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Fungus is nearly always a secondary infection, so it is important to find out the underlying cause, which could be water quality, parasites or a bacterial infection. Obviously these need to be resolved at the same time as treating the fungus. If the affected area is fairly small a combination of topical treatment and a long-term bath in malachite green or some other anti-fungal treatment should be successful. However, if the affected are is large, the outlook is poor.