A brief Guide to Cleaning and Disinfection in Wildlife Care
- Roger Valls Martínez
- Nov 20
- 6 min read
Over the years, I have realized that hygiene and biosecurity in general are one of the Achilles' heels of practically all wildlife facilities, from rescue centers or sanctuaries to zoos or private collections. The same happens in private homes, where — although the risks are lower — it is often handled even more inadequately. In this post, I want to provide some small keys and guidelines to lay the foundational knowledge on which a good hygiene and disinfection plan should be based, keeping both our animals and ourselves safe.
The Importance of Having a Good Plan
And nothing ever happens. Until it does. And then come the regrets, the urgent changes, and the patches that are useless but aim to cover years of management negligence. This is everyday life in many professional environments working with captive wildlife. It’s a shame because if we planned the biosecurity plan correctly from the start, we would save a considerable amount of money in veterinary care and an even greater amount of headaches. As I said, nothing happens until it does.
A fundamental part of a biosecurity plan is cleaning and disinfecting surfaces, whether in the animal enclosures themselves or in food preparation areas, veterinary surgery rooms, or any other part of the facilities (when I talk about facilities, I also mean the domestic environment, as the same applies in wildlife centers as in homes with animals). And it has a decisive impact on welfare, but above all on health, and therefore on the longevity of individuals. I have personally seen how implementing changes in the biosecurity protocols of some wildlife facilities can reduce annual mortality from 25% to 10%! In just one year!
Even so, these are processes that are often carried out incorrectly, whether due to ignorance, lack of training, overconfidence in certain products, or simply disinterest. That’s why understanding how and why each step works is essential to prevent disease, protect animals, and also ensure a safe environment for the people working with them.
So, let’s review the key points that determine the success of cleaning and disinfection, as well as the most common mistakes and how to avoid them. I want to create a quick and easy-to-read guide, without rambling and straight to the point. Here we go.
0. Cleaning and Disinfection. What Are They?
In the context of facilities or enclosures with animals, the terms cleaning and disinfection have distinct but complementary meanings within any biosecurity protocol:
Cleaning: Cleaning is the initial process aimed at removing visible dirt, including organic matter such as feces, urine, food, feathers, saliva, dust, or any other residue present on surfaces, utensils, or enclosures. This step is usually done with water, detergents, or physical agents (scraping, brushing) and its main function is to reduce microbial load by approximately 90%, while also allowing disinfectants to work properly. Cleaning does not destroy microorganisms on its own, but it removes most of them and it is essential because organic matter can harbor, protect, or even inactivate certain products (e.g., bleach).
Disinfection: Disinfection is the process carried out after cleaning and aims to inactivate or destroy most pathogenic microorganisms present on already cleaned surfaces. It is performed using chemical products (disinfectants) or physical agents (high temperature), applied according to specific concentrations and contact times. Disinfection does not guarantee the total elimination of all microorganisms but reduces microbial load to safe levels and is essential to prevent disease transmission in animal facilities.
1. Know Your Enemy. Which Microorganisms Do We Want to Eliminate?
Not all pathogens are equally sensitive to all disinfectants. In general terms:
Common bacteria, fungi, and enveloped viruses are usually eliminated with most disinfectants. E.g., Salmonella enterica, Aspergillus spp., Rabies virus.
Non-enveloped viruses, bacterial spores are much more resistant and require specific products, higher concentrations, or longer contact times. E.g., Canine parvovirus, Clostridium difficile.
Parasites that are not easily eliminated with common disinfectants and require specialized protocols. E.g., Toxoplasma gondii, Giardia duodenalis.
Therefore, before choosing a product, you must define your protocol objectives: Which areas and surfaces? Which potential pathogens do we want to eliminate? Then, review what microorganisms each disinfectant covers according to its registered label, and never assume it “works for everything.”
2. Choose the Right Product and Use It Correctly
There are numerous types of disinfectants, each with different compositions, uses, and indications. Their efficacy depends on several factors:
Active ingredient: Each substance has a different spectrum. Hypochlorite (bleach), quaternary ammonium compounds, peroxides, alcohols… Each works better for certain microorganisms and situations.
Concentration: Products are tested to act at a specific concentration. Using less reduces efficacy; using more may be toxic or damage surfaces.
Contact time: A very common mistake is applying the disinfectant and removing it too soon. Most need at least 10 minutes of continuous contact on the surface, which must remain visibly wet during that time.
Product stability: Some disinfectants degrade quickly after preparation, especially bleach. Fresh solutions should be used, check expiration dates, and store products in cool, dark places.
3. Is the Pre-Cleaning Done Correctly?
Cleaning and disinfection are two steps, not one (actually, there’s a third step, as you’ll see):
Cleaning: Removes organic matter like feces, food, blood, mud… This step is critical since organic matter protects microorganisms and inactivates many disinfectants, especially hypochlorite.
Disinfection: Apply the product to destroy remaining pathogens.
Drying: Finally, there is a crucial step for animal safety. Drying involves removing any disinfectant residue from surfaces before use, so it poses no risk to animals. This must be done on any surface that animals may contact directly or indirectly (food, bedding, enrichment materials…). It can be done mechanically (rags, towels) or via natural or forced ventilation.
Performing only the disinfection step is useless if the surface hasn’t been cleaned properly. And performing the first two steps without allowing drying can be even worse, as the cleaning/disinfection protocol itself could directly endanger the animals. Be careful!
Effectiveness of each stage in reducing microbial load highlights the importance of cleaning:
Cleaning alone can reduce microbial load by 90%.
Cleaning + Disinfection properly performed can reduce it up to 96%.
4. Environmental Factors That Can Ruin Disinfection
Even with the right product, efficacy can be affected by the environment:
Organic matter: Main cause of failure. Always clean first.
Surface type:
Smooth, non-porous surfaces (metal, glass, plastic) disinfect easily.
Porous, irregular, or cracked surfaces (wood, cement, hinges, ropes) trap microorganisms and require more work or specific products/methods.
Temperature: Most disinfectants work best above 20ºC, but very high temperatures can degrade them or accelerate evaporation. For example, quaternary ammonium compounds are less effective at 10ºC than 20ºC. Bleach evaporates instantly on very hot surfaces and becomes ineffective.
Water hardness and pH: Mineral-rich water can inactivate or reduce efficacy. Same for pH, whether from water (very hard water is very alkaline) or what is being cleaned (urine or fermented food is acidic). Check water hardness or use filtered water when necessary.
Presence of detergents or soaps: Many disinfectants (like bleach) are inactivated if soap residue remains after cleaning, mainly due to alkalinity. Always rinse thoroughly before applying the disinfectant.
5. Don’t Forget Cleaning Tools
Brushes, brooms, buckets, mops, and any tools used must also be cleaned and disinfected. Otherwise, they become contamination vectors.
Leftover solutions should be disposed of or stored according to product instructions, not randomly.
6. Safety for People and Animals
All cleaning and disinfectant products pose risks to animals and people. For safe work:
Use appropriate PPE: gloves, goggles, mask if irritant vapors.
Ventilate areas well.
Keep products out of animals’ reach.
Avoid using strong disinfectants in feeders or drinkers that may leave toxic residues.
Always consult safety data sheets and follow product instructions.
Avoid mixing incompatible products (e.g., bleach with ammonia).
7. Day-to-Day Biosecurity
An effective cleaning and disinfection program is part of a broader biosecurity system, including:
Continuous staff training.
Correct use of work clothing and dedicated footwear.
Access control.
Proper waste management.
Isolation protocols for sick or newly admitted animals.
Immediate consultation/communication in case of suspected diseases.
This should be applied proportionally, according to facility type (professional or domestic), number and diversity of animals, and facility characteristics. We cannot wear PPE designed for a nuclear disaster at home. If so, we should review which products we are using and how, because there may be less extreme alternatives. Protocols must be adapted proportionally to the risk.
I hope this brief cleaning and disinfection guide for animal care facilities has been useful. I greatly appreciate any comments, suggestions, or questions you may leave in the section below. And as always — see you next time!
Roger Valls Martínez
BIBLIOGRAPHY
Centre for Food Security and Public Health. (2025, october 30). Infection control and prevention. Iowa State University. https://www.cfsph.iastate.edu/infection-control/
Miller, E. A., & Schlieps, J. (Eds.). (2021). Standards for wildlife rehabilitation. National Wildlife Rehabilitators Association. Bloomington, MN.
Smith‑Blackmore, M. (2025, october). Cleaning, disinfection, and sanitation in shelter medicine. In M. Smith‑Blackmore (Ed.), MSD Veterinary Manual – Special Subjects: Shelter Medicine. Merck & Co., Inc. https://www.msdvetmanual.com/special-subjects/shelter-medicine/cleaning-disinfection-and-sanitation-in-shelter-medicine
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