Detection of A2142G, A2142C and A2143G clarithromycin mutations in Helicobacter pylori in Alexandria University Pediatric Hospital

Background: Helicobacter pylori (H. pylori)colonizes the stomach and affect almost 50% of the world’s population. Clarithromycin is considered a cornerstone for H. pylori treatment. Emergence of clarithromycin resistance (CLR-R) has played a major role in failure of H. pylori eradication both in adults and children.  Clarithromycin resistance is mostly due to mutations in 23S rRNA gene: A2142G, A2142C, and A2143G. The aim of the current study is to determine the prevalence of CLR-R among H. pylori infected children with prior clarithromycin treatment. Materials and Methods: Multiple endoscopic gastric biopsies were collected from 50 H. pylori infected children after cessation of clarithromycin-based treatment. Samples were subjected to histopathological examinations, rapid urease test (RUT) and simultaneous molecular detection of H. pylori infection as well as CLR-R by multiplex Real-Time polymerase chain reaction (PCR). Results: Histopathological examinations and RUT revealed H. pylori in 74% and 92% of samples respectively. Molecular detection of CLR-R showed that 62.5% positive H. pylori cases were not harboring any of the tested mutations, while 25% harbored 2143A-G single mutation. Double mutations (2142A-C and 2143A-G) were detected in only 4 cases. Statistical significant correlation existed between both RUT and PCR results as well as between histopathological findings and PCR test results. Conclusions: A combination of histopathogy, RUT and multiplex PCR procedures offers a real benefit in the simultaneous diagnosis of H. pylori infection along with clarithromycin resistance status. Other mechanisms of clarithromycin resistance need to be investigated to explain treatment failure in absence of the previously detected mutations

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

A Methodology for Investigating and Addressing Sexual and Reproductive Health Inequities in the Sustainable Development Agenda: Investigating and Addressing Sexual and Reproductive Health Inequities

Background: Countries are committed to the international agenda and essential to achieving sexual and reproductive health goal is their capability to integrate equity lens in structural social determinants framing of inequalities. The aim is to propose comprehensive practical methodology which can alert countries to the injustice of sexual and reproductive health inequalities and provide tool to guide evidence-based policies and actions. Method: The methodology was founded on literature review. This was followed by consultation meetings and workshops to drive scientific output. Finally, the methodology was applied on data in five Arab countries to illustrate its relevance. Results: There are five contributions made. First, integrating equity lens to conceptual framing of sexual and reproductive health inequalities. Second, operationalizing the framework by articulating comprehensive list of indicators, adding distribution of gender norms, and choosing two inequality measures (index of dissimilarity and concentration index redistribution need) to allow for assessment of magnitude and comparisons. Third, illustrating the responsiveness of the health system and its relative contribution as social determinant of health. Fourth, demonstrating unfairness of root social structures and of social configurations of sexual and reproductive health. Finally, using the decomposition analysis and six questions to identify entry points for actions and responsibilities. Conclusion: the proposed methodology provides countries clear way to assess severity and fairness of health-related conditions and not specifically sexual and reproductive inequalities. It offers an ethical urgency for addressing health inequities and guidance to main stream fairness in the full package of national policies

Impact of occult hepatitis B virus infection on antiviral therapy in chronic hepatitis C patients

Background: Occult HBV infection (OBI) can be defined by the presence of HBV-DNA in the serum of patients who are negative for HBsAg. The presence of OBI has been associated with a poor therapeutic response to alpha IFN in many, but not in all studies. Objective: The aim of our study was to assess the prevalence of OBI in the serum of Egyptian patients with CHC, and to evaluate its impact on the response to treatment with a combination of Peg-IFNα and RBV. Materials and methods: Fifty chronic HCV infected patients who were treated with Peg-IFNα once a week in combination with RBV for 48 weeks were included in this study. Patients were divided into two groups, group I which included 25 patients who achieved SVR and group II that included 25 patients who failed to achieve SVR (Non-SVR). Both patient groups were subjected to detailed questionnaire, clinical examination, routine laboratory investigations and virological studies. Results: No statistical significant difference was found in sex distribution regarding SVR and Non-SVR. The frequency of patients with low viral load has a statistically significant association with SVR patients compared to Non-SVR patients. The frequency of anti-HBc seropositivity has a statistically significant association with the Non-SVR patients compared to SVR patients. Out of 11 anti-HBc positive samples, 10 (90.9%) were positive for the pol and s genes while 9 (81.81%) were positive for the c gene. About 17 (34%) out of 50 patients included in the study were HBV-DNA positive. The frequency of HBV-DNA positive HCV patients has a statistically significant association with Non-SVR patients compared to the SVR patients (p < 0.05). Conclusion: The prevalence of OBI was higher in our CHCV patients. OBI was significantly associated with poor response to combined Peg-IFNα and RBV therapy

Assessment of hepatitis B immunization programme among school students in Qatar

تقييم برنامج تطعيم طلاب المدارس ضد التهاب الكبد B في قطر. حمد الرميحي، هناء المصري، شيرين شوقي، محمد آل ثاني، صلاح العويدي، محمد أحمد جناحي، معتز دربالة، خالد الأنصاري، روبرت أليسون. الخلفية: في عام 2010 ، تَبَنَّت قطر هدف خفض معدل انتشار فيروس التهاب الكبد B إلى أقل من 1% لدى الأطفال بحلول عام 2015. ولقد قدر استيطان فيروس التهاب الكبد B بإقليم شرق المتوسط في منظمة الصحة العالمية بدرجة متوسطة، لأن معدل انتشاره يتراوح بين 2% و 7%. وتشير التقديرات إلى أن 4.3 مليون شخص يعيشون مع العدوى بفيروس التهاب الكبد B في الإقليم. الهدف: أجريت هذه الدراسة لتقييم معدل الانتشار المصلي لفيروس التهاب الكبد B لدى الأطفال، والتغطية بالتطعيم ضد التهاب الكبد B، والتعرُّض المحتمل لعوامل الخطر، ومعرفة الآباء/الأوصياء بعدوى التهاب الكبد B. طرق البحث: لقد أجرينا هذه الدراسة المقطعية في قطر خلال العام الدراسي 2015/2016 ، واستخدمنا العينة العنقودية المتعددة المراحل لاختيار عينة ممثلة على الصعيد الوطني تضم 2735 طالباً في الصف الأول من المدرسة بعمر 5 سنوات وأكثر، وجمعنا الدم بوخز الإصبع وفحصناه بالاختبار السريع/اختبار نقطة الرعاية، واستخدمنا الاستبيان الذي يُدار ذاتيًا، والذي أعددنا رموزه مسبقاً، لتقييم معرفة الآباء/الأوصياء عن فيروس التهاب الكبد B، وجمعنا المعلومات حول التغطية بالتطعيم ضد فيروس التهاب الكبد B. النتائج: كانت جميع عينات الدم سلبية للمستضد السطحي لفيروس التهاب الكبد B HBsAg، وكان لدى القطريين المشاركين بالدراسة بطاقات تطعيم وتم تطعيمهم بالكامل، لكن 17.7 % من المشاركين بالدراسة من غير القطريين لم يحملوا بطاقة تطعيم، ولم يكن معظم آبائهم/الأوصياء عليهم على علم بحالة التطعيم لأطفالهم، مما يعرّض الأطفال لمخاطر متعددة لممارسات تنقل العدوى بالتهاب الكبد B. فقد كانت معرفة الآباء/ الأوصياء بالتهاب الكبد B منخفضة. الاستنتاج: لقد تفادت قطر تهديد التهاب الكبد B وحافظت على تغطية عالية لتطعيم الأطفال ضده

Emergence of carbapenem resistant gram-negative pathogens with high rate of colistin resistance in Egypt: A cross sectional study to assess resistance trends during the COVID-19 pandemic

The current study investigated the temporal phenotypic and genotypic antimicrobial resistance (AMR) trends among multi-drug resistant and carbapenem-resistant Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa recovered from Egyptian clinical settings between 2020 and 2021. Bacterial identification and antimicrobial sensitivity of 111 clinical isolates against a panel of antibiotics were performed. Molecular screening for antibiotic resistance determinants along with integrons and associated gene cassettes was implemented. An alarming rate (98.2%) of these isolates were found to be phenotypically resistant to carbapenem. Although 23.9 % K. pneumoniae isolates were phenotypically resistant to colistin, no mobile colistin resistance (mcr) genes were detected. Among carbapenem-resistant isolates, blaNDM and blaOXA-48-like were the most prevalent genetic determinants and were significantly overrepresented among K. pneumoniae. Furthermore, 84.78% of K. pneumoniae isolates co-produced these two carbapenemase genes. The plasmid-mediated quinolone resistance genes (qnrS and qnrB) were detected among the bacterial species and were significantly more prevalent among K. pneumoniae. Moreover, Class 1 integron was detected in 82% of the bacterial isolates. This study alarmingly reveals elevated resistance to last-resort antibiotics such as carbapenems as well as colistin which impose a considerable burden in the health care settings in Egypt. Our future work will implement high throughput sequencing-based antimicrobial resistance surveillance analysis for characterization of novel AMR determinants. This information could be applied as a step forward to establish a robust antibiotic stewardship program in Egyptian clinical settings, thereby addressing the rising challenges of AMR

Diagnosis and management of patients with Gaucher disease: an Egyptian expert opinion

Abstract Background Gaucher disease (GD), an autosomal recessive, lysosomal storage disorder, is caused due to mutations in the glucocerebrosidase (GBA) gene. GD can occur at any age and is classified as type 1 (non-neurologic), type 2 (infantile form, with acute early neurologic manifestation), and type 3 (subacute/chronic neuropathic form). The rarity of the disease and its overlapping symptoms with other diseases increase the delay in diagnosis. The Egyptian cohort of patients with GD is specifically different regarding the prevalence of type 3 as well as the severity and progression of the disease. The unavailability of precise diagnostic tests and lack of awareness among clinicians are the current challenges associated with diagnosing and managing GD in Egypt. Method An expert panel meeting was convened with 19 experts from Egypt to address the current unmet challenges in the diagnosis and management of GD from the region and to develop country-specific diagnostic algorithms based on the existing literature for pediatric and adult groups. In addition, management strategies and preventive measures were also discussed. Result The algorithms presented in this review can be implemented in clinical practice for the timely diagnosis of patients with GD in Egypt. Early diagnosis is crucial in selecting the best treatment for patients with GD, and evidence suggests that early initiation of therapy can result in better outcomes. Conclusion The evidence-based expert opinion presented in this review will help clinicians in the early initial diagnosis of GD in Egypt, leading to appropriate management of the disease