The bacteriology in adult patients with pneumonia and parapneumonic effusions: increased yield with DNA sequencing method.

The aim of this study was to use a 16S rDNA sequencing method in combination with conventional culture in patients with parapneumonic effusions (PPE) to evaluate the methods, study the microbiological spectrum, and examine the presence of bacteria within the different stages of PPE. Adults with community-acquired pneumonia (CAP) and PPE (n = 197) admitted to the Departments of Infectious Diseases at four hospitals in Stockholm County during 2011-2014 were prospectively studied. All patients underwent thoracentesis. Twenty-seven non-infectious pleural effusions were used as controls. The pleural samples were analyzed with culture, 16S rDNA sequencing, pH, glucose, and lactate dehydrogenase. Microbiological etiology was found in 99/197 (50%) of the patients with mixed infections in 20 cases. The most common pathogens were viridans streptococci (n = 37) and anaerobic bacteria (n = 40). Among the 152 patients with both methods performed, 26/152 (17%) and 94/152 (62%) had bacteria identified with culture and 16S rDNA sequencing respectively (p < 0.001). In 24/26 (92%) culture-positive cases, the same organism was identified by 16S rDNA. All controls were negative in both methods. Among the patients with complicated PPE and complete sampling, bacteria were found in 69/74 patients (93%), all detected with 16S rDNA sequencing, compared to 23/74 (31%) culture-positive samples (p < 0.001). Compared with culture, 16S rDNA sequencing substantially improved the microbiological yield, a microbiological diagnosis was achieved in almost all patients with complicated PPE, and the specificity seemed to be high. 16S rDNA sequencing should be used together with culture in patients with PPE to guide antibiotic therapy.

Rapid EUCAST disc diffusion testing of MDR Escherichia coli and Klebsiella pneumoniae: inhibition zones for extended-spectrum cephalosporins can be reliably read after 6†h of incubation.

Objectives: The need for rapid antibiotic susceptibility testing increases with escalating levels of antimicrobial resistance in Enterobacteriaceae. Our objective was to evaluate the accuracy of reading EUCAST disc diffusion, ROSCO ESBL and carbapenemase detection kits and the Mast Carbapenemase Activity Test (CAT-ID) disc, after 6 h of incubation. Methods: We used a collection of 128 isolates of Escherichia coli and Klebsiella pneumoniae with a wide variety of resistance mechanisms. Inhibition zones read from digital photo images with the BD Kiestra™ Total Lab Automation System after 6 h of incubation were compared with standard reading, after 18 h, of the same Mueller-Hinton agar plates. Results: For WT isolates, zones were generally smaller at 6 h than at 18 h. Cefotaxime had excellent categorical agreement of 99%, despite the high number of challenge isolates. However, for some other antimicrobials, hetero-resistant subpopulations were commonly invisible at 6 h, which resulted in an unacceptable number of errors when using standard EUCAST breakpoints. Accurate ESBL detection was possible at 6 h for isolates lacking other ß-lactamases. Carbapenemase detection was not reliable after 6 h. Conclusions: Inhibition zone reading at 6 h is an accurate method for susceptibility testing of extended-spectrum cephalosporins for Enterobacteriaceae. For other antimicrobials, 6 h reading can be used for preliminary reports of clearly resistant or susceptible isolates, preferably with application of adjusted breakpoints including an area of uncertainty between susceptible and resistant values.

Electronic structure origin of conductivity and oxygen reduction activity changes in low-level Cr-substituted (La,Sr)MnO3.

The electronic structure of the (La(0.8)Sr(0.2))(0.98)Mn(1-x)Cr(x)O3 model series (x = 0, 0.05, or 0.1) was measured using soft X-ray synchrotron radiation at room and elevated temperature. O K-edge near-edge X-ray absorption fine structure (NEXAFS) spectra showed that low-level chromium substitution of (La,Sr)MnO3 resulted in lowered hybridisation between O 2p orbitals and M 3d and M 4sp valance orbitals. Mn L3-edge resonant photoemission spectroscopy measurements indicated lowered Mn 3d-O 2p hybridisation with chromium substitution. Deconvolution of O K-edge NEXAFS spectra took into account the effects of exchange and crystal field splitting and included a novel approach whereby the pre-peak region was described using the nominally filled t(2g) ↑ state. 10% chromium substitution resulted in a 0.17 eV lowering in the energy of the t(2g) ↑ state, which appears to provide an explanation for the 0.15 eV rise in activation energy for the oxygen reduction reaction, while decreased overlap between hybrid O 2p-Mn 3d states was in qualitative agreement with lowered electronic conductivity. An orbital-level understanding of the thermodynamically predicted solid oxide fuel cell cathode poisoning mechanism involving low-level chromium substitution on the B-site of (La,Sr)MnO3 is presented.

Resistance to aztreonam-avibactam among clinical isolates of E. coli is primarily mediated by altered penicillin binding protein 3 and impermeability.

Herein, we investigated decreased susceptibility (DS; MICs 0.25-4 mg/L) and resistance (R; MICs >4 mg/L) to aztreonam-avibactam (ATM-AVI). Contemporary non-replicate clinical isolates of carbapenemase-producing Escherichia coli (n=90) (CP-EC) and ESBL-producing E. coli (n=12) (EP-EC) was used. CP-EC belonged to 25 distinct sequence types (STs) and all EP-EC belonged to ST405. All strains were isolated through 2019-2022 at the Karolinska University Laboratory, Stockholm, Sweden. ATM-AVI MICs were determined with broth microdilution and the EUCAST epidemiological cutoff value of 0.125 mg/L was used to define the wildtype (WT). Whole genome sequences (Illumina) were analyzed for detecting of resistance determinants among WT vs non-WT isolates. Among 102 isolates, 40 (39%) and 62 (61%) were WT and non-WT respectively. Among non-WT isolates 20 were R and 42 were DS. Resistance was observed among 14/47 NDM-producers, 5/43 OXA-48 group producers, and 1/12 EP-EC. DS was observed among 29/47 NDM, 13/43 OXA-48 group, and 3/12 EP-EC. Resistant isolates predominantly belonged to ST405 followed by STs 410, 361, 167, 617, and 1284. Presence of PBP3 inserts (YRIK/YRIN) were observed in 20/20 and presence of CMY-42 in 5/20 resistant isolates. Several mutations in the ftsI (encoding PBP3) and regulatory genes of outer membrane proteins (OmpC and OmpF) and efflux pumps (AcrAB-TolC) were detected. A ≥2-fold reduction in MICs were observed among 20/20 vs 7/20 isolates tested in the presence of the membrane permeabilizer PMBN and efflux inhibitor PAßN, respectively. In conclusion, resistance to ATM-AVI is a result of interplay of various determinants, including target alterations, deactivating enzymes, and decreased permeability.

Surface-Enhanced Raman Spectroscopy and Artificial Neural Networks for Detection of MXene Flakes' Surface Terminations.

The properties of MXene flakes, a new class of two-dimensional materials, are strictly determined by their surface termination. The most common termination groups are oxygen-containing (=O or -OH) and fluorine (-F), and their relative ratio is closely related to flake stability and catalytic activity. The surface termination can vary significantly among MXene flakes depending on the preparation route and is commonly determined after flake preparation by using X-ray photoelectron spectroscopy (XPS). In this paper, as an alternative approach, we propose the combination of surface-enhanced Raman spectroscopy (SERS) and artificial neural networks (ANN) for the precise and reliable determination of MXene flakes' (Ti3C2Tx) surface chemistry. Ti3C2Tx flakes were independently prepared by three scientific groups and subsequently measured using three different Raman spectrometers, employing resonant excitation wavelengths. Manual analysis of the SERS spectra did not enable accurate determination of the flake surface termination. However, the combined SERS-ANN approach allowed us to determine the surface termination with a high accuracy. The reliability of the method was verified by using a series of independently prepared samples. We also paid special attention to how the results of the SERS-ANN method are affected by the flake stability and differences in the conditions of flake preparation and Raman measurements. This way, we have developed a universal technique that is independent of the above-mentioned parameters, providing the results with accuracy similar to XPS, but enhanced in terms of analysis time and simplicity.

Measurement of lactate in pleural fluid rapidly identify infection and guide therapy.

BACKGROUND: Measurements of pleural fluid biomarkers for rapid identification of complicated parapneumonic effusion (CPPE) are crucial for optimal management. Previous studies for biomarker evaluation were however based on pleura culture, not modern DNA technique. Lactate has not been thoroughly studied earlier as a potential biomarker in this regard. OBJECTIVES: To evaluate whether the routine biomarkers pH, glucose, lactate dehydrogenase (LDH) measured in pleural fluid in a microbiological well characterised cohort could differentiate simple parapneumonic effusion (SPPE) from CPPE and if pleural fluid lactate could be of additional use in this discrimination. METHODS: Pleural fluid prospectively collected from adult patients (n = 112) with PPE admitted to the Departments of Infectious Diseases (DIDs) at four Stockholm County hospitals were characterised microbiologically with bacterial culture and 16S rDNA sequencing, and biochemically with pH, glucose, LDH and lactate. RESULTS: Forty and seventy two patients were categorised as SPPE/CPPE. The median values between SPPE/CPPE differed significantly for all biomarkers with varying overlap. Receiver operating characteristics (ROC) curves showed the area under the curve (AUC) for pH 0.905 (CI 0.847-0.963), glucose 0.861 (CI 0.79-0.932), LDH 0.917 (CI 0.860-0.974) and lactate 0.927 (CI 0.877-0.977), corresponding to best cut-off levels and sensitivity/specificity for pH of 7.255, 0.819/0.9, glucose 5.35 mmol/L, 0.847/0.775, LDH 9.8 µcat/L, 0.905/0.825 and lactate 4.9 mmol/L, 0.875/0.85. CONCLUSIONS: To distinguish between SPPE/CPPE, pH and LDH performed well, but optimal cut-off values differed from earlier established recommendations. Pleura lactate had the largest AUC of the investigated biomarkers and may be used in the analyses of PPE-staging.

Defect pairing in Fe-doped SnS van der Waals crystals: a photoemission and scanning tunneling microscopy study.

We investigate the effect of low concentrations of iron on the physical properties of SnS van der Waals crystals grown from the melt. By means of scanning tunneling microscopy (STM) and photoemission spectroscopy we study Fe-induced defects and observe an electron doping effect in the band structure of the native p-type SnS semiconductor. Atomically resolved and bias dependent STM data of characteristic defects are compared to ab initio density functional theory simulations of vacancy (VS and VSn), Fe substitutional (FeSn), and Fe interstitial (Feint) defects. While native SnS is dominated by acceptor-like VSn vacancies, our results show that Fe preferentially occupies donor-like interstitial Feint sites in close proximity to VSn defects along the high-symmetry c-axis of SnS. The formation of such well-defined coupled (VSn, Feint) defect pairs leads to local compensation of the acceptor-like character of VSn, which is in line with a reduction of p-type carrier concentrations observed in our Hall transport measurements.

A detailed mechanism of degradation behaviour of biodegradable as-ECAPed Zn-0.8Mg-0.2Sr with emphasis on localized corrosion attack.

In this study, advanced techniques such as atom probe tomography, atomic force microscopy, X-ray photoelectron spectroscopy, and electrochemical impedance spectroscopy were used to determine the corrosion mechanism of the as-ECAPed Zn-0.8Mg-0.2Sr alloy. The influence of microstructural and surface features on the corrosion mechanism was investigated. Despite its significance, the surface composition before exposure is often neglected by the scientific community. The analyses revealed the formation of thin ZnO, MgO, and MgCO3 layers on the surface of the material before exposure. These layers participated in the formation of corrosion products, leading to the predominant occurrence of hydrozincite. In addition, the layers possessed different resistance to the environment, resulting in localized corrosion attacks. The segregation of Mg on the Zn grain boundaries with lower potential compared with the Zn-matrix was revealed by atom probe tomography and atomic force microscopy. The degradation process was initiated by the activity of micro-galvanic cells, specifically Zn - Mg2Zn11/SrZn13. This process led to the activity of the crevice corrosion mechanism and subsequent attack to a depth of 250 µm. The corrosion rate of the alloy determined by the weight loss method was 0.36 mm·a-1. Based on this detailed study, the degradation mechanism of the Zn-0.8Mg-0.2Sr alloy is proposed.

Epitaxial growth and characterization of SnSe phases on Au(111).

Two-dimensional (2D) layered group IV-VI semiconductors attract great interest due to their potential applications in nanoelectronics. Depending on the dimensionality, different phases of the same material can present completely different electronic and optical properties, expanding its applications. Here, we present a combined experimental and theoretical study of the atomic structure and electronic properties of epitaxial SnSe structures grown on a metallic Au(111) substrate, forming almost defect-free 2D layers. We describe a coverage-dependent transition from a metallicß-SnSe to a semiconductingα-SnSe phase. The combination of scanning tunneling microscopy/spectroscopy, non-contact atomic force microscopy, x-ray photoelectron spectroscopy/diffraction and angle-resolved photoemission spectroscopy, complemented by density functional theory, provides a comprehensive study of the geometric and electronic structure of both phases. Our work demonstrates the possibility to grow two distinct SnSe phases on Au(111) with high quality and on a large scale. The strong interaction with the substrate allows the stabilization of the previously experimentally unreportedß-SnSe, while the ultra-thin films of orthorhombicα-SnSe are structurally and electronically equivalent to bulk SnSe.

Evaluation of multi-sample 16S ribosomal DNA sequencing for the diagnosis of postoperative bone and joint infections during antimicrobial treatment.

OBJECTIVES: Clinicians worldwide struggle to identify the bacterial aetiology of bone and joint infections. Failure to unequivocally identify the pathogen is linked to poor clinical outcomes. We explored the added value of analysing multiple samples per patient with 16S ribosomal DNA (16S rDNA) sequencing in diagnosing postoperative bone and joint infections. All patients had received antimicrobials prior to sampling, and false-negative cultures could be suspected. Bone biopsies obtained from patients with postoperative bone and joint infections for cultures were also subjected to 16S rDNA sequencing. RESULTS: In 5/28 infectious episodes, sequencing identified the causative organism of the infection when cultures failed. In 8/28 episodes, the methods led to different results, potentially leading to different antimicrobial choices. The analysis of multiple samples per patient helped rule out potential contaminating pathogens. We conclude that 16S rDNA sequencing has diagnostic value for patients receiving antibiotic treatment. We regard the method as a complement to culturing when the cultures are negative. Multiple samples per patient should be analysed to determine the clinical significance of positive findings.

A highly durable graphene monolayer electrode under long-term hydrogen evolution cycling.

Achieving long term stability of single graphene sheets towards repeated electrochemical hydrogen evolution reaction (HER) cycling has been challenging. Here, we show through appropriate electrode preparation that it is possible to obtain highly durable isolated graphene electrodes, which can survive several hundreds of HER cycles with virtually no damage to the sp2-carbon framework and persistently good electron transfer characteristics.

Local geometry around B atoms in B/Si(1 1 1) from polarized x-ray absorption spectroscopy.

The arrangement of B atoms in a doped Si(1 1 1)-[Formula: see text]:B system was studied using a near-edge x-ray absorption fine structure (NEXAFS). Boron atoms were deposited via segregation from the bulk by flashing the sample repeatedly. The positions of B atoms are determined by comparing measured polarized (angle-dependent) NEXAFS spectra with spectra calculated for various structural models based on ab initio total energy calculations. It is found that most of boron atoms are located in sub-surface L[Formula: see text] positions, beneath a Si atom. However, depending on the preparation method a significant portion of B atoms may be located elsewhere. A possible location of these non-L[Formula: see text]-atoms is at the surface, next to those Si atoms which form the [Formula: see text] reconstruction.

Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is commonly diagnosed by reverse transcription polymerase chain reaction (RT-PCR) to detect viral RNA in patient samples, but RNA extraction constitutes a major bottleneck in current testing. Methodological simplification could increase diagnostic availability and efficiency, benefitting patient care and infection control. Here, we describe methods circumventing RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated or lysed samples. Our data, including benchmarking using 597 clinical patient samples and a standardised diagnostic system, demonstrate that direct RT-PCR is viable option to extraction-based tests. Using controlled amounts of active SARS-CoV-2, we confirm effectiveness of heat inactivation by plaque assay and evaluate various generic buffers as transport medium for direct RT-PCR. Significant savings in time and cost are achieved through RNA-extraction-free protocols that are directly compatible with established PCR-based testing pipelines. This could aid expansion of COVID-19 testing.

Strain and Charge Doping Fingerprints of the Strong Interaction between Monolayer MoS2 and Gold.

Gold-mediated exfoliation of MoS2 has recently attracted considerable interest. The strong interaction between MoS2 and Au facilitates preferential production of centimeter-sized monolayer MoS2 with near-unity yield and provides a heterostructure system noteworthy from a fundamental standpoint. However, little is known about the detailed nature of the MoS2-Au interaction and its evolution with the MoS2 thickness. Here, we identify the specific vibrational and binding energy fingerprints of this interaction using Raman and X-ray photoelectron spectroscopy, which indicate substantial strain and charge doping in monolayer MoS2. Tip-enhanced Raman spectroscopy reveals heterogeneity of the MoS2-Au interaction at the nanoscale, reflecting the spatial nonconformity between the two materials. Micro-Raman spectroscopy shows that this interaction is strongly affected by the roughness and cleanliness of the underlying Au. Our results elucidate the nature of the MoS2-Au interaction and guide strain and charge doping engineering of MoS2.

pH sensitivity of interfacial electron transfer at a supported graphene monolayer.

Electrochemical devices based on a single graphene monolayer are often realized on a solid support such as silicon oxide, glassy carbon or a metal film. Here, we show that, with graphene on insulating substrates, the kinetics of the electron transfer at graphene with various redox active molecules is dictated by solution pH for electrode reactions that are not proton dependent. We attribute the origin of this unusual phenomenon mainly to electrostatic effects between dissolved/dissociated redox species and the interfacial charge due to trace amounts of ionizable groups at the supported graphene-liquid interface. Cationic redox species show higher electron transfer rates at basic pH, while anionic species undergo faster electron transfer at acidic pH. Although this behavior is observed on graphene on three different insulating substrates, the strength of this effect appears to differ depending on the surface charge density of the underlying substrate. This finding has important implications for the design of electrochemical sensors and electrocatalysts based on graphene monolayers.

Correction: pH sensitivity of interfacial electron transfer at a supported graphene monolayer.

Correction for 'pH sensitivity of interfacial electron transfer at a supported graphene monolayer' by Michel Wehrhold et al., Nanoscale, 2019, DOI: 10.1039/c9nr05049c.

Introduction of a hydrolysis probe PCR assay for high-throughput screening of methicillin-resistant Staphylococcus aureus with the ability to include or exclude detection of Staphylococcus argenteus.

Many countries using sensitive screening methods for detection of carriage of methicillin-resistant Staphylococcus aureus (MRSA) have a sustained low incidence of MRSA infections. For diagnostic laboratories with high sample volumes, MRSA screening requires stability, low maintenance and high performance at a low cost. Herein we designed oligonucleotides for a new nuc targeted hydrolysis probe PCR to replace the standard in-house nuc SybrGreen PCR assay. This new, more time-efficient, PCR assay resulted in a 40% increase in daily sample capacity, with maintained high specificity and sensitivity. The assay was also able to detect Staphylococcus aureus clonal cluster 75 (CC75) lineage strains, recently re-classified as Staphylococcus argenteus, with a sensitivity considerably increased compared to our previous assay. While awaiting consensus if the CC75 lineage of S. aureus should be considered as S. argenteus, and whether methicillin-resistant S. argenteus should be included in the MRSA definition, many diagnostic laboratories need to update their MRSA assay sensitivity/specificity towards this lineage/species. The MRSA screening assay presented in this manuscript is comprised of nuc oligonucleotides separately targeting S. aureus and CC75 lineage strains/S. argenteus, thus providing high user flexibility for the detection of CC75 lineage strains/S. argenteus.

Enhanced absorption of TiO2 nanotubes by N-doping and CdS quantum dots sensitization: insight into the structure.

Anodization of titanium film sputtered on fluorine doped tin oxide (FTO) glass was performed to obtain highly ordered ∼2 µm long and ∼60 nm wide TiO2 nanotubes. The titania films were annealed in ammonia atmosphere to enable the doping with N. The annealing did not affect the nanotubular morphology and the porosity remained open which is a very important requirement for further deposition of CdS quantum dots. The analysis done by transmission electron microscopy (TEM) has shown that the N-doped nanotubes have a smaller interplanar distance as compared to the undoped ones, whose interplanar distance corresponded to anatase phase. This difference was attributed to the N doping and the Sn migration from the substrate, as demonstrated by energy dispersive spectroscopy (EDS) combined with electron energy loss spectroscopy (EELS). The near edge X-ray absorption fine structure (NEXAFS) analysis clearly demonstrated that also the doped TiO2 film has anatase phase. Regarding the chemical composition of the studied samples, the X-ray photoelectron spectroscopy (XPS) and synchrotron radiation photoelectron spectroscopy (SRPES) analyses have shown that N is incorporated both interstitially and substitutionally in the TiO2 lattice, with a decreased contribution of the interstitial after ionic sputtering. The shift of the valence band maximum (VBM) position for the doped TiO2 vs. the undoped TiO2 proved the narrowing of the band gap. The CdS/TiO2 films show bigger VBM shifting that can be attributed to CdS deposit. Comparing the absorption spectra of the bare undoped and doped TiO2 samples, it was noticed that the doping causes a red shift from 397 to 465 nm. Furthermore, the CdS deposition additionally enhances the absorption in the visible range (575 nm for undoped TiO2/CdS and 560 nm for doped TiO2/CdS films).

Electronic and Chemical Properties of Donor, Acceptor Centers in Graphene.

Chemical doping is one of the most suitable ways of tuning the electronic properties of graphene and a promising candidate for a band gap opening. In this work we report a reliable and tunable method for preparation of high-quality boron and nitrogen co-doped graphene on silicon carbide substrate. We combine experimental (dAFM, STM, XPS, NEXAFS) and theoretical (total energy DFT and simulated STM) studies to analyze the structural, chemical, and electronic properties of the single-atom substitutional dopants in graphene. We show that chemical identification of boron and nitrogen substitutional defects can be achieved in the STM channel due to the quantum interference effect, arising due to the specific electronic structure of nitrogen dopant sites. Chemical reactivity of single boron and nitrogen dopants is analyzed using force-distance spectroscopy by means of dAFM.

Microarray assessment of fibronectin, collagen and integrin expression and the role of fibronectin-collagen coating in the growth of normal, SV40 T-antigen-immortalised and malignant human oral keratinocytes.

Extracellular matrix proteins affect the growth and survival of epithelial tissues. Accordingly, surface coating with fibronectin and collagen is a common practice for promoting keratinocyte culture. In this study, the expression of fibronectin and collagen-related factors, including integrins, by normal (NOK), SV40 T-antigen-immortalised (SVpgC2a) and malignant (SqCC/Y1) human oral keratinocytes, under standardised, serum-free conditions, was investigated by using microarray analysis. Cell growth was also studied in the presence and absence of a matrix consisting of human fibronectin and bovine collagen type I (FN-COL). Fibronectin transcripts were abundant in all cells, whereas 16 of 29 collagen chains and 14 of 24 integrin subunits were variably detected. With regard to both the expression level and the number of transcripts, higher collagen and lower integrin expression was observed in SVpgC2a cells than in NOKs and SqCC/Y1 cells. The cell types differed with regard to colony-forming efficiency and the rate and kinetics of growth at high cell density. For all cell types, FN-COL coating consistently stimulated cell migration, without influencing growth in mass culture or clonal density. The results demonstrate the transcription of genes associated with the formation and function of fibronectin and collagen in oral epithelium, and variably altered expression patterns in transformed states, and show that keratinocyte lines can be successfully transferred without the stimulus from extracellular FN-COL.