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In this study, we examined aqueous extracts of the edible mushrooms Pleurotus ostreatus (oyster mushroom) and Lentinula edodes (shiitake mushroom). Proteome analysis was conducted using LC-Triple TOF-MS and showed the expression of 753 proteins by Pleurotus ostreatus, and 432 proteins by Lentinula edodes. Bioactive peptides: Rab GDP dissociation inhibitor, superoxide dismutase, thioredoxin reductase, serine proteinase and lectin, were identified in both mushrooms. The extracts also included promising bioactive compounds including phenolics, flavonoids, vitamins and amino acids. The extracts showed promising antiviral activities, with a selectivity index (SI) of 4.5 for Pleurotus ostreatus against adenovirus (Ad7), and a slight activity for Lentinula edodes against herpes simplex-II (HSV-2). The extracts were not cytotoxic to normal human peripheral blood mononuclear cells (PBMCs). On the contrary, they showed moderate cytotoxicity against various cancer cell lines. Additionally, antioxidant activity was assessed using DPPH radical scavenging, ABTS radical cation scavenging and ORAC assays. The two extracts showed potential antioxidant activities, with the maximum activity seen for Pleurotus ostreatus (IC50 µg/mL) = 39.46 ± 1.27 for DPPH; 11.22 ± 1.81 for ABTS; and 21.40 ± 2.20 for ORAC assays. This study encourages the use of these mushrooms in medicine in the light of their low cytotoxicity on normal PBMCs vis à vis their antiviral, antitumor and antioxidant capabilities.

Carbapenem-resistant Acinetobacter baumannii (CRAB) has become a critical concern that necessitates the development of novel antimicrobial approaches. One of the most promising innovative approaches for combating CRAB infections is using effective and lytic bacteriophages (phages), known as phage therapy. Therefore, we recovered and characterized a polyvalent lytic Salmonella_phage_VB_ST-SA173, producing lytic activity against 6 CRAB clinical isolates and 3 multidrug-resistant (MDR) Salmonella serovars. Throughout pH 2–10, and thermal stability at up to 60 °C, the phage maintained its stability and lytic activity against the tested isolates. The presence of a tailed phage with a characteristic prolate head and a contractile tail was detected by the transmission electron microscope (TEM). According to the Oxford nanopore sequencing data, the genome of Salmonella_phage_VB_ST-SA173 was 53,636 bp in size, contained 45.9% G + C, and had 53 opening reading frames (ORFs). According to the TEM, ORFs, and BLASTn analysis findings, it was proved that the Salmonella_phage_VB_ST-SA173 belongs to the Loughboroughvirus genus. The efficacy of the phage-formulated Carbopol 940 hydrogel in wound healing was assessed preclinically in an infected burn wound animal model with a CRABa clinical isolate. The survival rate was enhanced in the phage-treated group compared to the untreated control groups. Histopathological analysis showed improved wound healing in the form of apparently healthy skin with apparently normal epidermal and dermis layers. In conclusion, depending on its in vitro and physicochemical traits, the phage-loaded hydrogel is expected to be a promising candidate for clinical trials against human CRAB-related skin infections. Key points • A polyvalent Loughboroughvirus phage showed lytic activity against CRAB and Salmonella serovars. • The phage showed stability at a wide range of pH and temperature. • The phage hydrogel enhanced healing in the burn-wound animal model infected with CRABa.

New strategies against antimicrobial resistance are urgently needed to address the challenges and health consequences posed by extensively drug-resistant (XDR) clinical isolates. This study explored how effective the green-synthesized silver nanoparticles alone or in combination with meropenem are in combating XDR Klebsiella pneumoniae . Klebsiella pneumoniae ( K. pneumoniae ) isolates were collected from several clinical labs and identified. After carrying out antimicrobial susceptibility testing, XDR isolates were selected for genotypic analysis using ERIC-PCR, and antibiotic resistance genes were identified. Silver nanoparticles (AgNPs) were synthesized using a Camellia sinensis (green tea) extract and characterized using UV-Vis spectroscopy, transmission electron microscopy (TEM), and X-ray diffraction (XRD). Particle size analysis was conducted to determine the physicochemical properties of the synthesized AgNPs. The AgNPs antibacterial effect alone or in combination with meropenem was carried out using the agar-well diffusion method, and the minimum inhibitory concentration (MIC), multiple antibiotic resistance (MAR) index and fractional inhibitory concentration index (FICI) were determined. Of the collected isolates, 67 were identified as K. pneumoniae , and 92.5% were considered XDR. Results showed that 10 (14.9%) and 57 (85.1%) isolates exhibited MAR index from 0.58 to 0.74, and 0.79-1.00, respectively. Upon genotypic analysis, 29 isolates were selected for further studies based on their unique or significant clustering patterns. The synthesized AgNPs exhibited strong antimicrobial activity against XDR K. pneumoniae strains, with inhibition zones ranging from 10 mm to 25 mm. The MIC of AgNPs ranged from 336.17 to 672.35 µg/mL. The fractional inhibitory concentration index (FICI) proved enhanced antimicrobial activity with partial (34.5%) and complete synergistic (65.5%) effects in the tested 29 nonclonal clinical isolates when AgNPs were combined with meropenem. In conclusion, a combination of AgNPs with meropenem is a useful alternative approach in combating XDR K. pneumoniae . Further studies are recommended for the use of this approach in clinical settings based on its benefits to enhance treatment outcomes.

Structural variants (SVs) are one of the significant types of DNA mutations and are typically defined as larger-than-50-bp genomic alterations that include insertions, deletions, duplications, inversions, and translocations. These modifications can profoundly impact the phenotypic characteristics and contribute to disorders like cancer, response to treatment, and infections. Four long-read aligners and five SV callers have been evaluated using three Oxford Nanopore NGS human genome datasets in terms of precision, recall, and F1-score statistical metrics, depth of coverage, and speed of analysis. The best SV caller regarding recall, precision, and F1-score when matched with different aligners at different coverage levels tend to vary depending on the dataset and the specific SV types being analyzed. However, based on our findings, Sniffles and CuteSV tend to perform well across different aligners and coverage levels, followed by SVIM, PBSV, and SVDSS in the last place. The CuteSV caller has the highest average F1-score (82.51%) and recall (78.50%), and Sniffles has the highest average precision value (94.33%). Minimap2 as an aligner and Sniffles as an SV caller act as a strong base for the pipeline of SV calling because of their high speed and reasonable accomplishment. PBSV has a lower average F1-score, precision, and recall and may generate more false positives and overlook some actual SVs. Our results are valuable in the comprehensive evaluation of popular SV callers and aligners as they provide insight into the performance of several long-read aligners and SV callers and serve as a reference for researchers in selecting the most suitable tools for SV detection.

Background: Carbapenemase-producing Gram-negative (CPGN) bacteria impose life-threatening infections with limited treatment options. Rigor and rapid detection of CPGN-associated infections is usually associated with proper treatment and better disease prognosis. Accordingly, this study aimed at evaluating the phenotypic methods versus genotypic methods used for the detection of such pathogens and determining their sensitivity/specificity values. Methods: A total of 71 CPGN bacilli (30 Enterobacterales and 41 non-glucose-fermenting bacilli) were tested for the carbapenemase production by the major phenotypic approaches including, the modified Hodge test (MHT), modified carbapenem inactivation method (mCIM), combined disk test by EDTA (CDT) and blue-carba test (BCT). The obtained results were statistically analyzed and correlated to the obtained resistant genotypes that were determined by using polymerase chain reactions (PCR) for the detection of the major carbapenemase-encoding genes covering the three classes (Class A, B, and D) of carbapenemases. Results: In comparison to PCR, the overall sensitivity/specificity values for detection of carbapenemase-producing organism were 65.62%/100% for MHT, 68.65%/100% for mCIM, 55.22%/100% for CDT and 89.55%/75% for BCT. The sensitivity/specificity values for carbapenemase-producing Enterobacterales were, 74%100% for MHT, 51.72%/ 100% for mCIM, 62.07%/100% for CDT and 82.75%/100% for BCT. The sensitivity/specificity values for carbapenemase-producing non-glucose fermenting bacilli were, 62.16%/100% for MHT, 81.57%/100% for mCIM, 50/100% for CDT and 94.74%/66.66% for BCT. Considering these findings, BCT possess a relatively high performance for the efficient and rapid detection of carbapenemase producing isolates. Statistical analysis showed significant association ( p <  0.05) between bla NDM and/or bla VIM genotypes with MHT/CDT; bla KPC / bla GIM genotypes with CDT and bla GIM genotype with BCT. Conclusion: The current study provides an update on the performance of the phenotypic tests which are varied depending on the tested bacterial genera and the type of the carbapenemase. The overall sensitivity/specificity values for detection of CPO were 65.62%/100% for MHT, 68.65%/100% for mCIM, 55.22%/100% for CDT and 89.55%/75% for BCT. Based on its respective diagnostic efficiency and rapid turnaround time, BCT is more likely to be recommended in a resource-limited settings particularly, when molecular tests are not available.

Background Paromomycin is a 2-deoxystreptamine aminocyclitol aminoglycoside antibiotic with broad spectrum activity against Gram-negative, Gram-positive bacteria and many protozoa. This study introduces a strategy for paromomycin production through solid-state fermentation using Streptomyces rimosus subsp. paromomycinus NRRL 2455. Solid state fermentation has gained enormous attention in the development of several products because of their numerous advantages over submerged liquid fermentation. After selecting the best solid substrate, a time course study of paromomycin production was carried out followed by optimization of environmental conditions using response surface methodology. Paromomycin yields obtained using this technique were also compared to those obtained using submerged liquid fermentation. Results Upon screening of 6 different substrates, maximum paromomycin concentration (0.51 mg/g initial dry solids) was obtained with the cost-effective agro-industrial byproduct, corn bran, impregnated with aminoglycoside production media. Optimization of environmental conditions using D-optimal design yielded a 4.3-fold enhancement in paromomycin concentration reaching 2.21 mg/g initial dry solids at a pH of 8.5, inoculum size of 5% v/w and a temperature of 30 °C. Conclusion Compared to submerged liquid fermentation, solid state fermentation resulted in comparable paromomycin concentrations, cost reduction of raw materials, less energy consumption and waste water discharge, which have major implications in industrial fermentation. Therefore, solid state fermentation is a promising alternative to submerged liquid fermentation for paromomycin production. To the best of our knowledge, this is the first report on the optimized paromomycin production through solid state fermentation process.

Mushrooms are nutritious foods that are widely cultivated all over the world. They are rich in a range of compounds linked to improving functions of the immune system including carotenoids, alkaloids, lectins, enzymes, folates, fats, organic acids, minerals, polysaccharides, phenolics, proteins, tocopherols, terpenoids, and volatile compounds. In this study we investigated, the immunomodulatory activity in rats of the aqueous extracts of five of the most common edible mushrooms belonging to Family Basidiomycota-white-rot fungi including, Lentinula edodes, Agaricus bisporus , Pleurotus ostreatus , Pleurotus columbinus, and Pleurotus sajor-caju . Male Wistar albino rats were assigned to thirteen groups and Immunosuppression was induced by oral administration of dexamethasone (0.1 mg/kg), followed by oral administration of the mushroom extracts at low (200 mg/kg) and high (400 mg/kg) doses. A positive control group received the immune stimulant Echinacea extract Immulant® at (30 mg/kg), while the negative control group received only saline. From each animal, in each group, blood samples were collected after 15 days for complete blood counts and for measurement of immunologic parameters, including lysozyme activity, nitric oxide (NO) production and serum cytokines including tumor necrosis factor-alpha (TNF-α), interferon-gamma (IFN-γ) and interleukin 1 beta (IL-1β) levels. Results have shown that white blood cells (WBCs) and lymphocytic counts were significantly boosted by high doses of each of the five mushroom extracts (207–289% increase for WBC and 153–175% for lymphocytes) with a significant increase in lysozyme activity (110–136% increase), NO concentration (159–232% increase) and cytokines as compared to the negative control group. Histopathological examination of the rats' spleen and thymus tissues has shown marked lymphocytic proliferation that was more obvious at the higher doses. In conclusion, our results showed that the five edible mushroom extracts revealed significant immunostimulatory effects preclinically particularly, at the higher doses (400 mg/kg) which can be considered the effective dose.

The emergence of multidrug-resistant pathogens and the growing burden of cancer worldwide demand novel therapeutic approaches. This study evaluated the biological activities of green-synthesized titanium dioxide nanoparticles (TiO₂ NPs) using Bacillus cereus cell-free supernatant and titanium tetra-isopropoxide precursor. Nanoparticles were analyzed and standard methods were employed to evaluate the antimicrobial, antibiofilm, and cell cytotoxicity. UV–Vis spectroscopy confirmed the synthesis of TiO₂ NPs with a characteristic peak at 360 nm. Transmission electron microscopy (TEM) revealed roughly spherical particles (8.8 ± 3 nm diameter). A Z-average hydrodynamic diameter of 328.1 nm (PDI, 0.439) was revealed by dynamic light scattering (DLS). According to the energy-dispersive X-ray spectroscopy (EDX) results, oxygen was 42.39% and titanium was 45.93%. The X-ray diffraction (XRD) measurement confirmed a crystalline anatase structure, with a prominent peak at 25.3° 2θ. Fourier transform infrared (FTIR) detected the characteristic Ti–O-Ti and vibrational band at 403.31 cm⁻ 1 . The nanoparticles demonstrated broad-spectrum antimicrobial activity with MICs of 78 μg/mL ( E. coli ), 156 μg/mL ( C. albicans ), 625 μg/mL ( E. faecalis ), and 2500 μg/mL ( S. aureus and P. aeruginosa ). At sub-MIC concentrations, TiO₂ NPs reduced biofilm formation in S. aureus by roughly 65.72% ± 0.01, in E. faecalis by 50.91% ± 0.02, and in P. aeruginosa by 38.4% ± 0.1. Cytotoxicity investigations revealed IC₅₀ values of 212.15 μg/mL (Caco-2) and 342.96 μg/mL (Vero cells), with a selectivity index of 1.62. Strong antiviral activity against HSV-1 was observed (74.74% inhibition at 60 µg/mL, EC₅₀ = 17.41 µg/mL, selectivity index = 19.7). Biogenic synthesis using B. cereus successfully produced highly crystalline, small-sized anatase TiO₂ nanoparticles demonstrating multifunctional biological activities including antimicrobial, antibiofilm, anticancer selectivity, and antiviral properties. Key points • Green synthesis via B. cereus yielded crystalline anatase TiO₂ NPs with nanoscale dimensions. • TiO₂ NPs demonstrated broad antimicrobial/antibiofilm effects and selective anticancer activity. • Strong antiviral potency against HSV-1 with excellent selectivity was observed

The Middle East has witnessed a greater spread of infectious Dengue viruses, with serotype 2 (DENV-2) being the most prevalent form. Through this work, multi-epitope peptide vaccines against DENV-2 that target E and nonstructural (NS1) proteins were generated through an immunoinformatic approach. MHC class I and II and LBL epitopes among NS1 and envelope E proteins sequences were predicted and their antigenicity, toxicity, and allergenicity were investigated. Studies of the population coverage denoted the high prevalence of NS1 and envelope-E epitopes among different countries where DENV-2 endemic. Further, both the CTL and HTL epitopes retrieved from NS1 epitopes exhibited high conservancies’ percentages with other DENV serotypes (1, 3, and 4). Three vaccine constructs were created and the expected immune responses for the constructs were estimated using C-IMMSIM and HADDOCK (against TLR 2,3,4,5, and 7). Molecular dynamics simulation for vaccine construct 2 with TLR4 denoted high binding affinity and stability of the construct with the receptor which might foretell favorable in vivo interaction and immune responses.

Background Multidrug-resistant (MDR) P. aeruginosa is a rising public health concern, challenging the treatment of such a ubiquitous pathogen with monotherapeutic anti-pseudomonal agents. Worryingly, its genome plasticity contributes to the emergence of P. aeruginosa expressing different resistant phenotypes and is now responsible for notable epidemics within hospital settings. Considering this, we aimed to evaluate the synergistic combination of fortimicin with other traditional anti-pseudomonal agents and to analyze the resistome of pan-drug resistant (PDR) isolate. Methods Standard methods were used for analyzing the antimicrobial susceptibility tests. The checkerboard technique was used for the in vitro assessment of fortimicin antibiotic combinations against 51 MDR P. aeruginosa and whole genome sequencing was used to determine the resistome of PDR isolate. Results Out of 51 MDR P. aeruginosa, the highest synergistic effect was recorded for a combination of fortimicin with β-lactam group as meropenem, ceftazidime, and aztreonam at 71%, 59% and 43%, respectively. Of note, 56.8%, 39.2%, and 37.2% of the tested MDR isolates that had synergistic effects were also resistant to meropenem, ceftazidime, and aztreonam, respectively. The highest additive effects were recorded for combining fortimicin with amikacin (69%) and cefepime (44%) against MDR P. aeruginosa. Resistome analysis of the PDR isolate reflected its association with the antibiotic resistance phenotype. It ensured the presence of a wide variety of antibiotic-resistant genes (β-lactamases, aminoglycosides modifying enzymes, and efflux pump), rendering the isolate resistant to all clinically relevant anti-pseudomonal agents. Conclusion Fortimicin in combination with classical anti-pseudomonal agents had shown promising synergistic activity against MDR P. aeruginosa. Resistome profiling of PDR P. aeruginosa enhanced the rapid identification of antibiotic resistance genes that are likely linked to the appearance of this resistant phenotype and may pave the way to tackle antimicrobial resistance issues shortly.