Transcriptomic analysis reveals the immune response mechanisms of Acrossocheilus fasciatus against Citrobacter freundii infection

Acrossocheilus fasciatus is an economically important freshwater fish species in China. In recent years, Citrobacter freundii infection has caused significant harm to the aquaculture industry. In this study, we performed histological observation and RNA‐seq analysis of the intestines and spleens of control (CK) and C. freundii infected A. fasciatus (EG). The results showed that infected fish exhibited abdominal haemorrhage, intestinal villous shedding, hydropic degeneration of hepatocytes and splenic sinus dilation with congestion. RNA‐seq analysis identified 3054 DEGs in the intestine and 7706 DEGs in the spleen, with 1247 overlapping DEGs identified by combined analysis. A substantial portion of these genes clustered within biological activities linked to immunity and metabolic regulation, particularly engaging immune‐related routes such as endoplasmic reticulum‐based protein maturation, alongside the complement system and coagulation signalling cascades. This study systematically reveals the synergy and division of labor between the intestine and spleen during C. freundii infection, providing fundamental data for understanding the immune response mechanisms of A. fasciatus and a theoretical basis for optimising disease prevention and control strategies.