Ornithobacterium rhinotracheale (ORT), is a bacterium that cause respiratory tract infection, has led to significant problems in the intensive poultry production. The current study aimed to isolate and identify ORT from broiler chickens, to detect antibacterial sensitivity and resistance of ORT isolates, and to test experimental infection of ORT in broiler chickens. One hundred eighty samples including tracheas, lungs and air sacs were subjected to isolation and phenotypic identification. Twelve suspected ORT isolates were used for molecular identification. Agar gel precipitation test was used to determine serotype of ORT isolates. Antibacterial sensitivity and resistance of ORT isolates were tested against 14 antibacterial drugs using standard disk diffusion technique. Pathogenicity of ORT was tested by experimental infection in broiler chickens. Results revealed that the incidence of ORT infection in broiler chickens in Assiut Governorate is 17.77% using isolation and phenotypic methods of identification, while it is 3.33% using molecular identification. Serological identification of ORT isolates indicated that all tested isolates, were belonged to serotype A. All ORT isolates were resistant to gentamycin, amoxycillin and cephradine with 100% incidence, where, 100% isolates were sensitive to colistin and doxycycline, 50% of isolates were sensitive to ampicillin and streptomycin, and 16.67% of isolates were sensitive to neomycin and trimethoprim. Living Newcastle attenuated vaccine, Lasota vaccine, exaggerates the clinical signs and lesions of ORT experimental infection.

In this study a total number of 22 organ samples (including trachea, lung and kidney) from 22 broiler farms from northern Upper Egypt were collected from Mars 2017 to June 2018 from chickens showing clear clinical and pathological signs of Infectious Bronchitis. The samples were prepared and examined by real time RT-PCR for diagnosis of IBV. A total number of 11 samples were positive (50%) which were used for further isolation on SPF eggs by three blind serial passages. Positive samples that showed the pathogenic lesions of IB (curling and dwarfing of embryos) were collected and tested with real time RT-PCR (rRT-PCR) for more confirmation then a part from S1 gene sequence was amplified by RT-PCR and the product was sequenced and the data have been compared with other related IBV strains. The results indicate that the Egyptian virus in this study has an identity percent reached up to 89% with other recent Egyptian isolates. However, it reached 67% with classical vaccine strains like H120 and variant I like CR88 strain. The lowest identity was observed with M41 strain (59%) in this study. The phylogenetic tree compared to other isolates from Middle East and worldwide showed that this isolate is related to the IBV variant 2 group closely related to IBVEg/1265B/2012 strain and the Israeli strain IS/1494/06.

Quail meat has gained a reputation as an outstanding source of protein and other essential nutrients, giving it numerous advantages over other poultry species. However, quail production has some limitations. One of them is vulnerability to parasitic infections that produce severe economic losses. Consequently, this study aimed to determine the prevalence and molecular characterization of Anonchotaenia species infecting quails in Elbehera Governorate, Egypt. A total of 239 quails were examined for gastrointestinal parasites. The total prevalence of Anonchotaenia infection was 0.83%. The prevalence was 1.11% in the Edko district, but no infection was recorded in Rashid. The prevalence of infection in migrant quails was 2.21%, while no infection was recorded in domesticated quails. The prevalence was higher in males than in females. The 18S rRNA sequence of Egypt's Anonchotaenia species has 99% identity with Anonchotaenia brasiliensis. The phylogenetic tree of the 18S rRNA showed that sequence of Anonchotaenia sp. from Egypt is in the same clade as Anonchotaenia macrocephala from Brazil and Chile. Molecular characterization using 18S rRNA gene sequencing is valuable for parasitic helminth genetic identification in quails. The results presented a novel member of the genus Anonchotaenia in quails from Elbehera governorate, Egypt for the first time.

Avian infectious bronchitis virus (IBV) causes a major problem in broiler chickens due to increasing mortality and lowering body weight. This group of gammacorona viruses has the ability to emerge frequent new variants. In the present study, 18 broiler chicken farms from 7 Egyptian governorates that showed respiratory signs were sampled from 2019 to 2022. There were 11 farms positive for detection of IBV with real time RT-PCR. The samples were inoculated in specific pathogen free (SPF) embryos for three successive blind passages and the obtained viruses were sequenced for hypervariable region of spike protein (S1) to study their genetic diversity. The results showed that the S1 gene was clustered into two major groups, the first group has only one virus belong to classical vaccine strain of GI-1 lineage and the second group contain nine viruses belong to genotype GI-23 (variant II). They are further separated in two subgroups, first subgroup GI-23.2.1, contains 8 viruses, second subgroup contain one virus belong to genotype GI-23.2.2. The selection pressure analysis revealed episodic diversifying selection on multiple sites, with positive selection observed at five amino acid residues of the S1 protein, as demonstrated by FEL models. The recombination analysis of the S1 gene reveled two viruses with recombination events. The F1282-7-IB-2022 exhibited a slight recombination from IS/1494/2006 and a larger recombination from M41-2004. Meanwhile, the F1282-8-IB-2022 had a minor recombination of strain 4/91-1998 and a larger recombination from the Egyptian strain IBV-D1344/2/4/10-EG. The 3D structural models of hypervariable region HVR of S1 protein also showed that the recent viruses in this study from subgroup GI-23.2.1 (F1282-6-IB-2022) have high structural similarity with vaccine strain D274 and local vaccine seed virus IBV-EG/1212B-2012 than classic or variant GI-23.2.2 subgroup. These results can support efforts to compare the efficacy of local and imported vaccines both in-vivo and in-vitro and to help in controlling the disease.

In this study, examination of infected cattle infested with tick, identification of collected tick samples were based on the12S rDNA PCR products as Rhipicephalus annulatus, the GenBank accession number is (OP650242). A total of 72 blood samples from crossbred cattle of both sexes were examined clinically and in the laboratory. Out of these, 43 cattle were healthy, while 19 (26.38%) had theileriosis and 10 (13.88%) had babesiosis. Hemogram analysis revealed distinct anemia patterns, with Babesia-infected cattle displaying macrocytic hypochromic anemia and theileria-infected ones showing normocytic normochromic anemia, both with reduced platelet counts. Babesia-infected cattle had elevated total leukocyte counts, neutrophilia, eosinophilia, and lymphopenia, while Theileria-infected cattle had decreased total leukocyte counts, neutropenia, lymphocytosis, and eosinophilia. In infected cattle, serum biochemistry showed increased ALT, AST, creatinine, and urea levels in both Babesia and Theileria infections. There was decreased serum protein, and albumin, in both cases. Oxidative stress revealed elevated serum malonaldehyde (MDA), reduced glutathione peroxidase (GPx) and   catalase (CAT) levels in infected animals compared to controls. After administering Imidocarb dipropionate (1mg/kg S/C) and Buparvaquone (1ml/20kg I/M) to animals with babesiosis and theileriosis, respectively, there was a positive change in the hematological and biochemical measures, bringing them closer to the normal values. There is a genuine danger to the cattle industry in Egypt due to the existence of babesiosis, theileriosis, and their vector. Modern techniques like PCR should be utilized for precise monitoring and to prevent spread of such diseases. Furthermore, adverse effect of babesia and theileria on hematological and biochemical parameters can be eliminated through the appropriate use of Imidocarb dipropionate and Buparvaquone for babesiosis and theileriosis respectively.

FADV has caused high economic losses in poultry industry in Egypt in the last few years. The study aimed to detect and genetically characterize the fowl adenovirus (FAdV) species prevalent in Egyptian commercial broiler chicken flocks during 2023. The 63 suspected samples were collected from Egyptian broiler chickens from 5 governorates during 2023. The molecular characterization was performed by using polymerase chain reaction (PCR) and the positive samples was isolated in primary chicken embryo liver (CEL) cells. The genetic characterization of 8 selected samples represented different governorates by sequencing of loop 1 (L1) of the hexon gene. Clinically, the poultry suffered from depression, watery diarrhea, and ascites and decreased body weight with a mortality rate of 10–30%. The post-mortem inspection showed liver was pale, enlarged with petechial haemorrhage. 27 out of 63 samples (42.8%) were positive by PCR. The molecular charctersation of the L1 hexon gene’s revealed that the FADV (from Eg-ANY1-2023 to EG-ANY4-2023) genetically charcterized as FADV-D 2/11 strains, the FADV-EG-ANY5-2023 to FADV-EG-ANY8-2023 genetically characterized as FADV E/8a and FADV E/8b. By mutation analysis, the strains in our study related to FADV-E/8a (FADV-EG-ANY5, ANY6) had R171K in the HVR4 and strain related to 8b (FADV-EG-ANY6, ANY7) had S95N in the HVR2 and A91T between HVR1 and HVR2 compared to other reference strains. Thus, these findings demonstrate that many mutated virus genotypes are circulating in commercial chicken flocks. Further research is needed to study the pathogencity of these strains and implement control measures and vaccine production to prevent economic loss in the poultry industry.