Pseudomonas aeruginosa infection is difficult to treat due to the presence of antibiotic resistance determinants. Here, we report the genome sequence of a multidrug-resistant P. aeruginosa strain isolated from a patient with a urinary tract infection in 2015.

Recently, Coronavirus has been given considerable attention from the biomedical community based on the emergence and isolation of a deadly coronavirus infecting human. To understand the behavior of the newly emerging MERS-CoV requires knowledge at different levels (epidemiologic, antigenic, and pathogenic), and this knowledge can be generated from the most related viruses. In this study, we aimed to compare between 3 species of Coronavirus, namely Middle East Respiratory Syndrome (MERS-CoV), Severe Acute Respiratory Syndrome (SARS-CoV), and NeoCoV regarding whole genomes and 6 similar proteins (E, M, N, S, ORF1a, and ORF1ab) using different bioinformatics tools to provide a better understanding of the relationship between the 3 viruses at the nucleotide and amino acids levels. All sequences have been retrieved from National Center for Biotechnology Information (NCBI). Regards to target genomes’ phylogenetic analysis showed that MERS and SARS-CoVs were closer to each other compared with NeoCoV, and the last has the longest relative time. We found that all phylogenetic methods in addition to all parameters (physical and chemical properties of amino acids such as the number of amino acid, molecular weight, atomic composition, theoretical pI, and structural formula) indicated that NeoCoV proteins were the most related to MERS-CoV one. All phylogenetic trees (by both maximum-likelihood and neighbor-joining methods) indicated that NeoCoV proteins have less evolutionary changes except for ORF1a by just maximum-likelihood method. Our results indicated high similarity between viral structural proteins which are responsible for viral infectivity; therefore, we expect that NeoCoV sooner may appear in human-related infection.

Background: Candida species are one of the most important opportunistic fungal pathogens that cause both superficial and systemic infections, especially in immunocompromised individuals. Considering the sharp increase in the rate of Candida infections, and resistance to commonly used antifungal agents in the last decades; this study was conducted to determine the rate of resistance among clinical isolates of Candida species, and to characterize some of the resistant genes among resistant isolates collected in Khartoum.  Methods: This is a cross-sectional laboratory-based study included 100 pre-screened Candida species isolates from Khartoum state hospitals. Chromogenic media was used for Candida isolation and/or identification. The standard disc diffusion method was performed to investigate the susceptibility to fluconazole, itraconazole, and amphotericin. Following genomic DNA extraction, the entire ERG11 gene was amplified from some C. albicans resistant isolates, sequenced, and further analyzed. Results: Out of 100 clinical isolates collected, 51% were C. albicans, followed by C. glabrata (31%), C. krusie (8%), C. tropicals (5%), and C. dupliniens (5%). Resistance rate was 23% for fluconazole, 4% for itraconazole, while there were no amphotericin resistant isolates detected. C. albicans ERG11 gene sequence reveals 15 different mutations. Among these, three (D116E, E266D, and V488I) were missense mutations; however, these substitutions do not contribute to fluconazole resistance. Conclusion: C. albicans was found to be the most common species. Resistance against fluconazole was observed most frequently; however, mutations in ERG11 are unlikely to be the reason behind fluconazole resistance among these isolates.

Background: Self-medication with antibiotics (SMA) is one of the common factors which precipitate antimicrobial resistance, yet if effective implementations are amended it can be effortlessly controlled. The present study aimed to estimate the prevalence and predictors of SMA in Sudan. Methods: The study adopted a cross-sectional study design conducted in all Sudan states between June and December 2021. Multi-stage stratified cluster sampling was used. A semi-structured questionnaire was used for data collection. Descriptive statistics were used to present the data. Binary logistic regression was computed to investigate the possible factors which associated with SMA. Results: Out of 1492 participants surveyed, 71.3% utilize antibiotics as self-medication. The derived reasons for SMA were convenience (63.3%) and cost-saving (34.8%). Tonsillitis was the most common ailment behind SMA (55.5%). Log-binominal regression revealed that non-insured and low level of education participants were more likely to predict SMA. Regarding the practice, 40% changed the dose and/or antibiotics mainly owing to improvement (53.7%) or worsening of the condition (37.9%). The most commonly used antibiotic was amoxicillin/clavulanic acid (32.5%). Conclusions: Two out of three individuals in Sudan practice SMA mainly to manage upper respiratory tract ailments. Thus, the necessity of implementing an antimicrobial stewardship program throughout the country, as well as implementing effective legislation to prohibit dispensing antibiotics without prescription is urgently required.

Renal transplantation provides the best long-term treatment for chronic renal failure. Singlenucleotide polymorphisms (SNPs) play a major role in the understanding of the genetic basis of many complex human diseases. Also, the genetics of human phenotype variation could be understood by knowing the functions of these SNPs. It is still a major challenge to identify the functional SNPs in a disease-related gene. This work explored how SNPs mutations in HLA-DRB1 gene could affect renal transplantation rejection. This study was carried out in Ahmed Gasim Hospital, Renal Dialysis Center during the period, from September 2012 to November 2013. Blood samples from five Sudanese patients (different families) with known renal transplantation rejection were collected before hemodialysis, furthermore one blood sample for control. DNA sequences results and detected SNPs were analyzed using bioinformatics tools (BLAST, SIFT, nsSNP Analyzer, PolyPhen, I-mutant, BioEdit, CPH, Chimera, Box shade and Project Hope). In addition, international databases were used for datasets [NCBI, Uniprot]. Results showed that, three SNPs were detected; two of three SNPs were predicted as tolerant or benign (rs1059575, novel) and one was deleterious (rs17885437). This study concluded that the identification of pathological SNPs could be an answer to unknown causes for a lot of organ transplantation rejection cases. * Corresponding author. M. M. Hassan et al. 223

Introduction: Vulvovaginal candidiasis (VVC) is a yeast infection of the vulva, which is caused by Candida species and affects women worldwide. Pregnant women are more vulnerable to VVC due to certain risks. Moreover, their offspring are also exposed to the risk of preterm birth. In this context, ascertaining the burden of VVC is of paramount importance and this meta-analysis was conducted to estimate the occurrence of VVC among pregnant women in Africa. Methodology: Database search was carried out through PubMed, Scopus, Science-Direct, and Google Scholar from the date of inception until December 2020. All the studies on the prevalence of VVC among African pregnant women were included in the analysis. The pooled prevalence was estimated based on the Random-effect model DerSimonian-Laird approach with Freeman- Tukey double arcsine transformed proportion. Heterogeneity was assessed using I2 test and subsequently explored using subgroup and meta-regression analysis. Results: A total of Sixteen records having a sample size 4,185 were included in this study. The overall prevalence of VVC was pooled at 29.2% (CI 95%: 23.4 – 33.0). Subgroup analysis revealed a higher prevalence in Eastern Africa, followed by Western Africa and North Africa (35%, 28%, and 15% respectively). Moderator analysis indicated that the studies that used advanced methods of detection had a higher prevalence (p = 0.048). In addition, the large sample size was associated with higher prevalence (p ≤ 0.001). No other moderators were found to be statistically significant. Conclusions: The overall prevalence of VVC among African pregnant women is comparable to other studies worldwide. However, appropriate identification techniques and larger sample size could likely be associated with an increased prevalence. Our findings necessitate the need for further investigations to determine the geographical distribution of VVC across African regions.

Background Dispensing antibiotics without prescription (DAwP) is a widespread practice, especially in developing countries, contributing to antibiotic resistance. Community pharmacists play a significant role in promoting rational use of antibiotics by refraining from DAwP, and providing drug information to patients. This study aimed to evaluate community pharmacists’ knowledge, attitude and practice, and to assess the factors behind DAwP. Methods A cross-sectional study was conducted in 2020 among random sample of community pharmacists in Sudan. Online semi-structured questionnaire was used for data collection. The association between dependent and independent variables was assessed using Chi-square test; a P -value less than 0.05 was considered significant. Results Of the 1217 pharmacists who participated, the majority were female (n = 645, 53%). Most pharmacists have a B. Pharm degree (n = 1026, 84%) and less than 5 years’ experience (n = 718, 59%). Notably, the majority of community pharmacists have good knowledge (n = 735, 61.7%), which is significantly associated with years of experience (P < 0.00). More than half (n = 623, 52.2%) of the pharmacists have above average score of practice. Nearly all the pharmacists who participated have a positive attitude in relation to DAwP (n = 1204, 98.9%). More than half of the pharmacists were DAwP for tonsillitis (n = 817, 67%), wound infection (n = 766, 62.9%), and urinary tract infection (n = 664, 54%). The leading factor behind DAwP was the low socioeconomic status of the patients (n = 624, 51%). Additionally, 47% of the pharmacists (n = 572) thought that they were knowledgeable enough to DAwP. Conclusion Despite their positive attitude and average level of knowledge regarding DAwP, Sudanese community pharmacists frequently are DAwP for tonsillitis. Low patients’ socioeconomic status was the leading factor behind DAwP. Accordingly, extensive work from health authorities to improve the accessibility and affordability of the health system as well as the development of an antibiotic stewardship program are required to diminish DAwP.

The HLA-DRB1 gene encodes a protein that is essential for the immune system. This gene is important in organ transplant rejection and acceptance, as well as multiple sclerosis, systemic lupus erythematosus, Addison’s disease, rheumatoid arthritis, caries susceptibility, and Aspirin-exacerbated respiratory disease. The following Homo sapiens variants were investigated: single-nucleotide variants (SNVs), multi-nucleotide variants (MNVs), and small insertions–deletions (Indels) in the HLA-DRB1 gene via coding and untranslated regions. The current study sought to identify functional variants that could affect gene expression and protein product function/structure. ALL target variants available until April 14, 2022, were obtained from the Single Nucleotide Polymorphism database (dbSNP). Out of all the variants in the coding region, 91 nsSNVs were considered highly deleterious by seven prediction tools and instability index; 25 of them are evolutionary conserved and located in domain regions. Furthermore, 31 indels were predicted as harmful, potentially affecting a few amino acids or even the entire protein. Last, within the coding sequence (CDS), 23 stop-gain variants (SNVs/indels) were predicted as high impact. High impact refers to the assumption that the variant will have a significant (disruptive) effect on the protein, likely leading to protein truncation or loss of function. For untranslated regions, functional 55 single-nucleotide polymorphisms (SNPs), and 16 indels located within microRNA binding sites, furthermore, 10 functionally verified SNPs were predicted at transcription factor-binding sites. The findings demonstrate that employing in silico methods in biomedical research is extremely successful and has a major influence on the capacity to identify the source of genetic variation in diverse disorders. In conclusion, these previously functional identified variants could lead to gene alteration, which may directly or indirectly contribute to the occurrence of many diseases. The study’s results could be an important guide in the research of potential diagnostic and therapeutic interventions that require experimental mutational validation and large-scale clinical trials.