Transcription profiles of chicken liver and spleen in response to infection with avian pathogenic Escherichia coli at different stages.

Avian pathogenic Escherichia coli (APEC) is an extraintestinal pathogen that causes diverse local and systemic infections in poultry and poses a potential zoonotic threat. Although extensive research has addressed its antimicrobial resistance, virulence factors, and host immune responses, the temporal transition from early infection to recovery remains poorly characterized. Here, we established a systemic infection model in broilers by inoculating the pectoral muscle with E. coli O18:K1 and monitored sequential changes in organ weights and indices, serum biochemistry, and histopathology. Parallel RNA-sequencing of liver and spleen tissues delineated stage-specific transcriptional reprogramming. Peak mortality occurred 2 days post-infection (dpi) and ceased at 5 dpi. The infected and uninfected control groups differed significantly in organ weights and indices and blood biochemical indicators at 2 dpi; however, many indicators recovered by 5 dpi in the infected group. Liver transcriptomics during acute infection revealed concerted downregulation of minichromosome maintenance (MCM) family genes and concurrent suppression of the cell cycle and DNA repair pathways. By 5 dpi, these genes and pathways were reactivated, mirroring the transition from pathology to recovery. Key immune mediators in the spleen (IL1B, IL6, FOS, PTGS2, JUN, and NFKBIA) were enriched in immune response pathways and displayed a temporal switch from activation to repression, underscoring the dynamic regulation imposed by this immune organ. Collectively, our data provide a comprehensive spatiotemporal map of the molecular and immune landscape that demarcates the infection and recovery phases of APEC in broilers.