Be proactive rather than reactive with equine biosecurity

“In the equine industry, true biosecurity is hard to achieve because horses move around a lot, and many diseases are always present,” says Ontario Veterinary College infectious disease specialist Dr. Scott Weese. “However, it's still important to try to prevent diseases from entering and to have plans in place to manage any outbreaks.”  With frequent horse movements, endemic pathogens and emerging diseases, there is a need for improved understanding and motivation to adopt better infection control practices.

Infection control begins in the barn and works best when the focus is pro-active rather than reactive.  This includes having an access management plan, proper quarantine protocols for new and returning horses, and training EVERYONE who comes on to the property or handles the horses.

Access Management

Controlling how horses, humans, equipment and vehicles can move into and around your farm are all aspects of access management aimed to reduce the transmission of pathogens.  

Access management begins at the entrance, where a training facility may use fencing and gated entries to restrict access to the stables and training areas, ensuring only authorized personnel can enter.  Procedures at controlled access points such as hand sanitizing and boot cleaning help prevent the spread of infections.  Both staff and service providers need to be made aware of any infection control measures in place.  Clean outerwear that has not been worn to another barn are also recommended to prevent potential spread of disease.

A sign in procedure can be made mandatory for visitors.  A log can be helpful to help trace the problem in the event of a disease outbreak. Providing guided tours can ensure they do not enter restricted areas.  Additional signage can let visitors know where they can and cannot go.

Controlled access zones can designate specific areas for different activities, such as quarantine zones for new arrivals and separate zones for resident horses, with controlled access points to manage movement.

Isolation/Quarantine

When horses return home or new horses arrive, such as from a sale, it is a good idea to implement quarantine and/or isolation protocols.  Ideally this involves housing in a separate building away from your resident horses, but it may be the end of an aisle with several empty stalls in between.  

New and returning horses are kept separate and monitored for at least 14 days.  This involves twice daily temperature checks and health checks including watching water consumption, appetite, urination, manure and any signs of illness.

Turn out paddocks should also be away from other resident equines, especially if that includes higher risk horses like broodmares and foals.  

Effective quarantine includes using separate equipment for isolated or quarantined horses to avoid cross-contamination.  This includes water buckets, feed tubs, grooming equipment as well as wheelbarrows, brooms, pitchforks and other cleaning tools.   

Ideally, new and returning horses are handled by separate staff.  Otherwise, quarantined horses are worked with last & hands are washed before & after each interaction.  Strategically placed alcohol-based sanitizers can also be used.  If wash stations are limited, this makes it easier for staff and visitors to follow infection control protocols.  Disposable gloves, disposable shoe covers & protective clothing are also best practices.  Barn cats and other pets should not be allowed to enter the quarantine area.

If you have a number new or returning horses in quarantine and one shows signs of illness, it should be further separated into isolation and seen by a veterinarian ASAP.  Horses should remain in isolation until cleared by the vet, as the horse may have recovered from clinical signs but still be infectious.  Signage once again should alert unauthorized persons at the entrance of any areas used for isolation or quarantine.

Not Sharing is Caring and Hygiene Practices

Of course, those new or returning horses should be housed in a stall that has been both cleaned and disinfected prior to their arrival.  

Cleaning involves removing all visible manure, bedding and soil before washing the area with soap and water and then allowing it to dry.  Then apply a disinfectant such as Virkon or other disinfectant recommended by your veterinarian.  All disinfectants have strengths and weaknesses and are best used for specific purposes.   Bleach has drawbacks as hard water can affect its effectiveness, it can be inactivated by organic material, and it can be irritating to the horse.  Steer clear of pressure washers as they can aerosolize certain viruses.  

An often-misused step, if you will pardon the pun, is the foot bath.  One cannot just walk through without first going through the same routine as mentioned above, both cleaning and disinfecting.  First remove debris from the footwear, including the soles using a brush or hose to get all the dirt out of the treads.  Immerse the entire bottom of footwear in the disinfectant and scrub.  Following the contact time on the product label is important and a dirty footbath does little in the way of boosting biosecurity.  Then wash your hands.  Other options include dedicated footwear and disposable shoe covers.

Hand hygiene cannot be overstated as one of the most important infection control measures.  Best practices on application time for the soap or alcohol-based sanitizer is 20 – 30 seconds.

Everyone knows not to share communal water, but it is also important not to become blasé about biosecurity when it comes to filling or refilling water buckets. Submersing a hose from one bucket to the next or letting it touch the buckets can be a free ride for a pathogen looking for its next host.  So instead of multi-tasking while filling buckets, one could be enjoying a beverage with their free hand. 

Not sharing should extend beyond grooming equipment to tack, pads, blankets, and of course medical supplies like syringes, needles and dewormers.

More disease prevention measures include minimizing the presence of rodents and insects by keeping feed secure, eliminating standing water and regular removal of manure from stalls and paddocks and as well as management of manure storage areas.

Vaccination

Vaccination is a crucial aspect of equine healthcare, but vaccines do not provide immediate protection; it can take days or weeks for a horse to develop optimal immunity after vaccination, so timing is very important.  Planning ahead will allow vaccines to be given well in advance of the next stressor such as travelling or competition.  

While no vaccine boasts 100% immunity, horse owners can rest assured that they are taking proactive steps to maintain their horse's health, minimizing the risk of unexpected veterinary expenses.  Vaccines significantly reduce the risk of disease which means if a vaccinated horses does get sick, they will generally experience milder symptoms and recover more quickly.

Working closely with a veterinarian to develop and maintain a vaccination program is an important step for optimal equine health.  In addition to core vaccinations, your vet will know what diseases are endemic and emerging in your region or regions you will be travelling to.   The frequency of your vaccinations or boosters will depend on a number of factors including special circumstances, such as an extended vector season or even a significant wound if it is incurred over 6 months after a Tetanus shot.  The length of your competition season may also necessitate a booster of certain shots to maintain optimal immunity. 

Emerging Diseases

Infection control specialist Dr. Weese says, “Understanding potential mechanisms of transmission is the basis of any infection control or biosecurity program.”

Most diseases in horses are caused by pathogens that mainly infect horses. They can spread continuously without needing long-term hosts (like the equine flu virus).  They can remain in the horse without causing symptoms for a long time (like Strangles). Some cause infections that can come back at any time (like equine herpesvirus).  Others may be part of the normal bacteria in horses but can cause disease if given the chance (like staphylococci and Enterobacteriaceae).

Horses can spread these germs even if they seem healthy, before showing symptoms, after recovering, or as part of their normal bacteria. This makes it hard to identify which horses are infectious. Some symptoms, like fever and diarrhea, strongly suggest an infection, but any horse can potentially spread germs. Therefore, it's important to have strong infection control practices to manage the risk.

In 2024, the Equine Disease Communication Center (EDCC) reported 577 Alerts for 813 confirmed cases of disease in North America. The most frequently reported disease was Strangles with 186 cases. Because Strangles is not reportable in all states or provinces the disease is likely much more prevalent than reported to the EDCC. Other frequently reported illnesses include: 153 West Nile Virus (WNV), 125 Eastern Equine Encephalitis (EEE), 109 Equine Infectious Anemia, 73 Equine Herpesvirus- Neurologic, 8 Equine Herpesvirus- Respiratory, 34 Equine Influenza.

1. Strangles: A bacterial infection caused by Streptococcus equi, leading to swollen lymph nodes and respiratory issues.  It is highly contagious and spread through contact.  This could be nose-to-nose between horses or via contaminated surfaces or equipment such as: shared halters, lead shanks, cross ties, feed tubs, stall walls, fencing, clothing, hands, the hair coat from other barn pets, grooming tools, water buckets, communal troughs. 

After an outbreak, cleaning should involve removal of all organic material from surfaces and subsequent disinfection of water containers, feeders, fences, stalls, tack and trailers. 

1. West Nile Virus (WNV): a mosquito-borne virus leading to neurological issues such as inflammation of the brain and spinal cord.  WNV can be fatal and survivors can have residual neurological deficits for a period of months to permanent disability.

2. Eastern Equine Encephalitis (EEE): another virus transmitted by mosquitos Eighty to ninety percent of infected horses develop acute and fatal neurologic disease.  

3. Equine Infectious Anemia (EIA): is a blood-bourne virus which can be transmitted by insects, medical equipment or passed from mare to foal in utero.  With no treatment or cure, horses confirmed positive by a Coggins test can be quarantined for the rest of their life but are usually euthanized.

4. Equine Herpesvirus (EHV): This virus had multiple strains and can cause both abortion and neurologic symptoms.  Spread via aerosol particles from nasal discharge or from contaminated surfaces.  There are vaccines for respiratory and abortive strains but not the neurologic form of EHV-1 (EHM).

These diseases highlight the importance of biosecurity and vaccination in managing equine health.  West Nile Virus and Eastern Equine Encephalitis are among the core vaccinations recommended by veterinarians.

In February 2025, Equine Guelph partnered with the Equine Disease Communication Center (EDCC), to help horse owners assess and manage infectious disease risks with the relaunch of Equine Guelph’s Biosecurity Risk Calculator (TheHorsePortal.com/BiosecurityTool).  The interactive free tool is full of useful information from quarantine protocols, best practices for cleaning, and easy to understand practical access management tips.  In just 10 minutes, you can assess and minimize biosecurity threats for your barn.

"Applying routine and basic biosecurity is the best way to prevent infectious diseases," says Dr. Nathaniel White the Director of the EDCC. "This includes isolation of new horses introduced to facilities, monitoring horses' temperature and preventing horse to horse contact while traveling and keeping vaccinations up to date. Being aware of disease prevalence using information from the EDCC and the updated "Biosecurity Risk Calculator" can help owners use management practices to decrease disease risk." 

Equine Infection Control Measures During Transport

Pre-transport preparations entail more than just having your paperwork in order.

Taking the time to clean and disinfect the trailer or make sure the trailer you have hired always cleans between loads is of paramount importance.  If the trailer smells like horses, it was not adequately cleaned.  Perform a horse health check before you leave the property.  It is not worth the gamble to stress a horse with travel when it is ‘not-quite right’.  

Being particular about your horses traveling companions is just as important as the cleanliness of the trailer.  Avoid travelling with horses from other locations as being in close quarters increases the risk of picking up an infectious disease.

Tie the horse loosely if possible.  Horses tied short are less ability to lower their head to clear mucus.  Allowing freedom of head movement can reduce stress and the bacterial load in the airways.  Similarly, hay nets that are hung high, encouraging a high head position, and introducing dust and debris, can challenge mucous clearance.

Ventilation is another important consideration as improving air exchange can reduce the dust and mold spores hanging in the air.  Drafts on the other hand can blow particles around in the trailer.

Many prefer shipping in leather halters because they will break in an emergency but there is a biosecurity benefit too as they are easier to clean.  Bacteria can linger in the webbing of polyester halters.

Biosecurity is just as important on the road and when visiting other venues. Disease is easily spread through equipment sharing.  While visiting venues off the farm be sure to bring your own broom and shovel for cleaning your trailer.  Be sure to pack a thermometer along with your tack and other equipment.  Clean & disinfect your equipment when you get ready to leave your off-site location.

Upon returning to the home farm, the cycle begins again, monitoring horses for possible delayed onset of symptoms.

To ensure effective infection control, it is crucial to maintain a proactive approach starting right in the barn with a plan. Implementing access management, enforcing proper quarantine protocols for new and returning horses, and thoroughly training everyone who enters the property or handles the horses are essential steps. By taking these practical steps, we can significantly reduce the risk of infections and promote a healthier environment for all.

#Soundbites - How closely do you follow your veterinarian’s advice if it conflicts with your gut feeling about your horse?

Article by Bill Heller

Bruce Brown

         That’s a good question. I usually have a good enough relationship with my vets. I really trust their judgment. It seems like nowadays there aren’t many vets who would do something you don’t want, something that you really don’t need, whatever it takes to get a horse in a race. That’s not in our game anymore. I have in my head what I think, but usually it matches well with my vets. 

Kelly Breen

I probably use a vet’s recommendation, maybe 85 percent of the time. I have gone against their recommendation because of my gut. Usually, my gut is the right answer. For sure, there are times when my gut is wrong. But sometimes the scientific answer is not always correct. Generally, the advice given from the vet is the textbook version, and not everything is textbook in horse racing.

Charlie Baker

Well, if it conflicts with my gut feeling, percentage wise, I would say 65 percent I’d follow the vet. It all depends on the situation. Is it one I’ve dealt with in the past? If so, I would use my experience, especially if it’s a younger vet, one fresh out of school. If I’m totally confident in my vet, I listen to him.

Carla Gaines

That’s a good question. You always want to do what’s best for the horse. You kind of have to go along with the veterinarian. These days, with just being way more cautious—not that it was irrelevant before—if you have a gut feeling that a horse is fine, you still do diagnostics to make sure your horse is fine.

Ian Wilkes

Ian Wilkes

You talk to him. Common sense prevails.

Burl McBride

  I stick with my gut feeling, but I do trust my vets because I can’t see an X-ray. I can’t see an ultrasound. I’m pretty opinionated. These horses will talk to you if you listen. 

Leonard Powell

A lot of times, I would use the vet for a sounding board. I’d really consider his opinion. Ninety-ninety percent of the time we come to a consensus.

Tom Proctor

I don’t ask a veterinarian for advice. I have a license. They have a license.

Probiotics – The key to a well-balanced equine gut

Article by Kerrie Kavanagh

It is no surprise that the health maintenance of the racehorse is a top priority for trainers. And probiotics can be used as a treatment modality to manipulate the gut microbiome to improve or maintain health. Equine studies to date have shown that probiotic strains can offer an advantageous approach to minimising disturbances in the gut microbial populations, repair these deficiencies—should they occur—and re-establish the protective role of the healthy gut microbiome. Other probiotic-associated health benefits include reducing diet-related diseases such as colic and laminitis, preventing diarrhoea, conferring host resistance to helminth infection, improving stress-related behavioural traits (e.g., locomotion) and even promote the development of an effective gut-brain communication pathway. 

Probiotics have been used by humans for more than 5,000 years with their development closely linked to that of dairy products and fermented foods. Today, probiotics are seen as an excellent non-pharmaceutical way to improve the health of both humans and animals, and there are a plethora of products to choose from. But what exactly is a probiotic, and how do they work? Why would your horse need one? What types of probiotics are available for horses? These are all questions that horse trainers ask frequently, which we will attempt to answer here. 

The Equine Gut Microbiome

Probiotics and the equine microbiome can benefit from a valuable symbiotic relationship; probiotics are seen as a restorative treatment modality for the gut, to re-establish the bacterial populations there and also to re-establish the protective role that the health gut microbiome confers to the host. But when we discuss the equine microbiome, what are we really talking about? 

The gut microbiota/microbiome can be categorised by anatomical location such as the oral microbiota/microbiome in the mouth and the intestinal microbiota/microbiome in the intestines, etc. Therefore, the gut microbiome pertains to the microbiota in the gastrointestinal tract. This population of microorganisms (bacteria, fungi, viruses, protozoa) is referred to as the ‘microbiota’ of the gut, while the term ‘gut microbiome’ refers to the genetic material associated with these microorganisms. The microbiome can be defined as the sum of the microbes and their genomic elements in a particular environment. If we look at the definition of the microbiome having the propensity to an equation, then any equation must be balanced; to maintain that balance is key. If the microbial community exists in an environment in a balanced state, then any upset or disturbance to the microbial populations will cause the balance to shift (known as dysbiosis). To maintain the balance, we need to firstly understand the way the microorganisms exist within their community (i.e. their microorganism-to-microorganism interactions and also microorganism-to-environment interactions) and secondly, their functioning role. If we can understand their (microorganism) position and role, then we can maintain the balance or re-establish the balance if a shift occurs.  

The human intestinal microbiome is now recognised as an organ and likewise, the equine intestinal microbiome is deemed an ‘organ’ of the body and is vital for the breakdown of complex food and subsequent release of energy, protection against the pathogenic bacterial colonisation and in regulating the immune system and metabolic functions. There has been much debate regarding the content of the healthy equine microbiome, and even to deduce what ‘healthy’ or ‘normal’ is requires a level of understanding of the microbiota associated with healthy horses. This question has been posed by many researchers and frankly has yet to be answered with certainty. There are many reasons why the ‘normal’ microbiota keeps eluding us; and this can be attributed to the many reasons as to why the gut microbiota (of a healthy horse) can be affected (see Figure 1). It is thought that the diversity of the human gut microbiota and the general assembly of microbial communities within the gut (with the dominant phyla being classed as belonging to Firmicutes and Bacteroidetes) is a shared hypothesis across most species (i.e., humans and animals share a similar gut microbiome structure). Firmicutes and Bacteroidetes have been shown to constitute the main dominant phyla in equine, bovine, canine and feline gut microbiome studies indicating the cruciality of the role they play in the maintenance of a healthy microbial ecology in the gastrointestinal tract. Several studies do agree that dominant phyla of the equine gut microbiota are obligate anaerobes: the gram-positive Firmicutes and the gram-negative Bacteroidetes; other phyla are identified as Proteobacteria, Verrucomicrobia, Actinobacteria, Euryarchaeota, Fibrobacteres and Spirochaetes. Ninety-five percent of the  Firmicutes phyla contains the Clostridia genus in addition to genera related to gut health such as Lachnospiraceae, Faecalibacterium and Ruminococcaceae. The other main dominant phyla, Bacteroidetes, on the other hand contains a large variety of the genus. 

Role of the Equine Gut Microbiota

The role of the gut intestinal microbiota serves to protect and prevent disease. The gut microbiota has several purposes: prevention of pathogen colonisation by competing for nutrients, enrichment and maintenance of the intestinal barrier—their ability to renew gut epithelial cells and repair damage to the mucosal barrier, the breakdown of food and releasing energy and nutrients, such as synthesising vitamins D and K and also conserving and restoration of the immune system by the formation of antimicrobial metabolites and blocking access to the binding sites of the mucosal wall. The gut microbiota is also thought to play some role of influencing the neuro-active pathways that affect behaviour. It is not surprising to see that gut disorders and gastrointestinal diseases can arise when gut dysbiosis occurs. The role of the gut microbiota may have even more importance than is realised and may have a role to play with developing illness or disease later in life.

The microbial colonisation of the intestinal tract begins at birth. The foal begins its colonisation through contact with the microbiota of the mare’s vaginal and skin surfaces plus the surrounding environments to which the foal is exposed and reaches a relatively stable population by approximately 60 days in age. It is perhaps a fight for dominance to achieve establishment in the gut among the bacterial populations that sees the foal’s microbiota as being more diverse and quick to change when compared to that of the older horse. The subsequent colonisation of the intestinal tract will reflect the foal’s diet, changing environment, introduction to other animals, ageing and health.

Figure 1: Factors that can lead to gut dysbiosis

What exactly is a probiotic?

The word ‘probiotic’ is of Greek origin meaning ‘for life’ and the WHO/FAO have defined probiotics as ‘live microorganisms which when administered in adequate amounts confer a health benefit on the host’.  People have long believed that exposure to non-pathogenic microorganisms can benefit the health of humans and animals. The thinking behind this is that daily consumption of sufficient numbers of ‘good’ microorganisms (either bacteria or fungi) can maintain a healthy population of microorganisms in the gut and benefit overall health.  

Probiotics are used to manipulate the bacterial populations of the gut in order to re-establish the delicate microbial balance there which, in turn, confers health benefits on the host. As the benefits associated with some of the ‘good’ bacteria within the gut became known, these were referred to as probiotic bacteria. 

How do probiotics work?

There are 4 main mechanisms by which probiotics are thought to exert their effects.

1. By inhibiting pathogen colonisation in the gut through the production of antimicrobial metabolites or by competitive exclusion; in other words, they prevent the ‘bad’ bacteria from growing in the gut.

2. By protecting or re-stabilising the commensal gut microbiota, probiotics can be a means to re-establish the balance of the gut microbial populations.

3. By protecting the intestinal epithelial barrier, they maintain the health of the intestinal wall.

4. By inducing an immune response, probiotics can boost the immune response and help prevent disease.

If we consider the definition of a probiotic as ‘live non-pathogenic microorganisms that, when administered in adequate amounts, confer a health benefit on the host’, then this reference to ‘adequate amounts’ must be emphasised, and the dose administered is critical to ensure that the probiotic has the desired effect. For horses, we must consider the route through the digestive tract that the probiotic strains must travel to arrive at their destination is a distance over 15 metres long. It is a race for survival! The gastrointestinal system has many obstacles along the passage such as the acidic stomach environment and the dangers of exposure to bile and digestive enzymes, in which they must survive. The initial dose of ‘live’ probiotic strains is therefore crucial to ensure survival in the gut. Prebiotics are ingredients such as carbohydrates and fibre, which promote the growth of these probiotic bacterial/yeast strains in the gut. Prebiotics are essentially the food for the probiotic strains and can help form a symbiotic relationship with the probiotic to improve the overall health status of the horse. 

Why would you need to give your horse a probiotic?

Gut dysbiosis is a fluctuation or disturbance in the population of microorganisms of the gut, which may be linked to a wide range of diseases in horses. Gut dysbiosis can be caused by many factors ranging from dietary changes, antibiotics, disease, intense exercise and training, age, worms, environment, travel, or even minor stress events—resulting in major consequences such as colic. Dysbiosis is generally associated with a reduction in microbial species diversity. 

Diet is one of the major factors contributing to gut dysbiosis. Unlike the ruminant cattle and sheep that use foregut fermentation, horses are hindgut fermenters. The large intestine is the main area where fermentation occurs. The horse utilises the microbial enzymes of the hindgut microbial population in the colon and caecum to break down the plant fibres (cellulose fermentation) sourced mainly from grasses and hay. The horse itself does not possess the hydrolytic enzymes that are required to break the bonds of the complex structures of the plant carbohydrates (in the form of celluloses, hemicelluloses, pectins) and starch; so therefore, it strongly relies on the microbiota present to provide those critical enzymes required for digestion. The main phyla Firmicutes and Bacteroidetes possess enzymes capable of breaking down the complex carbohydrates (such as starch and cellulose).

Research has shown that forage-based diets (grasses and hay) promote the most stable gut microbiomes, but ultimately the equine athlete requires far more energy than a forage-based diet can supply. Supplementing the diet with concentrates containing starch such as grain, corn, barley and oats can affect the number and type of bacteria in the gut. Optimising diet composition is so important as carbohydrate overload—as seen with high-starch diets (>1g/kg body weight per meal)—can change the populations of bacteria in the gut, alter pH, upset digestion and the gut environment, and ultimately result in diseases such as colitis, colic and laminitis. The correct diet is essential for maintaining the delicate balance of bacterial populations. Probiotics can be used to either replace the bacteria missing in the gut and/or can help maintain the delicate microbial balance even in the face of adversity such as abrupt dietary changes, antibiotic treatment and stress.

What types of probiotics are available for horses?

There are several probiotic products on the market, and most are in powder or liquid form. There are two main categories of probiotics: generic and autogenous. Generic probiotics are off-the-shelf products that contain specific strains of bacterial or yeast, singularly or in combination. The Lactobacillus and Bifidobacterium families, Enterococci and yeasts such as Saccharomyces cerevisae and boulardii are the most common equine probiotic strains. Advantages of generic probiotics are that they are widely available, easy to administer, and they may be beneficial to horse health (if the strains are alive in sufficient numbers). Autogenous probiotics are specifically formulated using bacteria obtained from the horse’s own faecal sample and, as such, are uniquely adapted to that individual animal. These host-adapted bacteria are more likely to survive in the gut than non-adapted generic strains and can quickly replenish absent or low levels of bacteria unique to the individual horse, thus maintaining health.

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