Koi Bacteria Diseases


Taken from “Understand aeromonas, pseudomonas pathogenic bacteria in Koi ponds” by Tom Holder.

I am extremely grateful to Tom Holder the master distributor world wide of the revolutionary product KoiZyme also known as Genesyz for permission to reproduce this article on aeromonas and pseudomonas pathogenic bacteria.

One of the most important things in keeping your pond and your fish healthy is understanding pathogenic bacteria. There are a wide variety of pathogenic bacteria that can infect your pond. By far the most common are aeromonas and pseudomonas. These two bacteria kill more Koi each year than all the other pathogens combined. Understanding how these pathogens live, eat and attack your Koi is vital to controlling them.

Aeromonas and pseudomonas cause ulcers (also known as hole in the side disease), fin rot, mouth rot and tail rot. If left untreated the damage they inflict will eventually kill the fish. Many hobbyists believe that their ponds do not have either of these bacteria when their fish are not currently experiencing any of the above symptoms. This simply is not true. Aeromonas and/or pseudomonas exist in almost every Koi pond the world. You must understand that it is possible for Koi to be around these bacteria and NOT be infected. Koi have a defense mechanism that helps protect them against these bacteria. This defense is made up of primarily their slime coat and their immune system. It is important not to have a false sense of security because all your fish appear healthy. This can change quickly. The big question is: How much aeromonas and pseudomonas can Koi be exposed to without getting sick?

In 2000 when KoiZyme was first introduced to the Koi hobby, many hobbyists and dealers conducted their own tests to verify KoiZyme did what it claimed. Most of these people were kind enough to share their test results, as well as information on the condition of their fish at the time of testing, with Koi Care Kennel. Conducting these tests were relatively simple. A sample of pond water prior to dosing with KoiZyme was sent to a lab to determine how much aeromonas and pseudomonas was present. The pond was then treated with the five initial treatments of KoiZyme. Once these treatments were completed, another pond water sample was sent to the lab for testing. A comparison of the before and after test results verified a significant reduction in aeromonas and pseudomonas. At Koi Care Kennel we reviewed test results from around the country and found some most interesting information. One pond that was tested had 22,000 C.F.U’s (Colony Forming Unit) of aeromonas prior to dosing with KoiZyme. Most of the fish were experiencing various degrees of ulcers or fin rot. In this particular pond 22,000 C.F.U’s of aeromonas were enough to cause problems in the majority of the fish. Another pond tested had 86,000 C.F.U’s of aeromonas prior to dosing with KoiZyme. All the fish in this pond were healthy with no signs of ulcers of any kind. From this example, it can be seen that there is no set level of aeromonas that will cause ulcers. Other factors can enter in to the picture here, such as the virility of different strains of bacteria, etc., however for the sake of simplicity, what is most important to remember from this discussion is that the overall health of the Koi plays a huge role in how much pathogenic bacteria a fish can be exposed to and not get sick.

In an effort to help you manage aeromonas and pseudomonas in your pond, I have come up with some terminology that will hopefully help you to visualize the relationship between pathogenic bacteria and Koi health. Let me emphasize that this is NOT some scientific theory based on mounds of research, but a simple explanation meant to help the hobbyist understand some basics.

If you had your pond tested for aeromonas and pseudomonas, you would get back from the lab a C.F.U. count telling you how much pathogenic bacteria was in your pond. Imagine this number as a RED LINE representing the pathogenic bacteria level in the pond posing a threat to the fish.As mentioned earlier, fish have a defense mechanism against pathogens. Each fish has its own individual tolerance level to the RED LINE based on the condition of its slime coat and the strength of its immune system. Now take a number of C.F.U’s that represents the highest level of pathogenic bacteria that an individual fish can be exposed to without getting sick. Imagine this number as a BLUE LINE. To have a totally healthy pond with no sick fish, each individual Koi would have a BLUE LINE higher than the RED LINE of the pond. For example, if an individual Koi had a BLUE LINE of 25,000 C.F.U’s (the highest level of pathogenic bacteria he could withstand without exhibiting symptoms) and the ponds RED LINE was 18,000 C.F.U’s, the fish would remain healthy and safe. On the other hand, if this individual Koi’s BLUE LINE was 15,000 C.F.U’s, it would be sick because it could not tolerate the 18,000 C.F.U’s in the pond.

Let me give you a classic example of how this relationship works. This example may also help some Koi dealers and hobbyists the next time a dealer is blamed for selling a sick fish. A hobbyist we’ll call John has had his pond for some time and for the past three years all his fish have been healthy with no infections or problems. John decides it is time to finally go out and buy that special show quality Koi he has always wanted. He visits his friendly Koi dealer, looks around and sees nothing but healthy, beautiful fish. He feels confident in spending the money for the Koi he has always wanted. He buys it, takes it home, and quarantines it for three weeks. Lets say he even treats it for parasites and flukes during the quarantine period. At last, he puts it in his pond and it gets sick with ulcers and fin rot. How many times have you heard John say it was the dealers fault. John’s collection has been healthy for the past three years. His pond is not the problem, just look at his healthy fish.

Lets take a look at what could have happened:

John’s pond had a RED LINE of 40,000 C.F.U’s. All his fish were healthy. They had BLUE LINES of lets say, 45,000 C.F.U’s.

Now, lets look at the dealers pond. He works hard to keep his ponds clean and healthy.When tested, that show tank had a RED LINE of 10,000 C.F.U’s. The fish John bought had a BLUE LINE of 20,000 C.F.U’s. It was healthy in that show tank when it was sold. But what happens when that fish with a BLUE LINE of 20,000 C.F.U’s is put in a pond with a RED LINE of 40,000 C.F.U’s? It gets sick because it cannot tolerate that level of bacteria.

Obviously, this scenario does not pertain to sick fish being bought and sold. But it is easy to see what can happen with the red line and blue line when moving fish from one pond to another without knowing what the RED LINE value is in each of the two ponds. Even if you did know the pathogenic bacteria levels in the two ponds, how do you determine the BLUE LINE of the fish being moved? What can you do?

Fighting the battle on two fronts

Keeping your Koi healthy and your pond healthy is a battle. And it’s a battle you want to fight on two fronts. On the first front you want to work on lowering the RED LINE in your pond. That is, you want the pathogenic bacteria level as low as possible. You do this by focusing on good mechanical filtration to remove the Koi waste as quickly and as thoroughly as possible. Use KoiZyme to combat the proliferation of aeromonas and pseudomonas. At the same time you want to work on the second front, raising the BLUE LINES – the ability of the fish to tolerate pathogenic bacteria. This means raising the overall health of your fish, and strengthening their immune system. To accomplish this, water quality must be kept as high as possible. Check ammonia, nitrite and nitrate levels keeping them within acceptable limits. Do periodic major water changes. Diet is very important to the overall health of the fish. They are what they eat. Feed a quality staple food and vary their diet. Feed collard greens, kale, romaine lettuce, citrus fruit, watermelon and defrosted frozen peas. Adding a paste food as a way to get extra vitamins and fatty acids in your Koi’s diet is always a good idea. See our website for a paste food recipe that the fish love! www.KoiZyme.com

Another factor that can dramatically affect the relationship between the RED LINE and the BLUE LINE is parasites. In fact, it throws the red line/blue line relationship right out the window. Parasites can bore through the protective slime coat of the fish allowing any existing opportunistic pathogenic bacteria to cause ulcers regardless of the BLUE LINE. Even with an extremely low RED LINE in your pond, the moment parasites are introduced, secondary infections from the existing pathogenic bacteria no matter how few can occur. Keeping your pond parasite free is critical to maintaining healthy fish.

It is easy to assume that when ulcers develop, an aeromonas problem exists. However, if the pond is well maintained and the fish are well cared for, parasites could very well be the problem. A microscope is needed to confirm the presence of parasites. If you don’t yet have a microscope, you really ought to get one. It is a necessary tool in the Koi hobby. Check with your local Koi club to see if you can get a member with a microscope to help you take a scraping of your Koi. If you don’t have access to a microscope, then it may be a good idea to treat for parasites anyway. Use a safe and effective parasitic treatment such as Proform-C. This product can be used in water temperatures as low as 50 degrees (F).

Ultimately, the main goal is to get the RED LINE as low as possible and the BLUE LINE as high as possible. Good mechanical filtration to remove Koi waste and the use of KoiZyme is the most effective way to lower the RED LINE in your pond. Raising the BLUE LINE of the fish is achieved by giving attention to providing a healthy diet and insuring the best water quality possible. Keep in mind stress will lower the BLUE LINE of a Koi quickly, and remember that as the seasons change and water temperatures fluctuate, the Koi’s immune system is affected, thereby lowering the BLUE LINE of the fish as well. The bigger the margin between the RED LINE and the BLUE LINE the better the chances the fish have of staying healthy.

You can win the battle against pathogenic bacteria if you fight the battle on BOTH fronts.


Koi Medications Koi Pond Treatment and Fish Health water disease used Koi MedicationsKoi Pond Treatment and Fish Health

Ever since Adam and Eve sinned in the Garden of Eden, man has been struggling with the problems of an imperfect world such as weeds, death and disease. This is very true for the Koi keeper who over the years has been forced to experiment with different chemicals and compounds in the quest to find the ‘magic bullet’ that will successfully treat his Koi.

Pond treatments are big business and it is evident how much as Koi keepers we are cursed with disease when viewing the range of bottles, boxes and powders stocked by Koi dealers to treat our Koi.

Once opened, many of the different branded treatments look very similar as they share very similar formulations, tried and tested over time. Historically, there has been very little financial incentive for pharmaceutical companies to research new aquatic medications when confronted with extensive research costs and the limited market compared with the incentives for finding new drugs for the human medicine.

Some of the chemicals used in the hobby today have been introduced (and recently restricted) from fish farming and other disciplines, including human medicine. With several treatments under potential threat of withdrawal from our hobby, and the change in Koi keepers’ opinions away from chemical treatments, alternative methods are starting to enter the market.

As science becomes progressively applied to Koi keeping and in this age of information overload, more questions are being asked of what Koi are subjected to when treated for disease. Are the treatments environmentally friendly? Are there alternatives? Why do we use them? How do they work? What are the side effects for our Koi, filter and pond?

All medications are used for their toxic effects on the target disease organism, whether bacteria, fungi or parasites. Unfortunately, most medications are also toxic to Koi as well as filter bacteria and aquatic plants.

The approach to chemotherapy in the pond environment is quite unique in the pet industry in that the water is usually treated instead of the animal. The chemical dose is determined by the volume of the pond rather than the size or number of Koi. In this way, when using a long-term bath treatment it is necessary to know the precise volume of the pond rather than the size or weight of the diseased animals.

This has many obvious benefits in that the fish can be treated without being handled and potentially thousands of fish can be treated in a single action (a real benefit for the Koi farmer). Yet, the cost of treating 20 Koi in a pond compared with 20 Koi in a bowl would unavoidably be more expensive; but as most pond treatments are inexpensive, this still does not prove to be a financial problem.

Larger specimen Koi (and other large pond fish) suffering from certain bacterial conditions are sometimes better treated individually with antibiotic injections. In contrast, in this situation it is essential to know the size of the fish and the cost of the treatment is directly related to the weight of fish treated.

Chemotherapy (chemical treatment) immediately conjures up thoughts and images of cancer treatment and the appalling associated side effects such as loss of weight and hair. Such graphic side effects are due to the treatment also being toxic to the host. The key factor is treating with a dose that is sufficiently concentrated to kill the disease but not the host. The same is true in Koi chemotherapy.

It is better not to treat at all rather than under-dose as under-dosing stresses the fish and does not eradicate the target pathogen, perhaps even enabling future generations of that disease to become more resistant to treatment. This is already the case with some bacteria that are resistant to antibiotics and some parasites being resistant to insecticides where the application of the medication has been inappropriate.

What do Koi medications treat?

There are four categories of pathogen (disease-causing organisms): viruses, bacteria, fungi and parasites.

Very briefly, viruses cause diseases such as carp pox and are responsible for a number of notifiable diseases such as SVC in carp, and more recently KHV. Viral diseases cannot be treated because of their mode of action and this is why most of the notifiable diseases in the UK are viral. Once a fish has contracted the disease, it is untreatable and down to the fish’s own immune response to attack the virus. Notifiable disease is a disease listed by DEFRA/CEFAS whereby any occurrence of such a disease must be reported to DEFRA/CEFAS who control the movement of these fish and thus control the spread of the untreatable viral disease. (Notifiable diseases are responsible for closing down fish farms as a result of the strict practices that infected sites have to carry out.)

Fish, just like humans, can be vaccinated against certain viral diseases where they are inoculated with a weakened form of the virus that stimulates the body to produce anti-bodies against that virus. In future infections by that virus the body is at an advantage in that it already possesses the antibodies to attack the virus. The fish is then immune to that virus. Although trialed in Koi, fish vaccination is more common in fish farming and can be carried out using a dip or bath.

Bacteria are responsible for causing external complaints such as fin rot, gill rot, ulcers and ‘mouth fungus’ and are usually treated by dosing the water with a chemical treatment. Internal bacterial complaints which may cause haemorrhaging and possibly dropsy are better targeted using an injection of antibiotics. Antibiotics are only available under prescription from a vet and injections are only really suitable for larger fish. Vets can also prescribe antibiotic food.

Fungus is responsible for the cotton wool-like growths found on wounds or abrasions. Fungus is often quite difficult to treat, especially in advanced cases, as the protruding fungus growth is the tip of the iceberg in that out of sight, the fungus is penetrating deep into the living fish tissue. Unlike the other categories of disease, fungus is not contagious and affected Koi will not infect healthy and intact Koi.

Parasites can attack the exterior and interior of fish and range in size from being microscopic (Chilodinella, Trichodina) to those visible by the naked eye (Fish Louse, Anchor Worm, White Spot) up to those several centimetres long such as leeches and tapeworms. Parasites on wild fish remain in a finely balanced relationship where their level of infection does not cause the death of the host. It is in the parasite’s interests to keep its host alive. In captivity in a Koi pond, however, Koi and parasite relationships can become unbalanced causing the death of the host. Treatments for parasites vary according to the location of the parasite (internally/externally), the size of the parasite and its lifecycle.

What treatments are used?

It is no coincidence that many proprietary pond medications are very similar in colour and appearance. Most of them follow very similar formulae with differences occurring in the refinement of chemicals used, chemical concentrations and minor adjustments to the base formula. Other chemicals are used on their own and for toxic implications cannot be mixed with other active ingredients.

Commonly used chemicals include malachite green, formalin, acriflavine, potassium permanganate, methylene blue, antibiotics and salt. A Koi keeper at one time or other will have used at least one of the above to treat their Koi so it is pertinent to know what effect these chemicals have on the disease, fish and the pond environment.

How do medications work?

Malachite Green

Malachite is a strong dark green dye that has even been used as an antiseptic in wounds in humans. Different grades are available but the less toxic zinc-free malachite green is used in ponds to treat fungus and microscopic external parasites such as Chilodinella, Costia and White Spot.

Due to its broad action, malachite is often the foundation to many pond medications. Malachite is toxic to humans as well as fish and is a cancer-causing substance. Care must be taken when using it especially if in powder form as it is extremely concentrated in this form. Fish unavoidably absorb malachite through their gills and being a cumulative toxin it is stored in fish flesh. Its use in trout farming has recently been restricted as there is evidence that fish reaching the market contain traces of malachite green.

A replacement for malachite that is less risky to humans is being researched but as malachite is so effective and readily available, the financial incentive to research and develop an alternative is very small when considering the small size of the pond market. Such a change will only occur through legislation banning the use of malachite in certain circumstances.

Malachite permeates through cell membranes of parasites and fungi where it interferes with respiratory and metabolic processes within the cells. Consequently, treated pathogens are unable to generate energy within their cells, eventually dying.

If Koi are overdosed with malachite their cells suffer the same effects on a massive scale, potentially killing the Koi. There is no antidote for malachite over dose.


Formalin is a solution of approximately 40% formaldehyde gas. It is a clear, colourless, pungent and highly toxic solution. Regularly used with malachite green (Leteux-Meyer mixture) as the effect of the two combined chemicals is greater than the sum of each if used individually. It is very effective against microscopic external parasites such as White Spot, Chilodinella and Trichodina.

Formalin is a universal disinfectant and works by damaging the structure of proteins that form the structure of cells and the genetic information within the cells themselves. Technically described as a protein precipitator, formalin denatures proteins unselectively which unfortunately will also include Koi tissue, so the correct dosing is critical.


The antiseptic nature of acriflavine is known from its uses in human medicine as a treatment for mouth and throat infections and for disinfecting wounds. It is a deep yellow powder that dissolves easily in water and can be used to treat bacteria, fungi and particular parasitic infections. It is absorbed through cell membranes where it reacts with DNA inside the cells. This disrupts the pathogen’s ability to reproduce causing an accelerated death and preventing the spread of the infestation. It is still not clear why acriflavine has this effect on DNA within cells.

Potassium Permanganate

This is a dark purple crystal effective against bacteria and external parasitic infections and is routinely the treatment for dipping newly-harvested or imported Koi. It is a very toxic chemical that can quite easily kill fish if even slightly over dosed. Its mode of action can be seen by the naked eye in that it forms manganese dioxide giving surfaces a brown colouration. This forms a manganese-protein complex in contact with proteins (fish skin, mucus, parasites, bacteria) which interferes with the protein synthesis of the organism, causing death.

Its effect is greatly reduced by a high organic content in the water as the potassium permanganate reacts with the organic molecules in the water rather than the target organisms.

In the Second World War during the years of rationing, when tights and stockings were in very short supply, to remain fashionable, ladies regularly took potassium permanganate baths to turn their legs brown! This is not to be recommended.

Methylene Blue

Methylene blue comes as a very dark green powder, appearing blue when dissolved in water. Once very fashionable, methylene blue is now considered a ‘traditional’ medication for bacterial, fungal and parasitic infections. It is now used less frequently as it is highly toxic to plants and will wipe out the bacteria in a biofilter. It is easily absorbed through cell membranes and affects cell activity by raising oxygen consumption within cells. Its mode of action is unclear but it is thought that its action is similar to that of other dyes.


Antibiotics (literally means ‘against life’) are naturally occurring chemicals produced by fungi or bacteria that have an antibacterial effect. Antibiotics are now manufactured and produced synthetically but have the same effect.

The use of antibiotics in the UK is controlled by prescription to limit their use to treating worthy cases rather than allow their widespread use to prevent disease that would increase bacterial resistance. This has already been seen with antibiotics such as oxolinic acid and oxytetracycline which are now useless against many bacteria. This has been one of the major issues in recent years when treating ulcers in imported pond fish where the ulcer does not respond to antibiotic treatment due to bacterial resistance.

Antibiotics can be added to water in short term baths and dips, fed orally in medicated food or given via injection. They must not be added to a tank or pond as they will wipe out any biofiltration.

Their mode of action is varied and ranges from the interference of cell membrane formation in developing bacteria to the inhibition of genetic apparatus within microbes, preventing cell division and the multiplication of bacteria. As bacterial infections spread rapidly it is vital to stop the bacteria from dividing and multiplying and antibiotics achieve just that, unless the bacteria are resistant to that antibiotic.


Salt (sodium chloride) can have several therapeutic effects on Koi and is used quite regularly by some Koi keepers as a preventative as well as a treatment. It has effective antiseptic properties and can be used as a tonic in mild concentrations to stimulate the Koi’s metabolism. It can also be added to ponds to reduce nitrite toxicity. Used as a dip or a long-term bath, salt can also be used as a treatment against external parasites such as Trichodina, Argulus and Lernaea.

In stronger concentrations, salt is believed to have a three-fold effect on parasites. Acts as a skin irritant increasing mucus production, throwing off skin parasites – the high sodium ion concentration is toxic to external parasites – the osmotic change will cause parasites to implode.

If treating ulcerated fish, the addition of salt to the water also reduces the influx of water into Koi, taking pressure off its kidney functions. It is important to remember that salt will remain in a pond system until it is removed with a water change.

As it can be seen, the mode of action of many Koi medications is at the cellular level, attacking cell membranes or activities within the cell. Medications are not usually selective in their action but quite crude, with Koi surviving by virtue of their size and complexity in relation to the smaller, susceptible pathogen. Consequently, pathogens of just one or a few cells in size are easier to treat (and kill) than the more complex and larger parasites.

Medications are nearly always toxic to Koi and humans and administered on the basis that at the recommended dose rates, they are more toxic to the pathogen that the Koi. This is why medications should never be overdosed.

It is essential to acknowledge that while most disease problems are the result of a water quality problem, pond medications will not solve a water quality problem but only treat the disease. Therefore always try to identify and solve the cause of the problem before treating it.

Essential Facts for Treating Koi

1. Only treat your Koi once you have made a definite diagnosis.
2. Pond treatments will kill pathogenic organisms, but only your Koi are able to heal themselves. They will only be able to recover from disease if the water quality is ideal.
3. Pond treatments cannot be used as a substitute for a quality pond environment. When treating for disease, carry out any corrective husbandry as a priority, otherwise the Koi will continue to suffer from stress and ill health.
4. Always aerate your pond vigorously when treating, as pond treatments have a negative impact on dissolved oxygen.
5. Know the volume of your pond and filter system (in gallons or litres). Volume in gallons: Calculate the volume in cubic feet and multiply answer by 6.25. Volume in litres: Calculate the volume in cubic feet and multiply answer by 28.375.
6. Never leave a bath or bowl of treated Koi unattended. By definition, bath/bowl treatments involve high doses that can cause fish to deteriorate rapidly.
7. Always complete a course of treatment, especially when treating against external parasites.
8. Please also check out this UK Pond Doctor site:


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