Evaluation of Two Portable Hyperspectral-Sensor-Based Instruments to Predict Key Soil Properties in Canadian Soils.

In contrast with classic bench-top hyperspectral (multispectral)-sensor-based instruments (spectrophotometers), the portable ones are rugged, relatively inexpensive, and simple to use; therefore, they are suitable for field implementation to more closely examine various soil properties on the spot. The purpose of this study was to evaluate two portable spectrophotometers to predict key soil properties such as texture and soil organic carbon (SOC) in 282 soil samples collected from proportional fields in four Canadian provinces. Of the two instruments, one was the first of its kind (prototype) and was a mid-infrared (mid-IR) spectrophotometer operating between ~5500 and ~11,000 nm. The other instrument was a readily available dual-type spectrophotometer having a spectral range in both visible (vis) and near-infrared (NIR) regions with wavelengths ranging between ~400 and ~2220 nm. A large number of soil samples (n = 282) were used to represent a wide variety of soil textures, from clay loam to sandy soils, with a considerable range of SOC. These samples were subjected to routine laboratory soil analysis before both spectrophotometers were used to collect diffuse reflectance spectroscopy (DRS) measurements. After data collection, the mid-IR and vis-NIR spectra were randomly divided into calibration (70%) and validation (30%) sets. Partial least squares regression (PLSR) was used with leave one out cross-validation techniques to derive the spectral calibrations to predict SOC, sand, and clay content. The performances of the calibration models were reevaluated on the validation set. It was found that sand content can be predicted more accurately using the portable mid-IR spectrophotometer and clay content is better predicted using the readily available dual-type vis-NIR spectrophotometer. The coefficients of determination (R2) and root mean squared error (RMSE) were determined to be most favorable for clay (0.82 and 78 g kg-1) and sand (0.82 and 103 g kg-1), respectively. The ability to predict SOC content precisely was not particularly good for the dataset of soils used in this study with an R2 and RMSE of 0.54 and 4.1 g kg-1. The tested method demonstrated that both portable mid-IR and vis-NIR spectrophotometers were comparable in predicting soil texture on a large soil dataset collected from agricultural fields in four Canadian provinces.

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 internal transcribed spacer (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 min/sample) species identification promptly after the initial culture.

Fourier Transform Infrared Spectroscopy as a Tool to Study Milk Composition Changes in Dairy Cows Attributed to Housing Modifications to Improve Animal Welfare.

Animal welfare status is assessed today through visual evaluations requiring an on-farm visit. A convenient alternative would be to detect cow welfare status directly in milk samples, already routinely collected for milk recording. The objective of this study was to propose a novel approach to demonstrate that Fourier transform infrared (FTIR) spectroscopy can detect changes in milk composition related to cows subjected to movement restriction at the tie stall with four tie-rail configurations varying in height and position (TR1, TR2, TR3 and TR4). Milk mid-infrared spectra were collected on weekly basis. Long-term average spectra were calculated for each cow using spectra collected in weeks 8-10 of treatment. Principal component analysis was applied to spectral averages and the scores of principal components (PCs) were tested for treatment effect by mixed modelling. PC7 revealed a significant treatment effect (p = 0.01), particularly for TR3 (configuration with restricted movement) vs. TR1 (recommended configuration) (p = 0.03). The loading spectrum of PC7 revealed high loadings at wavenumbers that could be assigned to biomarkers related to negative energy balance, such as ß-hydroxybutyrate, citrate and acetone. This observation suggests that TR3 might have been restrictive for cows to access feed. Milk FTIR spectroscopy showed promising results in detecting welfare status and housing conditions in dairy cows.

Diagnosis of idiopathic amyotrophic lateral sclerosis using Fourier-transform infrared spectroscopic analysis of patient-derived skin.

One of the great challenges in identifying effective therapy in many neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), is the lack of reliable biomarkers. In this study, we applied infrared imaging microspectroscopy, a valuable technique to investigate biomolecule fingerprints and secondary structure of proteins within biological tissue. We hypothesized that, since skin and CNS have the same embryonic origin, spectral differences associated with ALS-specific pathological events will be readily detectable through skin testing using this technique. Cells from healthy individuals and ALS patients were isolated from skin biopsies in order to generate tissue-engineered in vitro skin (TES). Infrared spectra of the generated TES were recorded using a focal-plane-array Fourier transform infrared (FPA-FTIR) spectrometer, and hierarchical cluster analysis of the spectral data was performed in order to establish clear differences between the tested TES specimens. Interestingly, our analyses showed that it was readily possible to discriminate ALS- and control-TES solely based on differences in associated FTIR spectra, mainly located between 1149 and 1473 cm-1, attributed to disruption of phospholipid cell membranes, extracellular matrix remodeling or cholesterol accumulation. Spectral differences within the TES samples may therefore be associated with disease state, paving the way for the identification of biomarkers in ALS.

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.

Cell Seeding on UV-C-Treated 3D Polymeric Templates Allows for Cost-Effective Production of Small-Caliber Tissue-Engineered Blood Vessels.

There is a strong clinical need to develop small-caliber tissue-engineered blood vessels for arterial bypass surgeries. Such substitutes can be engineered using the self-assembly approach in which cells produce their own extracellular matrix (ECM), creating a robust vessel without exogenous material. However, this approach is currently limited to the production of flat sheets that need to be further rolled into the final desired tubular shape. In this study, human fibroblasts and smooth muscle cells were seeded directly on UV-C-treated cylindrical polyethylene terephthalate glycol-modified (PETG) mandrels of 4.8 mm diameter. UV-C treatment induced surface modification, confirmed by Fourier-transform infrared spectroscopy (FTIR) analysis, was necessary to ensure proper cellular attachment and optimized ECM secretion/assembly. This novel approach generated solid tubular conduits with high level of cohesion between concentric cellular layers and enhanced cell-driven circumferential alignment that can be manipulated after 21 days of culture. This simple and cost-effective mandrel-seeded approach also allowed for endothelialization of the construct and the production of perfusable trilayered tissue-engineered blood vessels with a closed lumen. This study lays the foundation for a broad field of possible applications enabling custom-made reconstructed tissues of specialized shapes using a surface treated 3D structure as a template for tissue engineering.

Development of an NDIR CO2 sensor-based system for assessing soil toxicity using substrate-induced respiration.

The eco-toxicological indicators used to evaluate soil quality complement the physico-chemical criteria employed in contaminated site remediation, but their cost, time, sophisticated analytical methods and in-situ inapplicability pose a major challenge to rapidly detect and map the extent of soil contamination. This paper describes a sensor-based approach for measuring potential (substrate-induced) microbial respiration in diesel-contaminated and non-contaminated soil and hence, indirectly evaluates their microbial activity. A simple CO2 sensing system was developed using an inexpensive non-dispersive infrared (NDIR) CO2 sensor and was successfully deployed to differentiate the control and diesel-contaminated soils in terms of CO2 emission after glucose addition. Also, the sensor system distinguished glucose-induced CO2 emission from sterile and control soil samples (p ≤ 0.0001). Significant effects of diesel contamination (p ≤ 0.0001) and soil type (p ≤ 0.0001) on glucose-induced CO2 emission were also found. The developed sensing system can provide in-situ evaluation of soil microbial activity, an indicator of soil quality. The system can be a promising tool for the initial screening of contaminated environmental sites to create high spatial density maps at a relatively low cost.

Rapid identification of community-associated methicillin-resistant Staphylococcus aureus by Fourier transform infrared spectroscopy.

The emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) carrying Panton-Valentine leukocidin is a worldwide problem. Their identification is based currently on costly and complicated molecular methods. This article describes a simple method for differentiating CA-MRSA from hospital-associated (HA) epidemic MRSA pulsed-field gel electrophoresis types using Fourier transform infrared (FTIR) spectroscopy. The 47 CA-MRSA isolates included 3 Southwest Pacific (resembling USA1100), 24 CMRSA7 (resembling USA400/MW2), 19 CMRSA10 (resembling USA300), and 1 European ST80, while HA-MRSA were represented by 27, 16, 11, 15, 7, and 8 Canadian epidemic isolates CMRSA1 through CMRSA6 respectively, plus 25 nontyped Canadian HA-MRSA. Principal component analysis (PCA), self-organized maps (SOMs), and the K-nearest neighbor (KNN) method were used to cluster the isolates based on chemometric analysis of FTIR spectra of dried films of stationary-phase cells grown on Que-Bact® Universal Medium No. 2 (Quelab Laboratories, Montreal, QC, Canada). First-derivative normalized data from a single narrow spectral region (1361-1236 cm(-1), suggesting differences in protein amide III and nucleic acid phosphodiester contents) allowed 98% correct classification by KNN, 93% by SOMs, and 92% by PCA. FTIR spectroscopic analysis of cells grown on Que-Bact® Universal Medium No. 2 offers a rapid and simple alternative to molecular methods for routine identification of CA-MRSA epidemic isolates.

Effect of dissolved oxygen on two bacterial pathogens examined using ATR-FTIR spectroscopy, microelectrophoresis, and potentiometric titration.

The effects of dissolved oxygen tension during bacterial growth and acclimation on the cell surface properties and biochemical composition of the bacterial pathogens Escherichia coli O157:H7 and Yersinia enterocolitica are characterized. Three experimental techniques are used in an effort to understand the influence of bacterial growth and acclimation conditions on cell surface charge and the composition of the bacterial cell: (i) electrophoretic mobility measurements; (ii) potentiometric titration; and (iii) ATR-FTIR spectroscopy. Potentiometric titration data analyzed using chemical speciation software are related to measured electrophoretic mobilities at the pH of interest. Titration of bacterial cells is used to identify the major proton-active functional groups and the overall concentration of these cell surface ligands at the cell membrane. Analysis of titration data shows notable differences between strains and conditions, confirming the appropriateness of this tool for an overall charge characterization. ATR-FTIR spectroscopy of whole cells is used to further characterize the bacterial biochemical composition and macromolecular structures that might be involved in the development of the net surficial charge of the organisms examined. The evaluation of the integrated intensities of HPO(2)(-) and carbohydrate absorption bands in the IR spectra reveals clear differences between growth protocols. Taken together, the three techniques seem to indicate that the dissolved oxygen tension during cell growth or acclimation can noticeably influence the expression of cell surface molecules and the measurable cell surface charge, though in a strain-dependent fashion.

Evaluation of Fourier transform infrared spectroscopy for the rapid identification of glycopeptide-intermediate Staphylococcus aureus.

OBJECTIVES: To evaluate Fourier transform infrared (FTIR) spectroscopy as a rapid method for distinguishing glycopeptide-intermediate Staphylococcus aureus (GISA) from glycopeptide-susceptible methicillin-resistant S. aureus (MRSA) and to compare three data analysis methods. METHODS: First-derivative normalized spectra of dried films of bacterial growth on Que-Bact Universal Medium No. 2 were examined by singular value decomposition to identify key spectral regions. Region selection was analysed by principal component analysis (PCA), self-organizing maps (SOMs) and the K-nearest neighbour (KNN) algorithm. The initial data set included 35 GISA (including GISA Mu50 and heterogeneous GISA Mu3) and 25 epidemic MRSA. The regions were then tested using enlarged data sets that included 22 sporadic and 85 additional epidemic MRSA. RESULTS: Epidemic MRSA and GISA/hGISA were separated into two distinct clusters on the basis of spectral data from regions 1352-1315 and 1480-1460 cm(-1), the former providing 100% correct classification by all three analyses and the latter providing 96.67% correct by PCA, 98.34% by SOM and 100% by KNN. The 1480-1460 cm(-1) region was more effective for distinguishing GISA/hGISA from a set combining sporadic and epidemic MRSA, with two GISA/hGISA and four sporadic MRSA misclassified by PCA and SOM (92.69% correct), while the KNN method misclassified three of the four sporadic MRSA (93.90% correct). The addition of 85 other epidemic MRSA this set increased the fraction of correctly classified isolates to 96.41% and 97.01% by PCA, SOM and KNN, respectively. CONCLUSIONS: As only 6 of 167 isolates were misclassified, FTIR spectroscopy may provide means of rapid and accurate identification of GISA and hGISA among isolates of MRSA.

Epidemiological typing of methicillin-resistant Staphylococcus aureus strains by Fourier transform infrared spectroscopy.

A rapid and simple typing system is needed for controlling the spread of epidemic methicillin-resistant Staphylococcus aureus (MRSA), currently one of the most widespread multi-resistant nosocomial pathogens in Canadian hospitals. Fourier transform infrared (FTIR) spectroscopy was used to subtype 85 isolates representing five strains of epidemic Canadian MRSA (CMRSA). Spectral fingerprints of whole cells grown on Que-Bact(R) Universal Medium No. 2 were transformed to first derivative peak-height normalized files and examined visually and by singular-value decomposition (SVD). Distinguishing spectral regions were processed by principal component analysis (PCA), self-organizing map and K-nearest neighbor supervised cluster analysis. Among the visually identified regions, 1070-1050 and 1155-1137 cm(-1) were found suitable for discrimination of CMRSA-4 and CMRSA-2 respectively, while CMRSA-1, CMRSA-3, and CMRSA-5 each exhibited distinctive spectral profiles in the 1123-1094 cm(-1) region. The combination, 1123-1094, 1174-1154 and 2904-2864 cm(-1) separated the five CMRSA with 84.6% correct classification by PCA. Five clusters were also obtained using the SVD-selected regions 1096-1066, 1118-1090 and 2914-2880 cm(-1), with 87.8% correct classification based on visual examination of the PCA scores plot and 97% based on supervised cluster analysis. These results demonstrate that FTIR spectroscopy has considerable potential as a rapid (1-hour) and simple method for MRSA strain typing and monitoring in clinical settings.

Rapid identification of coagulase-negative staphylococci by Fourier transform infrared spectroscopy.

Coagulase-negative staphylococci (CNS), frequently associated with both community-acquired and nosocomial bloodstream infections, must be distinguished from Staphylococcus aureus for clinical purposes. Conventional methods are too laborious and time-consuming and often lack sensitivity to CNS. Fourier transform infrared (FTIR) spectroscopy combined with the use of a universal growth medium (Que-Bact Universal Medium No. 2) and chemometrics was evaluated for its potential as a rapid and simple clinical tool for making this distinction. FTIR spectra of 11 methicillin-sensitive and 11 methicillin-resistant CNS isolates as well as 25 methicillin-sensitive, 47 methicillin-resistant, 34 borderline oxacillin-resistant and 35 glycopeptide intermediate S. aureus isolates were obtained from dried films of stationary-phase cells grown on the universal medium. Principal component analysis (PCA), self-organizing maps, and the K-nearest neighbor algorithm were employed to cluster the different phenotypes based on similarity of their FTIR spectra. PCA of the first-derivative normalized spectral data from a single narrow region (2888-2868 cm(-1)) yielded complete differentiation of CNS from both methicillin-sensitive and methicillin-resistant S. aureus. The rate of correct classification was somewhat reduced, from 100% to 90%, after inclusion of borderline oxacillin-resistant and glycopeptide intermediate S. aureus strains in the data set. Differentiation based on the data in broader spectral regions was much less reliable. The results of this study indicate that with proper spectral region selection, FTIR spectroscopy and cluster analysis may provide a simple and accurate means of CNS species identification.

Differentiation of group I and group II strains of Clostridium botulinum by focal plane array Fourier transform infrared spectroscopy.

A method was developed for whole-organism fingerprinting of Clostridium botulinum isolates by focal plane array Fourier transform infrared (FPA-FTIR) spectroscopy. A database of 150,000 infrared spectra of 44 strains of C. botulinum was acquired using a FPA-FTIR imaging spectrometer equipped with a 16 x 16 array detector to evaluate the ability of FTIR spectroscopy to differentiate the 44 strains. The database contained strains from C. botulinum groups I and II producing botulinum neurotoxin of serotypes A, B, E, and F. All strains were grown on each of three agar media (brain heart infusion, McClung Toabe agar base, and universal) prior to spectral acquisition. Given the dependence of the infrared spectra of microorganisms on the composition of the growth medium, the spectra were initially separated into three subsets corresponding to the three growth media employed. However, the replicate spectra of all strains, regardless of growth medium, were properly clustered by hierarchical cluster analysis based on differences in their infrared spectral profiles in three narrow spectral regions (1,428 to 1,412, 1,296 to 1,284, and 1,112 to 1,100 cm(-1)). The dendrogram generated from the FTIR data revealed complete separation between group I and group II strains. The spectral differences between group I and group II strains allowed accurate classification of C. botulinum strains at the group level in two blind validation studies (n = 40). These results demonstrate that FPA-FTIR spectroscopy has the potential for rapid discrimination of group I and group II C. botulinum strains in less than 3 min per sample.

Heterospectral two-dimensional correlation spectroscopy of mid-infrared and Fourier self-deconvolved near-infrared spectra of sugar solutions.

The mid- and near-infrared (mid-IR and NIR) spectra of aqueous solutions of glucose and fructose, fructose and galactose, and glucose and galactose were recorded and analyzed by heterospectral two-dimensional correlation spectroscopy (H2D-CS) to determine characteristic NIR wavelengths for each sugar. Fourier self-deconvolution (FSD) was applied to the NIR spectra prior to H2D-CS analysis to help resolve the strongly overlapping sugar absorptions. Examination of the H2D-CS data gave characteristic absorption wavelengths for glucose, fructose, and galactose. The wavelengths identified by H2D-CS were then used to develop multiple linear regression (MLR) calibrations for the quantitative analysis of mixtures of the three sugars in solution. This approach gave comparable results to MLR calibrations based on wavelengths selected by examination of the first- and second-derivative spectra of solutions of the individual sugars.

Investigation of the potential utility of single-bounce attenuated total reflectance Fourier transform infrared spectroscopy in the analysis of distilled liquors and wines.

A new Fourier transform infrared (FTIR) spectroscopic method based on single-bounce attenuated total reflectance (SB-ATR) spectroscopy was developed for the analysis of distilled liquors and wines. For distilled liquors, a partial least-squares (PLS) calibration was developed for alcohol determination based on the SB-ATR/FTIR spectra of mixtures of ethanol and distilled water. An independent set of 12 different distilled liquor samples was predicted from the PLS calibration, and a standard deviation of the differences for accuracy (SDD(a)) between actual and predicted values of 0.142% (v/v) was obtained. The potential utility of SB-ATR/FTIR spectroscopy for the analysis of wines was initially evaluated based on a comparison with Fourier transform near-infrared (FT-NIR) spectroscopy and FTIR spectroscopy using a flow-through transmission cell. PLS calibrations for alcohol, total reducing sugars, total acidity and pH were developed using pre-analyzed wine samples (n = 28), and for SB-ATR/FTIR spectroscopy, the SDD(a) for the leave-one-out cross-validation statistics were of the order of 0.100% (v/v), 0.707 g L(-1), 0.189 g L(-1) (H2SO4), and 0.230, respectively. Overall, the SB-ATR/FTIR results were better than those obtained using FT-NIR spectroscopy and comparable to those obtained with transmission FTIR spectroscopy. A PLS calibration based on preanalyzed wine samples (n = 72) for the prediction of 11 different components and parameters in wines by SB-ATR/FTIR spectroscopy was subsequently developed and validated using an independent sample set (n = 77). Good coefficients of correlation between the reference and predicted values for the validation set were obtained for most of the components and parameters except citric acid, volatile acids, and total SO2. The results of this study demonstrate the suitability of SB-ATR/FTIR spectroscopy for the routine analysis of distilled liquors and wines.

Accelerating bacterial identification by infrared spectroscopy by employing microarray deposition of microorganisms.

A microarray method for the deposition of bacteria onto an agar slide was developed to accelerate the formation of microcolonies. Representative microarrays each consisting of 40 micro-spots of five replicates of eight foodborne bacteria (Yersinia enterocolitica, Staphylococcus aureus, Salmonella typhimurium, Listeria monocytogenes, Enterobacter cloacae, Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli) were printed on a Brain Heart Infusion (BHI) agar slide using a contact micro-spotting robotic system. Within 3 h, sufficient bacterial cells were obtained to allow accurate identification of the microorganism by infrared spectroscopy. This approach allows a "complete-in-a-single-day" analysis of a large array of samples.