Lifesaving Library

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Disease Control — The Role of Sanitation Training Playbook

Overview and Introduction

When we think about disease prevention, we often think of vaccinations and medical care or treatments, and sometimes forget the important role of sanitation. Unlike in a more controlled and sterile environment such as a veterinary hospital, animals in shelters have contact with numerous surfaces, including floors, walls, outdoor yards, walking paths and communal living spaces, as well as an array of people (the public, staff, volunteers).

In addition, many animals enter shelters in non-optimal health; more often than not, they are stressed and have no history of vaccination. It’s a perfect cocktail for infection. In some cases, animals have already been exposed to various diseases before coming into the shelter and will be “shedding” with or without showing any blatant symptoms. So, with diseases everywhere and far too many opportunities for transmission, many might think that disease spread is inevitable. However, there’s hope!

With appropriate intake protocols (such as completing vaccinations and physical exams before animals go into the general population or the adoption areas, providing adequate enrichment for ongoing stress reduction, and following a comprehensive sanitation plan), shelters can reduce exposure and increase their animals’ overall immunity to disease. Thus, increasing public health and herd health are likely positive outcomes.

Sounds good in theory, right? Just keep things clean and the animals will stay healthy. But many of us know that our housing configurations, workforce and budgets have a significant impact on how well or how often we clean our shelter environment.

This playbook gives a brief overview of considerations that every shelter can and should make when it comes to sanitation. Additionally, a few sample standard operating procedures (SOPs) and video tutorials are provided to demonstrate proven lifesaving strategies that can be modified easily to fit within an existing operation and/or budget. For more specific feedback on your sanitation plan, please contact your regional team or the Best Friends shelter outreach team at

Sanitation Considerations and Needs

The following describes steps to follow to create a customized sanitation plan, including things to consider along the way for successful disease prevention.

Step 1: Establish a sanitation plan leader

This role traditionally falls on the kennel manager. Regardless of your organization’s workforce structure, someone will need to be responsible for evaluating current protocols, researching efficacy of practice, writing new or revising old practices, and training staff and/or volunteers tasked with ongoing sanitation. Since efficacy of practice is critical for success, Best Friends recommends that a veterinarian or someone equally knowledgeable about shelter medicine serves as an advisor throughout this process.

Step 2: Understand the difference between cleaning and disinfecting

Looks can be deceiving! For all intents and purposes, cleaning simply refers to the removal of organic material and debris. Many shelters appear clean but are still breeding grounds for disease. Disinfecting is the actual application of chemicals to remove pathogens, and it is the most important part of effective sanitation. Protocols should be written to reflect this difference, as well as the expectations for these differences. Some items may simply need to be cleaned daily, but not disinfected. In fact, excessive cleaning can lead to unnecessary stress on the animals, which lowers their immune systems and aids in the spread of disease.

Step 3: Determine what needs to be cleaned vs. disinfected

As noted above, some items need more than just simple cleaning. Germs are often spread throughout the shelter environment via animal and human traffic. So, instead of focusing solely on animal housing areas (e.g., cat and dog kennels, communal rooms), we suggest looking at things with the following lens:

  • High-contact areas and surfaces: Items or surfaces that many animals will come in contact with (should be disinfected regularly)
  • High-risk areas and surfaces: Surfaces that will touch juvenile animals or those not protected by vaccination, or surfaces that have had contact with an ill animal (should be disinfected in between use or animals)
  • Low-contact areas and surfaces: Items or surfaces that few animals and people will come in contact with, but have potential for some disease transmission (e.g., fomite transmission) (should be cleaned regularly and disinfected as needed)
  • Low-risk areas and surfaces: Items or surfaces that animals and people will not come in contact with (should be cleaned as needed or required)

One way to proceed with this step is to identify all areas and surfaces of your shelter and rate them according to the categories given above. For example:

Area/Item Risk Rating
Office areas (animals not permitted) Low-risk area/surface
Office areas (animals permitted) High-contact area/surface
Main lobbies and hallways High-contact area/surface
Animal intake housing areas High-risk area/surface
Transport or field service vehicles High-risk area/surface
General population housing High-risk area/surface
Office furniture Low-contact area/surface
Appliances and computer equipment Low-risk area/surface
Hands, shoes and clothing: staff
(with all animal access, including intake animals)
High-risk area/surface
Hands, shoes and clothing: volunteers
(with limited animal access)
High-contact area/surface
Bedding, toys, etc.: reusable High-contact area/surface
Bedding, toys, etc.: non-reusable Low-risk area/surface
Storage areas: non-animal materials Low-risk area/surface
General laundry: shared throughout population High-risk area/surface

Step 4: Select cleaning and disinfecting agents

Once you have outlined what items, areas and surfaces need to be cleaned and/or disinfected, it’s time to decide what cleaning and disinfecting products to use. First and foremost, know that there is no one perfect product that works for every environment, operation, surface or situation. Animals with contagious diseases may need different disinfectants than those without. Certain areas of your shelter may be fine with regular household cleaning agents, while others are not.

As with choosing medications and treatments for efficacy, you’ll need to do research and consult with veterinarians experienced in shelter medicine before committing to a particular product. For example, bleach is a great disinfectant, except when it’s exposed to biomaterial such as feces.

So, how do you decide? We suggest looking at an array of products and consulting both vendors and medical professionals about the particulars of your operation and population. To make the decision process easier, we’ve included a chart from the UC Davis Koret Shelter Medicine Program on the next page. The chart provides insight into each available product as well as its efficacy for certain contagions, and the cautions of use. Keep in mind that you may need to keep several products on hand if your situation varies regularly.

Note: Once a product is selected for a specific surface or area, the manufacturer or vendor will dictate the frequency of cleaning, the proper application, and the setting or contact time for best efficacy. These are all critical pieces of your sanitation plan and protocols.

Step 5: Establish the order of cleaning

Once you know what needs to be cleaned, with which products, and what the proper application is, you will need to outline the order of cleaning in your sanitation plan. Order is particularly important, not simply because we want public areas cleaned before opening to the public, but because this step represents the greatest chance for transmission. Unless each area or surface is cleaned by a new person — or personal protective equipment (PPE) such as gloves, gowns and foot coverings are changed in between individual areas and surfaces — transmission rates are nearly doubled.

To minimize this risk, Best Friends recommends first cleaning the areas where the healthiest animals are housed, followed by stray/intake holding areas, and finally isolation areas or quarantined areas where sick animals are housed. When possible, we
recommend that within each area, juvenile or younger animals are cleaned first. While the time it takes to make these shifts and determinations can seem burdensome, the payoff is a healthier (and most likely quicker moving) population.

Disinfectant Product Good Points Cautions
Rescue, formerly branded as Accel (accelerated hydrogen peroxide)

Formulations: Rescue Concentrate (most economical), Rescue RTU (faster-acting), Rescue Wipes (faster-acting)
Good detergent activity and effective in the presence of organic material, making it a one-step product. Short contact time (1-10 min. depending on concentration or formulation). Marketed efficacy against non-enveloped viruses and dermatophytes. Liquid concentrate for easy dilution. Various application (e.g., spray bottles, hose-end applicators, centralized systems, pump-up foamers). No independent research available yet to verify Pure Oxygen (product by the same company) shampoo’s efficacy against dermatophytes (m. canis).
Potassium peroxymonosulfate (e.g., Virkon or Trifectant) Completely inactivates un-enveloped viruses and dermatophytes when used correctly. Some detergent activity.
Relatively good activity in the face of organic matter. Short contact time (5-10 min. depending on pathogen).
Dry powder form. Not designed for easy application through hose-end applicator systems (can be applied through specialized delivery systems). Leaves visible residue on some surfaces.
Seven-day shelf life once diluted.
Sodium hypochlorite (bleach)
Usually used at 1:32 dilution of 5% household bleach (1/2 cup per gallon), applied to clean, non-porous surface
Completely inactivates un-enveloped viruses when used correctly. Effective against dermatophytes at high concentration (1:10); however, this dilution is caustic. Very inexpensive.
Stable for 30 days once diluted if stored correctly.
Significantly inactivated by organic matter, exposure to light, or extended storage.
No detergent activity. Surfaces must be pre-cleaned and all organic matter removed prior to disinfection – thus always a two-step process. Corrosive to metal.
Calcium hypochlorite (e.g., Wysiwash) Completely inactivates un-enveloped viruses when used correctly. Can be used in hose-end applicator system (specific to this product). Dry tablet form. No detergent activity. Dry form is irritating to mucous membranes if inhaled.
Sodium dichloroisocyanurate
(e.g., Bruclean)
Completely inactivates un-enveloped viruses when used correctly. Less corrosive to metal than bleach. Less of a respiratory irritant than bleach. Dry tablet form. Dry form is irritating to mucous membranes if inhaled. Requires multiple-step process for cleaning and disinfection via a specialized applicator.
Quaternary ammonium compounds (e.g., Roccal, Parvo-sol, A33, Maxxon, many others) Some detergent activity. Only moderate inactivation by organic matter (less than bleach). Low tissue toxicity when diluted correctly. Not reliably effective against un-enveloped viruses or dermatophytes. Potential to be toxic to cats, causing tongue ulcers.
Chlorhexidine (e.g., Nolvasan) Very low tissue toxicity. Relatively expensive. Not reliably effective against un-enveloped viruses or dermatophytes.
Alcohol (e.g., ethanol, isopropyl alcohol)
Usually in hand sanitizers
Less irritating to tissue than quaternary ammonium or bleach. Moderately effective against calicivirus at higher concentration. Not reliably effective against parvovirus or dermatophytes.

Step 6: Establish written protocols for cleaning and disinfecting

After outlining the areas and surfaces, products and order of sanitation, the next step is establishing written protocols for each area or surface. At minimum, each written protocol should include:

  • Schedule: How often is the area or surface to be cleaned and/or disinfected (after each use, daily, weekly, annually, during or after an outbreak)?
  • Product: What cleaning and disinfection products are to be used and how should they be applied? (Include in detail the correct process for dilution and contact time.)
  • Responsible party: Who is responsible for writing the protocol, following the protocol and ensuring that the protocol is being followed?
  • Quality check: Who will check, how will you check and how often will you check to make sure the process is being done correctly?

We’ve provided a few sample protocols in the “Sample Procedures” section below. Editable copies can be provided if you need a working draft. 

Step 7: Train staff and volunteers (and the public)

Once you have written protocols, it’s time to train (or in many cases, re-train) your team on your new protocols. Training staff and volunteers is already an ingrained part of most progressive shelters and should come naturally. If not, we’ve provided video links below from the ASPCA that can act as tutorials for staff and volunteers to learn the basics of cleaning (daily, spot-cleaning) and disinfecting (deep-cleaning). Because viewing these videos alone likely won’t speak to the specifics of your operations, we recommend that each staff member and volunteer be given a copy of the written protocol to refer to, and that ongoing training is offered to those who deviate.

Training shouldn’t stop there. Best Friends also recommends that you work on training members of the public or shelter visitors regarding sanitation. As noted above, human traffic is one of the biggest reasons for poor sanitation and the spread of disease.

Cleaning a contaminated environment is only half the battle. You should have adequate signage about animals with health concerns or risks, and signage about protocols (e.g., no hands in kennels, wear gloves when visiting certain populations). Hand sanitizers or hand-washing stations should be abundant and easily accessible. These are great ways to reduce disease risk and keep your population healthy.

Step 8: Verify efficacy

With your new products and protocols in place, you might feel that you have completely reduced your risk for disease spread and you now have airtight sanitation practices. Two questions remain, though: Are they working? And how do you know? Occasional review of practices within a healthy population, and frequent review for at-risk populations, can ensure that these practices are serving their purpose. In many cases, it not only reaffirms the practice itself, but can motivate the workforce to continue them.

While options vary depending on what disease you are trying to prevent, most veterinarians can easily access efficacy via live culture. Streaking bacterial cultures from non-sanitized cages, exam surfaces and other high-contact surfaces and comparing those to ones that were recently cleaned is one way to go about verifying success. Another great tool is GloGerm, a product that fluoresces under an ultraviolet light designed to mimic the spread of germs. (The product is available at for under $20 a bottle.) GloGerm can be used in a variety of ways; for example, it can be secretly sprinkled on the backs of kennels or cages prior to cleaning, and staff can be rewarded if they successfully get it all out.

The larger point is this: Make sure your protocols are working for you, not against you, and try to have fun while doing it!

Sample Procedures and Other Sanitation Resources

Following the steps above will likely help you create and maintain a well-sanitized and healthy environment, but we know that it’s easier said than done. So, to help guide you along your journey, we’re including a few sample procedures and other resources that you might find helpful as you finalize your sanitation plan.

Links to presentations about sanitation or cleaning protocols:

Links for sample protocol documents:

Download the PDF

Version 1, July 2019