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Intracellular inclusions containing chlamydia-like organisms are frequently observed in the gill epithelial cells of Atlantic salmon, Salmo salar L., cultured in fresh water in Ireland. In this study, the causative agent was identified in four separate freshwater sites, using 16s rRNA sequencing, as ‘ Candidatus Clavochlamydia salmonicola’. Histopathology and real-time (RT) PCR were used to further assess infections. The prevalence of infection ranged from 75–100% between sites and infection intensity was highly variable. No significant lesions were associated with these infections. As a diagnostic tool, RT-PCR proved marginally more sensitive than histopathology. The fate of ‘ Candidatus Clavochlamydia salmonicola’ in Atlantic salmon post-seawater transfer was investigated in a 12-week marine longitudinal study. Both RT-PCR and histopathological examination indicate that the organism disappears from the gills 4–6 weeks post-transfer. [ABSTRACT FROM AUTHOR]

The prevalence and geographical distribution of the recently described endosymbiont 'Candidatus Branchiomonas cysticola' in Atlantic salmon Salmo salar gill epithelial cell cysts was investigated in seawater-farmed fish suffering proliferative gill inflammation (PGI). To this end, we developed a specific and sensitive real-time PCR assay for detection of the bacterium. 'Ca. B. cysticola' was found to be highly prevalent in Atlantic salmon gills sampled over 7 yr and from 17 geographically distant seawater locations in Norway and Ireland. 'Ca. B. cysticola' was found in significantly greater quantities in fish with large numbers of epitheliocysts, and fluorescence in situ hybridization confirmed its localisation within cysts. 'Ca. Piscichlamydia salmonis', a bacterium previously linked to epitheliocysts, was identified at relatively low levels of infection, apparently independent of epitheliocyst prevalence. These results suggest that 'Ca. B. cysticola' is the main cyst-forming bacterium in seawater-farmed Atlantic salmon in the studied countries. Our results also suggest a relationship between load of 'Ca. B. cysticola' and extent of pathological changes. Taken together with a previously described association between epitheliocyst load and severity of PGI in Norwegian salmon, the results could indicate a role for 'Ca. B. cysticola' in gill diseases such as PGI.