Multi-agent in situ hybridization confirms Ca. Branchiomonas cysticola as a major contributor in complex gill disease in Atlantic salmon

•In situ hybridisation of Ca. Branchiomonas cysticola shows that the bacterium is associated with inflammation and necrosis in which histologically detectable epitheliocysts were not visible.•New multiplex real-time PCR assays and RNA scope in situ hybrdizaton methods for a list of gill pathogens represent a rapid and sensitive diagnostic tool.•The results from multiplex real-time PCR and in situ hybridisation corresponded well.