Avian pathogenic Escherichia coli (APEC) infection is responsible for great economic losses to the poultry industry worldwide and there is increasing evidence of its zoonotic importance. In this study, 219 E. coli isolates from 84 poultry flocks in Egypt, including 153 APEC, 30 avian fecal E. coli (AFEC), and 36 environmental E. coli, were subjected to phylogenetic grouping and virulence genotyping. Additionally, 50 of these isolates (30 APEC from colisepticemia and 20 AFEC) were subjected to a more-extensive characterization which included serogrouping, antimicrobial susceptibility analysis, screening for seven intestinal E. coli virulence genes (stx1, stx2, eae, espP, KatP, hlyA, and fliCh7), multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and in vivo virulence testing. More than 90% of the total APEC examined possessed iroN, ompT, hlyF, iss, and iutA, indicating that Egyptian APECs, like their counterparts from the United States, harbor plasmid pathogenicity islands (PAIs). The majority of APEC and AFEC were of phylogenetic groups A, B1, and D. For the 50-isolate subgroup, more than 70% of APEC and 80% ofAFEC were multidrug resistant. Among the subgroup of APEC, MLST analysis identified 11 sequence types (ST) while seven STs were found among AFEC. Based on PFGE, the genetic relatedness of APEC and AFEC ranged from 50%-100% and clustered into four primary groups at 50% similarity. Two of the eight APEC strains tested in chickens were able to induce 25% mortality in 1-day-old chicks. APECs were distinguished from AFECs and environmental E. coli by their content of plasmid PAI genes, whereas APEC isolated from colisepticemia and AFEC were not distinguishable based on their antimicrobial resistance patterns, as both groups were multidrug resistant. Avian E. coli strains from broiler flocks in Egypt show similar sequence types to E. coli associated with human infection.

The complete genome sequence of a virulent Newcastle disease virus (NDV) isolated from chickens in Egypt was determined and compared to the sequence of NDV strains isolated from different parts of the world. The genome is 15,186 nucleotides (nt) long and consists of 6 genes in the order of 3'-N-P-M-F-HN-L-5'. The genome contains a 55-nt leader region at the 3' end and a 114-nt trailer region at the 5' end. Interestingly, the phylogenetic analysis showed that strain Egypt is closely related with the NDV strains isolated in China. In addition, the sequence of the fusion protein cleavage site of strain Egypt was identical to that of the NDV strain recently isolated in Mali. Determination of complete genome sequences of additional NDV strains from Africa is necessary to understand the epidemiology of currently circulating viruses in Africa.

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Avian influenza (AI) is a contagious disease caused by type A influenza viruses. In spite of the mild nature of H9N2 low pathogenic AIV, the virus was isolated from frequent disease outbreaks with high mortality in different parts of the world. In this study, forty-two layer and broiler chicken farms (21/each) suspected to be infected with AIV of different breeds and ages during 2012 -2014 were examined at Sharkia Governorate. The occurrence of AI in chickens using HI assay was 40.47%. Subtyping for H9 and H5 subtypes has been done by specific antisera. The H9 was detected in 30.95% and H5 was 9.52%. However, the occurrence of NDV in chickens was 23.80%. The selected seven AIV isolates representing broiler and layer flocks were confirmed by rRT-PCR using primers and probes specific for Matrix gene, H9 gene, H5 gene and H7 gene. Seven isolates were positive for M. gene indicating AI virus detection, and then 6 out of 7 isolates were positive for H9 gene but negative for H5 and H7 genes. The last isolate was positive for H5 gene, negative for H9 and H7 genes. The phylogenetic analysis for HA gene of the Six H9 AIV isolates showed the placement of the Egyptian viruses within the same lineage of H9N2 viruses that circulated in the region with the parent strain (A/Quail/ Egypt/ 113413v/2011) of G1/97 lineage and other strains that circulating in the Middle East. The circulating H9N2 AIV genetic analysis is pointing to a minor evolution of H9N2 viruses. But at the same time the co-circulation of H5 & H9 subtypes of AIV could be a risk for emergence of new AI viruses. Also, concurrent infection with viral (IBV and NDV) as well as bacterial agents (MG, Salmonella and E. coli) are considered the main cause behind increased mortality in H9N2 positive flocks.

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