I ended up using bio-coated nuclei only after 20 years of not using any kind of antibiotic.
A prudent measure. Topical applications of antibiotics are infinitely better than systemic indications, especially for prophylaxis. Aside from being more economical it also reduces the likelihood of increased resistance in other species.
Even then, the efficacy of antibiotics applies mainly to bacteria, not viruses. Retro-viral indications are exceeding complex, expensive to trace and even more difficult to apply.
Water quality is everything. In most aquaculture settings, all known pathogens are generally presumed to be present however not in great enough concentrations to cause disease or mortality. Wholesale slaughter of bugs en-mass leaves dead bodies which decay, giving rise to accelerated levels of ammonia and other nasty compounds.
For example, whirling disease in salmonids is caused by the parasite
Myxobolus cerebralis, but pointless to treat so long as it continuously proliferates in annelids. Namely the aquatic worm Tubifex tubifex
. Unless these are eliminated entirely from the ecosystem there is little chance for habitat rehabilitation, but even then a major food source has been removed thus a double edged sword for the fish.
In nature you can fight the water, but the water always wins. As they say, it's always best to let sleeping bears lay.