Make sure that when you do treat with antibiotics, that you follow the recommended course, especially when fish improve. This is a point that many aquarists do not follow based on conversations and feedback over the years, as often a well meaning aquarist will purchase just enough medication for one dose or two when three or four are the minimum required. Then what will happen is the fish may improve somewhat and the aquarist assumes all is good, but then the fish go “downhill” and subsequent treatments with the same antibiotic are not as effective if at all as the disease pathogen have built an immunity to this antibiotic.
I have had aquarists confront me stating “I thought you said this medication would work, the fish got better, but then they got sick again and now they are worse than before”. When I dug deeper I found that only one or two treatments had been used and this is the common result when one treats with most antibiotics this way.
An exception is Triple Sulfa (or any Sulfa) which are not true antibiotics, rather Sulfas are antimicrobials. That said about Sulfas, they too are much more effective when the full course is followed.

Change Medications when Ineffective;

Since fish treatment (especially bacterial infections, not Ich or other more positively identified diseases) is far from an exact science, it is important to try another antibiotic if after three treatments no results are seen. Also if some results are seen, but the fish goes backwards as to remission of symptoms, I would recommend changing antibiotics/antimicrobials as there may be bacterial resistance (often weak treatments such as Melafix or Pimafix will result this way).

As I note in this article, the majority of aquatic diseases are gram negative which make treatments with antibiotics such as Kanamycin or other gram negative antibiotics a good choice. This is no guarantee that the disease pathogen will respond. Sometimes combinations of Kanamycin and Nitrofurazone give a wide spectrum treatment, other times you may have to try very different antibiotics such as Erythromycin or Metronidazole (Erythromycin is often a good choice for usually aerobic gram positive eye infections) while Metronidazole is sometimes a better choice than Kanamycin or Minocycline for anaerobic gram positive bacterial infections with the side benefit of mild effectiveness for internal and some external parasites.

The bottom line is to read the other pages of this article such as Aquarium Medications Two, antimicrobials, antibiotics and to UNDERSTAND the strengths and weaknesses of each antibiotic used. You need to know whether aerobic, anaerobic, gram negative, or gram positive are what you will need for treatment.
For instance after finding some success with subsequent backslide in treatment success with a mild aerobic gram positive treatment such as Melafix, the next course may be a treatment with a stronger gram positive medication. Kanamycin Sulfate is both aerobic gram positive and negative, although more so as to gram negative and may be a good next course of action in THIS example (the addition of Nitrofurazone would increase effectiveness in difficult cases); while Erythromycin which is primarily only gram positive (aerobic as well) would be stronger yet (although it would be much more harsh on your bio filter).

The above example is just this, an example and a case of a less common gram positive infection. The use of Erythromycin for example with no effectiveness would likely indicate a totally wrong medication choice, which would not be too unlikely since gram negative infections such as Aeromonas, Vibrio, Columnaris are much more common in aquariums.
Using Erythromycin as an example again, if it was/is effective for a suspected case of Columnaris; the facts are your fish did not have Columnaris since Columnaris is gram negative and Erythromycin is almost strictly gram positive.

This general principle does not apply to the use of medicated baths using Methylene Blue or Potassium Permanganate and salt, only the optional antibiotics used in any bath (antibiotics should not be used with Potassium Permanganate).
Also as noted earlier, sometimes combinations will allow for better effectiveness than each medication by itself (I would call this the cocktail effect which is employed in human treatments as well).
See these articles for more about Fish Baths: “Aquarium Disease Prevention; Fish Baths” or Fish Baths, Dips, Swabs

This principle also applies to chemical treatments for suspected protozoan infestations:

One point that I often used for both me or clients when microscopic evaluation was not possible and/or practical was how fish responded to a medication was often a determining factor in what the disease actually was/is.
Three diseases often get confused (for good reason in my opinion), however treatment effectiveness is often a determining factor, see below;
*COSTIA: Formaldehyde
*VELVET: Copper Sulfate, Acriflavin, Methylene Blue
*SPOROZOA: Nitrofurazone (if anything)

Finally, often diseases are mis-identified, such as Fungus.
A good example is the use of Nitrofurazone which is found in different forms in many brands of Fungus treatment, HOWEVER this is not usually effective for true Fungus/Saprolegnia cases. If your treating for Fungus and switch to a product containing Nitrofurazone, likely your aquarium has Aeromonas and care should be taken to prevent this in the future.
See: Aquarium Aeromonas

Consider Water Conditions when Medications Ineffective;

Back up Bio-Filtration

As noted earlier in this article, water changes before each dose are important to the effectiveness of treatment. The other aspect that may be important is the use of backup bio filtration. This is especially important when using medications such as Erythromycin that are hard on aerobic gram positive bacteria as well as nitrifying bacteria (which although are gram negative, these bacteria are often quickly killed by Erythromycin).
Having a separate sponge filter, bio media, even gravel in a healthy tank that can be added as needed to the tank under treatment can go a long way in making a treatment effective as a soaring ammonia level in an aquarium can nullify the benefits of any treatment. I recommend testing ammonia during a treatment, especially with Erythromycin and Tetracyclines, and then add this bio media at the first sign of an ammonia increase.
If this is not possible or in addition the above suggestion, the use of SeaChem Stability or similar facultative bacterial aids should be added approximately 12 hours after each medication treatment/dosing to aid in maintaining your bio filter

Remove Carbon (& other chemical filter media)

Although most experienced keepers are aware of this, many “newbies” are not and that is the use of activated carbon in filters can and will remove most aquarium treatments/medications. If the carbon in your filter has not been changed in over 8 weeks, it likely will not be too effective at removing your medication from your aquarium/pond (likely it has become more of a media for bio filtration).
If you use filter cartridges, the answer is simple in most instances; simply (& carefully) slit the back of the cartridge and pour out the carbon so that the mechanical part of your filter cartridge can still be used.

Also note that some other types of chemical filter media such as Boyd’s Chemi-Pure or Bio-Chem Zorb can also remove medications and should be temporarily discontinued during use of aquarium medications/treatments.

Carbon or other similar chemical filter media can be replaced after treatment is finished or added to the filter temporarily for 2 hours prior to each subsequent treatment then removed again.
SeaChem Purigen is another good product to use during treatment intervals or after treatment. This product can be used with Carbon and compliments carbon in that Purigen removes many organic compounds carbon cannot remove that are toxic and often interfere with treatments.
The purpose of this is to remove any residual toxins that may have built up during each treatment dose; however this not required, only an option to improve water conditions during treatment).

Mineral treatments (such as Regular Wonder Shells), Buffers, or similar water chemistry additives can safely be used during aquarium medication treatments.

If bio filtration additives are required, such as SeaChem Stability due to ammonia or nitrite issues, these can be added about 50% of the time between each treatment dose.

Change Water

Changing water immediately prior to each treatment can improve effectiveness and lower the possible toxicity of treatment.
A 20% (or larger) can cut back on organics in the water column that can often absorb many medications (such as Malachite Green or many antibiotics), thus lowering effectiveness. As well some medications break down after 24-48 hours and can leave mildly to moderately toxic chemicals behind which a water change (or even running carbon in a filter for an hour or two) prior to the next treatment can help lower/remove.

Tetracycline and Malachite Green are two examples of treatments/medications that can be both more effective and less toxic if water changes (and/or carbon filtration) are performed immediately prior to a new or follow up treatment.

Why I do not use Diagnostic Charts:

Readers of my Aquarium Information sites might also note that I do not use diagnostic charts; the reason is simple, most of the ones posted on the internet or elsewhere are way over simplified and can mislead an average aquarist into miss-diagnosis often resulting in frustration. I will admit I have seen a few that have better flow charts than others, however even these do not take variables into account (which may often include water conditions/parameters that can effect correct diagnosis of disease pathogen).
My point is understanding each medication and how it works, where and where not it works as well as knowing more about the possible disease pathogens is far more important in my opinion than a “one chart fits all” diagnostic chart.
An example would be a fish with a Red Sore; first one needs to determine whether this was caused by another fish, then if not one should find out water parameters, tank conditions and similar. If this tank has poor circulation with a high bio load/DOC (dissolved organic compounds) this is likely caused by Aeromonas or similar since this is an Anaerobic bacteria that thrives in these kinds o water conditions. Columnaris can also cause similar symptoms and is also an opportunistic bacteria where improving electrolytes such as calcium would also help, however with Aeromonas you would want to address the water conditions foremost before treatment otherwise your medication results may be poor leading one to believe that used the wrong medication when in fact the medication could not help the fish over come perfect conditions for this bacteria.

This is an important point, as when medications do not work, it is often not a problem with the medications which is often assumed, but with water parameters and the choice of medication for the problem.
For example you cannot use Neomycin for a severe Aeromonas infection along with poor water conditions and then say medications do not work. In this case Aeromonas is a gram negative anaerobic bacteria that is much more resilient in low circulation, low oxygen water that is low in electrolytes, it also requires a gram negative treatment such as Kanamycin, not a primarily gram positive treatment such as Neomycin.
This point also extends to parasitic diseases such as “Ich” as many medications such as Malachite Green are not only more effective in water with pH above 7.2 and a GH over 150 ppm, it is less stressful to the fish and the necessary electrolytes such as Calcium further buffer and aid in osmoregulation that further helps a fish resist the infestation.

To further summarize why diagnostic charts are generally to be avoided in my opinion is just that, these are opinions that are often vague and even true medical doctors (as per many of my friends in the Medical Profession) often make educated guesses based on a lot more information at hand than the average aquarist has at their disposal (myself included), not to mention a lot more training than most aquarists have. This is important as several studies of online human diagnostic web sites have found the vast majority to be highly inaccurate when put to the test with real subjects where a true medical diagnosis has been confirmed. How can we expect an aquatic diagnostic web site to be nay more accurate when they have less tools and vastly less money at their disposal?

Effect of Water Parameters

So, please make sure all your water parameters are where they should be, if for example your ammonia levels are high, all the medication in the world will not help, in fact they will only exasperate the problem. Make sure you have proper water circulation and even more importantly enough dissolved oxygen and low waste particulates, otherwise your Redox Balance can be adversely affected (this is not to say Redox Potential needs to be worried about for the average aquarist). Adequate calcium levels (which can be partially measured by kH) are very important to proper osmotic proper osmotic function. For more information here see this article; CALCIUM, KH, AND MAGNESIUM IN AQUARIUMS; How to maintain a Proper KH, why is calcium important
If any of the above parameters are out of sorts, you will have trouble affecting a cure, even with proper medication.

And above, proper efficient water changes (with proper electrolytes; salt magnesium, calcium) can do wonders without medication, so use ALL medications sparingly!!

Medication misinformation

I would like to address the common anecdotal comments made by many about the harmful side effects of medications. While almost every medication has a side effect that can harm or kill your fish, applying over use or misuse as a reason to not use a medication is poor aquarium husbandry and even in human treatments what can cure can also harm.

An anecdotal comment often stated is that use of antibiotics will kill your nitrifying bacteria, while this is true it is ONLY true with new bio filters (newly established aquariums), with many gram positive antibiotics, or over use of others.
Although true nitrifying bacteria (Autotrophic bacteria) are gram negative, these bacteria are seriously impacted by gram positive rather than gram negative medications in particular Erythromycin (for reasons that are as of yet not totally understood; See Aquarium Nitrogen Cycle; Nitrification).
The majority of aquarium infections (especially in marine aquaria) are gram negative. So the use of gram negative antibiotics such as Kanamycin (which is primarily gram negative) have a lower risk of a nitrifying bacteria die-off than when used properly/carefully in an established aquarium. Some antibiotics are more mixed such as the Tetracycline families which are often equally divided such as Minocycline; however Tetracycline Hydrochloride is primarily gram positive.
References: What are Bacteria; http://www.dls.ym.edu.tw/ol_biology2/ultranet/Eubacteria.html , Cloudiness in Water.

Another example is Kanamycin Sulfate, this antibiotic can be very harmful on the Kidneys however this is one of the better kidney disease treatments available over the counter for fish you just do not want to abuse or over use it.

Another example is Malachite Green, this has been shown in studies to be carcinogenic when used in large quantities yet in studies using this chemical at established therapeutic levels, Malachite Green has not shown to pose this danger (I reference this source in my Malachite Green section)

Yet one more piece medication misinformation, I would more classify as jumping to conclusions (I state it this way, as often well informed aquarists and forums will make assumptions based on poor scientific method, however I have to give credit for good intention and simply trying to solve a problem). In this area two products by API; Melafix and Pimafix have recently fallen victim to this. I recommend reading page four of this article specifically dealing with these treatments: ORGANIC TREATMENTS.

Basically I have read aquarists in forums stating Pimafix should not be used due to Clove Oil being in this product, however this is akin to stating a human should never use Tylenol as over use (especially with alcohol) can lead to liver failure, however this is not likely used properly with normal water changes between doses (which I recommend with all medications). A similar product; Melafix has been blamed for the death of Labyrinth/Pencil fish, which I am not doubting as the sources (such as Fish Lore) are reputable, however since I and others have conducted tests with Melafix at double dose with Labyrinth fish with no ill effects, I think we have to look scientifically at what the trigger may be (I explore this problem further on page four of the Medications article as noted earlier).

Making False Assumptions when Medicating

This is similar to the above section however I am referring here to aquarium or pond keepers use of medications vs. the previous section dealing with anecdotal advice.

A good example is the use of Erythromycin or Melafix for treating Columnaris which as a Fact is gram negative and then assuming your use of Erythromycin cured this ailment when laboratory tests prove this impossible. What likely happened is some other part of your tank maintenance procedure took care of this opportunistic infection OR quite simply your fish did not even have Columnaris, rather Streptococcus or FNT Disease or other gram positive diseases.

Changing water or otherwise improving water conditions can often allow a fish to overcome an opportunistic infection (such as Aeromonas), thus easily allowing the aquarium keeper to assume that a treatment cured his/her fish.

My point is that this hobby is often driven by anecdotal assumptions that I would like readers to avoid by thinking more scientifically. A controlled study of medication use would include control groups, exact maintenance/water change procedures and more to keep different medication tests accurate. Obviously the aquarium or pond keeper when confronted with sick fish does not have time or multiple aquariums/ponds to perform these tests. However by changing water before treatments (even before each additional treatment), keeping water parameters where they should be for the fish kept, and knowing what each treatment method can and cannot effect, as well as proven/known effective treatments for bacterial & parasitic pathogens can allow an aquarist to know when an infection treatment is the best possible.
So please understand the importance of healthy water parameters, and knowing what a medication can and cannot due rather than listening to or making your own anecdotal assumptions.

Best Used By or Expiration Dates

Despite common belief, 95% of medications are still quite effective well past their expiration/best used by dates often printed on packages (generally an antibiotic is at least 90% + effective 6-12 months after said date). The exception is Tetracycline Hydrochloride which can become toxic past its expiration date, although even then it takes well over a year for this to happen (generally years).
Many organic treatments such as Melafix can last for years past their expiration dates (I used some Melafix that was two years past its date with positive and measured results).

These “dates” are in part made by regulations (often under false assumptions) as well as companies that manufacture these products who know that when you discard a medication you will likely purchase a replacement. Either way, neither reason is based on good science which includes many studies, as well as my own multiple controlled tests over the years.

If you doubt this, a quick search on the internet, including medical sites will prove this correct, so do not believe what you read on Yahoo Answers or similar anecdotal sites.

Here is one such site:
Harvard Medical School; Drug Expiration Dates - Do They Mean Anything?

Gram Negative/ Gram Positive Bacteria

Here are a few terms:

*Gram-negative bacteria are pathogenic, as they can cause disease in a host organism and have a thin cell wall. Gram negative bacterial infections are much more common in fish, especially marine. These bacteria that will NOT retain a crystal violet dye during the Gram stain process.

Please click picture to enlarge

Here are some Gram Negative Bacteria:

-Aeromonas (anaerobic)
-Furunculosis; Aeromonas-salmonicida (anaerobic)
-Vibrio (anaerobic)
-Flavobacterium (Columnaris) (aerobic)
-Pseudomonas (aerobic)
-Streptobacillus (anaerobic)
-Salmonella (anaerobic)

Aerobic Chemolithotrophic Bacteria:
Nitrifying bacteria
-Nitrobacteraceae (aerobic)
-Nitrobacter (aerobic)
-Nitrococcus (aerobic)
-Nitrospina (aerobic)
-Nitrospira (aerobic)
-Nitrosococcus (aerobic)
-Nitrosolobus (aerobic)
-Nitrosomonas (aerobic)

Anaerobic Chemotrophic Bacteria
-Erythrobacter (anaerobic)

- Cyanobacteria (Oxygenic Phototrophic)

*Gram-positive bacteria do not always cause a disease in the host organism and have a very thick cell wall.
Gram positive infections are less common in fish (or aquaria in general). These are the bacteria that retain a crystal violet dye during the Gram stain process.

Here are some Gram Positive Bacteria:

-Mycobacterium (aquatic tuberculosis)
- Streptococcus (Pyogenic Hemolytic Streptococci, Oral Streptococci,Enterococci, Lactic Acid Streptococci, Anaerobic Streptococci)
-Pseudonocardia (anaerobic)
-Staphylococcus (aerobic)

*Of the above bacteria noted, Flavobacterium (Columnaris), Vibrio, Aeromonas, & Pseudomonas cause the vast majority of diseases in aquariums/ponds AND these are gram negative. It should also be noted that Aeromonas and Vibrio are generally anaerobic, so keeping a well circulated/oxygenated aquarium or pond is important for their prevention and treatment.
Mycobacterium is an occasional problem that is gram positive.

I have cited much of the information for this section from this source:
Classification of Bacteria

Contraindications (& Medication Mixing)

Food Delivery of Medications;

For many internal infections soaking medications in food or the use of prepared medicated food is the best coarse of action (in freshwater, marine fish do not usually require delivery of medication via food due to their constant drinking of water around them). I prefer to use frozen foods such as Blood worms or Brine Shrimp (sometimes FD Brine Shrimp), I soak these foods in a few tablespoons of water for about 10-15 minutes then add everything to the aquarium (or pond).

These are the foods I find work best for internal infections when soaked; Metronidazole, Neomycin, Oxytetracycline, Piperazine, and Levamisol. Generally a dose intended for 2 gallons of water treatment will work for a 15 minute fish food soak
For instance with Neomycin, this would mean .10 grams (or one measure) of the brand "SeaChem Neoplex" per each fish food soak twice per day (usually for 7-10 days)

FOR EACH MEDICATION ARTICLE, PLEASE CLICK THE TOP LINKS, OR BELOW:
ANTIBIOTICS/ ANTIMICROBIALS
PARASITE & CHEMICAL TREATMENTS
ORGANIC TREATMENTS

How to Make a Percent-% Solution:

Sometimes it is necessary to mix your own chemical solutions such as Methylene Blue, Malachite Green, Potassium Permanganate, etc.

Simply put; to make a 1% Malachite Green aqueous solution; use a 100 ml bottle, then add 1 gram of Malachite Green to your bottle and bring the volume up to 100 ml.
As another example, to make a 2.30% Methylene Blue aqueous solution; use a 100 ml bottle, then add 2.3 grams of Methylene Blue to your bottle and bring the volume up to 100 ml.

See this equation:
% solution = (dry mass in grams / volume in ml) * 100

QUICK SUMMARY:

I have stated this in other articles as well that I personally have resisted adding disease charts as these proliferate all over the internet, many are very “cookie cutter” in their descriptions. I feel first understanding prevention methods followed then by a knowledge of antibiotics, chemical treatments, and organic treatments will go much further in treatment and disease prevention than a disease chart that has a one size fits all approach.
I recommend reading this companion article about Aquarium Disease Prevention for more information that will help you make an educated choice when treatment of fish is required, rather than a “dart on the wall” approach.
“Aquarium Disease Prevention”

Also I recommend reading some of the specific disease articles such as “Columnaris/ Saprolegnia”, Ichthyophonus, and many others founds here: “Aquatic Information, Resources”, “Aquarium & Pond Answers” or other disease specific articles found on the internet or elsewhere.

For some pictures of fish anatomy that may be useful in disease recognition, please visit this article: “Aquarium Answers; Fish Anatomy”