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Disease control in an aquarium is a very in-depth and complicated subject. There is a lot of biology and chemistry involved and every aspect of fish care can affect disease control. However, there are some basic principals involved that are very frequently overlooked when actually dealing with cases of illness.
One very common mistake is not looking at the full cause of a disease. There are two requirements for an illness to occur. One is that the pathogen is present. The other requirement is that the fish is stressed enough for its immune system to be weakened enough to allow that pathogen to actually cause an infection. There are very few pathogens that can cause an infection without any stress in the fish. The pathogens that can do this are rare.
Most people simply see a problem and ask what is causing it (looking for the name of the disease). If they happen to already know what is causing it they want to know what to treat it with. In almost every case this is all that is discussed. However, to maintain health and not simply have to deal with disease after disease the original cause must be addressed. This means the original stressor needs to be indentified and corrected.
There are many possible stressors in the aquarium. They can be water parameters (keeping fish in parameters too far from their natural range) or shock from parameters changing too quickly. There are behavioral issues, like an aggressive fish in the tank or a schooling species that does not have a large enough school. Water quality is a very common stressor. Many people like to leave good enough alone. The problem with this is that it can simply cause a slow deterioration in the water quality and therefore the health of the fish, sometimes taking years to have full effect (which can be a sudden outbreak of disease or ‘mystery’ deaths). High water quality must be maintained. \
Another very easily overlooked possible stressor is diet. Very few people think of diet as a possible stressor, but a poor diet can cause a wide range of physiological problems in fish. These are stressful as well and can cause an array of health problems.
Many problems with fish health are hard to see and understand. It is not hard to see the salt grain like white spots of ich, but things like water quality and diet are more abstract and many people have a hard time understanding that they can become severe problems. When keeping animals in captivity the keeper must look beyond the immediate appearance of the animal. Thriving long term needs to always be the main goal. This means that in many cases fish that are perfectly healthy in all observable aspects may not really be thriving at all.
People have a tendency to assume all is well when all seems well. This means that they assume their current practices are good and when things do come up that suggest there is a problem, they do not examine them further. For example, if an aquarist keeps the same diet and water change schedule for five years they assume this is good because they did it for so long and there were no issues. But when a fish becomes ill or dies for no apparent reason this aquarist may either try to blame some coincidental recent event (like a filter cleaning or water change) or even blame the death on ‘old age’. But when this is a fish that could and should live to be 10-20 years old and the fish died at the age of 5 there is a strong reason to believe something is wrong with the current care.
The differences between short term health and thriving long term can be very subtle. In many cases the differences can be as simple as minor behaviors, subtle color differences, and many other things that many aquarists may not even notice. Breeding is a good sign that fish are thriving in all but the most easily bred species.
Pushing the limits of the fish is a common way to cause unnecessary stress. When keeping fish outside of their natural parameter ranges people simply state that a few generations of captive breeding have changed the fish enough to now deal with different parameters. This is partially true. The fish can tolerate and do very well in parameters outside of their natural range. But this is not the end of the story. In almost every case the fish would still do much better if kept in its natural parameters. Fish evolved in their natural parameters for hundreds of thousands to millions of years. A few generations in captivity is not going to undo the evolution that brought them to their current physiology and adaptations. The fish can do very well in other parameters if they are far enough from their wild ancestors, but even then they do even better and truly thrive if kept in conditions that mimic the waters they are native to.
In almost every single case when there is something wrong, one of if not the only and best way to fix the problem is with water changes. Water quality can always be better, which can help reduce stress in fish. Water changes alone can fix many if not most of the problems commonly encountered in aquariums. The only exceptions to this is when there is something about the water change itself that is causing stress. For example, if the aquarist matches the temperature perfectly only to have the hot water run out halfway through filling the hot water runs out. Since the aquarist did match the temperature when he started willing the tank he doesn't think temperature is an issue, so the problem persists. Sometimes there are certain problems that can develop with the source water. One situation that I ran in to while running an aquarium store was a sudden outbreak of ich. My coworkers and boss thought it was because I was doing water changes that were too large (over 60%) and the shock of the cooler water caused the ich. I had been doing full cold water changes all winter with no problems, so I didn't believe this was the issue. I had noticed that around the same time the tap water smelled like chlorine, moreso than usual. After some research I found out that since it had been raining more recently so most likely the water company was putting extra chlorine and/or chloramine in the tap water, so much so that even standard dosing of teh dechlorinator was not able to detoxify it all. I started double dosing the dechlorinator and the ich went away immediately. Another less frequent issue is caused when the aquarist is altering the parameters for a tank and unaltered tap water is used for a water change. This can change the parameters in the tank too quickly and stress the fish. This makes it very important to always use buffers and additives if they are going to be used at all.
In many cases simply dealing with the original stressor is enough to completely treat the illness. Once the fish is no longer stressed by the original stressor its immune system can return to normal functioning and may be able to fight off the pathogen on its own. This can be very beneficial because it can mean that no chemical medications are needed. Chemical medications themselves can be a source of stress for many fish. Some medications will kill the nitrifying bacteria in the filter. This means that once treating for the illness is over, the aquarist is now dealing with a tank that is no longer cycled but is fully stocked, which can cause stress and lead to more illness. Many medications can simply kill certain tank inhabitants like plants, invertebrates, and more sensitive species of fish. I try to avoid using any medications at all whenever possible. Very rarely am I pushed to using medications. When I do I try to use either Pimafix or Melafix. Both use plant extracts as their active ingredients. Pimafix is good for treating fungal infections, most commonly seen as white cotton like growths. Melafix is good for bacterial infections, most commonly seen as red patches, ulcers, etc. It is also good for helping healing from injuries like scrapes and bite wounds.
When fish are too far along in the illness for correcting the original stressor to be adequate treatment, other steps must be taken. This is usually in the form of medications. Ideally the fish is moved to a fully cycled hospital tank so that the medication does not stress the other tank inhabitants or effect the nitrifying bacteria in the main tank. It is vital that the hospital tank is not any more stressful than the main tank. If it is it will simply cause the problem to continue or allow for more illnesses to develop in addition to the original illness. This means that the décor in the hospital tank must be adequate for the species being treated (something as simple as a PVC pipe can make all the difference for the fish). The water quality must be maintained at least as high as the water quality in the main tank. Putting a sick fish into a bare hospital room like tank with water quality lower than that in the main tank is not helping anything. This adds stress and reduces the chances of survival dramatically for the fish.
Proper identification of any illness is also vital for proper treatment. There are many books and online resources available to assist in proper identification of illness, as well as the availability of other fish enthusiasts in online forums.
Another thing that can make a huge difference in the likelihood of success is what the aquarist keeps on hand. Having treatment and medication options ready to be used at any moment can make a huge difference in how well the fish does. At the very least aquarium salt should be on hand at all times. Salt treatments can be a natural, effective, and safe treatment option, a great second step after water changes. I also suggest having both Pimafix and Melafix on hand. I would consider it a good thing if you bought both and wasted your money because you simply never needed to use them, that is a good problem to have. I think any other medications are too specific and are not worth it. Having such specific medications would require you to simply stock up on medications for every illness out there.
Once a fish has been successfully treated it should be quarantined to ensure it is not just incubating the pathogen. Once the quarantine period is up (a bare minimum of two weeks) the fish may be returned to the main tank. Many people use water from the main tank to do water changes on the hospital tank. This can allow for a stress free reintroduction back into the tank by keeping the parameters in the hospital tank identical to those in the main tank.
Keeping notes about any illness can be very helpful later on. Keeping detailed notes about anything that has to do with an aquarium can be invaluable. Proper note keeping can help identify otherwise undetectable stressors (such as every year as the weather is dry the pH in the tap water changes and causes stress). It can also help determine the proper mode of treatment when an illness becomes a problem again.
In conclusion, water changes alone will prevent treat most of the problems you would have otherwise encountered. I suggest a minimal water change schedule of 25% weekly, larger if necessary to keep the nitrate concentration under 20ppm before a water change. If problems arise do not increase the size of the water changes, but increase the frequency. Many times this will require daily water changes to fix the problem, but is very effective.