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    Establishing Safe And Effective Quarantine And Isolation Protocols For Your Animal Sanctuary

    A person in a tyvek suit and booties enters a quarantine area with three turkeys in it.
    A few minutes to suit up far outweighs the risks!

    This resource was updated as part of the veterinary review process. It was originally published on April 4, 2018.

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    Veterinary Review Initiative
    This resource has been reviewed for accuracy and clarity by a qualified Doctor of Veterinary Medicine as of February 2023.

    Check out more information on our Veterinary Review Initiative here!

    Regardless of the species for whom you care, it’s important to implement protocols that protect them from infectious disease. While there are many important biosecurity measures that work to achieve this, effective quarantine and isolation protocols play a crucial role in reducing the risk of infectious disease spread. It may sound overly dramatic, but when properly implemented, these protocols can save lives!

    Quarantine vs. Isolation

    The goal of quarantine and isolation are the same – to prevent the spread of infectious disease – and sometimes people use these two words interchangeably. However, they are not entirely the same. Quarantine is the practice of keeping individuals who may be carrying a communicable (contagious) disease separated from others in order to prevent possible disease spread. Individuals may be quarantined because of confirmed or suspected exposure to a certain disease or, as in the case of new residents, because they have an unknown health history. Isolation, on the other hand, is the practice of separating an individual who has a suspected or confirmed communicable disease from others who could potentially become infected. The big difference between isolation and quarantine is that in the case of isolation, the resident is either clinically ill or confirmed to have a certain disease, whereas quarantine is a preventative measure put into place because a resident may have a communicable disease.

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    Don’t Wait!
    Even if you don’t need to implement quarantine or isolation measures currently, it’s important to be prepared to enact these measures when needed. This means not just being familiar with what goes into an effective quarantine or isolation policy, but also having necessary supplies available for when you need them. This may mean having a separate, cleaned quarantine area available for use, or personal protective gear and additional supplies on hand (or at the very least, knowing you can secure these quickly if needed).


    At an animal sanctuary, quarantine is often associated with new residents, but there may also be times when it is necessary to quarantine existing residents. The tricky thing with quarantine for new residents is that you are basically preparing for anything. Unlike an existing resident (or group of residents) who may have been exposed to a certain infectious disease, quarantine for new residents is crucial because they may have any number of diseases that could be spread to your other residents. Therefore, quarantine for new residents may look different than quarantine for existing residents. 

    Quarantine For New Residents

    Quarantine is critical for all new residents of any species, even if they appear healthy and even if you know exactly where the individual came from! Quarantine procedures protect the rest of your residents (and the humans that care for them) from infectious diseases that may not be producing clinical signs in a healthy-looking arrival – an entire herd or flock could be easily infected, and possibly even killed, by certain infectious diseases. 

    There are various scenarios in which a new arrival may be infectious (able to spread disease) but not showing signs of illness. For starters, a new resident could have a subclinical infection. This means they have an infection that produces no outward signs of disease. These individuals are often referred to as ‘carriers’ or ‘silent shedders.’ Examples of this may include waterfowl carrying avian influenza or goats carrying Johne’s disease. Because there are no obvious signs of illness, subclinical infections often go undetected, which, depending on the disease, could have devastating consequences. Secondly, the period during which an individual is infectious varies depending on the pathogen and doesn’t necessarily correspond to the period in which they are showing clinical signs of illness. An individual may be infectious before they show clinical signs of illness and/or the individual may remain infectious even after signs of illness have resolved. Depending on the disease, the individual may remain infectious for a limited period of time or for the duration of their life. Individuals who are infectious for life are often called ‘lifelong carriers.’ 

    There’s More To Intake Than Just Quarantine
    Quarantine plays a crucial role in proper intake procedures, but there are other measures you will need to implement to help keep everyone, including the new resident, safe. We recommend working with your veterinarian to determine the most appropriate intake protocols for the species you care for. You can read more about species-specific intake procedures here.

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    It’s a good idea to ask your veterinarian about their recommendations for quarantine procedures for each species you care for based on the specifics of your sanctuary and your region. In general, we recommend quarantining new residents for a minimum of 30 days, but your veterinarian may recommend a longer quarantine period for certain species or situations. The quarantine period should not end until the individual is deemed healthy based on a thorough evaluation, ongoing observation, and diagnostic test results. Depending on the species, your veterinarian may recommend infectious disease testing prior to introducing the individual to your residents. Any external parasites should be addressed, taking the parasite’s life cycle into account when determining that they are “parasite free.” Additionally, any concerning internal parasites should be treated following your veterinarian’s recommendations, and a post-treatment fecal sample should be evaluated to assess the efficacy of the treatment, if appropriate. If the new resident received treatment for a communicable illness, you must work with your veterinarian to determine when it is safe to discontinue quarantine and introduce them to other residents. 

    What About Lifelong Carriers?
    Depending on the species you rescue, it may be very likely that you will encounter a situation where a newly rescued individual has a disease that will cause them to be infectious for the remainder of their life. What to do in a situation like this very much depends on the specific disease and the prognosis of the individual. In cases where an individual has a disease that makes them infectious for life but that does not so negatively affect the quality of their life that euthanasia must be considered, you should work with your veterinarian to determine the best way to provide them with what they need while still providing responsible protection for your other residents. It can also be useful to connect with other caregivers who have experience caring for individuals with that particular disease. In the case of very common diseases, for example Caseous Lymphadenitis (CL) in sheep and goats, some sanctuaries create separate herds/flocks for positive and negative residents and implement other measures to reduce the risk of disease transmission while still providing the best care possible to infected individuals. Other times, sanctuaries may network with each other or with experienced and trusted adopters to place lifelong carriers of certain diseases in settings where the caregivers are experienced in the care of individuals with the disease and where the individual can live with others who have already been diagnosed with or exposed to the disease in question.

    Keep in mind that if you rescue multiple new individuals from different settings, you will need to quarantine them separately from each other. Simply adding a new resident to a quarantine area that is already housing another rescued individual puts both individuals at risk.

    Setting Up A Quarantine Area For New Residents

    Some sanctuaries have a designated quarantine space (or perhaps multiple designated quarantine spaces each designed to safely house a particular species), while others may opt to rearrange living areas when they know new residents are arriving in order to create a safe quarantine space. As long as the space meets the needs of the individuals who will be living there and offers enough separation to keep others safe, either scenario is acceptable, though without a designated quarantine area, you may find yourself scrambling if a new resident arrives unexpectedly. When designing a dedicated quarantine area (or identifying a space that could act as a quarantine area) consider the following:

    1. Location, Location, Location

    At a minimum, the quarantine area must prevent new residents from coming into contact with other residents (this includes nose-to nose or beak-to-beak contact through a fence!), as well as preventing contact with the new resident’s bodily excretions, secretions, and fluids. However, these are not the only ways in which infectious diseases can spread – some infectious diseases can also spread via aerosols (pathogens suspended in the air) or vectors (such as flies, mosquitos, rodents, lice, etc.). How far pathogens can be transmitted depends on various factors including the specific pathogen as well as environmental conditions, but again, since you are trying to “prepare for anything” the more distance and separation you can provide between quarantine areas and other living spaces, the better* (assuming other precautions listed below are followed as well). Creating a quarantine pen within a structure that also houses other residents who are susceptible to the same diseases could lead to trouble, as could setting up a quarantine area next door to other residents. Also keep in mind that any outdoor spaces quarantined individuals have access to must be considered off limits for all other residents (more on this below).

    Ideally, new residents of any species should be kept away from all other residents, regardless of species. Some diseases can be spread from one species to another, so this type of robust quarantine protocol will best ensure everyone’s safety. However, if this is not possible, you will need to make a well-informed decision about which residents are most at risk of disease spread. For example, chickens and turkeys share many of the same diseases, therefore, a quarantine area for a new chicken resident should provide as much distance and separation as possible from both other chickens, as well as turkeys (and other avian residents). However, be aware that some serious infectious diseases can spread between seemingly very different species (such as between birds and pigs, for example). If you are unsure of the diseases that can be spread between the species you care for, have a conversation with your veterinarian so you can create protocols that keep everyone safe.

    *Off-Site Quarantine
    Unfortunately, for some infectious diseases there is simply no such thing as safe on-site quarantine. This is particularly true in the case of certain reportable diseases, such as highly pathogenic avian influenza (HPAI). We recommend having a conversation with your veterinarian about the most appropriate intake protocols for your sanctuary. In some cases, quarantining residents off-site or temporarily suspending intake may be necessary.

    2. The Quarantine Area Must Meet The Needs Of The Species Who Will Live There

    While quarantine areas must be set up so that they prevent infectious disease spread to other residents, they must also meet the needs of the residents they will house. This means the space must provide appropriate predator protection, safe flooring, enough space, and other elements that are important based on the species’ (or individual’s) needs and natural behaviors (for example perches and nest boxes for chickens). It must also provide proper ventilation and be able to be maintained at a comfortable temperature. Because some species have vastly different needs in these areas, if you care for multiple species, you may need to have more than one quarantine area with each designed to meet the needs of a specific species (or group of similar species). To learn more about the housing needs for farmed animal species, check out our resources here

    3. The Quarantine Area Should Be Easy To Disinfect

    All quarantine areas will need to be cleaned regularly, just like other living areas, and when a new resident finishes their quarantine and moves to another area, the space will need to undergo a more rigorous cleaning process in order to get it ready for other residents. Ideally, this entails disinfecting the space, so be sure to consider how easily this can be done. You really don’t know what disease(s) you may find yourself dealing with, so it’s best to be prepared. In the event that a new resident has a serious communicable disease, you will need to make sure the space is safe to be used again in the future. Non-porous walls and flooring are easiest to disinfect, but may not be appropriate for all of your residents. Many large animals, for example, really do best on dirt floors, but dirt isn’t exactly easy to clean. In the event of a pathogen that can live in dirt flooring, you will have to work with your veterinarian or a professional who specializes in that particular pathogen to determine what needs to be done in order to protect future residents from illness. In some cases, it may be a matter of waiting for a specific amount of time before allowing certain species to live in that space again. In other instances, there may be a treatment that can be used to decontaminate the dirt flooring.

    Keep in mind that it is more than just the walls and floors that may need to be disinfected. You may need to disinfect all elements in the space, including the water unit, food bowls, nest boxes, and so on. Whenever possible, opt for materials and supplies that are easy to disinfect.

    Depending on the issue, outdoor spaces may need to be addressed as well. Some diseases, such as Johne’s disease, can survive for up to a year in many environments. Because of this, there may be certain diagnostic tests that are done or signs of disease that you look for before new residents are given access to outdoor quarantine areas, but mostly you just need to be aware that you could find yourself in a situation where a quarantine area cannot be used for certain species until enough time elapses where contagion is no longer an issue.

    Establishing Quarantine Protocols

    Preventing infectious disease spread goes far beyond the specifics of the quarantine area. In addition to the transmission routes described above (direct contact with an infected individual or their fluids, aerosols, and vectors), fomites (contaminated inanimate objects such as shoes, clothing, tools, equipment, food/water dishes, etc.) can also play a role in disease spread. It is important to establish quarantine protocols that account for all of the main routes of disease transmission. This includes the following:

    1. Protective Gear

    Protective gear must be required in all quarantine areas regardless of if the new resident appears ill or not. Remember, a new resident could be infectious without showing outward signs of illness. You don’t want to find yourself in a situation where you discover that a new resident has a communicable disease that has likely already spread to other residents (or to the humans they have had contact with) because proper precautions were not taken.

    Anyone entering the quarantine area should wear gloves and full body covering, and they should also either wear boot covers or use foot baths (read more about foot baths in the textbox below). This practice will not only reduce the possibility of transferring disease to residents in other areas, it will also help protect staff from zoonotic disease (diseases that can be transmitted between humans and other animals). These protective coverings should not be used outside of this quarantine space, or you will defeat the purpose of wearing them in the first place! If you have more than one quarantined individual/group, folks should change into different gear for each group, particularly if the residents did not come from the same place originally. However, even if you rescued multiple individuals who are now being housed in separate quarantine areas, there may be times when it is wise to wear different gear with each group, especially if one individual or group is showing signs of illness but the others are not.

    A Note About Foot Baths
    Foot/boot baths commonly come up in discussions of quarantine, isolation, and biosecurity more generally, but some experts have raised concerns that due to the likelihood of incorrect use, foot baths may not be as effective as we need them to be. First, you must use an appropriate solution and concentration. Second, this solution must be changed regularly. Third, in order to work effectively, shoes must be thoroughly cleaned, with all organic material removed, before using the foot bath (this can be very difficult in outdoor settings). And lastly, it is imperative that shoes be soaked for an appropriate amount of time (following package or veterinarian instructions). Quickly dipping shoes that are covered in feces and/or mud into a foot bath is not an effective biosecurity measure.

    Be sure to also have procedures in place to deal with used protective gear. Disposable items should be discarded after use in a receptacle kept in or directly outside of the quarantine area (keeping resident safety in mind – you don’t want residents ingesting or getting tangled in protective gear). Protective gear that must be laundered (such as fabric coveralls), should be discarded in a designated receptacle in or near the quarantine area and should be washed separately from other laundry. It’s best to wash this laundry in hot water and you may also want to use bleach to disinfect.

    2. Cleaning Protocols

    Because cleaning tools can act as fomites, ideally, you should have designated tools that are used only to clean the quarantine area and are not used anywhere else (including in other quarantine areas). If this is not possible, all tools and cleaning supplies must be thoroughly disinfected before being used in other areas. To prevent accidental mix-ups, it’s a good idea to have a system in place for easily identifying quarantine tools (perhaps a “QUARANTINE” label or the use of color coding to indicate the tool is only for quarantine, or only for a specific quarantine area). If cloth rags are used for cleaning, these should be discarded in a designated receptacle to be laundered with soiled protective gear from the quarantine space. 

    Because urine, feces, and contaminated bedding can also be a source of disease spread, it’s important to keep old bedding that has been removed while cleaning quarantined areas away from other residents and their living spaces. If you typically spread old bedding on your sanctuary’s pastures, wait to do so with bedding from quarantined spaces until new residents have been evaluated by a veterinarian and they have given you the all clear. If you compost old bedding and then use that compost around the sanctuary, it’s a good idea to either have a separate compost pile/area for bedding from quarantine areas or to discard quarantine bedding in the trash to prevent possible disease transmission. 

    3. Feeding And Other Supplies

    Food and water bowls, wheelbarrows used to move hay, water hoses, and other items can also act as fomites. Just as cleaning tools should not be used elsewhere unless they are first disinfected, other items used in the quarantine space should also be confined to that space whenever possible. You can use labels or color coding to mark all quarantine supplies. Food and water bowls, as well as any brushes used to clean them should stay in/near the quarantine area. They should not be taken to non-quarantine areas for cleaning. 

    It’s also a good idea to have a designated receptacle to store food, as well as designated scoops, in or directly outside the quarantine space. If hoses are used for cleaning or to fill drinking water vessels, these should not be taken into the quarantine area unless they are solely used in this space. Shared hoses should stay out of the quarantine space, and when filling a drinking water vessel, should be held or positioned so that the end of the hose does not sit in the drinking water. When dumping out old drinking water, be sure to do this in an area where the water will not run into other resident spaces or into walkways. 

    Supplies that are used outside of quarantine areas should not be brought into the quarantine space, whenever possible, and if they are brought in, they must be thoroughly disinfected. Because it can be difficult to thoroughly disinfect certain items, it’s best to limit things that come and go from the space to just the absolute essentials. For example, if you must use a wagon or wheelbarrow to bring hay to the quarantine space, you should leave this outside the quarantine area and carry the hay into the space rather than bringing in the wheelbarrow/wagon.

    4. Guests

    In general, it’s a good idea to limit the number of people coming and going from quarantined areas whenever possible because you really do not know what pathogens new residents may be carrying. Restricting these areas to only essential personnel can reduce the likelihood of human movement contributing to disease spread. Additionally, because a new resident could be carrying a zoonotic disease, keeping guests away from these spaces is wise. While we recommend excluding quarantine areas from your tour route and preventing all guests from entering quarantine areas, be aware that children under 5 years old, adults over 65, pregnant people, and folks with a weakened immune system are particularly vulnerable to zoonoses.

    If guests are allowed to walk sanctuary grounds unaccompanied by sanctuary personnel, keep in mind that they could be exposed to harmful pathogens if they are able to reach into the quarantine area through or over a fence. If possible, establish quarantine areas on parts of the property where guests are not allowed. If this is not possible, make sure fencing is such that visitors cannot make contact with quarantined resident(s) or the things they have come into contact with.

    5. Signage

    Protocols only work if people follow them, and they can’t follow them if they don’t know about them! Quarantined areas should have prominent signage that alerts people to the fact that a particular area is quarantined and also explains the requirements of entering the space (such as who can enter and what protective gear is required). Signage can also play an important role in altering visitors to where they can and cannot go. However, don’t rely on signage alone! An excited guest may not notice (or may simply disregard) signage telling them not to touch a quarantined individual if it’s easy to reach through or over the fence.

    Quarantine For Existing Residents

    If there is a concern that existing residents may have been exposed to a communicable disease, quarantine may be recommended to prevent possible spread to other sanctuary residents, and in some cases quarantine may actually be required by local officials. Depending on the specifics, an entire sanctuary may be put under quarantine to prevent possible disease spread beyond sanctuary grounds. 

    Quarantine of existing residents is often (though not always) enacted in response to a confirmed or potential exposure to a specific disease. Therefore, unlike with quarantine for new residents, where you are protecting others from any number of communicable diseases and must consider all possible transmission routes, in the case of quarantine for a specific disease, you can enact targeted quarantine measures based on factors such as 1) how the pathogen spreads, 2) which species, breeds, and/or individuals are most susceptible, 3) how long the pathogen can survive in the environment, and 4) which disinfectants are most effective against it. Whereas we recommend a quarantine period of at least 30 days for new arrivals, when enacting quarantine for a specific pathogen, your veterinarian may make different recommendations based on the incubation and infectious period of the disease. If reliable screening tests are available, the length of quarantine may hinge on these results.

    If existing residents need to be quarantined following a suspected or confirmed exposure while in their living space, they can typically remain where they are and you can quarantine them in their current living space and with their current herd/flock mates. However, if a resident was possibly exposed to an infectious disease while off site, they should typically be quarantined away from their living space and susceptible herd/flock mates who have not yet been exposed. Every situation will be different, so be sure to consult with your veterinarian about what practices are best given the specifics of the situation. If quarantine requires residents to be separated, you can follow the suggestions above regarding how to set-up a quarantine space. 


    If a resident tests positive for a communicable disease or is showing highly suspicious signs of a communicable disease, your veterinarian may recommend enacting isolation practices to prevent spread to other residents. Just as when using quarantine to protect against a specific disease, in this case you know what disease (or in some cases, diseases) you are dealing with and can make informed decisions about what protective measures are necessary to keep everyone safe. In some cases, you may find that you need to isolate a resident away from others and also quarantine their herd/flock mates to prevent spreading the disease to other sanctuary residents or living spaces. 

    We recommend you work closely with your veterinarian, making sure you understand the specifics of the disease and the risk it poses to other residents when considering isolation. Removing a resident from their companions is not something to be taken lightly, but it is also necessary in certain circumstances. Ask as many questions as necessary to make sure you have a good understanding of the situation, and if your sanctuary has a caregiving team, have a group conversation about all of the options. You can find more information about questions to ask and things to consider when deciding whether or not isolation is the right choice here. Remember that at a sanctuary you must consider the individual’s well-being when making decisions about their care, whereas your veterinarian may be strictly focused on best practices to prevent disease spread. Full isolation may be the most effective way to prevent disease spread, but by asking questions about the likelihood of the disease spreading (including how likely it is that the individual’s companions have already been exposed), the prognosis of the disease, and other preventative measures that can help keep others safe, you may find that total isolation is not necessary.

    When implementing isolation procedures, be sure to take the specifics of the pathogen into account. Different diseases will warrant different biosecurity measures. If you aren’t sure what is necessary, your veterinarian can help you determine what measures will help keep everyone safe. And just as with quarantine areas, make sure isolation areas have prominent signage that explains the requirements of entering the space.

    Record Keeping

    Record keeping is an important aspect of animal care. If a resident (or group of residents) requires quarantine or isolation, be sure to keep good notes for your files. The specifics of the situation will dictate what information is necessary to record – think about what type of information you may need in the future, either for your own records or to demonstrate to government officials that you are taking proper precautions, and make sure your record keeping system accommodates that.

    a series of animal graphics around a compass

    Knowing how and when to implement quarantine and isolation protocols is a critical aspect of animal care. We strongly recommend working closely with a trusted veterinarian in your region to develop robust incoming procedures for new residents that include effective quarantine protocols. If you find yourself faced with a specific infectious disease concern that might warrant quarantine or isolation of existing residents, be sure to gather as much information as you can so that you can and work closely with your veterinarian to determine the most appropriate next steps.  


    How To Start, Operate, And Develop A Farm Animal Sanctuary | Farm Sanctuary

    Evaluating The Efficacy Of Boot Baths In Biosecurity Protocols | Amass SF, Vyerberg BD, Ragland D, et al.

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