Search Results (1,860)

The rapid and accurate diagnosis of meningitis is critical for preventing severe complications and fatalities. This study addresses the need for accessible diagnostics in the absence of specialized equipment by developing a novel diagnostic assay. The assay utilizes dual-priming isothermal amplification (DAMP) with unique internal primers to significantly reduce non-specificity. For fluorescence detection, the dye was selected among Brilliant Green, Thioflavin T, and dsGreen. Brilliant Green is preferred for this assay due to its availability, high fluorescence level, and optimal sample-to-background (S/B) ratio. The assay was developed for the detection of the primary causative agents of meningitis (Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae), and tested on clinical samples. The developed method demonstrated high specificity, no false positives, sensitivity comparable to that of loop-mediated isothermal amplification (LAMP), and a high S/B ratio. This versatile assay can be utilized as a standalone test or an integrated assay into point-of-care systems for rapid and reliable pathogen detection. Full article

The multisystemic effects of COVID-19 may continue for a longer time period following the acute phase, depending on the severity of the disease. However, long-term systemic transcriptomic changes associated with COVID-19 disease and the impact of disease severity are not fully understood. We aimed to investigate the impact of COVID-19 and its severity on transcriptomic alterations in peripheral blood mononuclear cells (PBMCs) following 1 year of the disease. PBMCs were isolated from the peripheral blood of healthy control donors who did not have COVID-19 (C; n = 13), from COVID-19 patients without pneumonia (NP; n = 11), and from COVID-19 patients with severe pneumonia (SP; n = 10) after 1-year of follow-up. Following RNA isolation from PBMCs, high-quality RNAs were sequenced after creating a library. Differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElncRNAs) were identified using Benjamini–Hochberg correction and they were analysed for hierarchical clustering and principal component analysis (PCA). Intergroup comparisons (C vs. NP, C vs. SP, and NP vs. SP) of DEGs and DElncRNAs were performed and hub genes were determined. Functional enrichment analyses of DEGs and DElncRNAs were made using Metascape (v3.5.20240101) and the first version of NCPATH. The RNA sequencing analysis revealed 4843 DEGs and 1056 DElncRNAs in “C vs. NP”, 1651 DEGs and 577 DElncRNAs in “C vs. SP”, and 954 DEGs and 148 DElncRNAs in “NP vs. SP”, with 291 DEGs and 70 DElncRNAs shared across all groups, respectively. We identified 14 hub genes from 291 DEGs, with functional enrichment analysis showing upregulated DEGs mainly linked to inflammation and osteoclast differentiation and downregulated DEGs to viral infections and immune responses. The analysis showed that 291 common and 14 hub genes were associated with pneumonia and that these genes could be regulated by the transcription factors JUN and NFκB1 carrying the NFκB binding site. We also revealed unique immune cell signatures across DEG categories indicating that the upregulated DEGs were associated with neutrophils and monocytes, while downregulated DEGs were associated with CD4 memory effector T cells. The comparative transcriptomic analysis of NP and SP groups with 52 gene signatures suggestive of IPF risk showed a lower risk of IPF in the SP group than the NP patients. Our findings suggest that COVID-19 may cause long term pathologies by modulating the expression of various DEGs, DeLncRNAs, and hub genes at the cellular level. Full article

Background: Creutzfeldt–Jakob disease (CJD) and fatal familial insomnia (FFI) are prion diseases characterized by severe neurodegenerative conditions and a short duration of illness. Methods: This study explores the characteristics of hospitalizations for CJD and FFI in Spain from 2016 to 2022 using the Spanish National Hospital Discharge Database (SNHDD). Results: We identified a total of 1063 hospital discharges, including 1020 for CJD and 43 for FFI. Notably, the number of hospitalized patients with FFI showed a significant peak in 2017. The average length of hospital stay (LOHS) was 13 days for CJD and 6 days for FFI, with in-hospital mortality rates (IHM) of 36.37% for CJD and 32.56% for FFI. Among CJD patients, the average LOHS was 14 days, with a significantly longer duration for those who experienced IHM. Conclusions: The presence of sepsis or pneumonia and older age were associated with a higher IHM rate among CJD patients. The total estimated cost for managing CJD and FFI patients over the study period was EUR 6,346,868. This study offers new insights into the epidemiology and healthcare resource utilization of CJD and FFI patients, which may inform future research directions and public health strategies. Full article

Pneumonia has long been a significant concern in global public health. With the advancement of convolutional neural networks (CNNs), new technological methods have emerged to address this challenge. However, the application of CNNs to pneumonia diagnosis still faces several critical issues. First, the datasets used for training models often suffer from insufficient sample sizes and imbalanced class distributions, leading to reduced classification performance. Second, although CNNs can automatically extract features and make decisions from complex image data, their interpretability is relatively poor, limiting their widespread use in clinical diagnosis to some extent. To address these issues, a novel weighted cross-entropy loss function is proposed, which calculates weights via an inverse proportion exponential function to handle data imbalance more efficiently. Additionally, we employ a transfer learning approach that combines pretrained CNN model parameter fine-tuning to improve classification performance. Finally, we introduce the gradient-weighted class activation mapping method to enhance the interpretability of the model’s decisions by visualizing the image regions of focus. The experimental results indicate that our proposed approach significantly enhances CNN performance in pneumonia diagnosis tasks. Among the four selected models, the accuracy rates improved to over 90%, and visualized results were provided. Full article

Background: Malnutrition is a critical concern in ICU settings. It is associated with increased morbidity and mortality, yet its prevalence and impact on clinical outcomes in patients with stroke and traumatic brain injury (TBI) remain underexplored. Objective: To evaluate the prevalence and impact of malnutrition risk on clinical outcomes in ICU patients with TBI, ischemic stroke, and hemorrhagic stroke, and to identify key risk factors associated with malnutrition risk. Methods: This retrospective cohort study utilized electronic health records encompassing ICU admissions from 2017 to 2023. Patients with either stroke or TBI were included, with malnutrition risk assessed using the prognostic nutritional index. Data were extracted and analyzed to determine patient characteristics, clinical and laboratory parameters, and outcomes. Results: This study included 1352 patients (267 TBI, 825 ischemic stroke, and 260 hemorrhagic stroke patients, >30% with pneumonia at admission). Severe malnutrition risk at admission was observed in over 60% of patients. Stroke patients, particularly those with hemorrhagic stroke, exhibited a higher risk of malnutrition compared to TBI patients. Malnutrition risk was associated with significantly higher hospital mortality and increased need for mechanical ventilation. Predictive factors for malnutrition risk included advanced age, higher SOFA scores, lower FOUR and GCS scores, and the presence of pneumonia at admission. Conclusions: Risk of malnutrition is highly prevalent among ICU patients with TBI, ischemic, and hemorrhagic stroke, significantly impacting mortality and other clinical outcomes. Identifying and managing malnutrition early in the ICU setting is crucial for improving patient outcomes. Further prospective, multicenter studies are needed to validate these findings and develop effective interventions. Full article

The COVID-19 pandemic has altered respiratory infection patterns in pediatric populations. The emergence of the SARS-CoV-2 Omicron variant and relaxation of public health measures have increased the likelihood of coinfections. Previous studies show conflicting results regarding the impact of viral and bacterial coinfections with SARS-CoV-2 on severity of pediatric disease. This study investigated the prevalence and clinical impact of coinfections among children hospitalized with COVID-19 during the Omicron wave. A retrospective analysis was conducted on 574 hospitalized patients aged under 18 years in Russia, from January 2022 to March 2023. Samples from patients were tested for SARS-CoV-2 and other respiratory pathogens using qRT-PCR, bacterial culture tests and mass spectrometry, and ELISA. Approximately one-third of COVID-19 cases had coinfections, with viral and bacterial coinfections occurring at similar rates. Adenovirus and Staphylococcus aureus were the most common viral and bacterial coinfections, respectively. Viral coinfections were associated with higher fevers and increased bronchitis, while bacterial coinfections correlated with longer duration of illness and higher pneumonia rates. Non-SARS-CoV-2 respiratory viruses were linked to more severe lower respiratory tract complications than SARS-CoV-2 monoinfection. These findings suggest that during the Omicron wave, seasonal respiratory viruses may have posed a greater threat to children’s health than SARS-CoV-2. Full article

The worldwide emergence and dissemination of carbapenem-resistant Gram-negative bacteria (CRGNB) is a challenging problem of antimicrobial resistance today. Outbreaks with CRGNB have severe consequences for both the affected healthcare settings as well as the patients with infection. Thus, bloodstream infections caused by metallo-ß-lactamase-producing Enterobacterales can often have clinical implications, resulting in high mortality rates due to delays in administering effective treatment and the limited availability of treatment options. The overall threat of CRGNB is substantial because carbapenems are used to treat infections caused by ESBL-producing Enterobacterales which also exist with high frequency within the same geographical regions. A genome-based surveillance of 589 CRGNB from 61 hospitals across the federal state Hesse in Germany was implemented using next-generation sequencing (NGS) technology to obtain a high-resolution landscape of carbapenem-resistant isolates over a three-year period (2017–2019). The study examined all reportable CRGNB isolates submitted by participating hospitals. This included isolates carrying known carbapenemases (435) together with carbapenem-resistant non-carbapenemase producers (154). Predominant carbapenemase producers included Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii and Acinetobacter baumannii. Over 80% of 375 carbapenem-resistant determinants including KPC-, NDM-, VIM- and OXA-48-like ones detected in 520 Enterobacterales were plasmid-encoded, and half of these were dominated by a few incompatibility (Inc) types, viz., IncN, IncL/M, IncFII and IncF(K). Our results revealed that plasmids play an extraordinary role in the dissemination of carbapenem resistance in the heterogeneous CRGNB population. The plasmids were also associated with several multispecies dissemination events and local outbreaks throughout the study period, indicating the substantial role of horizontal gene transfer in carbapenemase spread. Furthermore, due to vertical and horizontal plasmid transfer, this can have an impact on implant-associated infections and is therefore important for antibiotic-loaded bone cement and drug-containing devices in orthopedic surgery. Future genomic surveillance projects should increase their focus on plasmid characterization. Full article

This paper addresses the significant problem of identifying the relevant background and contextual literature related to deep learning (DL) as an evolving technology in order to provide a comprehensive analysis of the application of DL to the specific problem of pneumonia detection via chest X-ray (CXR) imaging, which is the most common and cost-effective imaging technique available worldwide for pneumonia diagnosis. This paper in particular addresses the key period associated with COVID-19, 2020–2023, to explain, analyze, and systematically evaluate the limitations of approaches and determine their relative levels of effectiveness. The context in which DL is applied as both an aid to and an automated substitute for existing expert radiography professionals, who often have limited availability, is elaborated in detail. The rationale for the undertaken research is provided, along with a justification of the resources adopted and their relevance. This explanatory text and the subsequent analyses are intended to provide sufficient detail of the problem being addressed, existing solutions, and the limitations of these, ranging in detail from the specific to the more general. Indeed, our analysis and evaluation agree with the generally held view that the use of transformers, specifically, vision transformers (ViTs), is the most promising technique for obtaining further effective results in the area of pneumonia detection using CXR images. However, ViTs require extensive further research to address several limitations, specifically the following: biased CXR datasets, data and code availability, the ease with which a model can be explained, systematic methods of accurate model comparison, the notion of class imbalance in CXR datasets, and the possibility of adversarial attacks, the latter of which remains an area of fundamental research. Full article

Background: Protein-based pneumococcal vaccines (PBPVs) may offer expanded protection against Streptococcus pneumoniae and tackle the antimicrobial resistance crisis in pneumococcal infections. This study examined the safety and immunogenicity in healthy adults vaccinated with three doses of a protein-based pneumococcal vaccine containing pneumococcal surface protein A (PspA) (PRX1, P3296 and P5668) and in combination with a recombinant detoxified pneumolysin protein (PlyLD). Methods: This phase Ia randomized, double blind, placebo-controlled clinical study enrolled healthy adults aged 18–49 years. The participants were randomized into experimental (low-dose, medium-dose, high-dose) and placebo groups in a ratio of 3:1. Three doses of investigational vaccine were given to the participants with an interval of two months. Safety endpoints included the occurrence of total adverse reactions, solicited local and systemic adverse reactions, unsolicited adverse reactions, serious adverse events (SAEs), and several laboratory parameters. Immunogenicity endpoints included geometric mean titers (GMT) of anti-PspA (PRX1, P3296 and P5668) and anti-PlyLD antibodies level as determined by ELISA, seropositivity rates of PspA and PlyLD antibodies (>4-fold increase) and neutralization activity of anti-Ply antibody in serum. Results: A total of 118 participants completed the study of three doses. The candidate PBPV was safe and well-tolerated in all experimental groups. No vaccine-related SAEs were observed in this study. Most solicited adverse reactions were mild and transient. The most frequently reported solicited adverse reactions in the medium- and high-dose groups was pain at the injection site, while in the low-dose group it was elevated blood pressure. The immunogenicity data showed a sharp increase in the GMT level of anti-PspA-RX1, anti-PspA-3296, anti-PspA-5668, and anti-PlyLD antibodies in serum. The results also showed that the elicited antibodies were dosage-dependent. The high-dose group showed a higher immune response against PspA-RX1, PspA-3296, PspA-5668, and PlyLD antigens. However, repeat vaccination did not increase the level of anti-PspA antibodies but the level of anti-PlyLD antibody. High seropositivity rates were also observed for anti-PspA-RX1, anti-PspA-3296, anti-PspA-5668, and anti-PlyLD antibodies. In addition, a significant difference in the GMT levels of anti-Ply antibody between the high-, medium-, and low-dose groups post each vaccination were indicated by neutralization activity tests. Conclusions: The PBPV showed a safe and immunogenic profile in this clinical trial. Taking into consideration both safety and immunogenicity data, we propose a single dose of 50 µg (medium dose) of PBPV as the optimum approach in providing expanded protection against Streptococcus pneumoniae. Full article

Objectives: The aim of this study was to examine the impact of the pentraxin 3 (PTX3) serum level and angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism on the severity of radiographic pulmonary infiltrates and the clinical outcomes of COVID-19. Methods: The severity of COVID-19 pulmonary infiltrates was evaluated within a week of admission by analyzing chest X-rays (CXR) using the modified Brixia (MBrixa) scoring system. The insertion (I)/deletion (D) polymorphism of the ACE gene and the serum levels of PTX3 were determined for all patients included in the study. Results: This study included 80 patients. Using a cut-off serum level of PTX3 ≥ 2.765 ng/mL, the ROC analysis (AUC 0.871, 95% CI 0.787–0.954, p < 0.001) showed a sensitivity of 85.7% and specificity of 78.8% in predicting severe MBrixa scores. Compared to ACE I/I polymorphism, D/D polymorphism significantly increased the risk of severe CXR infiltrates, OR 7.7 (95% CI: 1.9–30.1), and p = 0.002. Significant independent predictors of severe CXR infiltrates include hypertension (OR 7.71), PTX3 (OR 1.20), and ACE D/D polymorphism (OR 18.72). Hypertension (OR 6.91), PTX3 (OR 1.47), and ACE I/I polymorphism (OR 0.09) are significant predictors of poor outcomes. Conclusion: PTX3 and ACE D/D polymorphism are significant predictors of the severity of COVID-19 pneumonia. PTX3 is a significant predictor of death. Full article

To evaluate the phytochemical composition, antibacterial, and antioxidant activity of successive extracts of Centaurea calcitrapa L. (C. calcitrapa) aerial flowering parts, they were assessed in vitro. Using a spectrophotometer, the sample absorbance at 517 nm was used to quantify the scavenging activity. The negative control was DPPH. In the current study, the diffusion using agar wells technique was adapted to measure antimicrobial activity. Phytochemical analysis was performed using the recommended standard procedures. The methanol extract of C. calcitrapa exhibited high levels of total phenolic acids expressed as gallic acid (GA), measured as (97.25 ± 0.73 mg GAE/g) content compared to the chloroform, acetyl acetate, and aqueous extracts (27.42 ± 0.29, 64.25 ± 0.96, and 17.25 ± 0.73 mg GAE/g), respectively. Additionally, the methanol extract had a higher total tannin (27.52 ± 0.53 mg TAE/g) content compared to the chloroform, ethyl acetate, and aqueous extracts (12.02 ± 0.55, 26.01 ± 0.81, and 7.35 ± 0.56 mg TAE/g), respectively, while the aqueous extract contains a lower percentage of flavonoids (141.10 ± 1.31 mg RTE/g) compared to the higher content achieved by the methanol extract (425.93 ± 1.27 mg RTE/g). The hydroxyl groups of the flavonoid and the phenolic compounds found in C. calcitrapa are essentially scavenging free radicals. Radical scavenging activity was highest in the methanol extract (IC50 = 2.82 μg/mL), aqueous extract (IC50 = 8.03 μg/mL), ethyl acetate extract (IC50 = 4.79 μg/mL), and chloroform extract (IC50 = 6.33 μg/mL), as compared to the standard scavenging activity (IC50 = 2.52 μg/mL). The antibacterial properties of C. calcitrapa against Gram-negative bacterial strains Klebsiella pneumoniae, Escherichia coli, Enterobacter aerogenes, and Acinetobacter baumanii, in addition to Gram-positive strains Staphylococcus haemolyticus, Enterococcus faecalis, and Staphylococcus aureus, revealed inhibition zone diameter. The findings of this investigation establish that the aerial flowering parts of C. calcitrapa have substantial antibacterial action against human infections, and the plant can serve as a significant antioxidant that can be employed to prevent and treat severe degenerative diseases brought on by oxidative stress. qPCR showed that C. calcitrapa extracts elevate both SOD1 and SOD2 (cellular oxidation markers) with remarkable folds (1.8-fold for SOD1 and SOD2) with ethyl acetate plant extract against ascorbic acid as a control. This result reflects that C. calcitrapa extracts have remarkable antioxidant activity. Full article

Systemic steroids are frequently used in critically ill patients for their anti-inflammatory properties. Potential benefits of these agents should be balanced against their known side effects. In this paper, we review trials assessing the use of systemic steroids in common conditions requiring admission to the intensive care unit. These include septic shock, the acute respiratory distress syndrome, severe pneumonia, COVID-19, and hypercapnic respiratory failure due to chronic obstructive pulmonary disease. We will mainly focus on well-conducted randomized controlled trials to determine whether steroids should be administered to critically ill patients presenting with these conditions. Full article

Antimicrobial resistance (AMR) is a global public health threat caused by the misuse and overuse of antibiotics. It leads to infections becoming difficult to treat, causing serious illness, disability, and death. Current antibiotic development is slow, with only 25% of current antibiotics exhibiting novel mechanisms against critical pathogens. Traditional medicinal plants’ secondary metabolites offer potential for developing novel antibacterial compounds. These compounds, often with strong antimicrobial activity, can be used to develop safe and effective antibacterial chemotherapies. This study investigated the antibacterial activity of Phyllanthus niruri Linn. extracts against a panel of bacterial pathogens using disc diffusion and microdilution assays and quantified by calculation of minimum inhibition concentration (MIC). Additionally, the effects of combinations of the extracts and selected conventional antibiotics were examined by sum of fractional inhibition concentration (ƩFIC) calculation and isobologram analysis. Liquid chromatography–mass spectrometry (LC-MS) phytochemistry analysis was used to identify noteworthy compounds in the active extracts and the Artemia nauplii bioassay was used to evaluate toxicity. The aqueous and methanolic extracts exhibited notable antibacterial activity in the broth microdilution assay against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) (MIC = 669 µg/mL and 738 µg/mL, respectively). The methanolic extract also showed noteworthy antibacterial action in the broth assay against Klebsiella pneumoniae (MIC = 738 µg/mL). The aqueous extract had noteworthy growth inhibitory activity against Bacillus cereus (MIC = 669 µg/mL), whilst the methanolic extract demonstrated good antibacterial activity against that bacterium (MIC = 184 µg/mL). The aqueous and methanol extracts showed minimal antibacterial action against Shigella flexneri and Shigella sonnei. The extracts were subjected to LC-MS analysis, which revealed several interesting phytochemicals, including a variety of flavonoids and tannins. The antibacterial activity and lack of toxicity of the P. niruri extracts indicates that they may be worthwhile targets for antibiotic development and further mechanistic and phytochemistry studies are required. Full article

Enterobacter hormaechei, one of the species within the Enterobacter cloacae complex, is a relevant agent of healthcare-associated infections. In addition, it has gained relevance because isolates have shown the capacity to resist several antibiotics, particularly carbapenems. However, knowledge regarding colonization and virulence mechanisms of E. hormaechei has not progressed to the same extent as other Enterobacteriaceae species as Escherichia coli or Klebsiella pneumoniae. Here, we describe the presence and role of the type 3 fimbria, a chaperone-usher assembled fimbria, which was first described in Klebsiella spp., and which has been detected in other representatives of the Enterobacteriaceae family. Eight Chilean E. cloacae isolates were examined, and among them, four E. hormaechei isolates were found to produce the type 3 fimbria. These isolates were identified as E. hormaechei subsp. hoffmannii, one of the five subspecies known. A mutant E. hormaechei subsp. hoffmannii strain lacking the mrkA gene, encoding the major structural subunit, displayed a significantly reduced adherence capacity to a plastic surface and to Caco-2 cells, compared to the wild-type strain. This phenotype of reduced adherence capacity was not observed in the mutant strains complemented with the mrkA gene under the control of an inducible promoter. Therefore, these data suggest a role of the type 3 fimbria in the adherence capacity of E. hormaechei subsp. hoffmannii. A screening in E. hormaechei genomes contained in the NCBI RefSeq Assembly database indicated that the overall presence of the type 3 fimbria is uncommon (5.94–7.37%), although genes encoding the structure were detected in representatives of the five E. hormaechei subspecies. Exploration of complete genomes indicates that, in most of the cases, the mrkABCDF locus, encoding the type 3 fimbria, is located in plasmids. Furthermore, sequence types currently found in healthcare-associated infections were found to harbor genes encoding the type 3 fimbria, mainly ST145, ST78, ST118, ST168, ST66, ST93, and ST171. Thus, although the type 3 fimbria is not widespread among the species, it might be a determinant of fitness for a subset of E. hormaechei representatives. Full article