Recombination-mediated dissemination of Methicillin-resistant S. aureus clonal complex 1 in the Egyptian health care settings.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a rapidly evolving pathogen that is frequently associated with outbreaks and sustained epidemics. This study investigated the population structure, resistome, virulome, and the correlation between antimicrobial resistance determinants with phenotypic resistance profiles of 36 representative hospital-acquired MRSA isolates recovered from hospital settings in Egypt. RESULTS: The community-acquired MRSA lineage, clonal complex 1 (CC1) was the most frequently detected clone, followed by three other globally disseminated clones, CC121, CC8, and CC22. Most isolates carried SCCmec type V and more than half of isolates demonstrated multi-drug resistant phenotypes. Resistance to linezolid, a last resort antibiotic for treating multidrug resistant MRSA, was observed in 11.11% of the isolates belonging to different genetic backgrounds. Virulome analysis indicated that most isolates harboured a large pool of virulence factors and toxins. Genes encoding aureolysin, gamma hemolysins, and serine proteases were the most frequently detected virulence encoding genes. CC1 was observed to have a high pool of AMR resistance determinants including cfr, qacA, and qacB genes, which are involved in linezolid and quaternary ammonium compounds resistance, as well as high content of virulence-related genes, including both of the PVL toxin genes. Molecular clock analysis revealed that CC1 had the greatest frequency of recombination (compared to mutation) among the four major clones, supporting the role of horizontal gene transfer in modulating AMR and hypervirulence in this clone. CONCLUSIONS: This pilot study provided evidence on the dissemination success of CA-MRSA clone CC1 among Egyptian hospitals. Co-detection of multiple AMR and virulence genes in this lineage pose a broad public health risk, with implications for successful treatment. The results of this study, together with other surveillance studies in Egypt, should be used to develop strategies for controlling MRSA infections in Egyptian health-care settings.

Comparative genotyping of SARS-CoV-2 among Egyptian patients: near-full length genomic sequences versus selected spike and nucleocapsid regions.

Several tools have been developed for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genotyping based on either whole genome or spike sequencing. We aimed to highlight the molecular epidemiological landscape of SARS-CoV-2 in Egypt since the start of the pandemic, to describe discrepancies between the 3 typing tools: Global Initiative on Sharing Avian Influenza Data (GISAID), Nextclade, and Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) and to assess the fitness of spike and nucleocapsid regions for lineage assignment compared to the whole genome. A total of 3935 sequences isolated from Egypt (March 2020-2023) were retrieved from the GISAID database. A subset of data (n = 1212) with high coverage whole genome was used for tool discrimination and agreement analyses. Among 1212 sequences, the highest discriminatory power was 0.895 for PANGOLIN, followed by GISAID (0.872) and Nextclade (0.866). There was a statistically significant difference (p = 0.0418) between lineages assigned via spike (30%) and nucleocapsid (46%) compared to their whole genome-assigned lineages. The first 3 pandemic waves were dominated by B.1, followed by C.36 and then C.36.3, while the fourth to sixth waves were dominated by the B.1.617.2, BA, and BA.5.2 lineages, respectively. Current shift in lineage typing to recombinant forms. The 3 typing tools showed comparable discrimination among SARS-CoV-2 lineages. The nucleocapsid region could be used for lineage assignment.

Genomics in Egypt: Current Status and Future Aspects.

Egypt is the third most densely inhabited African country. Due to the economic burden and healthcare costs of overpopulation, genomic and genetic testing is a huge challenge. However, in the era of precision medicine, Egypt is taking a shift in approach from "one-size-fits all" to more personalized healthcare via advancing the practice of medical genetics and genomics across the country. This shift necessitates concrete knowledge of the Egyptian genome and related diseases to direct effective preventive, diagnostic and counseling services of prevalent genetic diseases in Egypt. Understanding disease molecular mechanisms will enhance the capacity for personalized interventions. From this perspective, we highlight research efforts and available services for rare genetic diseases, communicable diseases including the coronavirus 2019 disease (COVID19), and cancer. The current state of genetic services in Egypt including availability and access to genetic services is described. Drivers for applying genomics in Egypt are illustrated with a SWOT analysis of the current genetic/genomic services. Barriers to genetic service development in Egypt, whether economic, geographic, cultural or educational are discussed as well. The sensitive topic of communicating genomic results and its ethical considerations is also tackled. To understand disease pathogenesis, much can be gained through the advancement and integration of genomic technologies via clinical applications and research efforts in Egypt. Three main pillars of multidisciplinary collaboration for advancing genomics in Egypt are envisaged: resources, infrastructure and training. Finally, we highlight the recent national plan to establish a genome center that will aim to prepare a map of the Egyptian human genome to discover and accurately determine the genetic characteristics of various diseases. The Reference Genome Project for Egyptians and Ancient Egyptians will initialize a new genomics era in Egypt. We propose a multidisciplinary governance system in Egypt to support genomic medicine research efforts and integrate into the healthcare system whilst ensuring ethical conduct of data.

Primary and secondary sludge treatment using ionizing radiation technology in Alexandria, Egypt.

Improving the treatment efficiency of sludge in Alexandria, Egypt, was studied to improve the primary and secondary sludge treatment efficiency, different doses ranging from 0.25 to 6 kGy of ionizing radiation were proposed and evaluated. The scope of This study is to assess the radiation-based treatment efficiency from physical, chemical, and biological perspectives and to compare between the conventional treatment method and the radiation-based treatment technology. To evaluate the performance of each treatment system, pH, oil and greases concentrations, total solid concentrations, BOD concentrations, COD concentrations, parasites, and microorganisms were assessed in the primary and secondary samples at different radiation doses (from 0.25 to 6 KGy), and in the conventionally treated samples. Irradiation by gamma radiation with a dose ranging from 0.25 to 6 kGy was efficient in reducing some of the physical contaminants. Oil & greases, Total Solids, BOD, COD concentrations were reduced significantly (p < 0.001) in a dose-dependent manner. Either primary or secondary sludge samples, total solid reduced significantly to about one-third of control concentration at six kGy. Six kGy able to reduce the BOD and COD concentrations in the primary sludge samples to that of the treated (after sludge dewatering) samples or less respectively and saved the secondary treatment stage. In primary and secondary sludge samples culture, E. coli, Staphylococcus aureus, and Vibrio spp were isolated as heavy growth on different culture media in the samples before radiation. After exposure to increasing doses of radiation, the number of isolated organisms decreased, however, the growth of Proteus, Acinetobacter, and vipro organisms was detected but in small numbers. No growth of any organism was noted at 5 kGy. On the other hand, in the secondary sludge samples, Proteus was isolated as heavy growth before radiation and After exposure to increasing doses of radiation, Moraxella spp. organisms were detected but in small numbers. By increasing the radiation doses, the free-living ciliates were decreased in the primary and secondary sludge samples. The free-living ciliates disappeared completely at 3 kGy. In the primary and secondary sludge samples, free-living ciliates reduction efficiency at 0.25 kGy was equivalent to the conventional treatment methods. So, we can conclude that radiation technology using Gamma rays at a dose higher than 5 kGy with a dose rate of 1.095 kGy/h is an effective technology for domestic and industrial waste sludge treatment from the environmental perspective and an experimental pilot plant study is required to optimize the cost of wastewater treatment through the use of irradiation technology.

Relation between Vitamin D Level and Cyclin-Dependent Kinase-1 Gene Expression in Egyptian Patients with Lupus Nephritis and their Impact on Disease Activity.

INTRODUCTION: Lupus nephritis (LN) is a common complication of systemic lupus erythematosus. Vitamin D and cycline-dependent kinase-1 (CDK1) have been implicated in its pathogenesis. The aim of this study was to determine the relation between vitamin D level and CDK-1 in lupus nephritis patients and their impact on disease activity. PATIENTS AND METHODS: The current study was conducted on 50 LN patients and 20 control subjects from Egyptian population using ELISA to assess vitamin D level in serum and TaqMan assay for CDK1 gene expression. RESULTS: Serum vitamin D level was significantly lower in LN patients and CDK-1 gene was down expressed in the majority of LN patients. A significant inverse correlation was found between vitamin D level and 24 h protein in urine, ANA, anti-dsDNA, CRP, with a significant positive correlation with renal biopsy indices, eGFR. There was a non-significant inverse correlation between vitamin D and CDK-1 (before RO-3306 addition) and a positive correlation after RO-3306. A significant positive correlation was found between CDK-1 gene expressions with urinary albumin/creatinine ratio. However, a significant positive correlation was found between CDK-1 (after RO-3306 addition) and proteinuria. While a significant positive correlation was found between CDK-1 expression (after RO-3306 addition) and ANA, a significant positive correlation was found between CDK-1 expression (before RO-3306 addition) and anti-dsDNA but CDK-1 is not associated with renal biopsy indices nor with activity indices of SLE. There was a positive correlation between CDK-1 gene expression and CRP before and after RO-3306 addition. CONCLUSIONS: Vitamin D deficiency acts as a risk factor for developing LN. CDK-1 may have an association with the diagnosis of LN but its association with the progression of staging of LN is still confusing.

Fecal carriage of ESBL-producing Escherichia coli in Egyptian patients admitted to the Medical Research Institute hospital, Alexandria University.

Commensal ESBL-producing E. coli represent a reservoir for resistance genes therefore, their detection is crucial to restrain the spread of beta-lactam resistance. Hence, the aim of the present study was phenotypic and genotypic characterization of commensal ESBL-producing E. coli obtained from the stool of patients at the time of admission and at the time of discharge from the Medical Research Institute hospital. A total of 70 E. coli isolates were collected from 35 patients and were categorized into Group A (samples obtained on admission) and Group B (samples obtained at the time of discharge). Phenotypically, 30 isolates were ESBL producers (40% of E. coli isolates collected on admission and 45.7% of the strains obtained at the time of discharge were ESBL producers). Most of them harbored one to three plasmids with sizes ranging from one kbp to ten kbp. Upon genotypic investigation, bla CTX-M was the most detected gene in 80% of ESBL strains, followed by bla TEM in 53.3% and the least detected was bla SHV in only 13.3%. By comparing group A and group B, ten patients were found to carry commensal ESBL-producing E. coli, in two patients these isolates carried ESBL genes that were identical on admission and on discharge. However, in eight patients, these isolates carried different ESBL genes, which were newly harbored during hospital stay. The high abundance of MDR commensal E. coli 48.57% together with the presence of 42.86% ESBL-producing commensal E. coli among our isolates represents an alarming threat, as they are frequently associated with the increased risk of infection, higher costs and longer hospital stay.

Human coronavirus OC43 and other respiratory viruses from acute respiratory infections of Egyptian children.

Respiratory infections have a significant impact on health worldwide. Viruses are major causes of acute respiratory infections among children. Limited information regarding its prevalence in Egypt is available. This study investigated prevalence of 10 respiratory viruses; Adenovirus, influenza A, B, respiratory syncytial virus (RSV), Parainfluenza virus (PIV)type 1-4, enterovirus, and human coronavirus OC43 (HCoV-OC43) among children in Alexandria, Egypt presenting with acute lower respiratory tract infections.The study was conducted on children <14 years of age selected from ElShatby Pediatric Hospital, Alexandria University, Egypt. One hundred children presenting during winter season with influenza-like illness were eligible for the study. Oropharyngeal swabs were collected and subjected to viral RNA and DNA extraction followed by polymerase chain reaction.Viral infections were detected in 44% of cases. Adenovirus was the most common, it was found in 19% of the patients. Prevalence of PIV (3 and 4) and enterovirus was 7% each. Prevalence of RSV and HCoV-OC43 was 5% and 3% respectively. Two percentage were Influenza A positive and 1% positive for influenza B. Mixed viral infection was observed in 7%.To the best of our knowledge, this is the first report of the isolation of HCoV-OC43 from respiratory infections in Alexandria, Egypt.