The aims of the present study were to isolate and serotype, determine the Seroprevalence, Drug susceptibility and diagnosis of infection by Polymerase Chain Reaction (PCR). In this study 460 serum samples and 220 tracheal swabs, 90 ovaries and oviduct swabs, 90 misshapen egg shells swabs were collected from 22 broiler breeder flocks of 5 companies. Serological results showed that all of the 22 flocks (100%) were positive for ORT infection. Ornithobacterium rhinotracheale (ORT) antibodies were detected in 289 (62/83%) out of the 460 serum samples. ORT was detected from tracheal swabs of seven flocks (31/81% or 3/18% out of 220 tracheal swabs). There was significant correlation between flock different ages and ORT titers (p<0.05), but correlation of flock ages and ORT isolates was not significantly different (p>0.05). Seven flocks infected with ORT were detected positive in PCR but bacteria were Isolated from only five culture. No ovaries and oviducts, misshapen egg shell swabs yielded ORT. A 784 bp fragment of the 16S rRNA gene was amplified using ORT specific primers in the PCR. All the isolates were identified as serotype A by Rapid Agglutination Test. Drug sensitivity test using standard disk diffusion technique was performed with 27 antibiotics. Antibiotic susceptibility for Quinolons family was seen more than the others and Cephalosporins family except to Cephalexin. The isolates were 80-100% susceptible to Tetracycline family and the most antibiotic resistant were seen for Aminopenicillins, Polypeptides, Sulfanamides and 80-100% resistant to Aminoglycoside family. Eighty percent of the isolates were resistant to Licomycin and 60% were moderate sensitive to Lincomycin. This study is the first report of prevalence of ORT, bacterial isolation, biochemical characteristics, serotyping and molecular method (PCR) in broiler breeder flocks in Guilan province of Iran.

Avian influenza type A viruses (AIV) can infect a broad range of hosts including human and birds, making them an important viral pathogen with zoonotic potential. Among birds, ducks are a known reservoir for many avian viruses including the AIV. During migration seasons in Iran, this bird species is generally at a high risk of being infected by free-living aquatic birds. In this study, 962 cloacal swabs were collected from domestic ducks at several live poultry markets (LPMs) of Gilan, Mazandaran and Golestan provinces of Iran in the year 2017. Preliminary assays such as HI, NI, MDT, ICPI and RT-qPCR suggested that 0.5% of the birds were infected by H3 low pathogenic influenza viruses (LPAI). Three isolates were selected for whole genome sequencing. The cleavage site of the HA genes showed a PEKQTR/GLF motif, an indicator of LPAI. Furthermore, BLAST and phylogenetic analyses of the HA gene showed high homology to the Eurasian lineage of H3N8 AIV (95.5–97.1% to several European and East Asian isolates). However, the NA genes showed high homology (at most 96.5–96.9%) to those belonging to AIV N2 subtype. Furthermore, internal genes showed high homology (96–98%) to a variety of duck-origin subtypes and glycoprotein combinations, which were different for each segment. This showed a complex reassortment between different subtypes. Our report is the first whole genome sequencing and complete characterization of H3N2 AIV from Iran. Such surveillance should continue to study the evolution and possible emergence of viruses with pandemic potential.