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Disinfection -- Principles, Methods and Madness

by Louisa Jaskulski, RVT
“Keep it clean!” is an essential aspect of animal husbandry.  We live in a soup of microscopic critters, of which some can cause serious disease for pets and/or humans.  The challenge is to keep the disease-causing critters under control, without driving ourselves to the point of complete insanity - anyone who cares for multiple birds (and/or other children or pets) knows this is a task which is never “done”.

The first line of defense against any disease is a good immune system. Maintaining our birds on a healthy diet, exercise, toys, love - a happy healthy bird will of course be more resistant to illness.  Simple precautions will limit exposure to illness as well – proper quarantine of sick birds and new birds; doing the appropriate testing; keeping cage, dishes, and toys etc separate; washing our hands between cages; even having dedicated clothes when servicing sick birds and their cages (I use an old oversize T-shirt over my clothes).

However, even with the best of care and precautions, illness happens in our birds.  And, when we are dealing with new birds coming into our homes from any source, there is always a certain amount of risk.  Many pathogens can be “stored” or transmitted on surfaces, dishes, our hands, or our clothes.  Some diseases are contagious.  Therefore, good cleaning protocols are essential.

Because of the importance of disease control in human hospitals, significant research has been done on this issue, with rating systems by the Center for Disease Control and the Environmental Protection Agency.  Basically, the levels of microbe control are Sanitizing, Disinfection, and Sterilizing.

Below is a brief summary of principles, techniques and products, with attention to some particular pathogens we commonly encounter.  This list is not meant to be exhaustive, but merely a guide.  Where I found information that a particular method or chemical kills or controls a particular pathogen, I cited it below.


Pathogens are any disease producing micro-organism or agent.  The four classes that I am addressing here are:  fungi, bacteria, viruses and protozoa.  The examples given are ones of particular importance to companion birds, and which are referenced in the disinfection discussion.

Fungi - Include molds and yeast.  Single celled, often with a rigid cell wall, reproduce by spores or budding.  Of frequent concern to us:  Aspergillis (fungal infection, usually involving the respiratory system), and Gastric Yeast (previously known as Megabacteria), usually involving the gastrointestinal system.

 Bacteria Each of these are a single cell, lacking a nucleus and organelles, consisting of a single double-stranded DNA molecule.  The cell divides rapidly by binary fission and with a high rate of mutation, and can infect all systems of the body.  Generally either round or rod shaped, and mostly divided into Gram Positive and Gram Negative (depending on how the cell wall does or does not take up Gram stain). Many of the bacteria we are concerned about as potential pathogens for birds are Gram negative.  Examples are Chlamydia psittaci, Pseudomonas and Enterobacteria (including Klebsiella).

A special class is Mycobacterium - slender acid-fast (a special stain) rods that cause tuberculosis.  Avian TB is usually caused by Mycobacterium avium, which is common in moist environments.

Viruses - Smaller than most bacteria, they are not “alive” in any traditional sense, as they have no independent metabolism, movement or ability to reproduce.  Viruses must insert themselves into host cells by various receptor/binding mechanisms, after which they use the host cell biochemical functions to make new viruses.

Viruses have a very simple structure, consisting only of genetic material (either DNA or RNA) surrounded by a protein coat (the capsid).  Some viruses also have an additional surrounding lipid membrane envelope and hence called “enveloped” or “lipid”.  Those without the additional envelope are called “non-enveloped”, “nonlipid” or “naked”.

As a general rule, enveloped viruses are not stable outside the body, and hence require close contact for transmission and are easier to destroy.  (Pox virus is an exception to this - it is large, enveloped, and very stable.)  Enveloped viruses include Borna virus (can cause Proventricular Dilation Disease (PDD)), and the Herpes virus that causes Pacheco’s/Papilloma disease.

A word about Borna virus, recently identified as causing Proventricular Dilatation Disease (PDD).  Research is showing that this virus is much more common in pet bird populations than previously thought, and that it does not necessarily progress to PDD.  It is a virus that attacks the nervous system resulting in nerve damage. It is now thought to be a cause of at least some feather destructive behavior.  This is an enveloped virus, fragile outside the body, with a structure that should be vulnerable to rigorous cleaning and disinfection.

Non-enveloped viruses can persist in the environment for long periods of time and are therefore more contagious and harder to eradicate.  Non-enveloped viruses include Polyoma virus, Papillomavirus, and the Circovirus that causes Psittacine Beak and Feather Disease (PBFD).

Protozoa - Single celled organisms, mostly free living with independent movement, can be parasitic. Can form cysts when environment is not conducive to them, and these cysts can be tough, persistent, and difficult to eradicate.  Examples are Giardia, Cryptosporidium, and Coccidia.


SANITIZING is intended to reduce the number of bacteria, viruses and molds on inanimate surfaces to safer levels by mechanical action and dilution.  This is our essential regular maintenance work.  Hot soapy water is your friend here.  Vacuuming, mopping, dishwashing, and laundering cage covers all help a lot. Cleaning perches and cages with lots of hot soapy water, products like Poop-Off or AviTech’s AviClean dilute bleach (1:250, ie: 1/8 cup per gallon water), Borax, or white vinegar are examples of basic cleaning. Home power washing and steam cleaners are other methods, as they remove pathogens by the mechanical action of lots of high pressure water.  (My steam cleaner puts out up to 270 degrees at 60 psi.)  These methods will prevent buildup of dirt and organic matter by virtue of elbow grease and physical removal, and hopefully get rid of a goodly percentage of pathogens in the process. This process of dilution makes it less likely that your bird will be exposed to enough pathogen to cause disease/infection.

Thorough cleaning is an essential precursor to any kind of effective disinfection, as disinfectants do not remove or penetrate organic matter, and will not work if organic matter is present.

NOTE about bleach - Do not use bleach and any soap/detergent together if you want the bleach to disinfect what you are cleaning.  Soap/detergent cancels the disinfection capabilities of bleach, though the bleach will still function as a “whitener” in your laundry.  Mix fresh bleach solutions daily.

 DISINFECTION is intended to destroy, inhibit, or prevent the growth of most infection-causing organisms, usually by use of chemical disinfectants (though commercial steam and high heat can also be used).  These chemicals are usually too strong to be applied to living tissue (skin, mucus membranes, or wounds).  To be a disinfectant, the chemical must be registered as such by the EPA, with the registration number on the label. and the label should list what kinds of things it has been proven to kill (these will usually be human pathogens, though some veterinary products do list animal pathogens).  Disinfectants are classified as being low- or intermediate-level.

Few studies have been done on avian strains of most of these pathogens, so we have to extrapolate - for example, Mycobacterium causes TB in humans and some disinfectants specifically cite Mycobacterium as one they kill.  Avian TB is caused by a strain of Mycobacterium, so I think we can assume that if it kills human Mycobacterium it should kill avian TB Mycobacterium too.

Likewise, the virus that causes Psittacine Beak and Feather Disease (PBFD) is a Circovirus which is the smallest known pathogenic animal virus, only 17-22 nanometers (too small for most air cleaners, I think?).  It is non-enveloped, and it is very difficult to kill.  Virkon-S kills the pig Circovirus, however, and structurally the two viruses are very similar, so it is probably safe to assume that Virkon-S will kill avian Circovirus as well.  UNFORTUNATELY, THIS CIRCOVIRUS IS EASILY DISTRIBUTED THROUGHOUT THE ENVIRONMENT ON FEATHER DANDER, WHERE IT CAN PERSIST FOR MONTHS.  Besides using a chemical like Virkon-S on cages and other non-porous items (like countertops), consider commercial steam cleaning for large surfaces, bake small items or large valuable cages, and throw out porous materials like wood and rope perches.

When using disinfectants, be careful to follow manufacturers’ directions as to concentration and contact time. “Contact time” is the minimum time the surface must remain wet with the chemical to be effective. Mixing too strong or too weak a solution, or using insufficient contact time, renders them less (or not) effective.


a) Low Level Disinfectants kill many “common” bacteria (such as Salmonella, E. coli, most Staphylococcus), many yeasts (including Megabacteria/gastric yeast), and some viruses. Useful for tasks such as normal “thorough” cage and surface. Does not kill resistant bacteria strains, non-enveloped viruses, Coccidia or Cryptosporidia.  These disinfectants include:

  • Undiluted alcohol with 10 minute contact time (since alcohol evaporates quickly, you will have to keep pouring more on to the surface, or submerge the item),
  • Chlorine bleach mixed 3/4 cup bleach to one gallon water for 5+ minutes contact time,
  • Chlorhexidine (Nolvasan, Virosan, etc) 3 oz. Chlorhexidine in one gallon water with 10 minute contact time, and
  • Tamed iodines (Betadyne, Povidone) with 10 minute contact time. These do not kill resistant strains of bacterial, non-enveloped viruses, Cryptosporidia, or Coccidia.

b)  Intermediate Level Disinfectants have a broader range of efficacy.

  • Bleach, mixed 1:10 (1.5 cups bleach in 1 gallon water) for 15+ minutes contact time (will kill Pseudomonas, molds, fungus, Pacheco’s virus, Mycobacterium, Polyoma virus, Giardia, probably PDD Borna virus.  Readily available and relatively cheap.  Fumes are irritating to mucus membranes.  Corrosive to metal.
  • Household Ammonia, 5% for 45+ minutes.  This is the best household disinfectant for Coccidia and Cryptosporidia. Also effective against intestinal worm eggs, fecal coliforms, Salmonella.


The following disinfectants can be ordered online.

  • Quaternary Ammonia Compounds such as Roccal, Wipe-Out - Mix product according to manufacturer specifications with contact time 10+ minutes. Will kill Chlamydia, among other things.
  • Third Generation Quaternary Ammonia, i.e.: Roccal-D Plus – Mix up to 1.5 fluid ounces per gallon of water; 10+ minutes contact time.  Do not mix with any other products.  Proven to kill 23 kinds of bacteria including Pseudomonas, Klebsiella, Enterobacter, Actinomyses, Salmonella, Mycoplasma; and Fungi including Aspergillosis and Candida; various viruses (including Herpes virus, Borna virus).
  • DisCide - a quaternary/alcohol synergistic formula - use full strength, contact time 1+ minutes, 10 minutes as a soak; non-irritating to skin, not corrosive. Kills Mycobacterium (avian TB), drug resistant Staph, Pseudomonas, Salmonella, drug resistant E. coli/Klebsiella, many viruses (including herpes, adenovirus) and fungi.  Comes as a liquid or as wipes.
  • Phenols such as Lysol, One Stroke Environ- 10+ minute contact time.  Needs ventilation and thorough rinsing. Be sure birds are not in the area when using. Very effective against Staphylococcus, Streptococcus, Pseudomonas, Mycobacterium, most enveloped viruses.  Not effective against non-enveloped viruses, fungi, yeast, spores, gram negative bacteria. CAUTION – VERY TOXIC TO CATS!
  • Syn-Phenol – potent detergent/disinfectant which has good residual effect, can penetrate organic matter better than many products and has a residual effect. Contact time is 10+ minutes to disinfect.  Mix ½ ounce in 1 gallon water. Kills Pseudomonas, Salmonella, Klebsiella, E. coli; Aspergillosis, candida, Herpes virus, among others. Less effective against non-enveloped viruses.
  • Virkon-S (potent combination of peroxidation, surfactants and organic acids) – at 2% kills 65 strains of virus, 400 strains bacteria, 100 strains of fungi, including pig Circovirus (PBFD), Aspergillosis, Mycoplasma, Avian Influenza.  This product is marketed primarily to farm operations.  Probably because it should not be released into waterways, you can no longer buy it in California, but it is widely available on the internet for delivery to other states and is not very expensive – a BIG tub of the powder costs around $100, which will clean a lot of aviaries, and is good for at least 2 years.

STERILIZATION kills all pathogens, including bacterial spores and Coccidia.  Most of these methods and chemicals not available to the general public.  However, we can use:

  • Boiling - for as long as you can, at least 30 minutes (but may not kill all bacterial spores, so is not a true sterilant);
  • Baking/Dry Heat - recommended for items that won’t melt or burn when heated to 340+ degrees Fahrenheit for 1 hour to ensure killing viruses, bacteria and fungi.  (Viral capsid proteins denature (ie; break down) above 150 degrees so that the virus is no longer infectious.)  In the case of large cages, find a company that does powder coating - the ovens that bake the powder coat paint on will be a high enough temperature to ensure sterilization.


Commercial steam cleaners heat water up to 380 degrees Fahrenheit, and can go to 1,000+ pounds per square inch. They often can accommodate adding a detergent or other chemical to the process.  They then extract the dirty water out of the house into a tank for disposal.  With the operator holding the nozzle close to the surfaces you are trying to clean, they should be able to effectively remove most pathogens, and kill many of them, so this can be a useful component of a thorough cleaning/disinfecting effort for most floors and fabric furniture (they are too intense for use on wood or walls). If the operator has a nozzle that can put out a narrow stream (in addition to the wide nozzles used for floors and furniture), this could be applied to cages as well -- but you need to ask to be sure the operator carries the narrow nozzle with them.

Commercial power washers can produce water up to 8,000 psi at temperatures in the low 300 degrees Fahrenheit. These function to just blast the dirt away.  These are very powerful machines, and may not be appropriate for indoor home applications.  They are very useful for outdoor aviaries, though!