Gill disease of farmed Atlantic salmon (Salmo salar) in the marine environment has emerged as a significant problem for the salmon aquaculture industry. Different types of marine salmon gill disease reported include amoebic gill disease (AGD), parasitic gill disease, viral gill disease, bacterial gill disease, zooplankton (cnidarian nematocyst)‐associated gill disease, harmful algal gill disease and chemical/toxin‐associated gill disease. The term ‘multifactorial gill disease’ is used when multiple distinguishable types of disease (as opposed to an obvious single primary type) are present. When gill disease is non‐specific, it is referred to as ‘complex gill disease’ (CGD) or ‘complex gill disorder’. These two terms are often used interchangeably and are overlapping. The significance of many infectious and non‐infectious agents that may be associated with CGD is often unclear. In this review, we summarise aspects of the different types of gill disease that are relevant to the epidemiology of gill disease and of CGD in particular. We also tabulate simultaneously occurring putative pathogens to explore the multifactorial nature of gill disease.

Complex gill disorder (CGD) is an important condition in Atlantic salmon aquaculture, but the roles of the putative aetiological agents in the pathogenesis are uncertain. A longitudinal study was undertaken on two salmon farms in Scotland to determine the variations in loads of CGD-associated pathogens (Desmozoon lepeophtherii, Candidatus Branchiomonas cysticola, salmon gill pox virus (SGPV) and Neoparamoeba perurans) estimated by quantitative PCR. In freshwater, Ca. B. cysticola and SGPV were detected in both populations, but all four pathogens were detected on both farms during the marine stage. Candidatus B. cysticola and D. lepeophtherii were detected frequently, with SGPV detected sporadically. In the marine phase, increased N. perurans loads associated significantly (p < 0.05) with increases in semi-quantitative histological gill-score (HGS). Increased Ca. B. cysticola load associated significantly (p < 0.05) with increased HGS when only Farm B was analysed. Higher loads of D. lepeophtherii were associated significantly (p < 0.05) with increased HGS on Farm B despite the absence of D. lepeophtherii-type microvesicles. Variations in SGPV were not associated significantly (p > 0.05) with changes in HSG. This study also showed that water temperature (season) and certain management factors were associated with higher HGS. This increase in histological gill lesions will have a deleterious impact on fish health and welfare, and production performance.

Desmozoon lepeophtherii is a microsporidian associated with gill disease in farmed Atlantic salmon (Salmo salar). Detection of the parasite in histologic tissue sections is challenging using common histochemical stains given that the small, widely distributed parasite spores typically occur individually or in small clusters. We compared the ability of 4 histologic methods to detect D. lepeophtherii spores in serial sections of Atlantic salmon gill tissue: hematoxylin and eosin (H&E), Gram–Twort (GT), calcofluor white (CW), and immunohistochemistry (IHC). Using CW as a benchmark to calculate a relative ratio, IHC consistently detected more spores than CW (median: 1.3), followed by GT (median: 0.2) and H&E (median: 0.1). IHC detected significantly more spores than GT (p < 0.05) and H&E (p < 0.05), and GT more than H&E (p < 0.05). We found significant underestimation of numbers of microsporidia spores in gill disease in Atlantic salmon using conventional histochemical stains and recommend the use of CW or IHC to detect the parasite in tissue sections.