Transcriptomic Analysis of the Rainbow Trout Response to Single and Co-Infections with Myxobolus cerebralis and Tetracapsuloides bryosalmonae at Sites of Parasite Entry

Parasitic infections, such as those caused by the myxozoans <i>Myxobolus cerebralis</i> and <i>Tetracapsuloides bryosalmonae</i>, pose major threats to wild and farmed salmonids due to severe tissue damage and impairment of the host immune system. While individual infections have been studied, limited information is available on the host response during co-infection. This study investigated the transcriptomic immune response of rainbow trout (<i>Oncorhynchus mykiss</i>) during single and sequential co-infections with <i>M. cerebralis</i> and <i>T. bryosalmonae</i> using RNA-seq. Trout were exposed to single infections (Mc or Tb) followed by co-infections (Mc⁺ or Tb⁺). Fish were sampled at 31 days post-single infection (1 day post-co-infection). RNA from gill and caudal fin (portal of parasite entry) was sequenced, followed by differentially expressed genes (DEGs) identification and GO and KEGG enrichment. In the caudal fin, Mc⁺ (1 day after co-infection with <i>T. bryosalomne</i>) fish showed mild immune activation with <i>C4B</i> upregulation, while Tb⁺ fish exhibited a stronger response involving <i>IFI44, ISG15, RSAD2, and TLR7</i> signaling. In gills, Mc⁺ fish showed moderate cytokine-related gene upregulation, while Tb⁺ (1 day after co-infection with <i>M. cerebralis</i>) fish displayed increased expression of humoral response genes (<i>C3</i>, immunoglobulin pathways) but suppression of genes involved in B cell development. These results indicate that the order of infection shapes the outcome of the host immune response, offering candidate targets at the host-pathogen interface.