An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases.

BACKGROUND: An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM: This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD: We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS: Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION: This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.

The methodological quality of systematic reviews regarding the Core Outcome Set (COS) development.

BACKGROUND: The Core Outcome Measures in Effectiveness Trials (COMET) working group proposed core outcome sets (COS) to address the heterogeneity in outcome measures in clinical studies. According to the recommendations of COMET, performing systematic reviews (SRs) usually was the first step for COS development. However, the SRs that serve as a basis for COS are not specifically appraised by organizations such as COMET regarding their quality. Here, we investigated the status of SRs related to development of COS and evaluated their methodological quality. METHODS: We conducted a search on PubMed to identify SRs related to COS development published from inception to May 2022. We qualitatively summarized the disease included in SR topics, and the studies included in the SRs. We evaluated the methodological quality of the SRs using AMSTAR 2.0 and compared the overall quality of SRs with and without protocols using the Mann-Whitney U test. RESULTS: We included 175 SRs from 23 different countries or regions, and they mainly focused on five diseases: musculoskeletal system or connective tissue disease (n = 19, 10.86%), injury, poisoning, or certain other consequences of external causes (n = 18, 10.29%), digestive system disease (n = 16, 9.14%), nervous system disease (n = 15, 8.57%), and genitourinary system disease (n = 15, 8.57%). Although 88.00% of SRs included randomized controlled trials (RCTs), only a few SRs (23.38%) employed appropriate tools to assess the risk of bias in RCTs. The assessment results on the basis of AMSTAR 2.0 indicated that most SRs (93.71%) were rated as ''critically low'' to ''low'' in terms of overall confidence. The overall confidence of SRs with protocols was significantly higher than that without protocols (P <.001). Compared to the SRs with protocols on Core Outcome Measures in Effectiveness Trials (COMET), SRs with protocols on PROSPERO were of better overall confidence (P = .017). CONCLUSION: The overall quality of published SRs regarding COS development was poor. Our findings emphasize the need for researchers to carefully select the disease topic and strictly adhere to the requirements of optimal methodology when conducting a SR for the establishment of a COS.

Network pharmacology and in vitro experimental verification unveil glycyrrhizin from glycyrrhiza glabra alleviates acute pancreatitis via modulation of MAPK and STAT3 signaling pathways.

Acute pancreatitis (AP) is a severe gastrointestinal inflammatory disease with increasing mortality and morbidity. Glycyrrhiza glabra, commonly known as Liquorice, is a widely used plant containing bioactive compounds like Glycyrrhizin, which possesses diverse medicinal properties such as anti-inflammatory, antioxidant, antiviral, and anticancer activities. The objective of this study is to investigate the active components, relevant targets, and underlying mechanisms of the traditional Chinese medicine Glycyrrhiza glabra in the treatment of AP. Utilizing various computational biology methods, we explored the potential targets and molecular mechanisms through Glycyrrhizin supplementation. Computational results indicated that Glycyrrhizin shows promising pharmacological potential, particularly with mitogen-activated protein kinase 3 (MAPK3) protein (degree: 70), forming stable complexes with Glycyrrhizin through ionic and hydrogen bonding interactions, with a binding free energy (ΔGbind) of -33.01 ± 0.08 kcal/mol. Through in vitro experiments, we validated that Glycyrrhizin improves primary pancreatic acinar cell injury by inhibiting the MAPK/STAT3/AKT signaling pathway. Overall, MAPK3 emerges as a reliable target for Glycyrrhizin's therapeutic effects in AP treatment. This study provides novel insights into the active components and potential targets and molecular mechanisms of natural products.

Oleanolic acid alleviate intestinal inflammation by inhibiting Takeda G-coupled protein receptor (TGR) 5 mediated cell apoptosis.

Oleanolic acid (OA) is a bioactive compound present in plant-based foods known for its beneficial impact on gastrointestinal health, specifically in alleviating diarrhea. Nonetheless, the underlying mechanisms by which OA mitigates gut epithelial damage have yet to be elucidated. In this study, OA significantly markedly ameliorated adverse effects induced by Dextran Sulfate Sodium (DSS), including weight loss and epithelial morphological damage in a murine model. Remarkably, compared to normal mice, standalone administration of OA had no discernible impact on the animals. Concurrently, we identified a significant up-regulation in the expression levels of TGR5 and BAX in the intestines of DSS-exposed mice, coupled with a decline in Bcl2 expression. Correlation analyses revealed a robust association between TGR5 and BAX expression. Oral administration of OA efficaciously counteracted these alterations. To probe the role of TGR5 in cellular apoptosis, further, a lentivirus transfection approach was utilized to induce TGR5 overexpression in intestinal epithelial cells (IPEC-J2). RNA sequencing indicated that TGR5 overexpression significantly influenced biological processes, particularly in modulating cellular activation and intercellular adhesion, in contrast to the control group cells. Functional assays substantiated that TGR5 overexpression compromised cell viability and accelerated apoptosis. Notably, OA treatment in TGR5-overexpressed cells restored cell viability, suppressed TGR5 and BAX expression, and augmented Bcl2 expression. In sum, our data suggest that OA mitigates intestinal epithelial apoptosis and bolsters cellular proliferation by downregulating TGR5. This research provides valuable insights into the prospective utility of OA as a functional food supplement or adjunctive therapeutic agent for enhancing gastrointestinal health.

Hesperidin Alleviates Acute Necrotizing Pancreatitis by Activating SIRT1 ‒ Molecular Docking, Molecular Dynamics Simulation, and Experimental Validation.

BACKGROUND: Acute necrotizing pancreatitis is a serious pancreatic injury with limited effective treatments. This study aims to investigate the therapeutic effects of hesperidin on L-arginine-induced acute pancreatitis and its potential targets. METHODS: The authors induced acute pancreatitis in mice by administering two hourly intraperitoneal injections of L-arginine-HCl, and evaluated the impact of hesperidin on pancreatic and lung tissues, plasma amylase activity, and myeloperoxidase content. Additionally, necrosis and mitochondrial function was tested in primary pancreatic acinar cells. The interactions between hesperidin and proteins involved in necrosis and mitochondrial dysfunction were further invested using in silico molecular docking and molecular dynamic simulations. RESULTS: Hesperidin effectively ameliorated the severity of acute necrotizing pancreatitis by reducing plasma amylase, pancreatic MPO, serum IL-6 levels, pancreatic edema, inflammation, and pancreatic necrosis. Hesperidin also protected against acute pancreatitis-associated lung injury and prevented acinar cell necrosis, mitochondrial membrane potential loss, and ATP depletion. In addition, hesperidin exhibited a high binding affinity with SIRT1 and increased the protein levels of SIRT1. The SIRT1 inhibitor EX527 abolished the protective effect of hesperidin against necrosis in acinar cells. CONCLUSION: These findings indicate that hesperidin alleviates the severity of acute necrotizing pancreatitis by activating SIRT1, which may provide insight into the mechanisms of natural compounds in treating AP. Hesperidin has potential as a therapeutic agent for acute necrotizing pancreatitis and provides a new approach for novel therapeutic strategies.

Characterization of the diastaphenazine/izumiphenazine C biosynthetic gene cluster from plant endophyte Streptomyces diastaticus W2.

Two phenazine compounds, diastaphenazine and izumiphenazine C, with complex structures and promising antitumour activity have been isolated from the plant endophytic actinomycete Streptomyces diastaticus W2. Their putative biosynthetic gene cluster (dap) was identified by heterologous expression and gene knockout. There are twenty genes in the dap cluster. dap14-19 related to shikimic pathway were potentially involved in the precursor chorismic acid biosynthesis, and dapBCDEFG were confirmed to be responsible for the biosynthesis of the dibenzopyrazine ring, the nuclear structure of phenazines. Two transcriptional regulatory genes dapR and dap4 played the positive regulatory roles on the phenazine biosynthetic pathway. Most notably, the dimerization of the dibenzopyrazine ring in diastaphenazine and the loading of the complex side chain in izumiphenazine C could be catalysed by the cyclase homologous gene dap5, suggesting an unusual modification strategy tailoring complex phenazine biosynthesis. Moreover, metabolite analysis of the gene deletion mutant strain S. albus::23C5Δdap2 and substrate assay of the methyltransferase Dap2 clearly revealed the biosynthetic route of the complex side chain in izumiphenazine C.

Effects of different alcohol and ultrasonic treatments on thermal and structural properties of zein-starch sodium octenyl succinate composite nanoparticles.

The objective of this study is to prepare zein/starch sodium octenyl succinate composite nanoparticles (ZSPs) via anti-solvent precipitation technology and characterize their colloidal properties. The effects of polar solvents, ultrasonic treatment time, and concentrations of starch sodium octenyl succinate were investigated. We measured the particle size distribution, hydrophobicity, and apparent structures of the composite nanoparticles. Ultrasonic treatment time (0-25 min) was found to play an important role in composite nanoparticle formation. The ZSP nanoparticles were with an average particle size in the range of 70 to 110 nm. When the ultrasonic treatment time exceeds 25 min, ZSPs became macroscopic particles. The fluorescence spectrum and three-phase contact angle indicated that ZSPs presented hydrophilicity with largest three-phase contact angle, which was 65.1°. Fourier transform infrared spectroscopy and scanning electron microscopy revealed that hydrophilic SSOS absorbed on the surface of zein nanoparticles via Van der Waals to improve their water solubility. The changes in solvent polarity and zein self-assembly are considered to be the main driving force for composite nanoparticles conformational transitions from α-helix to ß-sheet. Differential scanning calorimetry analysis indicated that ethanol combined ultrasonic treatment (10 min) was beneficial to enhance the thermal stability of composite nanoparticles, causing the highest Tg of 153.6°C. This work aims to provide a practical reference for formulating delivery systems using bioactive compounds containing zein as a carrier biopolymer. PRACTICAL APPLICATION: This work aims to provide a practical reference for formulating encapsulants for food and other bioactive compounds containing zein as a carrier biopolymer. Zein/starch sodium octenyl succinate composite nanoparticles formulated in this study provide novel stabilizers for emulsification systems or carriers of bioactive substances that can enhance the nutritional value, taste, or shelf life of foods.

Isolation and Characterization of New Phenazine Metabolites with Antifungal Activity against Root-Rot Pathogens of Panax notoginseng from Streptomyces.

Three new phenazine metabolites, strepphenazine A-C (1-3), along with a known compound baraphenazine E 4 were isolated from the culture broth of a Streptomyces strain YIM PH20095. The structures were elucidated based on the spectral data. Compounds 1-4 showed different antifungal activity against Fusarium oxysporum, Plectosphaerella cucumerina, Alternaria panax, and Phoma herbarum, which caused root-rot disease of Panax notoginseng with minimal inhibitory concentrations (MICs) of 16-64 µg/mL; compared with compound 4, compounds 1-3 showed better antifungal activity against some of these pathogenic fungi with MICs of 16-32 µg/mL, while compound 4 showed antifungal activity against F. oxysporum, P. cucumerina, and A. panax with the same MICs of 64 µg/mL. Thus, strain YIM PH20095 provides new sources for the development of biological control agents to prevent the infection of pathogenic fungi of P. notoginseng.

Two new phenazine metabolites with antimicrobial activities from soil-derived Streptomyces species.

Two new phenazine metabolites, 6-hydroxyphenazine-1-carboxamide (1) and methyl 6-carbamoylphenazine-1-carboxylate (2), were isolated from a soil-derived Streptomyces diastaticus subsp. ardesiacus strain YIM PH20246, and their structures were elucidated by extensive spectroscopic data analysis. The antimicrobial activities of the isolates were assayed. Compound 1 showed moderate antifungal and antibacterial activities against Fusarium oxysporum (ATCC 7808), Fusarium solani (ATCC 36031) and Plectosphaerella cucumerina (local isolate), Staphylococcus aureus (ATCC 25923) and Staphylococcus albus (ATCC 10231), respectively. Compound 2 exhibited moderate antifungal and antibacterial activities against F. oxysporum, F. solani, and Phoma herbarum, S. aureus, S. albus, and Bacillus subtilis, respectively.

Evaluation of the Effectiveness of Clinical Pharmacists' Consultation in the Treatment of Infectious Diseases: A Single-Arm, Prospective Cohort Study.

Background: With the implementation of Antimicrobial Stewardship Program, clinical pharmacists' consultation (CPC) for infectious diseases (ID) is gradually adopted by many hospitals in China. We conducted a cohort study to evaluate the effectiveness of CPC in ID treatment on patient outcomes and potential determinants. Methods: Based on a registry database, a prospective cohort study was conducted in Guizhou Provincial People's Hospital. The main exposure factor was whether clinician adopted the suggestion from clinical pharmacist. The outcome was effective response rate (ERR) of ID patients. The variables associated with the outcome (e.g., age, gender, severity of infection, liver function, and kidney function) were also prospectively recorded. A multilevel model was performed to analyze the factors related to ERR. Results: A total of 733 ID inpatients were included in the final analysis according to the predesigned inclusion and exclusion criteria. The proportion of clinical pharmacists' suggestions adopted by clinicians and ERR were 88.13 and 69.03%, respectively. Significant data aggregation (P < 0.05) for individuals at the level of department was observed. According to the two-level variance component model, liver dysfunction (Adjusted Odds Ratio (AOR) = 0.649, 95%Credible Interval (CI): 0.432-0.976), severity of infection (AOR = 0.602, 95%CI: 0.464-0.781), and adopting the suggestion from pharmacist (AOR = 1.738, 95%CI: 1.028-2.940) had significant association with ERR. Conclusion: Our study suggests that the effect of CPC on ID treatment is significant. The policy/decision makers or hospital managers should be cognizant of the critical value of clinical pharmacists in ID treatment.

Echinosporin antibiotics isolated from Amycolatopsis strain and their antifungal activity against root-rot pathogens of the Panax notoginseng.

Actinomycete strain YIM PH20520, isolated from the rhizosphere soil sample of Panax notoginseng collected in Wenshang, Yunnan Province, China, exhibited antifungal activity against root-rot pathogens of the Panax notoginseng. The structures of bioactive molecules, isolated from the ethyl acetate extract of the fermentation broth of the strain, were identified as echinosporin (1) and 7-deoxyechinosporin (2) based on extensive spectroscopic analyses. 1 exhibited antifungal activity against four tested root-rot pathogens of Panax notoginseng include Fusarium oxysporum, Fusarium solani, Alternaria panax, and Phoma herbarum with the MIC value at 64, 64, 32, and 64 µg/mL, respectively. 2 exhibited antifungal activities against F. oxysporum, F. solani, A. panax, and P. herbarum with the MIC value at 128, 128, 64, and 128 µg/mL, respectively. Based on the phylogenetic analyses, the closest phylogenetic relative of strain YIM PH20520 is Amycolatopsis speibonae JS72T (97.69%), so strain YIM PH20520 was identified as Amycolatopsis strain. To the best of our knowledge, this is the first report of echinosporin antibiotics isolated from Amycolatopsis strain besides Streptomyces strain and their antifungal activity against four tested root-rot pathogens of the Panax notoginseng. The results provide a reliable evidence for the following related biosynthetic investigations on Amycolatopsis strain YIM PH20520 due to echinosporins antibiotics' unique tricyclic acetal-lactone structures.