الفهرس 
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Abstract
Acute respiratory tract infections are of paramount importance in the poultry industry. Avian influenza virus (AIV), infectious bronchitis virus (IBV), Newcastle disease virus (NDV), Avian Pneumovirus (APV), Mycoplasma gallisepticum (MG), and E. coli have been recognized as the most important respiratory pathogens in poultry.
In this study, the prevalence of circulating respiratory pathogens, including bacteria such as Mycoplasma gallisepticum and Mycoplasma synoviae and viruses such as AIV-H9 subtype and IBV, were investigated in 68 broiler chicken flocks in Fayoum, Beni-Suef, Minia and Giza governorates during 2020.
Swabs from the trachea and choanal cleft and tissues from organs including trachea, lung, and air sacs were collected from broiler chickens suffering from respiratory manifestations and divided into two parts for Mycoplasma isolation molecular identification and another part for IBV and AIV-H9 viruses detection. Swabs and part of organs of the collected samples were transferred to PPLO broth and incubated overnight at 37°C till its color converted into yellow, then transferred into PPLO agar by running DROP technique and incubated in an inverted position at 37°C under high CO2 tension and checked after 3 days and daily up to 21 days till the appearance of the characteristic fried egg appearance of Mycoplasma under stereo-microscope after excluding Acloleplasma through Digitonin discs, then 1ml of PPLO broth had been used for DNA extraction by boiling method for molecular identification of different Mycoplasma spp. by PCR, from the 68 detected samples, 19 samples were MG, 6 samples were MS, 3 samples were mixed with MG and MS, and 15 samples were NoneMG-NoneMS Mycoplasmas while 25 samples were negative (including 8 Acholeplasma positive samples).
RNA extraction was done to the tissue part of the samples using special kits (Biospin virus RNA extraction kit), and qRT-PCR was applied to detect IBV and AIV-H9 subtype. Clinical signs and lesions varied according to the immune status of the flock and the number of infecting pathogens. Mortality rates in the flocks under investigation ranged from 0.3% to 30%. The highest mortality rate was observed in mixed infection (MG-H9-IB). IBV and AIV-H9N2 viruses were found to be more prevalent. 60, 36, 22, 15, and 9 flocks were found positive for IBV, AIV-H9, MG, NoneMG-NoneMS, and MS, respectively.
The most common mixed infection was AIV-H9, IBV, and MG (12 flocks), representing 17.6%. Mortality rates (during 3 days of illness after appearance of clinical signs suggesting viral infection) after single infection with MG, IBV, AIV-H9, and mixed virus infection of AIV-H9 with IBV ranged from 1.6, 0.3 to 4.9, 0.8 to 2.6 and 0.8 to 2.5%, respectively compared to mortality rates of mixed infection when Mycoplasma included which were 1.3 to 6.8, 2.6 to 11.2, 4.3 to 6.8 and 1.6 to 30% for MG-IBV, MS-IBV, MS-H9-IBV, and MG-H9-IBV, respectively. The immune status and age of birds at the time of field challenge, the hygienic conditions in the farm, and the role of the secondary bacterial agents had a significant effect on the mortality rates in such flocks.
Out of the 68 samples, 60 were positive for IBV, while 36 were positive for AIV-H9. The obtained results showed that mixed infection is more common in cases of respiratory affection in Egypt; the mixed infection in our study was detected in 75% (51 flocks) of the examined flocks, while single infection with each of the tested pathogens found in 25% (17 flocks). MG-AIV-H9 - IBV has been found to be the most common mixed infection (12 flocks), representing 23.5% of mixed infected flocks (51 flocks) and 17.6 % of total investigated flocks (68 flocks).