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Dr. Ahmed Samy Ibrahim
Immunogenetics, The Pirbright Institute, United Kingdom

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Research Keywords & Expertise

0 Avian virology
0 Control measures
0 Avian viral and/or bacterial mixed infection
0 Avian immune response
0 Avian vaccine development and evaluation

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Avian immune response

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Journal article
Published: 05 March 2021 in Antibiotics
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Migratory wild birds acquire antimicrobial-resistant (AMR) bacteria from contaminated habitats and then act as reservoirs and potential spreaders of resistant elements through migration. However, the role of migratory wild birds as antimicrobial disseminators in the Arabian Peninsula desert, which represents a transit point for birds migrating all over Asia, Africa, and Europe not yet clear. Therefore, the present study objective was to determine antimicrobial-resistant bacteria in samples collected from migratory wild birds around Al-Asfar Lake, located in Al-Ahsa Oasis, Eastern Saudi Arabia, with a particular focus on Escherichia coli virulence and resistance genes. Cloacal swabs were collected from 210 migratory wild birds represent four species around Al-Asfar. E. coli, Staphylococcus, and Salmonella spp. have been recovered from 90 (42.9%), 37 (17.6%), and 5 (2.4%) birds, respectively. Out of them, 19 (14.4%) were a mixed infection. All samples were subjected to AMR phenotypic characterization, and results revealed (14–41%) and (16–54%) of E. coli and Staphylococcus spp. isolates were resistant to penicillins, sulfonamides, aminoglycoside, and tetracycline antibiotics. Multidrug-resistant (MDR) E. coli and Staphylococcus spp. were identified in 13 (14.4%) and 7 (18.9%) isolates, respectively. However, none of the Salmonella isolates were MDR. Of the 90 E. coli isolates, only 9 (10%) and 5 (5.6%) isolates showed the presence of eaeA and stx2 virulence-associated genes, respectively. However, both eaeA and stx2 genes were identified in four (4.4%) isolates. None of the E. coli isolates carried the hlyA and stx1 virulence-associated genes. The E. coli AMR associated genes blaCTX-M , blaTEM , blaSHV , aac(3)-IV, qnrA, and tet(A) were identified in 7 (7.8%), 5 (5.6%), 1 (1.1%), 8 (8.9%), 4 (4.4%), and 6 (6.7%) isolates, respectively. While the mecA gene was not detected in any of the Staphylococcus spp. isolates. Regarding migratory wild bird species, bacterial recovery, mixed infection, MDR, and AMR index were relatively higher in aquatic-associated species. Overall, the results showed that migratory wild birds around Al-Asfar Lake could act as a reservoir for AMR bacteria enabling them to have a potential role in maintaining, developing, and disseminating AMR bacteria. Furthermore, results highlight the importance of considering migratory wild birds when studying the ecology of AMR.

ACS Style

Ibrahim Elsohaby; Ahmed Samy; Ahmed Elmoslemany; Mohammed Alorabi; Mohamed Alkafafy; Ali Aldoweriej; Theeb Al-Marri; Ayman Elbehiry; Mahmoud Fayez. Migratory Wild Birds as a Potential Disseminator of Antimicrobial-Resistant Bacteria around Al-Asfar Lake, Eastern Saudi Arabia. Antibiotics 2021, 10, 260 .

AMA Style

Ibrahim Elsohaby, Ahmed Samy, Ahmed Elmoslemany, Mohammed Alorabi, Mohamed Alkafafy, Ali Aldoweriej, Theeb Al-Marri, Ayman Elbehiry, Mahmoud Fayez. Migratory Wild Birds as a Potential Disseminator of Antimicrobial-Resistant Bacteria around Al-Asfar Lake, Eastern Saudi Arabia. Antibiotics. 2021; 10 (3):260.

Chicago/Turabian Style

Ibrahim Elsohaby; Ahmed Samy; Ahmed Elmoslemany; Mohammed Alorabi; Mohamed Alkafafy; Ali Aldoweriej; Theeb Al-Marri; Ayman Elbehiry; Mahmoud Fayez. 2021. "Migratory Wild Birds as a Potential Disseminator of Antimicrobial-Resistant Bacteria around Al-Asfar Lake, Eastern Saudi Arabia." Antibiotics 10, no. 3: 260.

Journal article
Published: 06 March 2020 in Pathogens
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Wild migratory birds are often implicated in the introduction, maintenance, and global dissemination of different pathogens, such as influenza A viruses (IAV) and antimicrobial-resistant (AMR) bacteria. Trapping of migratory birds during their resting periods at the northern coast of Egypt is a common and ancient practice performed mainly for selling in live bird markets (LBM). In the present study, samples were collected from 148 wild birds, representing 14 species, which were being offered for sale in LBM. All birds were tested for the presence of AIV and enterobacteriaceae. Ten samples collected from Northern Shoveler birds (Spatula clypeata) were positive for IAV and PCR sub-typing and pan HA/NA sequencing assays detected H5N8, H9N2, and H6N2 viruses in four, four, and one birds, respectively. Sequencing of the full haemagglutinin (HA) gene revealed a high similarity with currently circulating IAV in Egypt. From all the birds, E. coli was recovered from 37.2% and Salmonella from 20.2%, with 66–96% and 23–43% isolates being resistant to at least one of seven selected critically important antimicrobials (CIA), respectively. The presence of enzootic IAV and the wide prevalence of AMR enterobacteriaceae in wild birds highlight the potential role of LBM in the spread of different pathogens from and to wild birds. Continued surveillance of both AIV and antimicrobial-resistant enterobacteriaceae in wild birds’ habitats is urgently needed.

ACS Style

Nehal M. Nabil; Ahmed M. Erfan; Maram M. Tawakol; Naglaa M. Haggag; Mahmoud M. Naguib; Ahmed Samy. Wild Birds in Live Birds Markets: Potential Reservoirs of Enzootic Avian Influenza Viruses and Antimicrobial Resistant Enterobacteriaceae in Northern Egypt. Pathogens 2020, 9, 196 .

AMA Style

Nehal M. Nabil, Ahmed M. Erfan, Maram M. Tawakol, Naglaa M. Haggag, Mahmoud M. Naguib, Ahmed Samy. Wild Birds in Live Birds Markets: Potential Reservoirs of Enzootic Avian Influenza Viruses and Antimicrobial Resistant Enterobacteriaceae in Northern Egypt. Pathogens. 2020; 9 (3):196.

Chicago/Turabian Style

Nehal M. Nabil; Ahmed M. Erfan; Maram M. Tawakol; Naglaa M. Haggag; Mahmoud M. Naguib; Ahmed Samy. 2020. "Wild Birds in Live Birds Markets: Potential Reservoirs of Enzootic Avian Influenza Viruses and Antimicrobial Resistant Enterobacteriaceae in Northern Egypt." Pathogens 9, no. 3: 196.

Journal article
Published: 30 October 2019 in Infection, Genetics and Evolution
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Infectious bursal disease virus (IBDV), the agent of an immunosuppressive and sometimes lethal disease in chickens, is causing recurrent outbreaks in broiler chickens in Egypt. In particular, an antigenically modified isolate of very virulent IBDV (vvIBDV) called 99323 was detected in Egypt nearly twenty years ago; this isolate was shown to be experimentally controlled by an antigenically classical live vaccine. However, acute IBD is still reported, even in vaccinated flocks, and little is known about the genetic and antigenic properties of viruses currently circulating in Egypt. In the present study, ten samples collected in Egyptian broiler farms in 2015 as well as five samples collected in 2001 were analyzed. Genetic analyses of partial VP2 sequences revealed that 8 isolates clustered with vvIBDV strains, and 5 with tissue culture adapted and vaccine strains. Similar results were observed for partial VP1 sequences with the exception of isolate 160019, for which VP2 clustered with the vaccine strain Bursine while VP1 clustered with vvIBDV, suggesting reassortment. For isolates genetically related to vvIBDV, antigenic profiling revealed two patterns: while some isolates exhibited typical European vvIBDV reactivity with lack of binding of mAbs 5, other revealed extensive antigenic modifications, with lack of binding of mAbs 3, 5, 6, 8 and 9, similar to isolate 99323. These different patterns were associated with a single amino acid mutation at position 321 of VP2 that is located within peak PHI. Full genome sequencing was performed for three isolates, among which two were representative of the two antigenic patterns observed for vvIBDV as well as the reassortant isolate 160019. This study highlights the co-circulation of both antigenically typical and modified vvIBDV during the last fifteen years in Egypt.

ACS Style

Ahmed Samy; Céline Courtillon; François-Xavier Briand; Mohamed Khalifa; Abdullah Selim; Abd El Satar Arafa; Ahmed Hegazy; Nicolas Eterradossi; Sébastien M. Soubies. Continuous circulation of an antigenically modified very virulent infectious bursal disease virus for fifteen years in Egypt. Infection, Genetics and Evolution 2019, 78, 104099 .

AMA Style

Ahmed Samy, Céline Courtillon, François-Xavier Briand, Mohamed Khalifa, Abdullah Selim, Abd El Satar Arafa, Ahmed Hegazy, Nicolas Eterradossi, Sébastien M. Soubies. Continuous circulation of an antigenically modified very virulent infectious bursal disease virus for fifteen years in Egypt. Infection, Genetics and Evolution. 2019; 78 ():104099.

Chicago/Turabian Style

Ahmed Samy; Céline Courtillon; François-Xavier Briand; Mohamed Khalifa; Abdullah Selim; Abd El Satar Arafa; Ahmed Hegazy; Nicolas Eterradossi; Sébastien M. Soubies. 2019. "Continuous circulation of an antigenically modified very virulent infectious bursal disease virus for fifteen years in Egypt." Infection, Genetics and Evolution 78, no. : 104099.

Review article
Published: 01 January 2019 in Infection Ecology & Epidemiology
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Wild birds of the orders Anseriformes (mainly ducks, geese and swans) and Charadriiformes (mainly gulls, terns and waders) constitute the natural reservoir for low pathogenic avian influenza (LPAI) viruses. In Egypt, highly pathogenic avian influenza (HPAI) H5N1 and LPAI H9N2 viruses are endemic in domestic poultry, forming a threat to animal and human health and raising questions about the routes of introduction and mechanisms of persistence. Recently, HPAI H5N8 virus was also introduced into Egyptian domestic birds. Here we review the literature on the role of wild birds in the introduction and endemicity of avian influenza viruses in Egypt. Dabbling ducks in Egypt harbor an extensive LPAI virus diversity and may constitute the route of introduction for HPAI H5N1 and HPAI H5N8 viruses into Egypt through migration, however their role in the endemicity of HPAI H5N1, LPAI H9N2 and potentially other avian influenza virus (AIV) strains – by means of reassortment of viral genes – is less clear. Strengthened surveillance programs, in both domestic and wild birds, that include all LPAI virus subtypes and full genome sequencing are needed to better assess the wild–domestic bird interface and form a basis for evidence-based measures to limit and prevent AIV transmission between wild and domestic birds.

ACS Style

Mahmoud M. Naguib; Josanne H. Verhagen; Ahmed Samy; Per Eriksson; Mark Fife; Åke Lundkvist; Patrik Ellström; Josef D. Järhult. Avian influenza viruses at the wild–domestic bird interface in Egypt. Infection Ecology & Epidemiology 2019, 9, 1575687 .

AMA Style

Mahmoud M. Naguib, Josanne H. Verhagen, Ahmed Samy, Per Eriksson, Mark Fife, Åke Lundkvist, Patrik Ellström, Josef D. Järhult. Avian influenza viruses at the wild–domestic bird interface in Egypt. Infection Ecology & Epidemiology. 2019; 9 (1):1575687.

Chicago/Turabian Style

Mahmoud M. Naguib; Josanne H. Verhagen; Ahmed Samy; Per Eriksson; Mark Fife; Åke Lundkvist; Patrik Ellström; Josef D. Järhult. 2019. "Avian influenza viruses at the wild–domestic bird interface in Egypt." Infection Ecology & Epidemiology 9, no. 1: 1575687.

Journal article
Published: 01 January 2019 in Infection Ecology & Epidemiology
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Infectious bronchitis virus (IBV) represents a major threat to poultry production worldwide particularly when complicated with bacterial infection. In the present study samples were collected from forty broiler farms with respiratory manifestations to characterize IBV and E. coli. Bacteriophages were isolated and enriched from sampled farms to study its efficacy to control single and mixed infections with E. coli and IBV in vivo. Twelve out of forty farms were positive for IBV. Phylogenetic analysis of partial spike protein revealed that all positive cases clustered within the GI-23 genotype. Eight out of forty farms were positive for E. coli serogroups O26, O78, O86, O114, O119, with O125 found on three farms. Bacteriophage treatment delayed the onset and reduced the severity of clinical signs, and prevented the mortality associated with single and mixed infection with IBV and E. coli. Furthermore, in mixed infections, bacteriophage treatment significantly reduced E. coli as well as IBV shedding. Groups treated with bacteriophages showed a significant reduction of E. coli shedding that gradually decreased over time, in contrast to higher and gradually increasing shedding without bacteriophage treatment. In conclusion, bacteriophage treatment significantly reduced the pathogenicity and shedding of IBVand E. coli in mixed infections.

ACS Style

Maram M. Tawakol; Nehal M. Nabil; Ahmed Samy. Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens. Infection Ecology & Epidemiology 2019, 9, 1686822 .

AMA Style

Maram M. Tawakol, Nehal M. Nabil, Ahmed Samy. Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens. Infection Ecology & Epidemiology. 2019; 9 (1):1686822.

Chicago/Turabian Style

Maram M. Tawakol; Nehal M. Nabil; Ahmed Samy. 2019. "Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens." Infection Ecology & Epidemiology 9, no. 1: 1686822.

Review
Published: 24 February 2018 in Veterinary Sciences
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The avian respiratory system hosts a wide range of commensal and potential pathogenic bacteria and/or viruses that interact with each other. Such interactions could be either synergistic or antagonistic, which subsequently determines the severity of the disease complex. The intensive rearing methods of poultry are responsible for the marked increase in avian respiratory diseases worldwide. The interaction between avian influenza with other pathogens can guarantee the continuous existence of other avian pathogens, which represents a global concern. A better understanding of the impact of the interaction between avian influenza virus and other avian respiratory pathogens provides a better insight into the respiratory disease complex in poultry and can lead to improved intervention strategies aimed at controlling virus spread.

ACS Style

Ahmed Samy; Mahmoud M. Naguib. Avian Respiratory Coinfection and Impact on Avian Influenza Pathogenicity in Domestic Poultry: Field and Experimental Findings. Veterinary Sciences 2018, 5, 23 .

AMA Style

Ahmed Samy, Mahmoud M. Naguib. Avian Respiratory Coinfection and Impact on Avian Influenza Pathogenicity in Domestic Poultry: Field and Experimental Findings. Veterinary Sciences. 2018; 5 (1):23.

Chicago/Turabian Style

Ahmed Samy; Mahmoud M. Naguib. 2018. "Avian Respiratory Coinfection and Impact on Avian Influenza Pathogenicity in Domestic Poultry: Field and Experimental Findings." Veterinary Sciences 5, no. 1: 23.

Journal article
Published: 13 June 2017 in Antimicrobial Resistance & Infection Control
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The aim of this study was to determine the prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase production among Enterobacteriaceae isolated from ambulatory patients with gastrointestinal complaints admitted to El-Ahrar General Hospital, Zagazig, Egypt in the period between January 2013 and May 2013. One hundred and thirteen Enterobacteriaceae isolates were recovered from 100 consecutive Egyptian patients with community–onset gastrointestinal complaints. The fecal samples were plated directly on selective EbSA-ESBL Screening Agar and on MacConkey agar. Isolate identification was performed with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Screening for ESBLs and carbapenemases production was done by both the automated VITEK®2 system with AST N198 and by disk diffusion method. Real-time PCR and sequencing were used to characterize the resistance genes. Phylogroups of the E. coli isolates were determined by a triplex PCR-based method. Of 100 patients screened for fecal colonization with extended-spectrum β-lactamase -producing Enterobacteriaceae (ESBL-E) and carbapenemase- producing Enterobacteriaceae (CPE), 68 were colonized with ESBL-E whereas five patients were positive for CPE. One hundred and thirteen Enterobacterceae isolates were recovered from 100 fecal samples, they belonged to E. coli (n = 72), Klebsiella pneumoniae (n = 23), Enterobacter cloacae(n = 3), Salmonella spp. (n = 1) and other Enterobacterceae isolates (n = 14). The bla CTX-M gene was detected in 89.04% (65/73) of the ESBL-producing Enterobacteriaceae, whereas bla SHV and bla TEM were detected in 30.14% (22/73) and 19.18% (14/73) respectively. Three out of 5 carbapenem-resistant isolates harbored New Delhi metallo-beta-lactamase (NDM) and 2 produced Verona integron-encoded metallo- beta -lactamase (VIM). Twenty-two (47.83%) of the ESBL positive isolates were multidrug resistant (MDR). Phylogenetic analysis showed that, of the 51 ESBL-EC isolates, 17 belonged to group B2, 13 to group D, 11 to group A and 10 to group B1. Nearly two-thirds of the Enterobacteriaceae isolates recovered from feces of ambulatory patients with community–onset gastrointestinal complaints admitted to El-Ahrar General Hospital, Zagazig, Egypt were ESBL producers and one in every 20 patients included in our study was colonized by carbapenemase-producing Enterobacteriaceae. These high colonization rates are worrying, therefore prudent antimicrobial use should be adopted in Egyptian community settings.

ACS Style

H.M. Abdallah; N. Alnaiemi; E.A. Reuland; B.B. Wintermans; A. Koek; A.M. Abdelwahab; Ahmed Samy; K.W. Abdelsalam; C.M.J.E. Vandenbroucke-Grauls. Fecal carriage of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in Egyptian patients with community-onset gastrointestinal complaints: a hospital -based cross-sectional study. Antimicrobial Resistance & Infection Control 2017, 6, 1 -7.

AMA Style

H.M. Abdallah, N. Alnaiemi, E.A. Reuland, B.B. Wintermans, A. Koek, A.M. Abdelwahab, Ahmed Samy, K.W. Abdelsalam, C.M.J.E. Vandenbroucke-Grauls. Fecal carriage of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in Egyptian patients with community-onset gastrointestinal complaints: a hospital -based cross-sectional study. Antimicrobial Resistance & Infection Control. 2017; 6 (1):1-7.

Chicago/Turabian Style

H.M. Abdallah; N. Alnaiemi; E.A. Reuland; B.B. Wintermans; A. Koek; A.M. Abdelwahab; Ahmed Samy; K.W. Abdelsalam; C.M.J.E. Vandenbroucke-Grauls. 2017. "Fecal carriage of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in Egyptian patients with community-onset gastrointestinal complaints: a hospital -based cross-sectional study." Antimicrobial Resistance & Infection Control 6, no. 1: 1-7.

Original article
Published: 25 March 2017 in Archives of Virology
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Newcastle disease viruses (NDV) represent a major threat to poultry production worldwide. Recently in Egypt NDV circulated extensively, even in vaccinated farms. In the present study samples were collected from sixteen vaccinated broiler farms in animals exhibiting the typical gross lesions of NDV. Virus isolation and pathogenicity studies for positive samples were carried out in accordance to reference procedures and phylogenetic analysis was carried out based on partial sequences of the Fusion gene. Furthermore, in vivo investigation of the ability of heterologous antibody, induced by commercially available lentogenic strain-based vaccines, to efficiently reduce viral shedding was examined. Results revealed that all the sixteen farms were positive for the presence of NDV. Out of these fifteen were confirmed to due to velogenic viruses, based on a main death time (MDT) ≤ 48 hours and partial sequencing of the F gene that showed the presence of a polybasic amino acid motif. However, three patterns in the cleavage site of these velogenic viruses were identified in the present study. Phylogenetic analysis revealed that all fifteen isolates were clustered with class II genotype VIIb while the remaining isolate (B81) was class II genotype II. Results of the in vivo study revealed that adequate heterologous antibody levels, induced by the proposed vaccination program, sufficiently protected birds from morbidity and mortality. However, virus shedding was quantitatively affected in relation to the time of challenge after vaccination. Altogether, with an absence of vaccines able to induce homologous antibody to the presently circulating viruses, higher antibody levels, which depend on efficient and timely implementation of the vaccination program, are considered as highly important in relation to the reduction of virus shedding.

ACS Style

A. M. Saad; Ahmed Samy; Mohamed Ahmed Mohamed Ali Soliman; A. Arafa; A. Zanaty; M. K. Hassan; A. H. Sultan; Abdel-Hamid Bazid; A. H. Hussein. Genotypic and pathogenic characterization of genotype VII Newcastle disease viruses isolated from commercial farms in Egypt and evaluation of heterologous antibody responses. Archives of Virology 2017, 162, 1985 -1994.

AMA Style

A. M. Saad, Ahmed Samy, Mohamed Ahmed Mohamed Ali Soliman, A. Arafa, A. Zanaty, M. K. Hassan, A. H. Sultan, Abdel-Hamid Bazid, A. H. Hussein. Genotypic and pathogenic characterization of genotype VII Newcastle disease viruses isolated from commercial farms in Egypt and evaluation of heterologous antibody responses. Archives of Virology. 2017; 162 (7):1985-1994.

Chicago/Turabian Style

A. M. Saad; Ahmed Samy; Mohamed Ahmed Mohamed Ali Soliman; A. Arafa; A. Zanaty; M. K. Hassan; A. H. Sultan; Abdel-Hamid Bazid; A. H. Hussein. 2017. "Genotypic and pathogenic characterization of genotype VII Newcastle disease viruses isolated from commercial farms in Egypt and evaluation of heterologous antibody responses." Archives of Virology 162, no. 7: 1985-1994.

Journal article
Published: 01 March 2017 in Veterinary Sciences: Research and Reviews
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| Quail meat and egg production represent a promising source to cover the deficit in animal protein in developing countries including Egypt. However little is known about the prevalence and antibiotic resistance of major bacterial pathogens such as Escherichia Coli, Staphylococcus aureus Salmonella and Pasteurella spp. in Egyptian quail farms. Such information is important for drug choice and success of treatment as well as spotting the light on emerging antimicrobial resistance that represent major concern for public health. A total one hundred swabs and 500 organ samples were collected from apparently healthy and freshly dead quails respectively. Bacterial isolation and characterization were performed in accordance with the clinical laboratory standards and confirmed by PCR. In life birds, only E.coli and Salmonella could be recovered from Cloacal swabs, while in freshly dead birds all four pathogens disseminated in various organs with higher incidence of mixed compared to single infection. Different serotypes of E.coli and Salmonella could be recovered from dead birds however E.coli (O78) and S.enteritidis were recovered mainly from heart and liver. The recovered E.coli, S.aureus and P. haemolytica isolates recovered from mixed infection cases showed (57.1-100%) resistance to highly important antibiotic group (Doxycycline, Tetracycline, Trimethoprim sulfa methoxazole and Chloramphenicol) and showed dissimilar pattern of resistance to critical important antibiotic group. Salmonella isolates showed antibiotic resistance to Nalidixic acid (100%) and Nitrofurantoin (42.9%). Strict biosecurity measures are required to reduce the incidence of mixed bacterial infection and subsequently reduce the spread of antibiotic resistance genes between bacterial spp.

ACS Style

Eman M. Farghal; Ahmed Samy; Heba Roshdy. Wide Prevalence of Critically Important Antibiotic Resistance in Egyptian Quail Farms with Mixed Infections. Veterinary Sciences: Research and Reviews 2017, 3, 17 -24.

AMA Style

Eman M. Farghal, Ahmed Samy, Heba Roshdy. Wide Prevalence of Critically Important Antibiotic Resistance in Egyptian Quail Farms with Mixed Infections. Veterinary Sciences: Research and Reviews. 2017; 3 (1):17-24.

Chicago/Turabian Style

Eman M. Farghal; Ahmed Samy; Heba Roshdy. 2017. "Wide Prevalence of Critically Important Antibiotic Resistance in Egyptian Quail Farms with Mixed Infections." Veterinary Sciences: Research and Reviews 3, no. 1: 17-24.

Journal article
Published: 01 December 2016 in British Journal of Virology
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| Avian influenza H9N2 represents one of the most important challenges to poultry production worldwide. That is in addition to its ability to induce mortalities and reduce the productivity, it accused to be negatively affecting the avian immune response facilitating the secondary infection. Many reports take into account the genotypic and pathogenic characterization of H9N2 in avian species. However little is known about the impact of different strains on the innate immune response. In the present study, using quantitative real-time PCR, cytokines gene expression were examined in response to infection with two strains of Egyptian H9N2 (namely V3 and RSF/1) in chicken peripheral blood mononuclear cells (PBMC). Hemagglutinin gene sequence analysis of the two strains reveal high similarity with difference close to cleavage site (HARSSR/ GLF) and (PARSSR/GLF) for V3 and RSF/1 respectively. Results of growth kinetics in PBMCs showed that V3 replicated more efficiently comparing to RSF/1 at all-time points. Further, strain V3 induced significant up-regulation of IL-1b and IL-6 at 24 hours post infections (hpi) comparing to RSF/1. However, both strains induced significant up-regulations of interleukin (IL)-8 at 1 and 3hpi and interferon (IFN)-α late 24 and 48hpi. Altogether, our results suggest that the concurrent up-regulation of IFNα, IL-1b and IL-6 with higher viral load could represent an important feature affecting the viral pathogenicity and associated with impairment of innate immune response that in turn facilitate and magnify the effect of co-infections.

ACS Style

Ahmed Samy; Wesam Mady; Naglaa M. Haggag; Samah H. Mohamed; Ebtissam N. AlShamy; M.K. Hassan. Immune-Related Gene Expression in Response to Different Strains of Egyptian Low Pathogenic H9N2 Infection in Chicken Peripheral Blood Mononuclear Cells. British Journal of Virology 2016, 3, 166 -176.

AMA Style

Ahmed Samy, Wesam Mady, Naglaa M. Haggag, Samah H. Mohamed, Ebtissam N. AlShamy, M.K. Hassan. Immune-Related Gene Expression in Response to Different Strains of Egyptian Low Pathogenic H9N2 Infection in Chicken Peripheral Blood Mononuclear Cells. British Journal of Virology. 2016; 3 (6):166-176.

Chicago/Turabian Style

Ahmed Samy; Wesam Mady; Naglaa M. Haggag; Samah H. Mohamed; Ebtissam N. AlShamy; M.K. Hassan. 2016. "Immune-Related Gene Expression in Response to Different Strains of Egyptian Low Pathogenic H9N2 Infection in Chicken Peripheral Blood Mononuclear Cells." British Journal of Virology 3, no. 6: 166-176.

Journal article
Published: 23 July 2016 in Archives of Virology
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Following the introduction of highly pathogenic avian influenza (HPAI) virus subtype H5N1, the Egyptian government implemented a massive poultry vaccination campaign as the cornerstone of its policies to control the virus. The efficacy of vaccination has been evaluated primarily by measuring titers of antibodies inhibiting the hemagglutinating activity of the viral hemagglutinin (HA). However, other aspects of the host response remain poorly understood. In the present study, in addition to hemagglutination inhibition (HI) titers, cytokine profiles were examined and IFNγ concentrations were measured in vivo after immunization with a whole inactivated virus (WIV) prepared from a classical strain of clade 2.2.1.2 (C121) and an antigenic drift variant of clade 2.2.1.1 (V1063). The results revealed an earlier response and higher HI titers and IFNγ levels in sera from chickens immunized with C121, accompanied by significantly higher expression of IL8, IL10, and IL18 in the spleen and IL6 and IL10 in the bursa, compared to those immunized with V1063. Furthermore, stimulation of the HD11 cell line with C121 induced gradual upregulation of pro-inflammatory cytokines, which was observed at 24 hours post-inoculation (hpi), and became more pronounced at 48 and 72 hpi, accompanied by upregulation of IFNα. Conversely, V1063 induced very early transient higher expression of pro-inflammatory cytokines at 3 and 6 hpi accompanied by upregulation of IL10, which then decreased at 24, 48 and 72 hpi. In summary, our results provide evidence of a correlation between adaptive immune responses induced by WIVs and higher expression of IL10 and IL18 in addition to early induction of IFNα. These findings could be used to improve immune responses induced by WIVs.

ACS Style

Ahmed Samy; Mona I. El-Enbaawy; Ahmed A. El-Sanousi; Soad Nasef; Hirokazu Hikono; Takehiko Saito. Initiation and regulation of immune responses to immunization with whole inactivated vaccines prepared from two genetically and antigenically distinct lineages of Egyptian influenza A virus subtype H5N1. Archives of Virology 2016, 161, 2797 -2806.

AMA Style

Ahmed Samy, Mona I. El-Enbaawy, Ahmed A. El-Sanousi, Soad Nasef, Hirokazu Hikono, Takehiko Saito. Initiation and regulation of immune responses to immunization with whole inactivated vaccines prepared from two genetically and antigenically distinct lineages of Egyptian influenza A virus subtype H5N1. Archives of Virology. 2016; 161 (10):2797-2806.

Chicago/Turabian Style

Ahmed Samy; Mona I. El-Enbaawy; Ahmed A. El-Sanousi; Soad Nasef; Hirokazu Hikono; Takehiko Saito. 2016. "Initiation and regulation of immune responses to immunization with whole inactivated vaccines prepared from two genetically and antigenically distinct lineages of Egyptian influenza A virus subtype H5N1." Archives of Virology 161, no. 10: 2797-2806.

Journal article
Published: 01 May 2016 in Veterinary Microbiology
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H5N1 highly pathogenic avian influenza virus (HPAIV) continues to cause mortality in poultry and threaten human health at a panzootic scale in Egypt since it was reported in 2006. While the early focus has been in Asia, recent evidence suggests that Egypt is an emerging epicenter for the disease. Despite control measures, epizootic transmission of the disease continues. Here, we investigate the persistence of HPAIV across wild passerine birds and domestic poultry between 2009 and 2012 and the potential risk for continuous viral transmission in Egypt. We use a new weighted cross J-function to investigate the degree and spatial temporal nature of the clustering between sightings of infected birds of different types, and the risk of infection associated with direct contact with infected birds. While we found no infection in wild birds, outbreaks occurred year round between 2009 and 2012, with a positive interaction between chickens and ducks. The disease was more present in the years 2010 and 2011 coinciding with the political unrest in the country. Egypt thus continues to experience endemic outbreaks of avian influenza HPAIV in poultry and an increased potential risk of infection to other species including humans. With the current trends, the elimination of the HPAIV infection is highly unlikely without a complete revamp of current policies. The application of spatial statistics techniques to these types of data may help us to understand the characteristics of the disease and may subsequently allow practitioners to explore possible preventive solutions.

ACS Style

Kevin Yana Njabo; Linda Zanontian; Basma Sheta; Ahmed Samy; Shereen Galal; Frederic Paik Schoenberg; Thomas B. Smith. Living with avian FLU⬝Persistence of the H5N1 highly pathogenic avian influenza virus in Egypt. Veterinary Microbiology 2016, 187, 82 -92.

AMA Style

Kevin Yana Njabo, Linda Zanontian, Basma Sheta, Ahmed Samy, Shereen Galal, Frederic Paik Schoenberg, Thomas B. Smith. Living with avian FLU⬝Persistence of the H5N1 highly pathogenic avian influenza virus in Egypt. Veterinary Microbiology. 2016; 187 ():82-92.

Chicago/Turabian Style

Kevin Yana Njabo; Linda Zanontian; Basma Sheta; Ahmed Samy; Shereen Galal; Frederic Paik Schoenberg; Thomas B. Smith. 2016. "Living with avian FLU⬝Persistence of the H5N1 highly pathogenic avian influenza virus in Egypt." Veterinary Microbiology 187, no. : 82-92.

Review article
Published: 23 February 2016 in Infection, Genetics and Evolution
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It is almost a decade since the highly pathogenic H5N1 avian influenza virus (A/H5N1) of clade 2.2.1 was introduced to Egypt in 2005, most likely, via wild birds; marking the longest endemic status of influenza viruses in poultry outside Asia. The endemic A/H5N1 in Egypt still compromises the poultry industry, poses serious hazards to public health and threatens to become potentially pandemic. The control strategies adopted for A/H5N1 in Egyptian poultry using diverse vaccines in commercialized poultry neither eliminated the virus nor did they decrease its evolutionary rate. Several virus clades have evolved, a few of them disappeared and others prevailed. Disparate evolutionary traits in both birds and humans were manifested by accumulation of clade-specific mutations across viral genomes driven by a variety of selection pressures. Viruses in vaccinated poultry populations displayed higher mutation rates at the immunogenic epitopes, promoting viral escape and reducing vaccine efficiency. On the other hand, viruses isolated from humans displayed changes in the receptor binding domain, which increased the viral affinity to bind to human-type glycan receptors. Moreover, viral pathogenicity exhibited several patterns in different hosts. This review aims to provide an overview of the viral evolution, pathogenicity and vaccine efficacy of A/H5N1 in Egypt during the last ten years.

ACS Style

E.M. Abdelwhab; M.K. Hassan; Ahmed Abdel-Moneim; Mahmoud Naguib; A. Mostafa; I.T.M. Hussein; Abdelsatar Arafa; Ahmed Erfan; Walid Kilany; M.G. Agour; Z. El-Kanawati; H.A. Hussein; A.A. Selim; S. Kholousy; H. El-Naggar; E.F. El-Zoghby; Ahmed Samy; Munir Iqbal; Amal Eid; E.M. Ibraheem; S. Pleschka; J. Veits; Soad Nasef; M. Beer; T.C. Mettenleiter; C. Grund; M.M. Ali; Timm Harder; H.M. Hafez. Introduction and enzootic of A/H5N1 in Egypt: Virus evolution, pathogenicity and vaccine efficacy ten years on. Infection, Genetics and Evolution 2016, 40, 80 -90.

AMA Style

E.M. Abdelwhab, M.K. Hassan, Ahmed Abdel-Moneim, Mahmoud Naguib, A. Mostafa, I.T.M. Hussein, Abdelsatar Arafa, Ahmed Erfan, Walid Kilany, M.G. Agour, Z. El-Kanawati, H.A. Hussein, A.A. Selim, S. Kholousy, H. El-Naggar, E.F. El-Zoghby, Ahmed Samy, Munir Iqbal, Amal Eid, E.M. Ibraheem, S. Pleschka, J. Veits, Soad Nasef, M. Beer, T.C. Mettenleiter, C. Grund, M.M. Ali, Timm Harder, H.M. Hafez. Introduction and enzootic of A/H5N1 in Egypt: Virus evolution, pathogenicity and vaccine efficacy ten years on. Infection, Genetics and Evolution. 2016; 40 ():80-90.

Chicago/Turabian Style

E.M. Abdelwhab; M.K. Hassan; Ahmed Abdel-Moneim; Mahmoud Naguib; A. Mostafa; I.T.M. Hussein; Abdelsatar Arafa; Ahmed Erfan; Walid Kilany; M.G. Agour; Z. El-Kanawati; H.A. Hussein; A.A. Selim; S. Kholousy; H. El-Naggar; E.F. El-Zoghby; Ahmed Samy; Munir Iqbal; Amal Eid; E.M. Ibraheem; S. Pleschka; J. Veits; Soad Nasef; M. Beer; T.C. Mettenleiter; C. Grund; M.M. Ali; Timm Harder; H.M. Hafez. 2016. "Introduction and enzootic of A/H5N1 in Egypt: Virus evolution, pathogenicity and vaccine efficacy ten years on." Infection, Genetics and Evolution 40, no. : 80-90.

Journal article
Published: 01 February 2016 in Veterinary Microbiology
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In Egypt, two distinct lineages of H5N1 highly pathogenic avian influenza (HPAI) viruses, “classic 2.2.1.2” and “variant 2.2.1.1” strains, have evolved. The underlying host immune responses counteracting these viruses in chickens remain not well understood. In the present study, the cytokine responses to a classic strain (C121) and those to a variant strain (V1063) were compared in naïve and vaccinated chickens. In naïve chickens, the C121 replicated more efficiently than the V1063. Both the C121 and the V1063 increased interferon (IFN)-γ and interleukin (IL)-10 gene expression at 48 hours post inoculation (hpi) in the lung and spleen but the levels of these cytokines were lower in chickens infected with the C121 than those infected with the V1063. In contrast, in chickens vaccinated with inactivated C121-based vaccine, the C121 replicated less than the V1063. Both challenge with the C121 and that with the V1063 did not increase IFN-γ gene expression at 48 hpi; rather, the C121 increased IL-4 gene expression in the lung accompanied with lower viral titer and higher HI titers. These results suggested that the pathogenicity of HPAI viruses correlated with IFN-γ-producing helper and/or cytotoxic T cell responses in naïve chickens, whereas vaccine efficacy to HPAI viruses correlated with IL-4 producing helper T cell responses in the lung in vaccinated chickens. It implies that IL-4 in the lung, in addition to the traditional serum HI titers, could be used to screen novel vaccine strategies, such as strains, adjuvant, prime/boost protocols, against HPAI in chickens.

ACS Style

Ahmed A. Samy; Mona I. El-Enbaawy; Ahmed A. El-Sanousi; Soad Nasef; Mahmoud M. Naguib; E.M. Abdelwhab; Hirokazu Hikono; Takehiko Saito. Different counteracting host immune responses to clade 2.2.1.1 and 2.2.1.2 Egyptian H5N1 highly pathogenic avian influenza viruses in naïve and vaccinated chickens. Veterinary Microbiology 2016, 183, 103 -109.

AMA Style

Ahmed A. Samy, Mona I. El-Enbaawy, Ahmed A. El-Sanousi, Soad Nasef, Mahmoud M. Naguib, E.M. Abdelwhab, Hirokazu Hikono, Takehiko Saito. Different counteracting host immune responses to clade 2.2.1.1 and 2.2.1.2 Egyptian H5N1 highly pathogenic avian influenza viruses in naïve and vaccinated chickens. Veterinary Microbiology. 2016; 183 ():103-109.

Chicago/Turabian Style

Ahmed A. Samy; Mona I. El-Enbaawy; Ahmed A. El-Sanousi; Soad Nasef; Mahmoud M. Naguib; E.M. Abdelwhab; Hirokazu Hikono; Takehiko Saito. 2016. "Different counteracting host immune responses to clade 2.2.1.1 and 2.2.1.2 Egyptian H5N1 highly pathogenic avian influenza viruses in naïve and vaccinated chickens." Veterinary Microbiology 183, no. : 103-109.

Journal article
Published: 01 December 2015 in International Journal of Veterinary Science and Medicine
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In Egypt, two distinct genetic groups of HPAI H5N1 viruses are co-circulating: classic 2.2.1/C sub-clade and antigenic drift variant 2.2.1.1 clade isolated from vaccinated poultry flocks. The response of chicken innate immunity to both genotypes is not investigated, so far. In this study, expression of immune related genes (IL1b, IL4, IL6, IL8, IL10, IL18, IFNα and IFNγ) after infecting chicken macrophage cell line (HD11) and chicken peripheral blood Mononuclear cells (PBMC) with a classic and a variant strains was assayed using quantitative reverse-transcription real-time polymerase chain reaction assays (qRT-PCR). In HD11, the variant strain induced higher levels of IL1b and IL8 at 6 hours post infection (hpi), IL4 at 24 / 48 hpi and IFNα at 48 hpi than the classic strain. Conversely, the classic strain induced about 10-fold increase of IFNγ at 24 and 48 hpi and the virus replicated at higher level than the variant strain. The results of PBMC infection were similar to that reported from HD11 except for IFNγ gene expression that was higher at variant strain infected cells than that infected with the classic strain. After 24hpi skewing the innate immune response toward anti-inflammatory (humoral-associated) cytokines was different between HD11 (through IL4) and PBMC (through IL10). To sum up, the classic strain produced less cytokines which may indicate adaptation to evade the recognition by the innate immune system and explain its higher pathogenicity.

ACS Style

Ahmed Samy; M.I. El-Enbaawy; A.A. El-Sanousi; S.A. Abd El-Wanes; A.M. Ammar; H. Hikono; T. Saito. In-vitro assessment of differential cytokine gene expression in response to infections with Egyptian classic and variant strains of highly pathogenic H5N1 avian influenza virus. International Journal of Veterinary Science and Medicine 2015, 3, 1 -8.

AMA Style

Ahmed Samy, M.I. El-Enbaawy, A.A. El-Sanousi, S.A. Abd El-Wanes, A.M. Ammar, H. Hikono, T. Saito. In-vitro assessment of differential cytokine gene expression in response to infections with Egyptian classic and variant strains of highly pathogenic H5N1 avian influenza virus. International Journal of Veterinary Science and Medicine. 2015; 3 (1-2):1-8.

Chicago/Turabian Style

Ahmed Samy; M.I. El-Enbaawy; A.A. El-Sanousi; S.A. Abd El-Wanes; A.M. Ammar; H. Hikono; T. Saito. 2015. "In-vitro assessment of differential cytokine gene expression in response to infections with Egyptian classic and variant strains of highly pathogenic H5N1 avian influenza virus." International Journal of Veterinary Science and Medicine 3, no. 1-2: 1-8.

Journal article
Published: 02 April 2015 in Eurosurveillance
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A distinct cluster of highly pathogenic avian influenza viruses of subtype A(H5N1) has been found to emerge within clade 2.2.1.2 in poultry in Egypt since summer 2014 and appears to have quickly become predominant. Viruses of this cluster may be associated with increased incidence of human influenza A(H5N1) infections in Egypt over the last months.

ACS Style

A S Arafa; M M Naguib; C Luttermann; A A Selim; W H Kilany; N Hagag; Ahmed Samy; A Abdelhalim; M K Hassan; E M Abdelwhab; Y Makonnen; G Dauphin; J Lubroth; T C Mettenleiter; M Beer; C Grund; T C Harder. Emergence of a novel cluster of influenza A(H5N1) virus clade 2.2.1.2 with putative human health impact in Egypt, 2014/15. Eurosurveillance 2015, 20, 21085 -8.

AMA Style

A S Arafa, M M Naguib, C Luttermann, A A Selim, W H Kilany, N Hagag, Ahmed Samy, A Abdelhalim, M K Hassan, E M Abdelwhab, Y Makonnen, G Dauphin, J Lubroth, T C Mettenleiter, M Beer, C Grund, T C Harder. Emergence of a novel cluster of influenza A(H5N1) virus clade 2.2.1.2 with putative human health impact in Egypt, 2014/15. Eurosurveillance. 2015; 20 (13):21085-8.

Chicago/Turabian Style

A S Arafa; M M Naguib; C Luttermann; A A Selim; W H Kilany; N Hagag; Ahmed Samy; A Abdelhalim; M K Hassan; E M Abdelwhab; Y Makonnen; G Dauphin; J Lubroth; T C Mettenleiter; M Beer; C Grund; T C Harder. 2015. "Emergence of a novel cluster of influenza A(H5N1) virus clade 2.2.1.2 with putative human health impact in Egypt, 2014/15." Eurosurveillance 20, no. 13: 21085-8.

Comparative study
Published: 15 February 2012 in Archives of Virology
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Avian influenza due to highly pathogenic avian influenza (HPAIV) H5N1 virus is not a food-borne illness but a serious panzootic disease with the potential to be pandemic. In this study, broiler chickens were vaccinated with commercial H5N1 or H5N2 inactivated vaccines prior to being challenged with an HPAIV H5N1 (clade 2.2.1 classic) virus. Challenged and non-challenged vaccinated chickens were kept together, and unvaccinated chickens served as contact groups. Post-challenge samples from skin and edible internal organs were collected from dead and sacrificed (after a 14-day observation period) birds and tested using qRT-PCR for virus detection and quantification. H5N1 vaccine protected chickens against morbidity, mortality and transmission. Virus RNA was not detected in the meat or edible organs of chickens vaccinated with H5N1 vaccine. Conversely, H5N2 vaccine did not confer clinical protection, and a significant virus load was detected in the meat and internal organs. Phylogenetic analysis showed that the H5N1 virus vaccine and challenge virus strains are closely related. The results of the present study strongly suggest a need for proper selection of vaccines and their routine evaluation against newly emergent field viruses. These actions will help to reduce human exposure to HPAIV H5N1 virus from both infected live birds and slaughtered poultry. In addition, rigorous preventive measures should be put in place in order to minimize the public-health risks of avian influenza at the human-animal interface.

ACS Style

Mohamed K. Hassan; Walid H. Kilany; E. M. Abdelwhab; Abdel-Satar Arafa; Abdullah Selim; Ahmed Samy; M. Samir; Yvon Le Brun; Yilma Jobre; Mona M. Aly. Distribution of avian influenza H5N1 viral RNA in tissues of AI-vaccinated and unvaccinated contact chickens after experimental infection. Archives of Virology 2012, 157, 951 -959.

AMA Style

Mohamed K. Hassan, Walid H. Kilany, E. M. Abdelwhab, Abdel-Satar Arafa, Abdullah Selim, Ahmed Samy, M. Samir, Yvon Le Brun, Yilma Jobre, Mona M. Aly. Distribution of avian influenza H5N1 viral RNA in tissues of AI-vaccinated and unvaccinated contact chickens after experimental infection. Archives of Virology. 2012; 157 (5):951-959.

Chicago/Turabian Style

Mohamed K. Hassan; Walid H. Kilany; E. M. Abdelwhab; Abdel-Satar Arafa; Abdullah Selim; Ahmed Samy; M. Samir; Yvon Le Brun; Yilma Jobre; Mona M. Aly. 2012. "Distribution of avian influenza H5N1 viral RNA in tissues of AI-vaccinated and unvaccinated contact chickens after experimental infection." Archives of Virology 157, no. 5: 951-959.