Compartmentalisation is a new tool for disease management within a country. In aquaculture, the successful application of compartmentalisation is largely dependent on the system of production and the epidemiology of the disease(s) for which the compartment is being defined. Therefore, compartmentalisation may not be universally applicable across all systems and diseases. The paper examines the implementation of the concept, providing examples of specific industries, and discusses the application of hazard analysis and critical control points (HACCP) to the biosecurity of the system. The role of compartmentalisation in the management of aquaculture disease emergencies is also discussed.

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In Australasia, bonamiosis (the disease caused by haplosporidian parasites of the genus Bonamia) was first reported from the New Zealand dredge fishery in the 1980s, and was subsequently reported from oyster farms in both Australia and New Zealand.In New Zealand, Foveaux Strait separates Stewart Island from the South Island. The strait was famous for the quality of the dredge oyster beds that had been fished continuously since the 1860s and were believed to have been carefully managed through a limited effort fishery and a quota.In 1985, fishers reported the occurrence of large numbers of freshly dead oysters on the western central beds. Subsequent examination by aquatic animal health specialists from the Research Division of the Ministry of Agriculture and Fisheries (now the National Institute of Water and Atmospheric Research, Ltd.) revealed that affected oysters were infected with a species of the haplosporidian parasite, Bonamia exitiosus. Monitoring of the beds in the strait over the next 8 years documented the decline in catch and eventually, in 1993, the fishery was closed. Because of the shortage of oysters and the high prices that were anticipated, a number of aquaculture ventures began in New Zealand during the 1990s, mostly using suspended tray culture. However, attempts failed due to the disease. Also in the 1990s there were attempts to farm Ostrea angasi in Australia. Outbreaks of bonamiosis occurred in oyster farms in Tasmania, Victoria and Western Australia. The ongoing mortalities have made farming this type of oyster uneconomic in Western Australia. However, some farming of O. angasi is undertaken in New South Wales where bonamiosis has not been reported. This is one of the few examples of a non-introduced disease agent destroying a wild fishery and aquaculture. Recent research has suggested that the impact of the fishery may have triggered the epizootic in Foveaux Strait as well as causing outbreaks in cultivated oysters. This has lessons for fisheries managers.