Cleaning Effectively for Captive Herps Christina Miller Last update: Wednesday, April 22, 2009.

It is a popular belief that reptiles and amphibians are "dirty" animals. Although herps can harbour harmful bacteria (such as Salmonella), captive reptiles and amphibians are as clean and as healthy as how much effort is put into keeping the animal and the enclosure sanitary. Making sure your animal's enclosure is clean is one of the most important steps of preventing illness in both yourself and your pet. When people catch Salmonella from their pet herps, it is often because the animal's enclosure was poorly maintained, and became a cesspool of unhealthy microbes.


A little bit of microbiology...

Microorganisms (or microbes) are practically everywhere, this is a fact of life. Our environment (and ourselves!) is covered by billions to trillions of simple organisms like bacteria, simple fungi, protists, archaeans, and protozoans. Microbes tolerate a wide range of conditions that varies the different species, and they have different functions in their ecosystems. Some are necessary for decomposition of organic matter, others produce nitrogen which is vital for plant life, and some even live in the digestive tracts of herbivores and break down cellulose (plant fibre) for the animal.

Clearly, not all microbes are "bad." With the popularity of antibacterial and disinfecting products, it's no wonder that people generally seem to think that microorganisms are all disease-causing pests. What is important to understand is that most microbes do not cause disease, and pathogenic (disease-causing) microbes do not always cause disease. Some microbes only cause illness when they are found in a particular environment. They may be benign in other environments. For example, Salmonella is naturally found in the lower digestive tract of many reptiles and amphibians, but if Salmonella were to be found anywhere else in the body in sufficient numbers, such as the coelomic (body) cavity or an open wound, it would most certainly cause illness.

Pathogenic microbes can also be opportunistic. If something allows their numbers to suddenly multiply more than usual, they may cause illness, then. Microbes passively compete with each other for food in their environment. If there is a wide variety of microbes in the environment, this can keep each species in-check, since there are only so many nutrients to be consumed. When an extraneous factor like an antiseptic or disinfectant, or an antibiotic with a high specificity (there are many possibilities) kills off some microbes but not others, the remaining microbes can flourish since they have no more competition. If they have the potential to cause disease, with their increased numbers they just might. This is why some women become extremely vulnerable to yeast infections when they take an antibiotic for a completely different problem- the normal, "healthy" microbes are killed off by the antibiotic, so yeast are permitted to multiply and cause problems.

A weakened immune system can also allow microbe numbers to grow out of control. Think about when you do not sleep very much, you are often most vulnerable to catching a cold or the flu because a lack of sleep can weaken your immune system. Keep in mind that in humans, the common cold and the flu are caused by viruses, which are not microbes (because they are technically not alive), but the point still remains clear: A weakened immune system can allow disease to occur more readily from pathogens that are not typically causing illness. Stressed captive animals, including herps, can certainly suffer from these opportunistic infections, as well.


Microbes in captivity

When we consider herps in captivity, they are typically in closed environments that are much smaller than the natural environments their wild counterparts experience. In the wild, natural ecosystems are typically kept in some kind of balance- not a perfect balance because random events do occur that cause imbalances. But more or less, balance is preserved. Ecosystems house a host of different microorganisms that take part in so many biological processes (such as decompsition of organic waste, like carcasses, feces and dead plant life), and abiotic factors (like weather) also promote ecosystem "health." The average enclosure for a captive herp is hardly a complete, healthy ecosystem.

For a more pertinent example, we will consider why so many herps defecate in their water dishes in captivity. Indeed, many herps that live near water sources in the wild will eliminate in water. If they may drink from the same water, why would they do this?

Consider the nature of most bodies of water: Many of them are moving sources, like streams, creeks or rivers. This constant flushing could be considered like a "toilet," in that whatever organic waste that is dropped in there doesn't stick around very long. These water sources are also home to many other organisms- microbes, plants and animals, which could eat or decompose fecal matter. The take-home message here is that ecosystems are equipped to deal with things like excrement and dead bodies, so that these "dirty" objects do not turn into biohazards of microbe overgrowth. Also consider that the average water dish in a herp enclosure is not a fully-functional aquatic ecosystem. Microbes that are multiplying using the nutrients in organic waste will have little or no competition from other environmental microbes, and the next time the animal drinks or bathes in the water dish, these organisms that are not naturally found in the mouth or on the skin of this animal could potentially cause disease.

So what microbes are of concern in captivity, and why can they be so persistant? It varies depending on the type of microbe!

• Bacteria: This is a very large group of single-celled microbes, that basically live everywhere. They are vital in nutrient cycling in ecosystems, and not all may cause disease. Naturally, bacteria on or in the body are kept at a "manageable" level by the immune system. Some bacteria may cause serious illness even in relatively small numbers, such as the bubonic plague (Yersinia pestis), leprosy (Mycobacterium leprae), and anthrax (Bacillus anthracis). Some species of bacteria, when faced with harsh conditions, form highly resistant endospores. Endospores are very resistant to environmental stresses, including many disinfectant chemicals, yet they may still infect an organism if ingested or inhaled.
  
  
• Fungi: Like bacteria, fungi are a large group of organisms that live (almost) everywhere, and most are non-pathogenic. Fungi include simple yeast-like organisms, to slime molds, to mushrooms. Not all fungi are considered microorganisms. Many fungi are pathogenic, and can cause diseases such as aspergilliosis, candidiosis, dermatophytosis (like ringworm, which is not actually a worm!), and others.
  
  
• Protozoa: These are single-celled microbes, many are free-living and some are parasitic. Some serious disease-causing protozoa include Plasmodium (malaria), Trypanosoma (sleeping sickness or trypanosomiasis) and Cryptosporidium (cryptosporidiosis). Their lifecycles can be relatively simple to quite complex. Many species have an oocyst stage that is highly resistant to environmental stresses, including chemical disinfectants. Oocysts, like bacterial endospores, can be infective.
  
  
• Viruses: Although not technically considered microorganisms because they are not alive, environmental control of viruses is important so they are included here. Viruses always need a host cell in order to reproduce, however they do not always cause disease. They consist of DNA or RNA, a protein coat, and some have a lipid (fat) envelope (envelopped viruses, those that lack the envelope are called non-enveloped viruses). Viruses essentially "hijack" a host cell by injecting its DNA or RNA, and taking over the cell's function to produce more viruses.
  

Cleaning routines

Keeping your herp's home clean is the first step towards good health, and is often greatly underappreciated. Because we usually keep herps in closed, "pseudo-ecosystems," the enclosure will inevitably get dirty. To avoid some misconceptions, consider the following definitions:

• Clean: To rid something of unwanted dirt or waste.
• Disinfect: To reduce the number of pathogenic (disease-causing) microorganisms on an object or material, so that they are no longer a hazard.
• Disinfectant: A chemical used on inanimate objects (not living things) to destroy microorganisms.
• Sterilize: Killing or removal of all microorganisms on an object or material.
• Antiseptic: A chemical used on living tissue to reduce the number of microorganisms so that they are no longer a hazard.

Cleaning should be a daily routine for captive herps. Waste and any leftover, dead or spilled food should be removed from the enclosure. You will either have to spot-clean the substrate (remove the waste and substrate that was in contact with it, this must be done for any particulate substrate such as sand or soil), replace the section of substrate that has been soiled (like for paper towels or newspaper), or clean the dirty surface (in the case of a bare enclosure bottom, or indoor/outdoor carpeting). Cage furniture like water dishes, hides and branches should also be cleaned if soiled.

Note that "cleaning" does not mean a complete disinfection. For reusable cage furniture, water with a mild detergent (like dish soap) and a good scrubbing is often all that is necessary. The purpose of cleaning is to remove the material that potentially harmful microbes would find appetizing, and reduce their numbers in the process. Cleaning will still leave behind some microbes, but their complete eradication is not necessary. Disinfecting is not necessary on a daily basis for the average herp. Animals that are being quarantined because they are ill or because their health status is unknown would benefit from more frequent disinfection, but this would be excessive for most captive herps.


Disinfection

Sick animals in a hospital or quarantine situation would certainly benefit from routine disinfection, to reduce the number of environmental pathogens that could reinfect the animal. Disinfection should be performed regularly, from once a week to every day depending on the nature of the animal's illness. Effort should be made to reduce cross-contamination between the "sick" cage and other herp cages, including using disposable paper towels to scrub, and washing your hands thoroughly after cleaning or wearing disposable gloves while cleaning. A variety of disinfectants are available, and they should be used appropriately, as the product was intended. Typically, products should be left on a surface free of organic waste for 5-30 minutes, then rinsed off, to be effective. Many herp owners fail to realize that most disinfectants do not act immediately on all organisms, and that organic waste can reduce the effectiveness of many products.

A few definitions to consider:

• Antimicrobial: A chemical that kills or inhibits the growth of microbes, including bacteria, fungi, protozoals, etc. This is a very broad term.
• Bactericide or bacteriocide: A chemical that kills bacteria.
• Bacteriostatic: A chemical that limits the growth/reproduction of bacteria.
• Fungicide: A chemical that kills fungi or their spores.
• Fungistat: A chemical that limits the growth/reproduction of fungi.

Disinfectants can be categorized according to their chemical properties. Different chemicals are suitable for different situations, so this should be considered when selecting a disinfectant for use at home. The following is a summary of different classes of common disinfectants (Slomka-McFarland 2006):

• Iodophore solutions: Iodophores consist of iodine mixed with an agent to solubilize it, so that it stays in liquid form. The most well-known iodophore is povidone-iodine, brand name Betadine. It is available in solutions between 10-100% (higher concentrations are not available domestically), and it is a reasonably effective antimicrobial. It will not kill all bacterial spores, but it is quite effective against viruses, tuberculosis organisms and other mycoplasma. These products are inactivated by alcohol and organic debris, so a clean surface is necessary. It must be in contact for 1-5 minutes to be effective (dependant on the concentration). It also stains porous surfaces, including skin. Iodophores are best left as wound antiseptics.
  
  
• Chlorine: Household bleach is also known as sodium hypochlorite solution, it is useful in concentrations between 2-10%. It has a range of activity similar to iodophores. However, it is corrosive (damages metals), irritating to tissues (both the liquid and fumes), and its antimicrobial activity is decreases in alkaline water (high pH). Note that bleach combined with ammonia will create very toxic, hazardous fumes, so always read the label of any product before use.
  
  Bleach is best used on non-porous materials (made of plastic, glass, ceramic, metal or non-porous rock), which should first be cleaned of any gross dirt, and rinsed thoroughly. A 5% water and bleach solution (50 mL of bleach to 1 L of water, or 0.125-oz cup of bleach to 1 gallon of water) can be used to soak the equipment for a minimum of 10 minutes, then rinsed completely with hot water and allowed to air dry for at least 24 hours. Cage furniture that cannot be bleached includes porous substances that will not rinse completely, such as wood. "Baking" these items outside in natural sunlight for several days can destroy most if not all of the bleach residue, as sunlight deactivates chlorine, the chemical in bleach.
  
  
• Bisdiguanide compounds (biguanides): Chlorhexidine diacetate is the most commonly used biguanide compound, and can be found under the brand names Nolvasan or Clinicide. These chemicals have a decent range of activity, killing most gram-positive and some gram-negative bacteria, some enveloped viruses, some fungi, and mycoplasma (including TB organisms). It does not destroy bacterial spores. Its activity is not hindered by organic matter, and is generally effective as both a cage and instrument disinfectant (10 minute contact time) and for wound asepsis at the appropriate concentrations (read the product label).
  
  
• Quaternary ammonium compounds: Common brands include Quatsyl-D and Parvosol. These chemicals are effective against bacteria and TB organisms, somewhat effective against fungi, mycoplasma and enveloped viruses, and poor activity against nonenveloped viruses. Its activity is also inhibited by organic matter, inactivated by soaps, and it is not very effective in hard water. It can be used to disinfect non-porous equipment and instruments (minimum 10 minute contact time). I find the fumes of these products to be quite strong even when diluted appropriately, so thorough rinsing is advised.
  
  
• Alcohols: Ethyl alcohol (ethanol) and isopropyl alcohol (rubbing alcohol) can be used at concentrations between 60-90% as disinfectants. Alcohols are very effective against bacteria, but do not destroy spores. They are somewhat effective against viruses, and not very effective against fungi. Alcohol is inactivated by organic matter, and fumes can be irritating to eyes and mucous membranes. It can be used on non-porous surfaces and instruments, as well as unbroken skin. Minimum contact time is 20 minutes. They have no bacteriostatic property.
  
  
• Hydrogen peroxide: Hydrogen peroxide (a 3% solution, which is commonly available) is bacteriostatic, and only mildly bactericidal. One study found that a 3 hour soak in liquid hydrogen peroxide did not kill coccidian (protozoan) oocysts (Lee 2007). Hydrogen peroxide is more suitable as a wound antiseptic than a cage disinfectant. Stabilized hydrogen peroxide (compounds are added to decrease degradation) may be much more effective as an environmental disinfectant.

A less unpleasant-smelling but easy-to-use disinfectant that does not quite fall under the categories above is the subsequent application of table vinegar then hydrogen peroxide (or vice versa, the order does not matter). Table vinegar (acetic acid, usually between 4-8% in concentration) and hydrogen peroxide (3%, like found in most pharmacies) will form peracetic acid when combined, which is an effective disinfectant. Both chemicals must be kept in separate containers to be maximally effective. Once sprayed on the surface and rinsed with water, they leave very little residue and practically no odour (Stouffer 1999).

It should be noted that for amphibians that require disinfected equipment, mild disinfectants (such as an antibacterial dish soap) and hot water are recommended, or more diluted solutions of the products above. Trace amounts of strong cleaners (even ones suitable for reptiles) can seriously harm or kill amphibians because of their sensitive and highly porous skin. Many cage materials are very good at retaining fumes, for example aquarium silicone can retain bleach (Wright and Whitaker 2001).


How clean is "too clean?"

Sterile environments that are completely disinfected on a regular basis are probably unnecessary for good health of captive animals. While you can certainly keep a herp healthy for its lifetime in this manner, I personally do not believe this is necessary, and can in some situations be detrimental to the animal's health. Disinfecting not only removes pathogens, it removes "good" microbes that compete with the "bad" ones.

The concern of antimicrobial resistance is very real, where overuse of antimicrobial products like soaps can kill all but the "toughest" microbes, which will multiply and become common. This can leave us with so-called "superbugs," which when pathogenic can be devastating because they are so difficult to control.

However, this brings us to the question of whether semi-naturalistic environments that can "control" bad microbes can be maintained in captivity. This is another complex topic in itself, and involves setting up a deep layer of natural substrate mix, usually with live plants, that will theoretically contain good soil microbes that help break down waste. Gross waste products like uneaten food and fecal matter are removed, but soil is turned regularly to aerate lower layers and keep the substrate healthy. This practice is beyond the scope of this article, but readers are encouraged to learn more about naturalistic environments for captive herps.


Clean yourself!

Your own hygiene should also be taken into account. Scrub your hands with soapy water before and after handling each of your animals or working in any of their enclosures. You can easily unwillingly transmit microorganisms from cage to cage by not washing your hands. This can become a major threat to any established collection, and your health, as well.

Do not clean anything that has come in contact with your animals in a sink or with a cloth that is used by people, especially if these items are used with human food preparation. Keep your hands away from your face before washing them, do not eat or drink while working with your herps or their cages, and do not use items in common with your pets and yourself.


The take-home message

• Regular removal of excrements and uneaten food is important to avoid microbe overgrowth.
  
  
• Cleaning of cages and equipment can be performed very effectively with soap and warm water.
  
  
• Routine disinfection of cages and equipment is probably only necessary for sick or quarantined animals, that may act as disease reservoirs.
  
  
• Most disinfectants are inactivated by organic debris, and need 5-30 minutes of contact to be effective. This means that when you are disinfecting something, it needs to be thoroughly cleaned, then soaked in disinfectant.