| Summary: | Peer reviewed Gill disease is one of the most significant challenges facing global salmon aquaculture and in terms of economic impact; amoebic gill disease (AGD) caused by the free living protozoan Neoparamoeba perurans is perhaps the most destructive. However, gill disease is often multifactorial, with numerous putative pathogens identified as potentially playing a role. AGD was first described in Irish aquaculture in 1995. Between the years 1995 and 2010, there were sporadic and relatively minor outbreaks of AGD. Since the re-emergence of the disease in 2011/2012, greater focus has been placed on gill health. This research aimed to investigate gill disease and in particular the re-emergence of AGD caused by N. perurans in Irish aquaculture. Through this it was hoped to provide the industry with the tools and information to help improve management of gill disease as well as fish health and welfare. With respect to this, Chapter 2 of this thesis details the effort to develop and validate a real-time TaqMan® PCR assay to detect Neoparamoeba perurans in Atlantic salmon gills. Furthermore, it describes the use of this assay to monitor disease progression on a marine Atlantic salmon farm in Ireland in conjunction with gross gill pathology and histopathology. As molecular diagnosis of AGD remains a high priority for much of the international salmon farming industry, Chapter 3 evaluates the suitability of currently available molecular assays in conjunction with the most appropriate non-destructive sampling methodology. In addition it compares this methodology with traditional screening methods of gill scoring and histopathology. Chapter 4 addresses the complex and multifactorial nature of gill disorders. Co-infections are common on farms and there is a lack of knowledge in relation to interactions and synergistic effects of these agents. The advances in molecular diagnostics have made it possible in Chapter 5 to identify N. perurans as the causative agent in the earliest AGD outbreaks. In addition to this, a number ...
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