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Proteomics and Docking Study Targeting Penicillin Binding Protein and Penicillin-Binding Protein2a of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Sudan

Authors: Mohamed, Sofia B, Adlan, Talal A, Khalafalla, Nagla A et al.

Dec 2025

Whole genome sequencing of methicillin-resistant Staphylococcus aureus (MRSA) strain isolated from Sudan has led to a great deal of information, which allows the identification and characterization of some pivotal proteins. The objective of this study was to investigate the penicillin-binding proteins, PBP and PBP2a, of SO-1977 strain to have insights about their physicochemical properties and to assess and describe the interaction of some phytochemicals against them in silico. PBP and PBP2a from MRSA’s Sudan strain were found to be of great resemblance with some other strains. G246E single-nucleotide polymorphism was reported and identified in the allosteric binding site positioned in the non-penicillin-binding domain. The docked compounds demonstrated good binding energies and hydrogen bond interactions with residue Ser404 which plays crucial roles in β-lactam activity. This finding would contribute significantly to designing effective β-lactam drugs, to combat and treat β-lactam–resistant bacteria in the future.

Distribution of Colistin Resistance Genes Among Clinical Isolate of Gram-Negative Bacteria

Authors: abdalla,Amna, Musa,Hassan A, Abdelhalim,Khalid A et al.

Dec 2025

This study focuses on the identification and the distribution of Colistin resistance genes among Gram-negative bacteria isolated from clinical samples at the National Ribat Teaching hospital, in Khartoum, Sudan. A total of 165 Gram-negative isolated pathogens were as follow Klebsiella pneumoniae (73/44.2%), E. coli (53/32.1%), Pseudomonas aeruginosa (33/20%), Proteus vulgaris (6/3.6%), and Citrobacter freundii (2/1.2%), isolated between December 2019 and February 2020 from clinical samples at the National Ribat Teaching hospital in Khartoum, Sudan. Stock of all isolates were stored in 20% Glycerol-broth at -80°C for further subculture for antimicrobial susceptibility profile and resistance genes associated with Colistin resistance were identified. Colistin resistance associated genes (mcr-1, mcr-2, mcr-3, mcr-4, mcr-5) of Gram-negative isolates were determined by polymerase chain reaction (PCR) using appropriate primer sets. Out of 165; 11 isolates (7%) were resistance to Colistin antibiotic with MIC ≥ 9-10 μg/Ml. The majority 67% (4/6) of K. pneumoniae Colistin resistant strains were considered MDR. Three out of the 6 (50%) clinical Colistin-resistant K. pneumoniae isolates were resistant to carbapenems (meropenem ≤ 2 μg/ml). One of these 3 strains was resistant to all tested antibiotics. The remaining K. pneumoniae strains were susceptible to most tested antibiotics (Supplementary material Table A1). The two Colistin resistant P. vulgaris isolates were resistant to all antibiotics including the carbapenems (meropenem ≤ 2 μg/ ml) and were only susceptible to amikacin and ciprofloxacin. One Colistin resistant C. freundii isolate was only susceptible to amikacin, cotrimoxazole, and carbapenems. The Antibiotic resistant patterns were very low among P. aeruginosa isolates, as the majority of the isolates were shown more sensitive to most of the antibiotics. Only one Colistin resistant E. coli isolate was resistant to aminoglycoside and beta-lactam antibiotics. The gene detection by PCR revealed positive mcr-1 gene in 11/165 (7%) of the isolates; 6/73 (8%) were K. pneumoniae with highest mcr-1 gene among Colistin resistant K. pneumoniae 60% (6/10). 2/6 (33%) P. vulgaris, 1/53 E. coli, 1/33 (3%) P. aeruginosa, and 1/2 (50%) C. freundii. While only one (0.6%) K. pneumoniae isolate was found

Whole-genome sequence data of a Salmonella enterica serovar Rissen sequence type 8877 isolated from cracked table egg in Sudan

Authors: Elhassan, Mortada M.O., Adam, Habiba B.A., Fagir, Shaimaa S.A.O. et al.

Dec 2025

Salmonella enterica serovar Rissen is an emerging and impor- tant Salmonella serovar prevalent in live animals and foods from retail markets worldwide. Here, we describe the whole- genome sequence of Salmonella enterica Serovar Rissen Se- quence Type 8877 isolated from a cracked table egg in Su- dan. The whole-genome sequencing was obtained using Illu- mina Miseq platform. The quality of the sequenced read, the De novo assembly, and the sequencing typing was conducted by JEKESA pipeline ( https://github.com/stanikae/jekesa ). The assembled genome was also uploaded to the Center for Ge- nomic Epidemiology web server to determine acquired an- tibiotic resistance genes, predict the serovar, and the anti- genic profile. The genome of Salmonella enterica serovar Ris- sen 1-M1 was found to harbor 4,689 protein-coding genes, 96 RNA genes, and 115 pseudogenes, as predicted by NCBI Prokaryotic Genome Annotation Pipeline. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under accession JAPSFB0 0 0 0 0 0 0 0 0.

Properties of natural adsorbent prepared from two local Sudanese agricultural wastes mango seeds and date’s stones and their uses in removal of contamination from fluid nutrient

Authors: ElNasri, Nazar A.aziz, Wadidi, Nazar Abdallazim, Idris, Alkhair Abd Almahmoud et al.

Dec 2025

Background: In recent years, special attention has been focused on the use of natural adsorbents as an alternative to replace the conventional adsorbents, based on both the environmental and the economical points of view. The study aimed to produce natural absorbent (activated carbon) from two local agricultural wastes: mango seeds (MS) and date stones (DS) and their uses in removal of contamination from fluid nutrient. Chemical properties such as ash con tent, moisture content, carbon content percentage and percentage of methylene blue reduction of the two samples were investigated. Results: The results of study indicated that activated carbon produced from both MS and DS samples have the same pH value of 7 (neutral).The ash content of activated carbon prepared from mango seeds and date’s stones was 9.7 and 9.5%, respectively.Our statistical analysis showed no significant difference (p ≥ 0.05)for ash determinations, while the moisture content of (19.5 and 19.9%) was found for mango seeds and date’s stones, respectively. There was no signifi cant difference at p > 0.05 for moisture content of the two samples. A significant difference was observed in carbon contents for mango seeds (61.4%) and date’s stones (21.8%) at p ≤ 0.05). There was no significant difference at p > 0.05 for moisture content of the two samples. Statistical analysis showed significance difference (p ≤ 0.05) for carbon determination for both samples. The results also indicated that there was significant correlation between reduction in methylene blue and percentage of activated carbon. Conclusions: Activated carbon produced from MS and DS was found to be very effective in color removal and of acceptable quality in pH, carbon content, ash content, moisture content and solubility.

Extraction and Identification of Fungi from Different Sudanese Soil

Authors: Ibrahim, Nesreen A. A., Saeed, Humodi A., Saeed, Samar M. et al.

Dec 2025

The biosynthesis process utilizing fungi and other microorganisms is an essential sustainable method for the manufacture of nanomaterials, aligning with sustainable development goals. Consequently, the extraction and accurate identification of fungi from soil is strongly advised. In this study, various fungus species were collected from different Sudanese agricultural soil at various locations. Afterwards, the fungi were extracted and identified. The fungi have been isolated were then identified to the genus level and to the species according to the basis of macro morphological. Thus, the colonies were investigated for slow or for rapid growth, also based on topography and texture. Interestingly, the identification methods used for fungi isolated displayed that various fungi have been successfully identified. Thus, based on the culture method, there are fungal species of 121 species with 100% were recognized. However, based on the microscopic investigation there are 102 species of fungal species were identified. However, based on the molecular method the identified fungi were found to be 90 of the fungal species isolated.

Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan

Authors: Mohamed, Sofia B, Kambal, Sumaya, Ibrahim, Sabah A.E. et al.

Dec 2025

The ever increasing applications of bioinformatics in providing effective interpretation of large and complex biological data require expertise in the use of sophisticated computa tional tools and advanced statistical tests, skills that are mostly lacking in the Sudanese research community. This can be attributed to paucity in the development and promotion of bioinformatics, lack of senior bioinformaticians, and the general status quo of inadequate research funding in Sudan. In this paper, we describe the challenges that have encountered the development of bioinformatics as a discipline in Sudan. Additionally, we highlight on spe cific actions that may help develop and promote its education and training. The paper takes the National University Biomedical Research Institute (NUBRI) as an example of an institute that has tackled many of these challenges and strives to drive powerful efforts in the devel opment of bioinformatics in the country.

Genomic analysis of methicillin-resistant Staphylococcus aureus strain SO-1977 from Sudan

Authors: Ali,Mohamed S, Isa,Nurulfiza M, Abedelrhman,Faisal M et al.

Dec 2025

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is known as a leading cause of morbidity and mortality. Investigation of the MRSA’s virulence and resistance mechanisms is a continuing concern toward controlling such burdens through using high throughput whole Genome Sequencing (WGS) and molecular diagnostic assays. The objective of the present study is to perform whole-genome sequencing of MRSA isolated from Sudan using Illumina Next Generation Sequencing (NGS) platform. Results: The genome of MRSA strain SO-1977 consists of 2,827,644 bp with 32.8% G + C, 59 RNAs and 2629 predicted coding sequences (CDSs). The genome has 26 systems, one of which is the major class in the disease virulence and defence. A total of 83 genes were annotated to virulence disease and defence category some of these genes coding as functional proteins. Based on genome analysis, it is speculated that the SO-1977 strain has resistant genes to Teicoplanin, Fluoroquinolones, Quinolone, Cephamycins, Tetracycline, Acriflavin and Carbapenems. The results revealed that the SO-1977, strain isolated from Sudan has a wide range of antibiotic resistance compared to related strains. Conclusion: The study reports for the first time the whole genome sequence of Sudan MRSA isolates. The release of the genome sequence of the strain SO-1977 will avail MRSA in public databases for further investigations on the evolution of resistant mechanism and dissemination of the -resistant genes of MRSA.

Reverse vaccinology and immunoinformatics approaches for multi-epitope vaccine design against Klebsiella pneumoniae reveal a novel vaccine target protein

Authors: Elfadil, Mayada M., Samhoon, Samah Omer A., Saadaldin, Moaaz M. et al.

Dec 2025

Klebsiella pneumoniae (K. pneumoniae), a Gram-negative pathogen, is a leading cause of hospital-acquired in fections in Sudan and worldwide. The emergence of multidrug-resistant (MDR) strains has severely limited treatment options, underscoring the urgent need for an effective vaccine. In this study, we employed reverse vaccinology and immunoinformatics to design a novel multi-epitope vaccine targeting the hypervirulent NUBRI- K strain. Two conserved, non-host homologous iron acquisition proteins, IucA/IucC and FyuA, were prioritized as targets. The vaccine construct integrates six B-cell, six cytotoxic T lymphocyte (CTL), and six helper T lymphocyte (HTL) epitopes, linked by optimized spacers and fused to a β-defensin adjuvant. Computational analyses confirmed strong antigenicity (1.0429), non-allergenicity, and favorable solubility (0.477). Molecular docking revealed high-affinity binding to Toll-like receptor 4 (TLR4) ( 278.22 kcal/mol), stabilized by eight hydrogen bonds and two salt bridges. Structural validation showed that 91 % of residues were located in favored regions of the Ramachandran plot. Additionally, CABSflex 2.0 dynamics analysis confirmed stable vaccine–TLR4 interactions, with minimal residue-level fluctuations (RMSF <1.5 Å), indicating conformational stability of the complex. In silico immune simulations predicted potent humoral and cellular responses, including elevated IgG/ IgM titers, T-cell proliferation, and IFN-γ secretion. The construct was further optimized for mammalian expression, achieving an ideal GC content (48.27 %) and a codon adaptation index (CAI) of 1.0, facilitating efficient in silico cloning into the pcDNA3 vector. By targeting conserved iron acquisition systems, this vaccine candidate presents a promising strategy to combat antibiotic-resistant K. pneumoniae while minimizing selective pressure. Future in vitro and in vivo studies are warranted to validate its immunogenicity and protective efficacy

Green synthesis of silver nanoparticles using Sudanese Candida parapsilosis: a sustainable approach to combat antimicrobial resistance

Authors: Ibrahim, Nesreen A. A., Saeed, Humodi A., Saeed, Samar M. et al.

Dec 2025

Background Antimicrobial resistance (AMR) is a critical global health challenge, particularly in Sudan, where the overuse and misuse of antibiotics have driven the rise of multidrug-resistant (MDR) pathogens. Conventional antimicrobial strategies often fall short due to rapid resistance development and limited efficacy, highlighting the need for novel approaches. Nanotechnology offers promising alternatives, with silver nanoparticles (AgNPs) demonstrating potent broad-spectrum antimicrobial activity. This study aims to develop an eco-friendly synthesis of AgNPs using Candida parapsilosis (C. parapsilosis), an untapped yeast strain isolated from Sudanese soil, to combat AMR. Results Biosynthesis of AgNPs using C. parapsilosis was successfully confirmed through UV-Vis spectroscopy, X-ray diffraction (XRD), and high-resolution transmission electron microscopy (HRTEM), revealing well-defined nanoparticles. The biosynthesized AgNPs exhibited strong antibacterial activity against both ATCC reference strains and MDR clinical isolates of Gram-positive and Gram-negative bacteria, with inhibition zones increasing in a concentration-dependent manner. At optimal concentrations, inhibition zones reached 29 mm for Pseudomonas aeruginosa (P.aeruginosa) (ATCC 27853), while clinical isolates of Salmonella typhi (S. typhi) (24.5 ± 0.58 mm) and Escherichia coli (E. coli) (23.8 ± 0.79 mm) exhibited significant susceptibility. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays demonstrated potent bactericidal activity, particularly against E. coli and Klebsiella pneumoniae (K. pneumoniae) at 0.3125 mg/mL. Furthermore, AgNPs synergistically enhanced the efficacy of conventional antibiotics in a species- and antibiotic-dependent manner. The strongest synergy was observed in Enterococcus faecalis (E. faecalis) (up to 9.84-fold with Colistin) and Acinetobacter baumannii (A. baumannii) (up to 5.11-fold with Ceftazidime), suggesting that AgNP-enhanced antibiotic efficacy varies depending on bacterial species, nanoparticle synthesis method, and antibiotic type. Conclusions This study presents a novel and sustainable approach to tackling AMR by leveraging Sudanese yeast strains for the green synthesis of AgNPs. The findings underscore the potential of AgNPs as an effective antibacterial agent, both independently and in combination with conventional antibiotics, to combat MDR pathogens. By integrating microbiology and nanotechnology, this research offers a cost-effective and environmentally friendly

The impact of mutations on TP53 protein and MicroRNA expression in HNSCC: Novel insights for diagnostic and therapeutic strategies

Authors: Mahmoud, Ashraf Attia, Raih, Mohd Firdaus, Sage, Edison Eukun et al.

Dec 2025

The tumor suppressor protein p53 (TP53) is frequently mutated in various types of human malignancies, including HNSCC, which affects tumor growth, prognosis, and treatment. Gaining insight into the impact of TP53 mutations in HNSCC is crucial for developing new diagnostic and therapeutic methods. In this study, we aimed to investi gate the influence of mutations on the structure and functions of the TP53 protein and miRNA expression using computational analysis. The genomic data of patients with HNSCC were obtained from TCGA, and the impact of mutations on the TP53 gene was investigated using different bioinformatics tools. Results: The findings showed that the TP53 mutations increased TP53 expression levels in HNSCC and were associated with a poor prognosis. Furthermore, hsa-mir-133b expression was reduced in TP53- mutated samples, significantly affecting patient survival in HNSCC. Six mutations, including R273C, G105C, G266E, Q136H/P, and R280G, were identified as delete rious, carcinogenic, driver, highly conserved, and exposed. These mutations were located in the P53 domain, and PTM analysis revealed that R280G and R273C are at a methylation site, and R273C, Q136H/P, and R280G are located in the protein pocket. The docking research indicated that these mutations decreased the binding affinity for DNA, with R273C, R280G, G266E, and G105C displaying the most significant differ ences. The molecular dynamics analysis indicates that R280G, Q136H, and G105C mutations confer a gain of function by stabilizing the TP53-substrate complex. Conclu sions: Based on the research findings, the mutations on TP53 were found to have an impact on protein and miRNA expression, development, survival, and progression of HNSCC patients, and has-mir-133b could be a promising novel biomarker for mon itoring the progression of HNSCC. It was discovered that G105C and Q136H/P, as novel mutations, affect the function and structure of proteins causing HNSCC, which indicates that they could be interesting subjects for further investigation, diagnostics, and therapeutic strategies. Furthermore, the precise positioning of R280G and R273C within the methylation site and Q136H/P in the binding site has been documented for the first time. Moreover, the G105C, Q136H, and R280G mutations that stabi lized TP53 structure and altered its interaction dynamics with substrates may serve as novel potential diagnostic biomarkers in cancer, guiding patient stratification and personalized treatment strategies. The molecular dynamics analysis provides insights into how specific TP53 mutations impact protein structure, stability, and function upon substrate binding, highlighting their role in cancer biology and potential implications for therapeutic interventions. This paper provides a novel understanding of the mecha nisms by which these mutations contribute to the development of cancer.