The impact of immunosuppression on the mortality and hospitalization of Monkeypox: a systematic review and meta-analysis of the 2022 outbreak.

BACKGROUND: Limited data is available regarding the severity and mortality of Mpox in individuals with immunocompromised conditions. Therefore, we performed this meta-analysis to understand the impact of HIV- or non-HIV-associated immunosuppression on the severity of Mpox requiring hospitalization and mortality. METHODS: A thorough literature search was performed from 2022 up to January 2024. The results were presented as odds ratios (ORs). We only included patients who required hospitalization for severity rather than isolation. RESULTS: A total of 34 studies were included in this analysis. Our analysis did not find a significant difference in the hospitalization risk between HIV-positive individuals and those who were HIV-negative (OR = 1.03; P = 0.85; 7 studies; CD4 count of fewer than 200 cells/µL was less than 0.5% across all studies). Patients with a CD4 count lower than 200 cells/µL or an unsuppressed RNA viral load (> 200 copies/ml) had a significantly higher hospitalization risk (OR = 5.3, P < 0.001) and (OR = 3, P < 0.001), respectively. Most of the reported deaths were reported in patients with HIV with CD4 counts below 200 cells/µL, with some fatal cases occurring in non-HIV immunosuppressed patients, particularly organ transplant recipients. Based on the autopsy findings, Mpox was confirmed in multiple organs, particularly the digestive tract, lung, and testes. Furthermore, some studies documented cases of death that were suspected to be related to hemophagocytic lymphohistiocytosis (HLH) and immune reconstitution inflammatory syndrome (IRIS). Most of the death reports showed concomitant non-Mpox infections at the time of hospitalization and death CONCLUSIONS: Our finding shows that Mpox acts as an opportunistic pathogen in immunocompromised individuals. These individuals should be prioritized for early care and closely monitored for signs of deteriorating clinical conditions. Clinical manifestations and autopsy findings strongly suggest Mpox dissemination to multiple organs, particularly the digestive tract, and lungs. However, the presence of concomitant non-Mpox infections complicates the assessment of the attribution of Mpox to death. Caution should be exercised when interpreting data suggesting poorer outcomes in individuals with non-HIV immunosuppression, as current evidence is scarce and further research is needed.

The burden of persistent symptoms after COVID-19 (long COVID): a meta-analysis of controlled studies in children and adults.

BACKGROUND: Previous meta-analyses estimating the prevalence of the post-COVID-19 condition (PCC) were confounded by the lack of negative control groups. This may result in an overestimation of the prevalence of those experiencing PCC, as these symptoms are non-specific and common in the general population. In this study, we aimed to compare the burden of persistent symptoms among COVID-19 survivors relative to COVID-19-negative controls. METHODS: A systematic literature search was conducted using the following databases (PubMed, Web of Science, and Scopus) until July 2023 for comparative studies that examined the prevalence of persistent symptoms in COVID-19 survivors. Given that many of the symptoms among COVID-19 survivors overlap with post-hospitalization syndrome and post-intensive care syndrome, we included studies that compare the prevalence of persistent symptoms in hospitalized COVID-19 patients relative to non-COVID-19 hospitalized patients and in non-hospitalized COVID-19 patients relative to healthy controls that reported outcomes after at least 3 months since infection. The results of the meta-analysis were reported as odds ratios with a 95% confidence interval based on the random effects model. RESULTS: Twenty articles were included in this study. Our analysis of symptomatology in non-hospitalized COVID-19 patients compared to negative controls revealed that the majority of symptoms examined were not related to COVID-19 infection and appeared equally prevalent in both cohorts. However, non-COVID-19 hospitalized patients had higher odds of occurrence of certain symptoms like anosmia, ageusia, fatigue, dyspnea, and brain fog (P < 0.05). Particularly, anosmia and ageusia showed substantially elevated odds relative to the negative control group at 11.27 and 9.76, respectively, P < 0.05. In contrast, analysis of hospitalized COVID-19 patients compared to those hospitalized for other indications did not demonstrate significantly higher odds for the tested symptoms. CONCLUSIONS: The persistent symptoms in COVID-19 survivors may result from hospitalization for causes unrelated to COVID-19 and are commonly reported among the general population. Although certain symptoms exhibited higher odds in non-hospitalized COVID-19 patients relative to controls, these symptoms are common post-viral illnesses. Therefore, the persistent symptoms after COVID-19 may not be unique to SARS-CoV-2. Future studies including well-matched control groups when investigating persistent symptoms in COVID-19 survivors are warranted to draw a firm conclusion.

The innovation of AI-based software in oral diseases: clinical-histopathological correlation diagnostic accuracy primary study.

BACKGROUND: Machine learning (ML) through artificial intelligence (AI) could provide clinicians and oral pathologists to advance diagnostic problems in the field of potentially malignant lesions, oral cancer, periodontal diseases, salivary gland disease, oral infections, immune-mediated disease, and others. AI can detect micro-features beyond human eyes and provide solution in critical diagnostic cases. OBJECTIVE: The objective of this study was developing a software with all needed feeding data to act as AI-based program to diagnose oral diseases. So our research question was: Can we develop a Computer-Aided Software for accurate diagnosis of oral diseases based on clinical and histopathological data inputs? METHOD: The study sample included clinical images, patient symptoms, radiographic images, histopathological images and texts for the oral diseases of interest in the current study (premalignant lesions, oral cancer, salivary gland neoplasms, immune mediated oral mucosal lesions, oral reactive lesions) total oral diseases enrolled in this study was 28 diseases retrieved from the archives of oral maxillofacial pathology department. Total 11,200 texts and 3000 images (2800 images were used for training data to the program and 100 images were used as test data to the program and 100 cases for calculating accuracy, sensitivity& specificity). RESULTS: The correct diagnosis rates for group 1 (software users), group 2 (microscopic users) and group 3 (hybrid) were 87%, 90.6, 95% respectively. The reliability for inter-observer value was done by calculating Cronbach's alpha and interclass correlation coefficient. The test revealed for group 1, 2 and 3 the following values respectively 0.934, 0.712 & 0.703. All groups showed acceptable reliability especially for Diagnosis Oral Diseases Software (DODS) that revealed higher reliability value than other groups. However, The accuracy, sensitivity & specificity of this software was lower than those of oral pathologists (master's degree). CONCLUSION: The correct diagnosis rate of DODS was comparable to oral pathologists using standard microscopic examination. The DODS program could be utilized as diagnostic guidance tool with high reliability & accuracy.

Epidemiology of clinically isolated methicillin-resistant Staphylococcus aureus (MRSA) and its susceptibility to linezolid and vancomycin in Egypt: a systematic review with meta-analysis.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen that causes severe morbidity and mortality worldwide. For the establishment of national strategies to combat MRSA infection in each country, accurate and current statistics characterizing the epidemiology of MRSA are essential. The purpose of this study was to determine the prevalence of MRSA among Staphylococcus aureus clinical isolates in Egypt. In addition, we aimed to compare different diagnostic methods for MRSA and determine the pooled resistance rate of linezolid and vancomycin to MRSA. To address this knowledge gap, we conducted a systematic review with meta-analysis. METHODS: A comprehensive literature search from inception to October 2022 of the following databases was performed: MEDLINE [PubMed], Scopus, Google Scholar, and Web of Science. The review was conducted following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) Statement. Based on the random effects model, results were reported as proportions with a 95% confidence interval (CI). Analyses of the subgroups were conducted. A sensitivity analysis was conducted to test the robustness of the results. RESULTS: A total of sixty-four (64) studies were included in the present meta-analysis, with a total sample size of 7171 subjects. The overall prevalence of MRSA was 63% [95% CI: 55-70]. Fifteen (15) studies used both PCR and cefoxitin disc diffusion for MRSA detection, with a pooled prevalence rate of 67% [95% CI: 54-79] and 67% [95% CI: 55-80], respectively. While nine (9) studies used both PCR and Oxacillin disc diffusion for MRSA detection, the pooled prevalences were 60% [95% CI: 45-75] and 64% [95% CI: 43-84], respectively. Furthermore, MRSA appeared to be less resistant to linezolid than vancomycin, with a pooled resistance rate of 5% [95% CI: 2-8] to linezolid and 9% [95% CI: 6-12] to vancomycin, respectively. CONCLUSION: Our review highlights Egypt's high MRSA prevalence. The cefoxitin disc diffusion test results were found to be consistent with PCR identification of the mecA gene. A prohibition on antibiotic self-medication and efforts to educate healthcare workers and patients about the proper use of antimicrobials may be required to prevent further increases.

Seroprevalence of hepatitis B virus surface antigen (HBsAg) in Egypt (2000-2022): a systematic review with meta-analysis.

BACKGROUND: Hepatitis B infection seriously threatens global public health, especially in developing nations. Despite several investigations on HBV incidence, the national pooled prevalence remains unknown, particularly in populations at-risk at whom interventions should be primarily aimed. METHODS: A comprehensive literature search of the following databases: Medline [PubMed], Scopus, Google Scholar, and Web of Science was conducted following the PRISMA guidelines. I-squared and Cochran's Q were used to measure the heterogeneity between the studies. Publications that matched the following were included: Primary studies published in Egypt from 2000 to 2022 reported HBV prevalence based on HBsAg. We excluded any studies that were not performed on Egyptians or that were performed on patients suspected of acute viral hepatitis or studies focusing on occult hepatitis or vaccination evaluation studies, or national surveys. RESULTS: The systematic review included 68 eligible studies reporting a total of 82 incidences of HBV infection based on hepatitis B surface antigen with a total sample size of 862,037. The pooled national prevalence among studies was estimated to be 3.67% [95% CI; 3: 4.39]. Children under 20 with a history of HBV vaccination during infancy had the lowest prevalence of 0.69%. The pooled prevalence of HBV infection among pregnant women, blood donors, and healthcare workers was 2.95%, 1.8%, and 1.1%, respectively. While patients with hemolytic anemia and hemodialysis patients, patients with malignancies, HCC patients, and chronic liver disease patients had the highest prevalences at 6.34%, 25.5%, 18.6%, and 34%, respectively. Studies reporting HBV prevalence in urban settings compared to rural settings revealed a similar HBV prevalence of 2.43% and 2.15%, respectively. Studies comparing HBV prevalence in males and females revealed a higher prevalence among males (3.75%) than females (2.2%). CONCLUSION: In Egypt, hepatitis B infection is a significant public health issue. The blocking of mother-to-infant hepatitis B transmission, the scaling up of the scope of the existing vaccination program, and implementing new strategies, including screen-and-treat, may reduce the prevalence of the disease.

Prevalence of Vancomycin-resistant enterococci (VRE) in Egypt (2010-2022): a systematic review and meta-analysis.

BACKGROUND: Vancomycin-resistant Enterococci (VRE) represent a critical medical and public health concerns due to their association with serious nosocomial infections and a high risk of mortality. We aimed to reveal the pooled prevalence of VRE and antimicrobial resistance profiles among enterococci clinical isolates in Egypt. METHODS: A PubMed, Scopus, Google Scholar, and Web of Science literature search was carried out in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Only published studies documenting the prevalence of VRE between 2010 and 2022 were included. Using the random effects model and the 95% confidence intervals, the pooled estimate of VRE was calculated by MedCalc Version 20.113. Cochran's Q and I2 tests were used to evaluate the degree of heterogeneity, and publication bias was examined by visually examining the funnel plot and its associated tests (Begg's and Egger's tests). RESULTS: The pooled prevalence of VRE among enterococci clinical isolates in Egypt was estimated to be 26% (95% CI 16.9 to 36.3). E. faecalis had a greater pooled prevalence than E. faecium, with 61.22% (95% CI 53.65 to 68.53) and 32.47% (95% CI 27 to 38.2), respectively. The VanA gene is more frequent than the VanB gene among VRE, with a pooled prevalence of 63.3% (95% CI 52.1 to 73.7) and 17.95% (95% CI 7.8 to 31), respectively. The pooled resistance rate of linezolid was substantially lower than that of ampicillin and high-level gentamicin (HLG) 5.54% (95% CI 2.33 to 10%), 65.7% (95% CI 50.8 to 79.2%), and 61.1% (95% CI 47.4 to 73.9), respectively. CONCLUSION: The prevalence of VRE is alarmingly high in Egypt. It is imperative that antimicrobial stewardship activities and infection control programs are strictly adhered to and implemented to prevent further escalation of the problem.

Prevalence of occult hepatitis B virus infection in Egypt: a systematic review with meta-analysis.

BACKGROUND: Occult hepatitis B virus (HBV) infection (OBI) is a major public health problem. The clinical importance of OBI stems from the fact that it can be transmitted to healthy individuals at extremely low viral load levels. Additionally, immunosuppression has the potential to trigger viral replication, which can result in life-threatening liver decompensation. Despite several studies examining the prevalence of OBI, the pooled prevalence of OBI in Egypt remains unknown, particularly among blood donors and high-risk individuals, to whom intervention should be targeted. METHODS: A comprehensive literature search of the following databases was conducted from inception to October 2022 using the following keywords: occult hepatitis B virus infection or occult HBV infection or OBI and Egypt in MEDLINE [PubMed], Scopus, Google Scholar, and Web of Science. The review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement. I-squared and Cochran's Q were used to measure the heterogeneity between the studies, and based on the random effects model, results were reported as proportions (%) with a 95% confidence interval (CI). Analyses of subgroup analyses were conducted based on the target population. Sensitivity analyses were conducted using the leave-one-out approach to test the robustness of the results. RESULTS: A total of 50 studies with 62 estimations of OBI were included, 19 in patients who were HBsAg-negative and anti-HBc-positive and 43 in patients who were HBsAg-negative. The highest prevalence (41%) was among multi-transfused patients according to  studies that report occult hepatitis B virus prevalence in an HBsAg-negative population, while the pooled prevalence of OBI among patients on hemodialysis, patients with chronic hepatitis C infection, patients with hepatocellular carcinoma (HCC), and patients with liver cirrhosis was 17%, 10%, 24%, and 13%, respectively. On the other hand, among studies that report OBI prevalence in HBsAg-negative and anti-HBc-positive individuals, the pooled prevalence of OBI among blood donors, patients with chronic hepatitis C infection, and patients with HCC was 12%, 15%, and 31%, respectively. Also, the majority of studies examining the genetic background of OBI have found that genotype D is the most prevalent. CONCLUSION:  This study highlights the high prevalence in OBI among blood donors and high-risk populations in Egypt. The implementation of HBV nucleic acid amplification testing (NAT) may increase the safety of blood transfusions by excluding all HBV DNA-positive donations. However, the cost-effectiveness of these tests should be investigated.

Design and implementation of a hybrid MPI-CUDA model for the Smith-Waterman algorithm.

This paper provides a novel hybrid model for solving the multiple pair-wise sequence alignment problem combining message passing interface and CUDA, the parallel computing platform and programming model invented by NVIDIA. The proposed model targets homogeneous cluster nodes equipped with similar Graphical Processing Unit (GPU) cards. The model consists of the Master Node Dispatcher (MND) and the Worker GPU Nodes (WGN). The MND distributes the workload among the cluster working nodes and then aggregates the results. The WGN performs the multiple pair-wise sequence alignments using the Smith-Waterman algorithm. We also propose a modified implementation to the Smith-Waterman algorithm based on computing the alignment matrices row-wise. The experimental results demonstrate a considerable reduction in the running time by increasing the number of the working GPU nodes. The proposed model achieved a performance of about 12 Giga cell updates per second when we tested against the SWISS-PROT protein knowledge base running on four nodes.

A design of a parallel architecture for solving exact matching problem on DNA molecules.

This paper describes a parallel algorithm and its needed architecture for solving exact string matching problem on DNA molecules. The parallel algorithm is considered much more faster than sequential algorithms used to perform exact string matching; the whole matching process between a given string and a pattern is performed in only one clock cycle by activating a number of processing elements and grouping them into clusters that perform the comparison operation between the Pattern and the string simultaneously. A simple parallel architecture is also presented as the algorithms is performed using this parallel architecture. The system is considered a step towards a complete parallel processing architecture to solve computationally intensive applications of DNA.