaspora delbrueckii (40%) and Kluyveromyces marxianus (10%) were found in 12 Turkish traditional sourdough samples. S. cerevisiae was found to be the most dominant species in Aegean region while T. delbrueckii was the most frequently isolated species in Black Sea region. Some technological properties of isolated yeast species such as acidity development, resistance to NaCI and potassium sorbate, and yeast effect on bread quality were investigated. Breads were prepared by S. cerevisiae TGM38 strain demonstrated the highest bread volume compared the other yeasts used in the study. This study showed the yeast diversity and technological properties of traditional Turkish sourdough breads fermented by chosen yeast species.