Performance of 16S rRNA Gene Next-Generation Sequencing and the Culture Method in the Detection of Bacteria in Clinical Specimens.

Effective treatment of infectious diseases requires prompt and accurate bacterial identification and tailored antimicrobial treatments. Traditional culture methods are considered the gold standard, but their effectiveness diminishes for fastidious and hard-to-grow microorganisms. In recent years, molecular diagnostic tools such as 16S rRNA gene next-generation sequencing (16S NGS) have gained popularity in the field. We analysed data from samples submitted for 16S NGS between July 2022 and July 2023 at the Department of Advanced Translational Microbiology in Trieste, Italy. The study included samples submitted for both culture-based identification and 16S NGS. Conventional media were used for culture, and bacterial identification was performed using MALDI-TOF mass spectrometry. The V3 region of the 16S rRNA gene was sequenced using the Ion PGM platform. Among the 123 samples submitted, drainage fluids (38%) and blood (23%) were the most common, with requests predominantly from the Infectious Diseases (31.7%) and Orthopedic (21.13%) Units. In samples collected from patients with confirmed infections, 16S NGS demonstrated diagnostic utility in over 60% of cases, either by confirming culture results in 21% or providing enhanced detection in 40% of instances. Among the 71 patients who had received antibiotic therapies before sampling (mean 2.3 prior antibiotic days), pre-sampling antibiotic consumption did not significantly affect the sensitivity of 16S NGS. In routine microbiology laboratories, combining 16S NGS with culture method enhances the sensitivity of microbiological diagnostics, even when sampling is conducted during antibiotic therapy.

Vancomycin-Resistant Streptococcus thoraltensis: A Case Report of Bacterial Endocarditis and Review of Literature on Infections Caused by This Pathogen.

Streptococcus thoraltensis is a rare species, part of the viridans streptococcus group, found initially in rabbits and pigs, which can be vancomycin-resistant. We present the case of a 65-year-old patient, a smoker and chronic alcohol consumer with chronic obstructive pulmonary disease (COPD) and multiple dental foci who had been diagnosed with bacterial endocarditis caused by Streptococcus thoraltensis. The particular elements of the case consisted of an atypical clinical presentation with diarrheal stools, abdominal pain, concomitant damage to the aortic and tricuspid valves, the presence of large vegetations (>2 cm), and a vancomycin-resistant strain of Streptococcus thoraltensis. The evolution of the patient was unfavorable due to septic embolisms, respiratory failure requiring orotracheal intubation, and septic and cardiogenic shock. Infections with Streptococcus thoraltensis are challenging to treat because of the severity of the clinical form it causes and the pattern of antibiotic resistance in this germ. Based on our brief review, Streptococcus thoraltensis is an extremely rare human pathogen previously described as the etiologic agent of infectious endocarditis in only one case.

An Overview of the Factors Involved in Biofilm Production by the Enterococcus Genus.

Enterococcus species are known for their ability to form biofilms, which contributes to their survival in extreme environments and involvement in persistent bacterial infections, especially in the case of multi-drug-resistant strains. This review aims to provide a comprehensive understanding of the mechanisms underlying biofilm formation in clinically important species such as Enterococcus faecalis and the less studied but increasingly multi-drug-resistant Enterococcus faecium, and explores potential strategies for their eradication. Biofilm formation in Enterococcus involves a complex interplay of genes and virulence factors, including gelatinase, cytolysin, Secreted antigen A, pili, microbial surface components that recognize adhesive matrix molecules (MSCRAMMs), and DNA release. Quorum sensing, a process of intercellular communication, mediated by peptide pheromones such as Cob, Ccf, and Cpd, plays a crucial role in coordinating biofilm development by targeting gene expression and regulation. Additionally, the regulation of extracellular DNA (eDNA) release has emerged as a fundamental component in biofilm formation. In E. faecalis, the autolysin N-acetylglucosaminidase and proteases such as gelatinase and serin protease are key players in this process, influencing biofilm development and virulence. Targeting eDNA may offer a promising avenue for intervention in biofilm-producing E. faecalis infections. Overall, gaining insights into the intricate mechanisms of biofilm formation in Enterococcus may provide directions for anti-biofilm therapeutic research, with the purpose of reducing the burden of Enterococcus-associated infections.

A Tale of Two Pandemics: Antimicrobial Resistance Patterns of Enterococcus spp. in COVID-19 Era.

Although the COVID-19 pandemic has held the spotlight over the past years, the antimicrobial resistance (AMR) phenomenon continues to develop in an alarming manner. The lack of strict antibiotic regulation added to the overuse of antimicrobials fueled the AMR pandemic. This paper aims to analyze and identify the impact of the COVID-19 pandemic on antibiotic resistance patterns of Enterococcus spp. The study was designed as a retrospective observational study. Enterococcus spp. infections data were collected from one academic hospital in Cluj-Napoca, Romania over 18 months. A statistical analysis was performed to compare antibiotic resistance phenotypes identified. We recorded an increase in the isolation rates of Enterococcus spp. strains, from 26 isolates (26.53%) during Period A (November 2020-April 2021) to 42 strains (42.85%) during Period C (November 2021-April 2022). The number of strains with resistance to vancomycin increased from 8 during Period A to 17 during Period C. Of the total 36 strains with resistance to vancomycin, 25 were identified as E. faecium. SARS-CoV-2 patients (n = 29) proved to be at risk to develop an E. faecium co-infection (n = 18). We observed that strains with resistance to ampicillin (n = 20) and vancomycin (n = 15) are more often isolated from these patients. All changes identified in our study are to be considered in the light of COVID-19 pandemic, highlighting the threatening AMR phenomenon in Romania. Further studies should be performed to quantify the worldwide effects of these pandemics.

Easy and Affordable: A New Method for the Studying of Bacterial Biofilm Formation.

BACKGROUND: Bacterial biofilm formation (BBF) proves itself to be in the spotlight of microbiology research due to the wide variety of infections that it can be associated with, the involvement in food spoilage, industrial biofouling and perhaps sewage treatment. However, BBF remains difficult to study due to the lack of standardization of the existing methods and the expensive equipment needed. We aim to describe a new inexpensive and easy to reproduce protocol for a 3D-printed microfluidic device that can be used to study BBF in a dynamic manner. METHODS: We used the SolidWorks 3D CAD Software (EducationEdition 2019-2020, Dassault Systèmes, Vélizy-Villacoublay, France) to design the device and the Creality3D Ender 5 printer (Shenzhen Creality 3D Technology Co., Ltd., Shenzhen, China) for its manufacture. We cultivated strains of Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae and Pseudomonas aeruginosa. For the biofilm evaluation we used optical coherence tomography (OCT), scanning electron microscopy (SEM), Fourier Transform Infrared (FTIR) spectroscopy and crystal violet staining technique. RESULTS: Based on the analysis, Enterococcus faecalis seems to produce more biofilm in the first hours while Pseudomonas aeruginosa started to take the lead on biofilm production after 24 h. CONCLUSIONS: With an estimated cost around €0.1285 for one microfluidic device, a relatively inexpensive and easy alternative for the study of BBF was developed.

3D Printed Microfluidic Bioreactors Used for the Preferential Growth of Bacterial Biofilms through Dielectrophoresis.

A realistic modelling of the way biofilms form and evolve in time requests a dynamic approach. In this study, the proposed route uses continuous-flow bioreactors under controlled flow rates and temperature in the culture medium containing bacteria or fungi. 3D printed, Polylactic acid (PLA), flow-based bioreactors with integrated copper electrodes were used to investigate the effect of dielectrophoresis on the formation and growth of Staphylococcus aureus ATCC 25923, Enterococcus faecalis ATCC 29212, Pseudomonas aeruginosa ATCC 27853, and Klebsiella pneumoniae ATCC 13883 biofilms. Bacterial suspensions of 1McF turbidity have been prepared and circulated through the bioreactors. At the same time, a 30 V potential difference was applied on the system. The effect of the non-uniform electric field induced upon the bacterial cells was determined using quantitative methods, such as an adjusted microtiter plate technique, as well as spectral domain optical coherence tomography (SD-OCT) images. The morphology and the surface quality of the biofilms were investigated using Scanning Electron Microscopy (SEM) images. The results show that the different bacterial cells present a positive dielectrophoretic behaviour, with the preferential formation of biofilms in the high field gradient region.

Descriptive Analysis of Circulating Antimicrobial Resistance Genes in Vancomycin-Resistant Enterococcus (VRE) during the COVID-19 Pandemic.

COVID-19 offers ideal premises for bacteria to develop antimicrobial resistance. In this study, we evaluated the presence of several antimicrobial resistance genes (ARG) in vancomycin-resistant Enterococcus (VRE) isolated from rectal swabs from patients at a hospital in Cluj-Napoca, Romania. Rectal swabs were cultivated on CHROMID® VRE (bioMérieux, Marcy-l' Étoile, France) and positive isolates were identified using MALDI-TOF Mass Spectrometry (Bruker Daltonics, Bremen, Germany) and further analyzed using the PCR technique for the presence of the following ARGs: van A, van B, tet(M), tet(L), ermB, msrA, mefA, aac(6')-Im, aph(2)-Ib, ant(4')-Ia, sul1, sul2, sul3, and NDM1. We isolated and identified 68 isolates of Enterococcus faecium and 11 isolates of Enterococcus faecalis. The molecular analysis showed 66 isolates positive for the vanA gene and eight positive for vanB. The most frequent association of ARG in VRE was vanA-tet(M)-ermB. There was no statistically significant difference between Enterococcus faecium and Enterococcus faecalis regarding ARGs. Our work proves that during the COVID-19 pandemic, highly resistant isolates of Enterococcus were present in patients in the intensive care unit; thus, better healthcare policies should be implemented for the management and control of these highly resistant isolates in the future.

Enterococcus raffinosus, Enterococcus durans and Enterococcus avium Isolated from a Tertiary Care Hospital in Romania-Retrospective Study and Brief Review.

(1) Background: This paper aims to provide a description of non-faecalis non-faecium enterococci isolated from a tertiary care hospital in Romania and to briefly review the existing literature regarding the involvement of Enterococcus raffinosus, Enterococcus durans and Enterococcus avium in human infections and their antimicrobial resistance patterns; (2) Methods: We retrospectively analyzed all Enteroccocus species isolated from the "Prof. Dr. O. Fodor" Regional Institute of Gastroenterology and Hepatology from Cluj-Napoca during one year focusing on non-faecalis non-faecium Enterococci. A brief review of the literature was performed using case reports involving Enterococcus raffinosus, Enterococcus durans and Enterococcus avium; (3) Results: Only 58 out of 658 Enteroccocus isolates were non-faecalis non-faecium and met the inclusion criteria. These species were isolated more often (p < 0.05) from the surgical ward from mixed etiology infections with E. coli. In our review, we included 39 case reports involving E. raffinosus, E. durans and E. avium; (4) Conclusions: Isolation of non-faecalis non-faecium enterococci displays an emerging trend with crucial healthcare consequences. Based on the analysis of the case reports, E. avium seems to be involved more often in neurological infections, E. durans in endocarditis, while E. raffinosus displays a more heterogenous distribution.

Mixed Etiology COVID-19 Associated Pulmonary Aspergillosis (CAPA)-A Case Report and Brief Review of the Literature.

The SARS-CoV-2 pandemic has proved to be a significant risk addition for invasive infections with Aspergillus. Even though there are plenty of data about the COVID-19-associated pulmonary aspergillosis (CAPA), especially involving Aspergillus fumigatus, recent studies are presenting cases of CAPA involving more than one species of Aspergillus. We report the first case of a SARS-CoV-2 patient associating co-infection with, most likely, Aspergillus section Fumigati and Aspergillus section Flavi from Romania, and we review the existing medical literature in order to shed light upon mixed etiology cases of CAPA. Since mortality remains high in these cases, there is an acute need for more information about the interaction between SARS-CoV-2 and Aspergillus spp., and the therapies for CAPA. The emerging number of cases and the high mortality rate must be considered an incentive for future research.

Ethene Dimerization on Zeolite-Hosted Ni Ions: Reversible Mobilization of the Active Site.

The active site in ethene oligomerization catalyzed by Ni-zeolites is proposed to be a mobile Ni(II) complex, based on density functional theory-based molecular dynamics (DFT-MD) simulations corroborated by continuous-flow experiments on Ni-SSZ-24 zeolite. The results of the simulations at operating conditions show that ethene molecules reversibly mobilize the active site as they exchange with the zeolite as ligands on Ni during reaction. Microkinetic modeling was conducted on the basis of free-energy profiles derived with DFT-MD for oligomerization on these mobile [(ethene)2-Ni-alkyl]+ species. The model reproduces the experimentally observed high selectivity to dimerization and indicates that the mechanism is consistent with the observed second-order rate dependence on ethene pressure.

Fluid-driven metamorphism of the continental crust governed by nanoscale fluid flow.

The transport of fluids through the Earth's crust controls the redistribution of elements to form mineral and hydrocarbon deposits, the release and sequestration of greenhouse gases, and facilitates metamorphic reactions that influence lithospheric rheology. In permeable systems with a well-connected porosity, fluid transport is largely driven by fluid pressure gradients. In less permeable rocks, deformation may induce permeability by creating interconnected heterogeneities, but without these perturbations, mass transport is limited along grain boundaries or relies on transformation processes that self-generate transient fluid pathways. The latter can facilitate large-scale fluid and mass transport in nominally impermeable rocks without large-scale fluid transport pathways. Here, we show that pervasive, fluid-driven metamorphism of crustal igneous rocks is directly coupled to the production of nanoscale porosity. Using multi-dimensional nano-imaging and molecular dynamics simulations, we demonstrate that in feldspar, the most abundant mineral family in the Earth's crust, electrokinetic transport through reaction-induced nanopores (10-100 nm) can potentially be significant. This suggests that metamorphic fluid flow and fluid-mediated mineral transformation reactions can be considerably influenced by nanofluidic transport phenomena.

Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions.

Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https://zenodo.org/collection/user-nmrlipids ) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.

Mixed Mechanism of Lubrication by Lipid Bilayer Stacks.

Although the key role of lipid bilayer stacks in biological lubrication is generally accepted, the mechanisms underlying their extreme efficiency remain elusive. In this article, we report molecular dynamics simulations of lipid bilayer stacks undergoing load and shear. When the hydration level is reduced, the velocity accommodation mechanism changes from viscous shear in hydration water to interlayer sliding in the bilayers. This enables stacks of hydrated lipid bilayers to act as efficient boundary lubricants for various hydration conditions, structures, and mechanical loads. We also propose an estimation for the friction coefficient; thanks to the strong hydration forces between lipid bilayers, the high local viscosity is not in contradiction with low friction coefficients.

Bottom-up model of adsorption and transport in multiscale porous media.

We develop a model of transport in multiscale porous media which accounts for adsorption in the different porosity scales. This model employs statistical mechanics to upscale molecular simulation and describe adsorption and transport at larger time and length scales. Using atom-scale simulations, which capture the changes in adsorption and transport with temperature, pressure, pore size, etc., this approach does not assume any adsorption or flow type. Moreover, by relating the local chemical potential µ(r) and density ρ(r), the present model accounts for adsorption effects and possible changes in the confined fluid state upon transport. This model constitutes a bottom-up framework of adsorption and transport in multiscale materials as it (1) describes the adsorption-transport interplay, (2) accounts for the hydrodynamics breakdown at the nm scale, and (3) is multiscale.

Optimized molecular reconstruction procedure combining hybrid reverse Monte Carlo and molecular dynamics.

We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight ω of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.

Molecular simulations of supercritical fluid permeation through disordered microporous carbons.

Fluid transport through microporous carbon-based materials is inherent in numerous applications, ranging from gas separation by carbon molecular sieves to natural gas production from coal seams and gas shales. The present study investigates the steady-state permeation of supercritical methane in response to a constant cross-membrane pressure drop. We performed dual control volume grand canonical molecular dynamics (DCV-GCMD) simulations to mimic the conditions of actual permeation experiments. To overcome arbitrary assumptions regarding the investigated porous structures, the membranes were modeled after the CS1000a and CS1000 molecular models, which are representative of real microporous carbon materials. When adsorption-induced molecular trapping (AIMT) mechanisms are negligible, we show that the permeability of the microporous material, although not significantly sensitive to the pressure gradient, monotonically decreases with temperature and reservoir pressures, consistent with diffusion theory. However, when AIMT occurs, the permeability increases with temperature in agreement with experimental data found in the literature.

Diffusion coefficient and shear viscosity of rigid water models.

We report the diffusion coefficient and viscosity of popular rigid water models: two non-polarizable ones (SPC/E with three sites, and TIP4P/2005 with four sites) and a polarizable one (Dang-Chang, four sites). We exploit the dependence of the diffusion coefficient on the system size (Yeh and Hummer 2004 J. Phys. Chem. B 108 15873) to obtain the size-independent value. This also provides an estimate of the viscosity of all water models, which we compare to the Green-Kubo result. In all cases, a good agreement is found. The TIP4P/2005 model is in better agreement with the experimental data for both diffusion and viscosity. The SPC/E and Dang-Chang models overestimate the diffusion coefficient and underestimate the viscosity.