Complex Gill Disease (CGD) has emerged as one of the most significant health challenges in global salmon aquaculture, particularly affecting Atlantic salmon ( Salmo salar ) reared in marine environments. CGD represents one of the major health problems in salmon farming worldwide, as it causes severe gill damage, leading to respiratory distress, chronic stress, and, in severe cases, mortality. Despite its high prevalence in Chile, little is known about the molecular mechanisms associated with salmon’s response to CGD. In this study, we analyzed transcriptomic responses in gill filaments of Atlantic salmon naturally affected by CGD in open sea cages in the Patagonian fjords.
Gill samples were collected from healthy salmon and fish clinically affected by CGD. In the latter, gill filaments were classified into damaged tissue (CGDdt ) and undamaged tissue. RNA-Seq analysis revealed a marked immunometabolic imbalance between the two tissue types. In CGDdt samples, overexpression of proinflammatory genes (mmp9, ccl919, il8 ) was observed, along with activation of pathways associated with leukocyte recruitment and extracellular matrix remodeling. However, the down-regulation of processes related to cellular communication, structural organization, and tissue repair was also detected, suggesting a compromised regenerative capacity. In contrast, CGDndt samples maintained a transcriptomic profile similar to that of healthy fish, albeit with mechanisms associated with a state of preparedness to respond to infection, characterized by protein synthesis and ionic balance genes (5ntla, ca12 ). These results demonstrate the ability of Atlantic salmon to generate a localized inflammatory response in the gills affected by CGD. Understanding these processes is essential for designing diagnostic, preventive, and management strategies that mitigate the disease’s impact in salmon farming.
Acknowledgments : Fondecyt regular (1252231), Vicerrectoría de Investigación y Desarrollo de la Universidad de Concepción (VRID INICIACION, VRID Nº2025001383INI) and DICYT-USACH (082541RL_Ayudante; 1ra Convocatoria Apoyo asistencia a Eventos ) grants.