Background and Aim: Multidrug resistance (MDR) of Escherichia coli has become an increasing concern in poultry farming worldwide. However, E. coli can accumulate resistance genes through gene transfer. The most problematic resistance mechanism in E. coli is the acquisition of genes encoding broad-spectrum beta-lactamases, known as extended-spectrum beta-lactamases, that confer resistance to broad-spectrum cephalosporins. Plasmid-mediated quinolone resistance genes (conferring resistance to quinolones) and mcr-1 genes (conferring resistance to colistin) also contribute to antimicrobial resistance. This study aimed to investigate the prevalence of antimicrobial susceptibility and to detect beta-lactamase and colistin resistance genes of E. coli isolated from broiler farms in Egypt. Materials and Methods: Samples from 938 broiler farms were bacteriologically examined for E. coli isolation. The antimicrobial resistance profile was evaluated using disk diffusion, and several resistance genes were investigated through polymerase chain reaction amplification. Results: Escherichia coli was isolated and identified from 675/938 farms (72%) from the pooled internal organs (liver, heart, lung, spleen, and yolk) of broilers. Escherichia coli isolates from the most recent 3 years (2018-2020) were serotyped into 13 serotypes; the most prevalent serotype was O125 (n = 8). The highest phenotypic antibiotic resistance profiles during this period were against ampicillin, penicillin, tetracycline, and nalidixic acid. Escherichia coli was sensitive to clinically relevant antibiotics. Twenty-eight selected isolates from the most recent 3 years (2018-2020) were found to have MDR, where the prevalence of the antibiotic resistance genes ctx, tem, and shv was 46% and that of mcr-1 was 64%. Integrons were found in 93% of the isolates. Conclusion: The study showed a high prevalence of E. coli infection in broiler farms associated with MDR, which has a high public health significance because of its zoonotic relevance. These results strengthen the application of continuous surveillance programs.

Since it was first discovered, the low pathogenic avian influenza (LPAI) H9N2 subtype has established linages infecting the poultry population globally and has become one of the most prevalent influenza subtypes in domestic poultry. Several different variants and genotypes of LPAI H9N2 viruses have been reported in Egypt, but little is known about their pathogenicity and how they have evolved. In this study, four different Egyptian LPAI H9N2 viruses were genetically and antigenically characterized and compared to representative H9N2 viruses from G1 lineage. Furthermore, the pathogenicity of three genetically distinct Egyptian LPAI H9N2 viruses was assessed by experimental infection in chickens. Whole-genome sequencing revealed that the H9N2 virus of the Egy-2 G1-B lineage (pigeon-like) has become the dominant circulating H9N2 genotype in Egypt since 2016. Considerable variation in virus shedding at day 7 post-infections was detected in infected chickens, but no significant difference in pathogenicity was found between the infected groups. The rapid spread and emergence of new genotypes of the influenza viruses pinpoint the importance of continuous surveillance for the detection of novel reassortant viruses, as well as monitoring the viral evolution.

Salmonellosis is a major global pathogen in the poultry industry and is a significant public health concern. Ducks are known to be carriers of Salmonella. Therefore, monitoring salmonellosis is the most important strategy for preventing the disease. An experimental design was planned to study the pathogenicity of two Salmonella strains. One hundred and fifty chicks were divided into three groups; group one was inoculated with the Salmonella enteritidis strain, group two was inoculated with the Salmonella typhimurium strain, and group three was UN inoculated. Symptoms, postmortem lesions and mortality rate were recorded. The chick growth performance parameters were also determined. Using ANOVA for statistical analysis, there was a significant difference in body weight, body gain, feed consumption, and feed conversion ratio between the two infected groups and the blank group (uninoculated group). In this study, the prevalence of Salmonella enteritidis was (1.73%) and Salmonella typhimurium (0.43%) in imported ducklings in Egypt. Both Salmonella strains were subjected to an antimicrobial sensitivity test. It showed that Salmonella enteritidis had a 60% antimicrobial resistance profile and Salmonella typhimurium had a 20% antimicrobial resistance profile. Furthermore, genotypic characterization was performed and the seven virulence genes(stn, avrA, sopB, ompF, invA, Mgtc, Ssaq) were found. New pathological lesions of Salmonella infection were discovered, such as skull hemorrhage at 3 days and 6 days of age, and a liver similar to a button shape in necropsied infected chicks with Salmonella typhimurium at 21 days of age. Furthermore, hemorrhagic spots were observed on the duodenum. In the presence of Salmonella, Clostridium perferingens was discovered in a bacteriological investigation of duodenal lesions samples from infected chicks. At 30 days of age, administration of acetic acid (1%) as an alternative tool for controlling Salmonella. In conclusion, salmonellosis is a risk factor for necrotic enteritis, and using acetic acid to eliminate salmonella infection is insufficient.

Background and Aim: Rabbits are a highly sensitive species and susceptible to various bacterial pathogens that may be causative agents for early embryonic death. This study aimed to explore the administration of different bacterial agents in does suffering from early embryonic death. Furthermore, identification of genes associated with virulence was performed to identify the phenotypic and genotypic antimicrobial resistance patterns that may increase the virulence of pathogens and lead to early embryonic death. Materials and Methods: We isolated and identified bacterial agents in 106 samples from live and dead female rabbits that had undergone early embryonic death, including liver and intestine tissue, aborted fetuses, discharges, and vaginal swabs. Conventional polymerase chain reaction (PCR) was conducted to confirm the identity of the isolated bacterial strains and their virulence. Moreover, antibiotic resistance was studied phenotypically and genotypically. Results: We isolated Escherichia coli, Salmonella, Staphylococcus aureus, Pasteurella multocida, and Listeria monocytogenes. PCR confirmed typical identification except in P. multocida, which was confirmed as Gallibacterium spp. in some cases. The final percentage of detection was 34%, 30.2%, 16.9%, 13.2%, and 11.3%, respectively. Virulence properties were investigated using different designated genes. All Salmonella strains harbored invA, stn, avrA, and ompf genes, while the sopE gene was identified in 31.25%. E. coli strains harboring the iss gene lacked the shiga toxin (stx1) gene. L. monocytogenes and S. aureus strains harbored the hemolysin gene (66.7% and 33.4%, respectively). Multidrug resistance was detected phenotypically and genotypically in most strains. Each bacterial pathogen had a different antibiotic resistance profile. Conclusion: Multiple bacterial species may contribute to early embryonic death in does. Furthermore, the combined infection could be the main cause of early embryonic death. Thus, monitoring programs should bear this in mind and focus on the early detection of these bacterial agents in female rabbits to avoid embryonic death.

Newcastle disease (ND) is a highly contagious and economically significant viral infection that affects poultry globally, with recurrent outbreaks occurring even among vaccinated flocks in Egypt. Caused by the Newcastle disease virus (NDV), the disease results in substantial losses due to high mortality rates, decreased productivity, and the imposition of trade restrictions. This study aimed to develop a rapid, sensitive, and field-deployable diagnostic assay based on real-time reverse transcription recombinase-aided amplification (RT-RAA) for the detection of all NDV genotypes in clinical avian specimens. Primers and an exo-probe were designed based on the most conserved region of the NDV matrix gene. After testing ten primer combinations, the pair NDV RAA-F1 and RAA-R5 demonstrated the highest sensitivity, detecting as low as 6.89 EID₅₀/mL (95% CI). The RT-RAA assay showed excellent clinical sensitivity and specificity, with no cross-reactivity to other common respiratory pathogens such as avian influenza virus, infectious bronchitis virus, Mycoplasma gallisepticum or infectious laryngotracheitis virus. All 25 field samples that were tested positive by real-time RT-PCR, including those with high CT values (~35), were detected by RT-RAA in 2–11 min, indicating superior sensitivity and speed. The assay requires only basic equipment and can be performed under isothermal conditions, making it highly suitable for on-site detection in resource-limited or rural settings. The successful implementation of RT-RAA can improve NDV outbreak response, support timely vaccination strategies, and enhance disease control efforts. Overall, the assay presents a promising alternative to conventional diagnostic methods, contributing to the sustainability and productivity of the poultry sector in endemic regions.

The infectious bronchitis virus (IBV) causes a severe infectious disease in poultry, leading to significant financial losses. The prevention and treatment of this disease are extremely challenging due to the virus’s rapid mutation. Therefore, quick diagnosis of IBV infections is crucial for controlling the disease. This study aimed to develop a real-time reverse transcription recombinase-aided amplification (RT-RAA) method for IBV. The most effective primer combination was selected for further validation. To determine the assay’s analytical sensitivity, a serial dilution from 10⁵ to 10⁰ EID₅₀/mL was used, and the limit of detection was calculated. The assay could detect down to 10² EID₅₀/mL. The limit of detection (95% Confidence Interval) was 67 EID₅₀ per reaction. There was no cross-reaction with common poultry diseases. When analyzing 39 clinical samples, RT-RAA and RT-PCR showed 100% diagnostic sensitivity and specificity. In conclusion, the IBV RT-RAA detection method is rapid, sensitive, and specific. This approach can be used to improve IBV diagnosis at the point of need.