Presence of BlaPER-1 and BlaVEB-1 Beta-Lactamase Genes among Isolates of Pseudomonas Aeruginosa from Burn and Trauma Hospital Peshawar, Pakistan

Pseudomonas aeruginosa spp are the most prevalent bacteria that cause nosocomial infections in hospitals. Most antibiotics, including novel new β-lactams, are already resistant to them, and they can become resistant during treatment, which can make the treatment fail. P. aeruginosa isolates from ICU patients who had Per-1 and VEB-1 were the main focus of this study. These two ESBLs are the two most common in ICU patients who had them. 50 isolates were gathered from Peshawar\u27s LRH ICU facilities in the year 2021. The antibiotic susceptibility test was conducted in accordance with the Clinical and Laboratory Standards Institute\u27s standards (CLSI). The combination disc test used to identify isolates that produce ESBLs. Ceftazidime MIC was determined using the agar dilution method using particular primers, the PER-1 and VEB-1 genes were detected using polymerase chain reaction (PCR). Fifty-six percent patients (n=40) male, whereas forty percent (n=25) were female. Augmentin (96.6%, n=61) and cefpodoxim (86.7%, n=55) resistance was found in the majority of ICU isolates. Fifty isolates (77%) tested positive for ESBL, with 94 percent (n=47) carrying the PER-1 gene and VEB-1 gene 52 percent (n=26). Ten isolates had blaPER1 and blaVEB1 present at the same time, and seven of them amplified all three genes. ESBL producers were found in a large number of ICU P. aeruginosa isolates. Although blaVEB1 and blaPER1 were found in a small number of isolates, their frequency was very high. Furthermore, carbapenem resistance was negligible. Because of drug-resistant P. aeruginosa isolates, it is vital to monitor ICU centers

The Functions of Mediator in Candida albicans Support a Role in Shaping Species-Specific Gene Expression

The Mediator complex is an essential co-regulator of RNA polymerase II that is conserved throughout eukaryotes. Here we present the first study of Mediator in the pathogenic fungus Candida albicans. We focused on the Middle domain subunit Med31, the Head domain subunit Med20, and Srb9/Med13 from the Kinase domain. The C. albicans Mediator shares some roles with model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, such as functions in the response to certain stresses and the role of Med31 in the expression of genes regulated by the activator Ace2. The C. albicans Mediator also has additional roles in the transcription of genes associated with virulence, for example genes related to morphogenesis and gene families enriched in pathogens, such as the ALS adhesins. Consistently, Med31, Med20, and Srb9/Med13 contribute to key virulence attributes of C. albicans, filamentation, and biofilm formation; and ALS1 is a biologically relevant target of Med31 for development of biofilms. Furthermore, Med31 affects virulence of C. albicans in the worm infection model. We present evidence that the roles of Med31 and Srb9/Med13 in the expression of the genes encoding cell wall adhesins are different between S. cerevisiae and C. albicans: they are repressors of the FLO genes in S. cerevisiae and are activators of the ALS genes in C. albicans. This suggests that Mediator subunits regulate adhesion in a distinct manner between these two distantly related fungal species

Fungal–Bacterial Co-Infections and Super-Infections among Hospitalized COVID-19 Patients: A Systematic Review

This study systematically reviewed fungal–bacterial co-infections and super-infections among hospitalized COVID-19 patients. A PRISMA systematic search was conducted. On September 2022, Medline, PubMed, Google Scholar, PsychINFO, Wiley Online Library, NATURE, and CINAHL databases were searched for all relevant articles published in English. All articles that exclusively reported the presence of fungal–bacterial co-infections and super-infections among hospitalized COVID-19 patients were included. Seven databases produced 6937 articles as a result of the literature search. Twenty-four articles met the inclusion criteria and were included in the final analysis. The total number of samples across the studies was 10,834, with a total of 1243 (11.5%) patients admitted to the intensive care unit (ICU). Of these patients, 535 underwent mechanical ventilation (4.9%), 2386 (22.0%) were male, and 597 (5.5%) died. Furthermore, hospitalized COVID-19 patients have a somewhat high rate (23.5%) of fungal–bacterial co-infections and super-infections. Moreover, for SARS-CoV-2 patients who have a chest X-ray that suggests a bacterial infection, who require immediate ICU admission, or who have a seriously immunocompromised condition, empiric antibiotic therapy should be taken into consideration. Additionally, the prevalence of co-infections and super-infections among hospitalized COVID-19 patients may have an impact on diagnosis and treatment. It is crucial to check for fungal and bacterial co-infections and super-infections in COVID-19 patients

Characterization of Candida albicans Virulence using a Caenorhabditis elegans Infection Model

We screened a C. albicans cell wall mutant library for mutants that show attenuation in their ability to filament within the worm. Our results revealed three novel genes in regards to having a role in C. albicans Pathogenesis. The novel genes included 1) LRG1, 2) ECM9, and 3) PGA6. Our focus was on the characterisation of two of these genes that were found to cause a severe defect in filamentation upon their deletion, LRG1 and ECM9. We also applied the C. elegans infection model for the study of other novel C. albicans genes that was part of collaborative work and is presented in Chapter 4 of this PhD thesis

In vitro Utility of Zinc oxide Nanoparticles and Antifungal Drugs for the Treatment of Mycotic Mastitis in Dairy Cows in Egypt

Bovine mastitis is an inflammation of mammary gland parenchyma in cows. It is caused by multiple pathogens including bacteria and fungi. Mycotic mastitis is a secondary disease following improper frequent use of antibiotics or an unhygienic environment. The treatment of rising cases of mycotic mastitis is still controversial because of the rapid resistance acquired by the traditional use of antifungal drugs. The present study aimed to investigate the use of zinc oxide nanoparticles (ZnO-NPs), alternative therapy for traditional antifungal drugs, to combat fungal isolates from mastitic cows by examining the in vitro antifungal activity of ZnO-NPs. One hundred milk samples were aseptically collected from cows suffering from clinical mastitis in a governorate in Egypt. The fungal isolates were identified by their colony morphology and microscopical examination and subsequent underwent determining the MIC of traditional antifungal drugs and ZnO-NPs using the disc diffusion methods. Our results showed that 70% of milk samples were positive for mycotic mastitis with 30% yeasts, 15% molds, and 25% yeast and molds. Candida was the most common yeast species isolated. Rhodotorula, c. guilliermondii, c. parapsillosis, and c. albicans showed entire resistant (100%) to all traditional antifungal drugs whereas, the same isolates, except c. albicans, were susceptible to ZnO-NPs. Mold spp. were susceptible to ZnO-NPs and only Itraconazole, and Clotrimazole. ZnO-NPs are highly effective and promising inexpensive antimicrobial agent for the treatment of bovine mycotic mastitis

In Silico Identification of Novel Derivatives of Rifampicin Targeting Ribonuclease VapC2 of <i>M. tuberculosis</i> H37Rv: Rifampicin Derivatives Target VapC2 of <i>Mtb</i> H37Rv

The emergence of multi-drug-resistant Mycobacterium tuberculosis (Mtb) strains has rendered many of the currently available anti-TB drugs ineffective. Hence, there is a pressing need to discover new potential drug targets/candidates. In this study, attempts have been made to identify novel inhibitors of the ribonuclease VapC2 of Mtb H37Rv using various computational techniques. Ribonuclease VapC2 Mtb H37Rv’s protein structure was retrieved from the PDB databank, 22 currently used anti-TB drugs were retrieved from the PubChem database, and protein–ligand interactions were analyzed by docking studies. Out of the 22 drugs, rifampicin (RIF), being a first-line drug, showed the best binding energy (−8.8 Kcal/mol) with Mtb H37Rv VapC2; hence, it was selected as a parent molecule for the design of its derivatives. Based on shape score and radial plot criteria, out of 500 derivatives designed through SPARK (Cresset®, Royston, UK) program, the 10 best RIF derivatives were selected for further studies. All the selected derivatives followed the ADME criteria concerning drug-likeness. The docking of ribonuclease VapC2 with RIF derivatives revealed the best binding energy of −8.1 Kcal/mol with derivative 1 (i.e., RIF-155841). A quantitative structure–activity relationship study revealed that derivative 1’s activity assists in the inhibition of ribonuclease VapC2. The stability of the VapC2–RIF155841 complex was evaluated using molecular dynamics simulations for 50 ns and the complex was found to be stable after 10 nsec. Further, a chemical synthesis scheme was designed for the newly identified RIF derivative (RIF-155841), which verified that its chemical synthesis is possible for future in vitro/in vivo experimental validation. Overall, this study evaluated the potential of the newly designed RIF derivatives with respect to the Mtb VapC2 protein, which is predicted to be involved in some indispensable processes of the related pathogen. Future experimental studies regarding RIF-155841, including the exploration of the remaining RIF derivatives, are warranted to verify our current findings

In Silico Identification of Novel Derivatives of Rifampicin Targeting Ribonuclease VapC2 of M. tuberculosis H37Rv: Rifampicin derivatives target VapC2 of Mtb H37Rv

The emergence of multi-drug-resistant Mycobacterium tuberculosis (Mtb) strains has rendered many of the currently available anti-TB drugs ineffective. Hence, there is a pressing need to discover new potential drug targets/candidates. In this study, attempts have been made to identify novel inhibitors of the ribonuclease VapC2 of Mtb H37Rv using various computational techniques. Ribonuclease VapC2 Mtb H37Rv&rsquo;s protein structure was retrieved from the PDB databank, 22 currently used anti-TB drugs were retrieved from the PubChem database, and protein&ndash;ligand interactions were analyzed by docking studies. Out of the 22 drugs, rifampicin (RIF), being a first-line drug, showed the best binding energy (&minus;8.8 Kcal/mol) with Mtb H37Rv VapC2; hence, it was selected as a parent molecule for the design of its derivatives. Based on shape score and radial plot criteria, out of 500 derivatives designed through SPARK (Cresset&reg;, Royston, UK) program, the 10 best RIF derivatives were selected for further studies. All the selected derivatives followed the ADME criteria concerning drug-likeness. The docking of ribonuclease VapC2 with RIF derivatives revealed the best binding energy of &minus;8.1 Kcal/mol with derivative 1 (i.e., RIF-155841). A quantitative structure&ndash;activity relationship study revealed that derivative 1&rsquo;s activity assists in the inhibition of ribonuclease VapC2. The stability of the VapC2&ndash;RIF155841 complex was evaluated using molecular dynamics simulations for 50 ns and the complex was found to be stable after 10 nsec. Further, a chemical synthesis scheme was designed for the newly identified RIF derivative (RIF-155841), which verified that its chemical synthesis is possible for future in vitro/in vivo experimental validation. Overall, this study evaluated the potential of the newly designed RIF derivatives with respect to the Mtb VapC2 protein, which is predicted to be involved in some indispensable processes of the related pathogen. Future experimental studies regarding RIF-155841, including the exploration of the remaining RIF derivatives, are warranted to verify our current findings

In silico evaluation of the inhibitory potential of nucleocapsid inhibitors of SARS-CoV-2: a binding and energetic perspective

The COVID-19 outbreak brought on by the SARS-CoV-2 virus continued to infect a sizable population worldwide. The SARS-CoV-2 nucleocapsid (N) protein is the most conserved RNA-binding structural protein and is a desirable target because of its involvement in viral transcription and replication. Based on this aspect, this study focused to repurpose antiviral compounds approved or in development for treating COVID-19. The inhibitors chosen are either FDA-approved or are currently being studied in clinical trials against COVID-19. Initially, they were designed to target stress granules and other RNA biology. We have utilized structure-based molecular docking and all-atom molecular dynamics (MD) simulation approach to investigate in detail the binding energy and binding modes of the different anti-N inhibitors to N protein. The result showed that five drugs including Silmitasterib, Ninetanidinb, Ternatin, Luteolin, Fedratinib, PJ34, and Zotatafin were found interacting with RNA binding sites as well as to predicted protein interface with higher binding energy. Overall, drug binding increases the stability of the complex with maximum stability found in the order, Silmitasertib > PJ34 > Zotatatafin. In addition, the frustration changes due to drug binding brings a decrease in local frustration and this decrease is mainly observed in α-helix, β3, β5, and β6 strands and are important for drug binding. Our in-silico data suggest that an effective interaction occurs for some of the tested drugs and prompt their further validation to reduce the rapid outspreading of SARS-CoV-2. Communicated by Ramaswamy H. Sarma</p

Biodegradation of Azo Dye Methyl Red by Pseudomonas aeruginosa: Optimization of Process Conditions

Water pollution due to textile dyes is a serious threat to every life form. Bacteria can degrade and detoxify toxic dyes present in textile effluents and wastewater. The present study aimed to evaluate the degradation potential of eleven bacterial strains for azo dye methyl red. The optimum degradation efficiency was obtained using P. aeruginosa. It was found from initial screening results that P. aeruginosa is the most potent strain with 81.49% degradation activity and hence it was subsequently used in other degradation experiments. To optimize the degradation conditions, a number of experiments were conducted where only one variable was varied at a time and where maximum degradation was observed at 20 ppm dye concentration, 1666.67 mg/L glucose concentration, 666.66 mg/L sodium chloride concentration, pH 9, temperature 40 &deg;C, 1000 mg/L urea concentration, 3 days incubation period, and 66.66 mg/L hydroquinone (redox mediator). The interactive effect of pH, incubation time, temperature, and dye concentration in a second-order quadratic optimization of process conditions was found to further enhance the biodegradation efficiency of P. aeruginosa by 88.37%. The metabolites of the aliquot mixture of the optimized conditions were analyzed using Fourier transform infrared (FTIR), GC-MS, proton, and carbon 13 Nuclear Magnetic Resonance (NMR) spectroscopic techniques. FTIR results confirmed the reduction of the azo bond of methyl red. The Gas Chromatography&ndash;Mass Spectrometry (GC-MS) results revealed that the degraded dye contains benzoic acid and o-xylene as the predominant constituents. Even benzoic acid was isolated from the silica gel column and identified by 1H and 13C NMR spectroscopy. These results indicated that P. aeruginosa can be utilized as an efficient strain for the detoxification and remediation of industrial wastewater containing methyl red and other azo dyes