Molekulare Aspekte und chemische Inaktivierung von Influenza H5N1-Viren aus ägyptischen Hühnerbeständen von Ausbrüchen der Jahre 2006 bis 2010

The primary objective of the current study was to identify two of the highly pathogenic avian influenza virus (HPAIV) isolates of subtype H5N1 genotypically using one step Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), followed by sequence and phylogenetic analyses. A further objective was to determine in vitro the virucidal efficacy of four types of chemical disinfectants, namely Formalin, Glutaraldehyde, TH4® and Virkon®S at different concentrations and contact times on the two HPAI isolates. A/chicken/Egypt/0626/2006 (EGY06) and A/chicken/Egypt/1094/2010 (EGY10) were isolated from cloacal and tracheal swabs from broiler during HPAI H5N1 outbreaks in Egypt in 2006 and 2010. The first strain, EGY06, was isolated from a non-vaccinated flock in February 2006 in the Alexandria governorate. The second strain, EGY10, was isolated from a vaccinated flock in November 2010 in the Marsa Matrouh governorate. Classical identification of the two isolates was carried out in the Department of Poultry and Hygiene, Faculty of Veterinary Medicine, Alexandria University, Egypt. Molecular identification and genetic analyses were conducted in the Gene Analysis Unit of the National Laboratory for Veterinary Quality Control on Poultry Production (NLQP), Egypt. Using RT-PCR with specific sets of primers for H5 and N1 genes of AIV it was confirmed that the two isolates belonged to AI subtype H5N1. After molecular characterization and phylogenetic analysis of the HA and NA genes, the strain EGY06 was closely related to the 2006 predecessor Egyptian viruses of 2.2.1 clade, whereas EGY10 clustered within the classic 2.2.1/c group that commonly isolated from small-scale commercial farms and human since 2009. The efficacy of four chemical disinfectants to inactivate both isolates was carried out in accordance to the guidelines of the German Veterinary Medical Society (Deutsche Veterinärmedizinische Gesellschaft, DVG) for testing of disinfection procedures and chemical disinfectants. The experiments were performed using suspension tests without and with protein load (40% Bovine Calf Serum "BCS") as well as wood and gauze as a carriers (also loaded with BCS), at room temperature and incubation times of 15 to 120 min. The obtained results showed that the use of Glutaraldehyde, Formalin or TH4® 0.5% without protein load led to complete inactivation of the virus after 15, 30, 60 or 120 min contact time. Use of Virkon®S 0.5% with and without protein load led to survival of the virus even after 60 min. In contrast, using Formalin and TH4® (1% and 2%) with and without protein load led to complete inactivation of the virus even at the shortest contact time of 15 min. Similar results were obtained after using Glutaraldehyde 1%, while treatment of H5N1 with Glutaraldehyde 2% led to gel formation. After treatment of contaminated carriers (poplar wood and gauze) with Formalin, Glutaraldehyde and TH4® 0.5%, the virus was inactivated after 30 min. Concentration of 1% of the three disinfectants was sufficient to inactivate the two isolates within 15 min contact time, except in case of Virkon®S which required higher concentrations to give similar results. The study indicated that the four chemical disinfectants could efficiently inactivate the two tested H5N1 viruses when used at higher concentration than the manufacturers recommended. The results of the present thesis highlight the sensitivity of HPAIV H5N1 to different disinfectants, which may improve biosecurity measures on the farms and reduce the economic losses caused by HPAIV H5N1.Das primäre Ziel der aktuellen Studie war es, hoch pathogene aviäre Influenza- Viren (HPAIV) des Subtyps H5N1 genotypisch durch eine einschrittige Reverse Transkriptase- Polymerase-Kettenreaktion (RT-PCR) zu identifizieren und anschließend molekularbiologisch zu charakterisieren. Ein weiteres Ziel war, die Wirksamkeit von verschiedenen Konzentrationen und Einwirkungszeiten von vier chemischen Desinfektionsmitteln (Formalin, Glutaraldehyd, TH4® und Virkon®S) auf zwei Stämme (A/chicken/Egypt/0626/2006 "EGY06" und A/chicken/Egypt/1094/2010 "EGY10") des aviären Influenzavirus (AIV) des Subtyps H5N1 in vitro zu prüfen. Die beiden Isolate des AIV-Subtyps H5N1 wurden aus Kloaken- und Trachealtupfern von infizierten Masthühnerherden während der Ausbrüche aviärer Influenza (AI) 2006 und 2010 isoliert. Während der erste Stamm EGY06 aus einer nicht geimpften Herde im Februar 2006 im Gouvernement Alexandria isoliert wurde, wurde der zweite Stamm, EGY10, aus einer geimpften Herde im November 2010 im Gouvernement Marsa Matrouh isoliert. Die klassischen Methoden zur Identifizierung der beiden Isolate wurden in der Abteilung für Geflügel und Hygiene, Veterinärmedizinische Fakultät, Universität Alexandria, Ägypten durchgeführt. Die molekulare Identifizierung und genetische Analyse erfolgten in der Gen- Analyse-Einheit des Nationalen Labors zur Qualitätskontrolle der Geflügelproduktion (NLQP), Ägypten. Mittels RT-PCR unter Verwendung spezifischer Primersets für die H5 und N1 Gene konnte bestätigt werden, dass es sich bei beiden Isolaten um AIV des Subtyps H5N1 handelt. Der molekularen Charakterisierung und der phylogenetischen Analyse der HA und NA zufolge war der Stamm EGY06 sehr eng verwandt mit dem früher im Jahr 2006 isolierten klassischen Stamm und wurde dem Clade 2.2.1 zugeordnet. Im Gegensatz dazu wurde der Stamm EGY10 im klassischen 2.2.1/c Gruppe zugeordnet, welcher häufig von kleinen kommerziellen Farmen und menschlichen seit 2009 isoliert. Die Empfindlichkeit der Viren gegen verschiedene Desinfektionsmittel wurde auf Grundlage der Richtlinien der Deutschen Veterinärmedizinischen Gesellschaft (DVG) für die Prüfung von Desinfektionsverfahren und chemischen Desinfektionsmitteln geprüft. Die Experimente wurden mittels Suspensions-Test ohne und mit Proteinbelastung (40% Bovines Calf Serum (BCS)) sowie auf Keimträgern aus Holz und Gaze, die mit BCS belastet waren, bei Raumtemperatur und Einwirkzeiten von 15 bis 120 Min durchgeführt. Die Verwendung von Glutaraldehyd, Formalin oder TH4® in einer Konzentration von 0,5% führte ohne Proteinbelastung zu einer Inaktivierung der Viren nach allen Einwirkzeiten (15, 30, 60 und 120 Min). Die Verwendung von Virkon®S 0,5% mit und ohne Proteinbelastung führte zum Überleben des Virus sogar nach 60 Min. Demgegenüber führte die Verwendung von Formalin und TH4® in einer Konzentration von 1% und 2% mit und ohne Proteinbelastung zu einer vollständigen Inaktivierung des Virus sogar bei der kürzesten Einwirkungszeit von 15 Min. Ähnliche Ergebnisse wurden nach Verwendung von Glutaraldehyd in einer Konzentration von 1% beobachtet. Die Behandlung von H5N1 mit Glutaraldehyd in einer Konzentration von 2% führte zu einer Gelbildung. Nach der Behandlung von kontaminierten Keimträgern (Pappelholz und Gaze) mit Formalin, Glutaraldehyd und TH4® in Konzentrationen von 0,5% wurde das Virus nach 30 Min inaktiviert. Während eine Konzentration von 1% der drei Desinfektionsmittel ausreichend war, um die beiden Isolate in 15 Min Einwirkzeit zu inaktivieren, konnte dieses Ergebnis im Fall von Virkon®S nicht erreicht werden, und eine höhere Konzentration war erforderlich um ähnliche Ergebnisse zu erzielen. Die Studie zeigte, dass die vier chemischen Desinfektionsmittel, wenn die verwendeten Konzentrationen höher als die vom Hersteller empfohlenen Konzentrationen sind, beide getesteten H5N1 Viren effektiv inaktivieren. Die Ergebnisse dieser Studie bieten einen neuen Ansatz zur Verbesserung der Biosicherheitsmaßnahmen in Geflügelbeständen und können zur Reduzierung der wirtschaftlichen Verluste beitragen

Advancing the fight against tuberculosis: integrating innovation and public health in diagnosis, treatment, vaccine development, and implementation science

Tuberculosis (TB) remains one of the leading causes of infectious disease mortality worldwide, increasingly complicated by the emergence of drug-resistant strains and limitations in existing diagnostic and therapeutic strategies. Despite decades of global efforts, the disease continues to impose a significant burden, particularly in low- and middle-income countries (LMICs) where health system weaknesses hinder progress. This comprehensive review explores recent advancements in TB diagnostics, antimicrobial resistance (AMR surveillance), treatment strategies, and vaccine development. It critically evaluates cutting-edge technologies including CRISPR-based diagnostics, whole-genome sequencing, and digital adherence tools, alongside therapeutic innovations such as shorter multidrug-resistant TB regimens and host-directed therapies. Special emphasis is placed on the translational gap—highlighting barriers to real-world implementation such as cost, infrastructure, and policy fragmentation. While innovations like the Xpert MTB/RIF Ultra, BPaLM regimen, and next-generation vaccines such as M72/AS01E represent pivotal progress, their deployment remains uneven. Implementation science, cost-effectiveness analyses, and health equity considerations are vital to scaling up these tools. Moreover, the expansion of the TB vaccine pipeline and integration of AI in diagnostics signal a transformative period in TB control. Eliminating TB demands more than biomedical breakthroughs—it requires a unified strategy that aligns innovation with access, equity, and sustainability. By bridging science with implementation, and integrating diagnostics, treatment, and prevention within robust health systems, the global community can accelerate the path toward ending TB

Pivotal role of Helicobacter pylori virulence genes in pathogenicity and vaccine development

One of the most prevalent human infections is Helicobacter pylori (H. pylori), which affects more than half of the global population. Although H. pylori infections are widespread, only a minority of individuals develop severe gastroduodenal disorders. The global resistance of H. pylori to antibiotics has reached concerning levels, significantly impacting the effectiveness of treatment. Consequently, the development of vaccines targeting virulence factors may present a viable alternative for the treatment and prevention of H. pylori infections. This review aims to provide a comprehensive overview of the current understanding of H. pylori infection, with a particular focus on its virulence factors, pathophysiology, and vaccination strategies. This review discusses various virulence factors associated with H. pylori, such as cytotoxin-associated gene A (cagA), vacuolating cytotoxin gene (vacA), outer membrane proteins (OMPs), neutrophil-activated protein (NAP), urease (ure), and catalase. The development of vaccines based on these virulence characteristics is essential for controlling infection and ensuring long-lasting protection. Various vaccination strategies and formulations have been tested in animal models; however, their effectiveness and reproducibility in humans remain uncertain. Different types of vaccines, including vector-based vaccines, inactivated whole cells, genetically modified protein-based subunits, and multiepitope nucleic acid (DNA) vaccines, have been explored. While some vaccines have demonstrated promising results in murine models, only a limited number have been successfully tested in humans. This article provides a thorough evaluation of recent research on H. pylori virulence genes and vaccination methods, offering valuable insights for future strategies to address this global health challenge

An overview of the public health challenges in diagnosing and controlling human foodborne pathogens

Pathogens found in food are believed to be the leading cause of foodborne illnesses; and they are considered a serious problem with global ramifications. During the last few decades, a lot of attention has been paid to determining the microorganisms that cause foodborne illnesses and developing new methods to identify them. Foodborne pathogen identification technologies have evolved rapidly over the last few decades, with the newer technologies focusing on immunoassays, genome-wide approaches, biosensors, and mass spectrometry as the primary methods of identification. Bacteriophages (phages), probiotics and prebiotics were known to have the ability to combat bacterial diseases since the turn of the 20th century. A primary focus of phage use was the development of medical therapies; however, its use quickly expanded to other applications in biotechnology and industry. A similar argument can be made with regards to the food safety industry, as diseases directly endanger the health of customers. Recently, a lot of attention has been paid to bacteriophages, probiotics and prebiotics most likely due to the exhaustion of traditional antibiotics. Reviewing a variety of current quick identification techniques is the purpose of this study. Using these techniques, we are able to quickly identify foodborne pathogenic bacteria, which forms the basis for future research advances. A review of recent studies on the use of phages, probiotics and prebiotics as a means of combating significant foodborne diseases is also presented. Furthermore, we discussed the advantages of using phages as well as the challenges they face, especially given their prevalent application in food safety

Burnout among surgeons before and during the SARS-CoV-2 pandemic: an international survey

Background: SARS-CoV-2 pandemic has had many significant impacts within the surgical realm, and surgeons have been obligated to reconsider almost every aspect of daily clinical practice. Methods: This is a cross-sectional study reported in compliance with the CHERRIES guidelines and conducted through an online platform from June 14th to July 15th, 2020. The primary outcome was the burden of burnout during the pandemic indicated by the validated Shirom-Melamed Burnout Measure. Results: Nine hundred fifty-four surgeons completed the survey. The median length of practice was 10 years; 78.2% included were male with a median age of 37 years old, 39.5% were consultants, 68.9% were general surgeons, and 55.7% were affiliated with an academic institution. Overall, there was a significant increase in the mean burnout score during the pandemic; longer years of practice and older age were significantly associated with less burnout. There were significant reductions in the median number of outpatient visits, operated cases, on-call hours, emergency visits, and research work, so, 48.2% of respondents felt that the training resources were insufficient. The majority (81.3%) of respondents reported that their hospitals were included in the management of COVID-19, 66.5% felt their roles had been minimized; 41% were asked to assist in non-surgical medical practices, and 37.6% of respondents were included in COVID-19 management. Conclusions: There was a significant burnout among trainees. Almost all aspects of clinical and research activities were affected with a significant reduction in the volume of research, outpatient clinic visits, surgical procedures, on-call hours, and emergency cases hindering the training. Trial registration: The study was registered on clicaltrials.gov "NCT04433286" on 16/06/2020

<i>Staphylococci</i> in Livestock: Molecular Epidemiology, Antimicrobial Resistance, and Translational Strategies for One Health Protection

Livestock-associated Staphylococcus species—particularly Staphylococcus aureus (S. aureus), Staphylococcus pseudintermedius (S. pseudintermedius), and coagulase-negative staphylococci (CoNS)—pose escalating threats to animal health, food safety, and public health due to their evolving antimicrobial resistance (AMR) profiles. This review synthesizes recent insights into the molecular epidemiology, resistance determinants, and host adaptation strategies of these pathogens across food-producing animals. We highlight the role of mobile genetic elements (MGEs), clonal dissemination, and biofilm formation in shaping multidrug resistance (MDR) patterns. Diagnostic advancements, including MALDI-TOF MS, whole-genome sequencing (WGS), and PCR-based assays, are discussed alongside treatment challenges arising from therapeutic failures and limited vaccine efficacy. The review critically examines current AMR surveillance gaps and the need for integrative One Health frameworks that encompass animals, humans, and the environment. Novel tools such as metagenomics, real-time genomic surveillance, and artificial intelligence (AI)-driven analytics are proposed to enhance predictive monitoring and resistance management. Together, these insights underscore the urgency of coordinated, evidence-based interventions to curb the spread of MDR staphylococci and safeguard One Health

Managing demolition wastes using GIS and optimization techniques

Egypt has experienced vast urbanization and expansion in existing highways, leading to much demolition waste. Construction and demolition waste constitutes around half of the total municipal waste. So, these wastes must be appropriately managed to decrease their negative impacts. As a result, this research presents a framework that automatically detects demolishing wastes' location and optimizes utilized resources in demolition and transportation processes. It consists of three main components: the GIS module, the optimization module, and the decision-making module. Based on the raster image of the study region, the framework detects existing buildings that should be demolished to enable highways’ expansion. The GIS module is designated to quantify the volume of demolition waste in the studied area using ArcGIS Pro software. The optimization module determines the near-optimum combination of resources involved in the demolition process and waste transportation. These resources include labor crews, excavators, and trucks. The module performs multi-objective optimization using a non-dominated sorting genetic algorithm (NSGA-II). The optimization module considers three objectives in demolition and transportation processes: time, cost, and energy consumption. Finally, the decision-making module is developed to rank the Pareto front solutions. The Entropy Weight Method (EWM) is used to identify the weights of the three criteria. The estimated weights for time, cost, and energy consumption are 38.6%, 17.3%, and 44.1%, respectively. Subsequently, the TOPSIS technique is utilized to normalize, rank, and select the best solution. The proposed framework is applied to an actual case study that involves expanding the ring road project in Cairo to demonstrate its main features

Mass Spectrometry Technology and qPCR for Detection of Enterococcus faecalis in Diabetic Foot Patients

Diabetic foot ulcer (DFU) is one of the most serious and costly complications of diabetic patients. Enterococcus faecalis (E. faecalis) represents one of the most virulent microorganisms in diabetic foot infections (DFIs). We therefore aimed to study the frequency and precise identification of E. faecalis in DFU. Six hundred thirty specimens collected from diabetic foot patients were used in the current investigation. Biochemical identification was carried out by the Vitek® 2 system. Proteomic analysis was implemented by MALDI-TOF MS and confirmed by SYBER Green real-time polymerase chain reaction (SYBER Green qPCR). According to the results, the overall frequency of E. faecalis in patients with DFU was 8.25% (52/630). Out of 52 E. faecalis strains, 40 isolates were isolated from males and 12 from females. The results of biochemical identification revealed that 92.30% (48/52) of E. faecalis isolates were properly recognized at the species level. Whereas 100% (52/52) of E. faecalis isolates were properly recognized by MALDI-TOF MS as 44.23% (23/52), 51.92% (27/52) and 3.84% (2/52) with a score value ranging from 2.300 to 3.000, 2.000-2.299 and 1.700-1.999 Da, respectively. Seven E. faecalis virulence genes, including asa1, GelE, cylA, esp, hy1, VanA, and VanB, were detected by SYBER Green RT-PCR. In conclusion, E. faecalis was the utmost predominant single organism isolated from the DFIs. MALDI-TOF mass spectrometry is considered a fast, trustworthy and economic detection method for various significant microorganisms. E. faecalis isolates were also found to carry several virulence genes. Our findings may serve as an urgent issue for supplementary investigations of contagions caused by E. faecalis