LAUSR

Abstract Gill disease (GD) in farmed Atlantic salmon may be due to the impact of several agents that may interact. We followed the infections of four gill disease-associated agents during the first year of production in six farms; examining the correlation between their densities in the gills. These farms were located in an area with high risk of developing gill disease, and three of the farms were diagnosed with GD in the autumn. In the present study we show temporal changes in pathogens in salmon from all 6 farms, revealing recurring infection patterns by Desmozoon lepeophtherii and Candidatus Branchiomonas cysticola (C. B. cysticola), and large variation without an apparent pattern in densities of Ichthyobodo salmonis . Infections with the microsporidian D. lepeophtherii show a clear seasonal pattern, and high densities are associated with GD. Ca. B. cysticola appears not to be directly connected to the disease, albeit densities of this bacterium may coincide with high D. lepeophtherii densities. Amoebae ( Paramoeba spp.) were only sporadically detected with low densities. Salmon with low condition had elevated densities of D. lepeophtherii and Ichthyobodo spp., while no such pattern was seen for the other pathogens. Challenge studies are needed to substantiate the role of D. lepeophtherii in GD, but realistic challenge model (i.e. bath) has so far not been developed. Based on the present molecular screening, we suggest that D. lepeophtherii infections both may be responsible for GD, and cause runting in farmed salmon populations. Statement of relevance This is an epizootiological study of Atlantic salmon and gill diseases. There is much known about pathogen in connection with GD outbreak, less is known about the occurrence of potential pathogen in healthy farmed salmon or how such infections develop over time. High densities of the microsporidian parasite Paranucleospora theridion in the gills coincide with gill disease, making P. theridion a possible primary source to this condition. Densities of Paranucleospora theridion , Candidatus Branchiomonas cysticola and Ichthyobodo salmonis may be correlated in farmed salmon populations with gill disease. P.theridion and I. salmonis densities are elevated in Atlantic salmon with low condition (‘runts’).