Breath of Health: spectroscopy-based breath test for the detection of SARS-CoV-2.

BACKGROUND: Nucleic acid amplification tests (NAAT) are considered the gold standard for COVID-19 diagnosis. These tests require professional manpower and equipment, long processing and swab sampling which is unpleasant to the patients. Several volatile organic compounds (VOCs) have been identified in the breath of COVID-19 patients. Detection of these VOCs using a breath test could help rapidly identify COVID-19 patients. OBJECTIVE: Assess the accuracy of 'Breath of Health' (BOH) COVID-19 Fourier-transform infra-red (FTIR) Spectroscopy-based breath test. METHODS: Breath samples from patients with or without symptoms suggestive for COVID-19 who had NAAT results were collected using Tedlar bags and were blindly analysed using BOH FTIR spectroscopy. BOH Measures several VOCs simultaneously and differentiating positive and negative results. BOH results were compared to NAAT results as gold standard. RESULTS: Breath samples from 531 patients were analysed. The sensitivity of BOH breath test was found to be 79.5% and specificity was 87.2%. Positive predictive value (PPV) was 74.7% and negative predictive value (NPV) 90.0%. Calculated accuracy rate was 84.8% and area under the curve 0.834. Subgroup analysis revealed that the NPV of patients without respiratory symptoms was superior over the NPV of symptomatic patients (94.7% vs 80.7%, P-value < 0.0001) and PPV of patients with respiratory symptoms outranks the PPV of individuals without symptoms (85.3% vs 69.2%, P-value 0.0196). CONCLUSION: We found BOH COVID-19 breath test to be a patient-friendly, rapid, non-invasive diagnostic test with high accuracy rate and NPV that could efficiently rule out COVID-19 especially among individuals with low pre-test probability.

Bacillus cereus strains from donor human milk and hospital environment: uncovering a putative common origin using comparative analysis of toxin and infra-red spectroscopy profiles.

Bacillus cereus is reported as a common cause of toxin-induced food poisoning and of contamination in pasteurized human milk donations. As various toxins can be produced by B. cereus, the aim of this work was first to investigate the toxigenic potential and profiles of 63 B. cereus isolates from Amiens Picardie human milk bank. A comparison to the toxigenic profiles of 27 environmental B. cereus isolates harvested in the hospital in which this human milk bank is situated was performed. Toxin gene prevalences were the highest for nhe (ABC) and entFM followed by cytK and hbl(ACD). A 27% prevalence was found for ces human milk isolates, which is higher than previous works reporting on pasteurized milk and dairy products. No significant differences could be found between human milk and environmental isolates regarding toxin gene prevalences and/or toxin gene profiles. The second aim was to establish whether a B. cereus cross-contamination between human milk and the environment could occur. This was achieved with the help of Fourrier-transform infra-red spectroscopy which enabled the discrimination of 2 main clusters of 11 and 8 isolates, each containing human milk and Amiens Picardie human milk bank environmental isolates. For these two clusters, the time sequence showed that human milk isolates were the first to occur and might have contaminated the milk bank environment as well as other human milk donations. Routinely used on B. cereus isolates, Fourrier-transform infra-red spectroscopy could help in rapidly detecting such clusters and in limiting the spread of a B. cereus strain that might generate rejection of pasteurized donation by the human milk bank.

Development and validation of standard and real patient gallstone library using Fourier transform infra-red spectroscopy.

BACKGROUND: Analysis of the constituents of gallstones using various spectroscopic techniques assists in identification of the pathogenesis of gallstones. In the current study, using Fourier Transform Infra-Red (FTIR) Spectroscopy, a Gallstone Standard Library (GSL) and a Gallstone Real Patients' Library (GRPL) were developed and validated for gallstone composition analysis. METHODS: The study was conducted at the Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan. Pure standards (cholesterol, calcium carbonate, bilirubin and bile salts) and gallstone specimens were analyzed using FTIR Nicolet iS-5 Spectrometer from Thermo Fisher Scientific, USA. Thermo Scientific™ QCheck™ algorithm, embedded within the OMNIC™ software, was used to identify the unique spectral fingerprint of the patient samples to match with known, standard material. Matching of > 75% was considered acceptable. Validation for accuracy of the library was performed for twenty analyzed gallstones at an international reference lab. RESULTS: Concerted search analysis was performed against the developed GSL consisting of 71 "pure component" spectrum divided into 5 types to generate the library. For the Gallstone Real Patient Library (GRPL), 117 patient samples were analyzed. Ninety-eight gall stones (83.8%) out of 117 stones matched with the developed GSL. Majority stones were mixed stones (95.92%), with cholesterol being the primary component (91.83%). Results of the developed library were 100% in agreement with the reports received from the external reference lab. CONCLUSIONS: The library developed displayed good consistency and can be used for detection of gallstone composition in Pakistan and replace the traditional labor- and time-intensive chemical method of gallstone analysis.

Nosocomial outbreak of monoclonal VIM carbapenemase-producing Enterobacter cloacae complex in an intensive care unit during the COVID-19 pandemic: an integrated approach.

BACKGROUND: An outbreak of VIM carbapenemase-expressing Enterobacter cloacae complex occurred between March and October 2020 in an intensive care unit (ICU) of a tertiary care and teaching hospital in France. At the same time, the hospital was facing the COVID-19 first wave. AIM: To describe the management of an outbreak caused by a VIM-producing Enterobacter cloacae complex strain during the COVID-19 pandemic in an ICU and to show the importance of an integrated approach. METHODS: A multi-focal investigation was conducted including descriptive and molecular epidemiology, environmental screening, and assessment of infection prevention and control measures. FINDINGS: A total of 14 cases were identified in this outbreak with a high attributable mortality rate (85.7%). The outbreak management was coordinated by a crisis cell, and involved the implementation of multi-disciplinary actions such as: enhanced hygiene measures, microbiological and molecular analysis of patients and environmental E. cloacae complex strains, and simulation-based teaching. All 23 E. cloacae complex strains isolated from patients and environment samples belonged to multi-locus sequence type ST78 and carried bla-VIM4 gene. Using Fourier transform infrared spectroscopy, all but two isolates were also found to belong to a single cluster. Although the source of this outbreak could not be pinpointed, the spread of the strain was controlled thanks to this multi-focal approach and multi-disciplinary implementation. CONCLUSION: This investigation highlighted the usefulness of Fourier transform infra-red spectroscopy in the rapid typing of outbreak strains as well as the importance of an integrated approach to successfully fight against multidrug-resistant micro-organism dissemination and healthcare-associated infections.

Thermal properties of an exopolysaccharide produced by a marine thermotolerant Bacillus licheniformis by ATR-FTIR spectroscopy.

The novel exopolysaccharide (EPS-B3-15) produced by the marine thermotolerant Bacillus licheniformis strain B3-15, constituted by mannose and glucose, has been recently reported as a valuable biopolymer in pharmaceutical applications. To dynamically characterize the thermal behavior of the whole EPS-B3-15 system, the Attenuated Total Reflectance Fourier Transform Infra-Red spectroscopy technique was used over a temperature range from ambient to 78.5 °C. The molecular changes of EPS-B3-15 during the heating process were evaluated by the spectral distance (SD) and wavelet cross-correlation (XWT) analysis. The thermal analysis revealed that the EPS-B3-15 possessed high stability until 78.5 °C. As evaluated by SD and XWT, the molecular structure of EPS-B3-15 at 45 °C was partially modified, due to -OH groups and the -COOH and -OH interactions, conferring a new conformational structure to the biopolymer. The thermal characterization provides novel information about the molecular conformations of the whole EPS-B3-15 system at different temperatures. The thermostable EPS-B3-15 can be successfully employed for biotechnological, nanotechnological and material science applications even at high temperatures.

Batch-to-batch variation in domestic paints: Insights into the newly commercialized recycled paints.

A few recent studies attempted to evaluate the differentiation of paints at a production batch level and reported results depending largely on the paint type. The discrimination from production batches is much more random than brands and/or models levels and subject to many unknowns, which suggests that a particular production batch can suddenly present a substantially different composition than the one produced right before or right after it. To add to this existing complexity, most of the paint companies now propose a range of recycled paints among their products. These recycled paints are composed of wastes collected by recycling plants, sorted by their color and binder type (i.e. latex, alkyds), and mixed together in large tanks to form the basis material for future formulations. Quality controls on these recycled batches are voluntarily less precise, and a higher variation is expected in esthetic and chemical properties of the paint. In this project, we collaborated with a North American paint producer that gave us access to its samples, paint formulations recipes, and a summary of the quality controls and corrections they performed on each production batches. The whole study was conducted blindfold and a final verification was made with the manufacturer to evaluate the accuracy of the results. The data set comprised two models of regular paints and two models of recycled paint. Five different production batches were collected per model for a total of 20 samples analyzed by Microscopy, Infrared spectroscopy, Raman spectroscopy, and Pyrolysis GC/MS.

Proof-of-concept study to establish an in situ method to determine the nature and depth of collagen changes in dentine using Fourier Transform Infra-Red spectroscopy after sodium hypochlorite irrigation.

AIM: To establish a method using Fourier Transform Infra-Red spectroscopy (FTIR) to characterize the nature and depth of changes in dentinal collagen following exposure to sodium hypochlorite (NaOCl) during root canal irrigation in an ex vivo model. METHODOLOGY: Fourier Transform Infra-Red spectroscopy was used to assess the changes in dentinal collagen when the root canal was exposed to NaOCl. The changes in dentinal collagen caused by NaOCl irrigation of root canals in transverse sections of roots, at 0.5 mm from the canal wall and 0.5 mm from the external root surface, were assessed by FTIR. The data were analysed using paired t-test with 5% significance level. RESULTS: Fourier Transform Infra-Red spectroscopy confirmed that NaOCl exposure caused alterations in the chemistry and structure of collagen in dentine. FTIR spectra obtained from dentine surfaces and dentine adjacent to root canals exposed to NaOCl, all consistently showed degradation and conformational change of the collagen structure. FTIR data from the ex vivo model showed that the depth of effect of NaOCl extended to at least 0.5 mm from the canal wall. CONCLUSION: In extracted human teeth, NaOCl caused changes in dentinal collagen that were measurable by FTIR. In an ex vivo model, the depth of effect into dentine extended at least 0.5 mm from the canal wall.

On the Morphology and Composition of Particulate Matter in an Urban Environment.

Particulate matter (PM) plays a vital role in altering air quality, human health, and climate change. There are sparse data relevant to PM characteristics in urban environments of the Middle East, including Peshawar city in Pakistan. This work reports on the morphology and composition of PM in two size fractions (PM2.5 and PM10) during November 2016 in Peshawar. The 24 hous mass concentration of PM2.5 varied from 72 µg m-3 to 500 µg m-3 with an average value of 286 µg m-3. The 24 hours PM10 concentration varied from 300 µg m-3 to 1440 µg m-3 with an average of 638 µg m-3. The morphology, size, and elemental composition of PM were measured using Fourier Transform Infra Red (FT-IR) Spectroscopy and Scanning Electron Microscopy (SEM) with Energy Dispersive X-ray (EDX) Spectroscopy. The size of the analyzed particles by EDX ranged from 916 nm to 22 µm. Particles were classified into the following groups based on their elemental composition and morphology: silica (12%), aluminosilicates (23%), calcium rich (3%), chloride (2%), Fe/Ti oxides (3%), carbonaceous (49%), sulfate (5%), biogenic (3%). The major identified sources of PM are vehicular emissions, biomass burning, soil and re-suspended road dust, biological emissions, and construction activities in and around the vicinity of the sampling site.

Exopolysaccharide production in Anabaena sp. PCC 7120 under different CaCl2 regimes.

Influence of various levels of CaCl2 (0, 1, 10 and 100 mM) on exopolysaccharide production has been investigated in the cyanobacterium Anabaena 7120. At the concentration of 1 mM CaCl2, growth was found to be stimulatory while 100 mM was sub lethal for the cyanobacterial cells. Estimation of EPS content revealed that EPS production depends on the concentration of calcium ions in the immediate environment with maximum being at10 mM CaCl2. A possible involvement of alr2882 gene in the process of EPS production was also revealed through qRT-PCR. Further, FTIR-spectra marked the presence of aliphatic alkyl-group, primary amine-group, and polysaccharides along with shift in major absorption peaks suggesting that calcium levels in the external environment regulate the composition of EPS produced by Anabaena 7120. Thus, both quantity and composition of EPS is affected under different calcium chloride concentrations presenting possibilities of EPS with novel unexplored features that may offer biotechnological applications.

Standardization of Shodhita Naga with special reference to thermogravimetry and infra-red spectroscopy.

BACKGROUND: Standardization of Ayurvedic medicine is the need of hour to obtain desired quality of final product. Shodhana literally means purification, is the initial step to make drugs like metals, minerals and poisonous herbs suitable for further procedure. Shodhana of metals/minerals help to expose maximum surface area of drug for chemical reactions and also in impregnation of organic materials and their properties in the drug. Thermo-gravimetric analysis (TGA) facilitates in identifying the presence of organic matter and change in the melting point of metal whereas Fourier transform infra-red spectroscopy (FTIR) assists in identifying the presence of various functional groups. AIM: To standardize the process of Naga Shodhana and to study the change in chemical nature of Shodhita Naga in each media through TGA and FTIR. MATERIAL AND METHODS: Samanya and Vishesha Shodhana of Naga was carried out. Time taken for melting of Naga, physico-chemical changes in media used for Shodhana and weight changes after Shodhana were recorded. Samples of Naga were collected after Shodhana in each media for TGA and FTIR analysis. RESULTS: Average loss occurred during Shodhana was 6.26%. Melting point of Ashuddha Naga was 327.46°C, and it was 328.42°C after Shodhana. Percentage purity of Naga (percentage of lead in Naga) decreased after Shodhana from 99.80% to 99.40%. FTIR analysis of Shodhita Naga in each sample showed stretching vibrations particularly between C-H and C-N bonds that are indicating the presence of various organic compounds. CONCLUSION: According to TGA and FTIR analysis, Shodhana process increases melting point of Naga and initiation of new physico-chemical properties which are indicated by detection of large number of functional groups and organo-metallic nature of Shodhita Naga.

Impact of carbon source and variable nitrogen conditions on bacterial biosynthesis of polyhydroxyalkanoates: evidence of an atypical metabolism in Bacillus megaterium DSM 509.

Twenty bacterial strains were examined on their ability to produce polyhydroxyalkanoates (PHA) from different carbon sources under rich and depleted nitrogen conditions. Preliminary experiments with glucose as sole carbon source allowed to select PHA producing bacteria using FTIR spectroscopy. They were further tested with eight additional carbon substrates including organic, fatty acids or sugars. PHA content and monomer composition of four chosen strains (Pseudomonas putida mt-2, Bacillus megaterium DSM 90 and DSM 509, Corynebacterium glutamicum DSM 20137) were assessed by gas chromatography techniques for two cultural conditions: during growth phase on a mineral medium (MM) and after transfer of cells on a fresh MM without nitrogen (MM-N). For several carbon substrates, substantial amounts of PHA (up to 53% of the cell dry weight: CDW) were already obtained in MM for C. glutamicum DSM 20137 and the two B. megaterium strains; after transfer in MM-N, PHA contents remained constant except for B. megaterium DSM 509 where PHA production increased whatever the carbon source. P. putida mt-2 synthesized PHA under deprived nitrogen conditions. Highest PHA accumulation reached 48 and 77% of CDW with octanoic acid as substrate in B. megaterium DSM 90 and P. putida mt-2, respectively. Surprisingly, an atypical metabolic shift was observed for B. megaterium DSM 509 cultivated with nearly all unrelated carbon sources: whereas short chain length PHA (scl-PHA) were synthesized in MM, medium chain length PHA (mcl-PHA) were produced after transfer of cells into MM-N supplemented with the same substrate.