First report of Ochrobactrum anthropi isolated from bloodstream infection in Alexandria, Egypt

Background: Ochrobactrum anthropi ( O. anthropi) is a Gram-negative, nonfermenting bacillus, which has been recovered from clinical samples worldwide. However, it has never been reported from any clinical sample in Egypt. To the best of our knowledge, we report for the first time, the isolation of O. anthropi from bloodstream infection of a 75-year-old female patient. Ochrobactrum anthropi identification was performed using Vitek-2 system (BioMérieux, Marcy l’Etoile, France), and confirmed using 16S rRNA sequencing. The organism was further classified as O. anthropi subclade I, using recA sequence analysis. Susceptibility testing was carried out using broth microdilution method, and the isolate was found to be resistant to both ceftazidime and cefepime. Molecular investigation of genes conferring resistance to the third and fourth generation cephalosporins, showed that the isolate harbored blaOCH-6 gene, and that blaTEM, blaSHV and blaCTX-M were not present. This work highlights the first isolation of O. anthropi from bloodstream infection in Alexandria, Egypt

Prevalence of trimethoprim/sulfamethoxazole resistance genes among Stenotrophomonas maltophilia clinical isolates in Egypt

Stenotrophomonas maltophilia is an important multidrug resistant nosocomial pathogen. Trimethoprim/sulfamethoxazole (TMP/SMX) is considered the drug of choice for treatment of S. maltophilia infections, thus emerging resistance to TMP/SMX poses a serious threat. In the present study we aimed to investigate the frequency of TMP/SMX resistance genes (sul1, sul2, dfrA), and to evaluate their relatedness with integron 1 (int1), and insertion sequence common regions (ISCR) among 100 S. maltophilia from different clinical isolates in Egypt. Isolates were identified biochemically and confirmed by VITEK2. Detection of sul1, sul2, and dfrA genes, int1 and ISCR elements was performed by PCR. Among the 16 TMP/SMX resistant isolates, sul1 gene was detected in all of them, and it was associated with int1 gene presence in all resistant isolates. The sul2 gene was detected in 6 out of 16 resistant isolates (37.5%), and only 2 of the 16 resistant isolates (12.5%) harboured dfrA gene. ISCR was detected in 10 of the resistant isolates (62.5%) and in 4 of them it was associated with the presence of sul2 gene. Among the 84 TMP/SMX sensitive isolates, sul1 gene was detected in 15 (17.8%), int1 in 16 (19%) and ISCR in 6 (7.1%). None of the susceptible isolates had sul2 or dfrA genes. These findings point out an increasing frequency of TMP/SMX resistance genes among S. maltophilia clinical isolates in our region, so the adoption of prudent use of S. maltophilia antimicrobial agents and the establishment of a surveillance system are desperately needed

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

Impact of a service provider incentive payment scheme on quality of reproductive and child-health services in Egypt

A case-control, quasi-experimental study was designed (post-test only) to investigate the effect of a per-formance-based incentive payment scheme on behaviours of public-sector service providers in delivering a basic package of maternal and child-health services in Egyptian primary healthcare units. The results showed significant improvements in the quality of family-planning, antenatal care, and child-care services as reported by women seen in clinics where the incentive payment scheme was in operation as measured by various indicators, including both technical and inter-personal communication content. An analysis of characteristics of the service providers and clients found no significant or meaningful differences between the study groups, and the facilities of both the study groups were essentially the same. Some findings are suggestive of other influences on behaviours of the service providers not captured by the data-collection instruments of the study. Subsequent to this study, the payment scheme has been rolled out to other dis-tricts in Egypt

Co-Existence of blaNDM-1, blaOXA-23, blaOXA-64, blaPER-7 and blaADC-57 in a Clinical Isolate of Acinetobacter baumannii from Alexandria, Egypt

The increasing rates of antimicrobial resistance among carbapenem-resistant Acinetobacter baumannii in the Middle East and North Africa are one of the major concerns for healthcare settings. We characterised the first A. baumannii isolate harbouring five β-lactamases identified in Egypt. The isolate Ale25 was obtained from an ICU patient of a hospital from Alexandria. The isolate was phenotypically and genotypically screened for carbapenemase genes. The isolate was resistant to carbapenems, aminoglycosides, fluoroquinolones and cefiderocol. Whole-Genome Sequencing identified five β-lactamase genes, blaNDM-1, blaOXA-23, blaOXA-64, blaPER-7 and blaADC-57, together with other antibiotic resistance genes, conferring resistance to sulfonamides, macrolides, tetracyclines, rifamycin and chloramphenicol. Virulome analysis showed the presence of genes involved in adhesion and biofilm production, type II and VI secretion systems, exotoxins, etc. Multi-Locus Sequence Typing analysis identified the isolate as Sequence Types 113Pas and 2246Oxf, belonging to International Clone 7. Sequencing experiments revealed the presence of four plasmids of 2.7, 22.3, 70.4 and 240.8 Kb. All the β-lactamase genes were located in the chromosome, except the blaPER-7, gene which was found within the plasmid of 240.8 Kb. This study highlights the threat of the emergence and dissemination of these types of isolates.This research was funded by the MINISTRY OF SCIENCE AND INNOVATION (MCIN/AEI/10.13039/501100011033), grant number PID2020-116495RB-I00; the DEPARTMENT OF EDUCATION OF THE BASQUE GOVERNMENT (Research Groups of the Basque University System 2021), grant number Group IT1578-22, GIC21/18; and the ARAB ACADEMY FOR SCIENCE, TECHNOLOGY AND MARITIME TRANSPORT, grant number 2072

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

HIV prevalence and risk behaviors of male injection drug users in Cairo, Egypt

Objective: To measure HIV prevalence and related risk behaviors among male injection drug users (IDUs) in Cairo, Egypt in the context of the first survey wave of an integrated biological and behavioral surveillance system. Design and methods: Given the hidden nature of injection drug use, we used the peer-referral methodology of respondent-driven sampling in a cross-sectional study to recruit a sample of male IDUs in Cairo between May and August 2006. Behavioral data were collected through face-to-face interviews and serum was obtained for HIV antibody testing. Population estimates were produced using respondent-driven sampling Analysis Tool. Results: The study enrolled 413 male IDUs. The population estimated HIV prevalence was 0.6% (95% confidence interval 0.1-1.8). More than half (53.0%) reported injecting drugs with used needles or syringes and nearly one-third (32.4%) shared their used needle or syringe with one or more persons in the preceding month. Overall, 70.5% had sex in the preceding year, of whom 9.4% reported sex with male partners and 13.2% reported sex with commercial sex workers in the preceding 12 months. Ever use of a condom during sex was low with all partner types and only 5.8% ever had an HIV test. Conclusion: This first survey wave of integrated biological and behavioral surveillance system in Egypt to track the HIV epidemic among male IDUs found relatively low prevalence of infection compared to global estimates, though the figure is many times higher than the general population. In addition, risky injection practices and unprotected sex were high with sexual networks including men who have sex with men, female sex workers, wives, and other regular and casual partners. The respondent-driven sampling method was effective in recruiting male IDUs and the results are being used to inform surveillance and prevention programs

Evaluation of liver biopsy in Egyptian HBeAg-negative chronic hepatitis B patients at initial presentation: implications for therapy

Objectives: A subgroup of HBeAg-negative chronic hepatitis B (CHB) patients with alanine aminotransferase (ALT) and/or hepatitis B virus (HBV)-DNA levels below the cutoff values of international guidelines may have significant liver disease and miss the opportunity for early treatment. Histopathological changes of HBeAg-negative CHB patients at initial presentation irrespective of HBV-DNA and/or ALT levels to increase the likelihood of patients for treatment are evaluated. Methods: CHB patients attending Cairo Liver Center from January 2006 to May 2008 had biochemical, serological, and virological screening as well as liver biopsy that was assessed by Metavir score. Results: Fifty-two HBeAg-negative CHB patients (46 male and 6 female) with a median age of 37.5 years were included in the study. Significant fibrosis (\u3eor=F2) was found in 26% (5/19) of patients with serum HBV-DNA \u3c2,000 IU/ml, and 53% (21/40) of patients with ALT level \u3c2xULN. Liver biopsy increased candidacy for treatment by nearly 25% before implementation of the recommended lower ALT levels (30 U/l for male and 19 U/l for female patients), and by 21.2% after implementation of the lower ALT level. Implementation of the lower ALT level increased the candidacy of patients for treatment by 4% (two patients), whereas liver biopsy increased eligibility for treatment by 55.8 % (27/49). Conclusions: Liver biopsy is more reliable than either ALT or HBV-DNA levels in the decision to treat Egyptian HBeAg-negative CHB patients, even with the implementation of the recommended lower ALT levels

HIV Surveillance and Epidemic Profile in the Middle East and North Africa

HIV infection is the most devastating infection that has emerged in the recent history. The risk of being infected can be associated with both individual’s knowledge and behavior and community vulnerability influenced by cultural norms, laws, politics, and social practices. Despite that the countries in the Middle East and North Africa have succeeded in keeping low the HIV epidemic rates, the number of identified infected cases are increasing. Since the appearance of the first AIDS cases, all the national authorities devoted their efforts to abort the epidemic in its early stages. The rate of new HIV infections across the Middle East and North Africa region are not at an alarming level, but the need for a concerted effort from nation-states and nongovernmental organizations to stem the spread of the virus across the region is vital. Most countries of the region have put in place better information systems to track the HIV epidemic, yet the passive HIV/AIDS reporting remains the cornerstone in the HIV surveillance systems. Several countries still believe that their current strategies are optimal to the HIV status within their territories and that their national strategies are appropriate to their low epidemic status that is not expected to grow. Additionally, these countries fear that establishing an HIV national program to survey risk behaviors may be perceived as an approval of these behaviors that are culturally and religiously unacceptable. This background article aims to summarize the HIV surveillance strategies and epidemic profile in 17 Arab countries in the Middle East and North Africa. The article, also, displays the national surveillance system and the epidemic profile in Egypt and Lebanon as models for the region. This information aims to provide useful insights that may help the national authorities in finding out the best surveillance strategies that allow merging and collecting biological and risk data which is an integral part of their efforts to fight the HIV epidemic in the region

Child Health: Caring for the Future

The Arab world is a distinct geographic and cultural entity, with a complex demographic. Public Health in the Arab World reviews and dissects the public health concerns specific to this region. This volume will interest not only researchers, practitioners and students in the Arab world, but also the wider constituency of international public health specialists and social scholars interested in this region. With contributions from a multidisciplinary group of leading regional and international experts, this volume addresses a comprehensive range of contemporary topics, including the social determinants of health, and health issues in different population groups. Synthesizing a large body of knowledge in an accessible manner, the authors critique and adapt public health concepts, frameworks and paradigms to the context of the Arab world, engaging readers in current debates. This is a valuable addition to the library of anyone interested in global public health and in Arab world studies. Presents a diverse perspective on health issues through a multidisciplinary approach including public health, social and anthropological perspectives Describes the practical relevance of current theoretical debates, allowing readers to apply the theory in different frameworks Highlights the differences and commonalities between various Arab countries and population groups, helping readers understand the complexity of the regionhttps://fount.aucegypt.edu/faculty_book_chapters/2205/thumbnail.jp