Comparative trachea transcriptome analysis between avian infectious bronchitis virus and avian pathogenic E. coli individual infection and co-infection in SPF chickens

Avian infectious bronchitis virus (IBV) and avian pathogenic Escherichia coli (APEC) are two important respiratory pathogens in the chicken. The co-infection can lead to chronic complications and considerable economic losses in the poultry industry worldwide. In the present study, we compared differential transcriptional profiles in the trachea tissue of three infected groups (IBV, APEC, and co-infection) with the control group to investigate transcriptome profile changes at the early stage of the infection. After the challenge of SPF chickens with IBV IS-1494 like (GI-23) and APEC, serotype O78: K80, or co-infection, the trachea tissue was used for RNA extraction, and changes in the transcriptome were investigated by Illumina RNA-seq technique. Up-regulated and down-regulated differentially expressed genes (DEGs) in the transcriptome of each group's trachea were identified. Gene ontology category, KEGG pathway, and gene interaction networks (STRING analysis) were analyzed to identify relationships among differentially expressed genes. In general, the numbers of up-regulated genes were higher than of down-regulated genes. In the co-infection group, a more severe immune response and macrophage infiltration occurred; an important cluster of pathway signaling in this group's up-regulated genes was an apoptotic cluster, cytokine-mediated signaling cluster, and the PAMPs recognizing cluster. This is the first study to provide a general overview of transcriptome changes in the trachea at the early stage of infection with these pathogens. Keywords: avian infectious bronchitis virus; avian pathogenic E. coli; transcriptome; RNA-Seq.