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Yousif B Hamadalneel,1 Hifa O Ahmed,1 Marwa F Alamin,2 Walaa M Almahy,3 Zainab M Almustafa,3 Yousif M Yousif,3 Mohammed A Taha4 1Department of Clinical Pharmacy & Pharmacy Practice, Faculty of Pharmacy, University of Gezira, Wad Medani, Sudan; 2Department of Molecular Biology, Institute of Endemic Disease, Khartoum University, Khartoum, Sudan; 3Clinical Pharmacy & Pharmacy Practice, Pharmacy Program, Wad Medani College for Science and Technology, Wad Medani, Gezira State, Sudan; 4Pathology Center for Diagnosis and Research, Faculty of Medicine, University of Gezira, Wad Medani, SudanCorrespondence: Yousif B Hamadalneel, Department of Clinical Pharmacy & Pharmacy Practice, Faculty of Pharmacy, University of Gezira, Wad Medani, Sudan, Tel +249918026087, Email Yousefbekhet2020@gmail.comPurpose: Urinary tract infections exert a significant negative impact on an individual’s quality of life and cause significant economic and public health burdens. Therefore, this study was conducted to identify the common bacterial uropathogens associated with urinary tract infections in Wad Medani patients and their susceptibility to antibiotics.Patients and Methods: This was a cross-sectional study. All urine samples were collected from patients at Wad Medani and investigated at the Pathology Center for Diagnosis and Research, Faculty of Medicine, University of Gezira, Sudan, from the 1st of January 2021 to the 15th of October 2023.Results: A total of 2698 urine samples were analyzed during the three years study period, with a mean age of 45.29 ± 18.9 years. Among these patients, 1108 (41.8%) were positive for bacterial growth, and 888 (80.14%) were female. A total of 522 (47.1%) were gram positive bacteria (GPB), and 586 (52.9%) were gram negative bacteria (GNB). The most frequently isolated bacteria were S. aureus 42% (465/1108) and E. coli 38.5% (427/1108), while P. aeruginosa was less detected 3.4% (38/1108). Amikacin 91.5% was the most sensitive drug to isolated GPB, while cotrimoxazole 20.9% was the least sensitive drug. In particular, amikacin 94.1% (144/153) was the most sensitive drug to S. aureus, while cotrimoxazole 20.7% (80/386) was the least sensitive drug. Moreover, amikacin 91.5% was the most sensitive drug to the isolated GNB, while ampicillin 5.7% was the least sensitive drug. Notably, amikacin was the most sensitive drug to all the isolated GNB, and ampicillin was the least sensitive drug to all the isolated GNB.Conclusion: This study reported a moderate uropathogen isolation rate of 41.8%. S. aureus and E. coli were the most frequently isolated bacteria, most of which were from female patients. Remarkably, amikacin was the most sensitive drug to isolated GNB and GPB.Keywords: prevalence, antimicrobial, sensitivity patterns, uropathogens, Wad Medani, Sudan

Purpose: To evaluate the diagnosis and management of bacterial meningitis in adult Sudanese patients in accordance with the Infectious Diseases Society of America (IDSA) guidelines for bacterial meningitis management., Patients and Methods: A cross-sectional, retrospective study design was used to recruit all patients aged > 18 years who were diagnosed with or suspected of having bacterial meningitis and admitted to Wad Medani Teaching Hospital, Gezira State, Sudan, between January 2017 and October 2022., Results: In total, 201 patients were included in the analysis. The mean age of the participants was 44.1 ± 21.4 years, and 107 (53.2%) were male. Community-acquired bacterial meningitis accounted for 193 (96%) of the studied patients, and only 8 (4%) of the patients had healthcare-associated meningitis. Neuroimaging was utilized appropriately in 148 (73.6%) patients, blood cultures were not performed entirely, and lumbar puncture was seldom performed in 1 (0.5%) patient. Corticosteroids were appropriately administered to 65 (32.3%) patients, and antibiotics were administered appropriately to only 5 (2.5%) patients. Ceftriaxone 185 (76.1%) was the most frequently utilized antibiotic, followed by vancomycin 23 (9.5%). In terms of overall adherence, this study demonstrated that the IDSA guidelines were not followed at all in the treatment of patients with suspected bacterial meningitis., Conclusion: The results of this study contradict the IDSA guidelines for the standard of care for bacterial meningitis. Antibiotic regimens are often incorrect, corticosteroids are administered appropriately in approximately one-third of patients, and neuroimaging is reasonably utilized. This study raises attention to several important issues regarding the diagnosis of bacterial meningitis, including the lack of confirming microbiological tests and the reliance of the diagnosis primarily on CT and clinical examination., (© 2024. The Author(s).)

Introduction: Bone marrow kinase, or BMX, is alternatively referred to as endothelial tyrosine kinase (Etk). It plays a vital role in the processes of cell proliferation, survival, immune activation, and the modulation of diverse signaling pathways. Since there are few direct comprehensive studies linking BMX role with multiple cancers, this study aimed to utilize bioinformatic tools to conduct a comprehensive analysis of BMX across multiple cancers, assessing its potential role., Methods: Multiple databases including the Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), and University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN), have been used to explore BMX expression across different cancers, which has been further validated by using Gene Expression Omnibus (GEO) public datasets. In addition, we used the Kaplan-Meier plotter to estimate overall survival and cBioPortal for genetic alterations analysis. This study accommodates several other analyses like clinical parameters, immune cell infiltration, and DNA promoter methylation profiles to evaluate the general role of BMX in several cancers.  Results: The present investigation revealed that the BMX gene expression was significantly downregulated and could serve as an effective diagnostic biomarker in five types of cancers, namely breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), and rectum adenocarcinoma (READ) (all p < 0.05). Detailed analyses revealed notable downregulation of BMX in various clinical parameters such as age, gender, race, and cancer stage (all p < 0.05). To better understand the immunotherapeutic role of BMX, this investigation further examined the immune infiltration which exhibited positive correlations between BMX expression and the infiltration of immunological cells such as B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells, especially in COAD, LUAD, and LUSC (all p < 0.05). In addition, the present study has demonstrated that diminished BMX gene expression is correlated with an unfavorable prognosis in kidney renal clear cell carcinoma (KIRC), liver hepatocellular carcinoma (LIHC), sarcoma (SARC), and uterine corpus endometrial carcinoma (UCEC); thus BMX gene expression can be used as a prognostic target for these specific cancers. Also, the results showed that the promoter methylation level of BMX was significantly elevated in LUAD and LUSC, whereas it was significantly decreased in BRCA (all p < 0.001). Importantly, our findings of significantly low BMX expression in LUAD and LUSC, along with their methylation profiles suggest that the low expression of BMX across these cancers is due to epigenetic factors. However, genetic alteration analysis revealed that mutations existed in only approximately 2% of the TCGA samples., Conclusion: Our study revealed BMX as a diagnostic biomarker in BRCA, COAD, LUAD, LUSC, and READ and a prognostic biomarker in KIRC, LIHC, SARC, and UCEC. Furthermore, epigenetic variables may have a greater impact on BMX expression levels especially in LUAD and LUSC. This study also emphasized the role of BMX in the infiltration of immune cells, such as B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells, in certain cancers. The BMX expression level highlights the prognostic value and potential therapeutic potential of BMX., Competing Interests: Human subjects: Consent was obtained or waived by all participants in this study. Animal subjects: All authors have confirmed that this study did not involve animal subjects or tissue. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Khalafallah et al.)

Background: Embryonic stem cell-related gene (ESRG; also known as HESRG) is a long non-coding RNA (lncRNA). It is involved in the regulation of human pluripotent stem cells (hPSCs) self-renewal. ESRG gene has the ability to interact with chromatins, different RNA types, and RNA binding proteins (RBP); thus making ESRG be considered an oncogenic lncRNA, where its expression is detected in various tumor tissues. This study aimed to evaluate the prospective diagnostic and prognostic values of ESRG in various human cancers., Materials and Methods: The expression of ESRG in various cancers was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA), Tumor Immune Estimation Resource (TIMER), and University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN) databases. Moreover, the correlation between the expression of ESRG and clinical pathological parameters was analyzed using UALCAN. The effect of ESRG expression on the survival outcome was evaluated using Kaplan-Meier plotter, UALCAN, GEPIA, and TIMER. The correlation between ESRG expression and immune cell infiltration was studied by TIMER. Additionally, the genetic alterations were investigated cBioportal. Our findings were validated using the GEO2R database., Results: Our results showed ESRG to be significantly up-regulated in colon adenocarcinoma (COAD) and lung squamous cell carcinoma (LUSC) with p<0.001, in addition to rectum adenocarcinoma (READ), and uterine carcinosarcoma (UCEC) with p<0.01. Regarding pathogenic stages, there was a significant upregulation in stages 2, 3, and 4 compared to normal in COAD and stages 1, 2, and 3 for LUSC patients. The combined prognostic analysis showed that the up-regulated expression of ESRG was associated with better survival outcomes in patients with brain lower-grade glioma (LGG). Our results demonstrate a significant negative correlation between ESRG expression and the abundance of CD8+T cells in COAD, READ, LUSC, and UCEC. Additionally, ESRG was mutated in 0.77 (<1%) of the queried samples, and the most prevalent ESRG mutations are deep deletion mutations, followed by amplification., Conclusion: Analysis of ESRG across various cancer types elucidated its potential to be used as a diagnostic biomarker in COAD, LUSC, READ, and UCEC and a promising prognostic biomarker in LGG. Our findings provide useful insights for future research., Competing Interests: Human subjects: All authors have confirmed that this study did not involve human participants or tissue. Animal subjects: All authors have confirmed that this study did not involve animal subjects or tissue. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Fageer et al.)

Introduction In sub-Saharan Africa, including Sudan, there is commonly no local data on the bacterial profile or antibiotic resistance pattern. Therefore, to bridge these gaps, this study aimed to evaluate ceftriaxone resistance patterns and associated risk factors among different clinical samples. Methods This study was a laboratory-based, retrospective, cross-sectional study. All clinical specimens were obtained from patients at Wad Medani and examined at the Pathology Center for Diagnosis and Research, Faculty of Medicine, University of Gezira, Sudan, from January 2020 to October 2023. Results Overall, 1784 specimens exhibited bacterial growth over four years. Of these, 1260 (70.6%) were females. Approximately one-third of the 588 (33%) studied patients were aged 30 to 44 years. Of the studied samples, 1108 (62.1%) were urine, and 465 (26.1%) were wound swabs. Staphylococcus aureus  (697, 39.1%) and Escherichia coli  (656, 36.8%) were the most frequently encountered bacteria. Generally, ceftriaxone resistance has been evaluated in 150 positive culture samples. The overall ceftriaxone resistance rate was 106 (70.7%). The greatest proportion of ceftriaxone resistance was observed in 4/4 (100%) of Klebsiella spp. and 66/82 (80.5%) of E. coli strains. The type of isolate (95% Cl, p-value ; 0.006) and type of bacterial stain (95% Cl, p-value  0.013) have been significantly associated with ceftriaxone resistance, in which Gram-negative bacteria had a greater resistance rate of 98/132 (74.2%) than Gram-positive bacteria 8/18 (44.4%). Conclusions This study revealed a high rate of ceftriaxone resistance. The most resistant bacteria were Klebsiella spp. and E. coli . The type of isolate and bacterial stain were significantly associated with ceftriaxone resistance. Therefore, hospitals should immediately and significantly modify their antibiotic prescription policy to give doctors a consistent strategy for the rational, safe, and effective administration of antibiotics., Competing Interests: Human subjects: Consent was obtained or waived by all participants in this study. Ethical Committee, Ministry of Health, Gezira State, Sudan issued approval 12/6/2023. Animal subjects: All authors have confirmed that this study did not involve animal subjects or tissue. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Hamadalneel et al.)

Pathogens including viruses evolve in tandem with diversity in their animal and human hosts. For SARS-coV2 , the focus is generally for understanding such coevolution on the virus spike protein, since it demonstrates high mutation rates compared to other genome regions, particularly in the receptor-binding domain (RBD). Viral sequences of the SARS-coV2 19B (S) clade and variants of concern from different continents were investigated, with a focus on the A.29 lineage, which presented with different mutational patterns within the 19B (S) lineages in order to learn more about how SARS-coV2 may have evolved and adapted to widely diverse populations globally. Results indicated that SARS-coV2 went through evolutionary constrains and intense selective pressure, particularly in Africa. This was manifested in a departure from neutrality with excess nonsynonymous mutations and a negative Tajima D consistent with rapid expansion and directional selection as well as deletion and deletion-frameshifts in the N-terminal domain (NTD region) of the spike protein. In conclusion, we hypothesize that viral transmission during epidemics through populations of diverse genomic structures and marked complexity may be a significant factor for the virus to acquire distinct patterns of mutations within these populations in order to ensure its survival and fitness, explaining the emergence of novel variants and strains.