Infectious aetiologies in adult diarrhoea - Veterinary Practice
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Infectious aetiologies in adult diarrhoea

What should you do if you suspect infectious causes of diarrhoea in an adult horse?

The last two articles have discussed the most common aetiologies and treatment options for the causes of diarrhoea in the mature equine patient. This article will discuss the infectious aetiologies that can occur in the UK adult equine population with an overview of biosecurity protocols when infectious causes are suspected.

Clostridial enterocolitis

Clostridium difficile and Clostridium perfringens can both be associated with enterocolitis in horses. For the clinical signs associated with clostridial enterocolitis to occur, the normal gastrointestinal microbiome will have to become disrupted, allowing overgrowth of the clostridial species and subsequent toxin production.

C. difficile is a Gram-positive, rod-shaped, obligate anaerobe that requires oral transmission of the bacteria or its spores, whether this is via faeces, contaminated soil or fomite. The vegetative form of the bacteria does not survive for prolonged periods, but the spore is highly resistant to changes in environmental pressures.

C. difficile is found in the intestinal tract of normal horses to varying degrees and therefore culture does not confirm an infection. It appears that overgrowth of the bacteria is frequently associated with antibiotic (particularly cephalosporins) use and therefore should always be considered a possibility in antibiotic-induced diarrhoea. An overgrowth is also highly associated with hospitalisation, likely due to disruption of the normal microbiome.

C. difficile produces three toxins: toxin A (enterotoxin), toxin B (cytotoxin) and CDT (binary toxin). When testing, the most appropriate diagnostic modality is an ELISA for toxins A and B. It is possible to perform a PCR looking for the toxin genes, but this does not confirm a pathogenic C. difficile infection, just the presence of the bacteria containing the genes that code for the toxins.

C. perfringens is frequently found in the gastrointestinal tract of adult horses, with one study finding 35 percent of horses have C. perfringens in their intestine (Tillotson et al, 2002). That said, the production of their toxins (enterotoxin, α, β-1 and β-2) appears to be higher in horses affected with diarrhoea. Diagnosis must be made based on a faecal ELISA for enterotoxin due to the relatively ubiquitous nature of the bacteria in the equine population.

Clinical signs of clostridial enterocolitis will vary depending on the severity of the infection and toxin production but the disease is characterised by an increased permeability of the intestinal epithelial cells, cell lysis, mucosal inflammation and subsequent fluid and electrolyte secretion into the GI tract.

These changes can lead to a severe diarrhoea and endotoxaemia secondary to translocation of both bacteria and their toxins into the systemic circulation. Haematology and biochemistry can reveal systemic inflammatory response related signs including hypovolaemia, hypoalbuminaemia, neutropenia, elevated inflammatory proteins and even multi-organ failure.

Pathologically, the lesions appear to be distributed dependant on age, with foals less than one month old showing most signs in the small intestine compared with the colon and caecum in older animals. Histopathologically, there will often be a haemorrhagic, coagulative mucosal necrosis associated with oedema and congestion. There will also frequently be thrombosis of many of the blood vessels with subsequent autolysis.

Treatment of these cases should be based upon the severity of clinical signs and will often entail intensive fluid therapy with plasma transfusions to replenish albumin and prevent low colloidal oncotic pressures. Other treatments can include di-tri-octahedral smectite (Biosponge) (Lawler et al, 2008) as well as an appropriate antimicrobial choice including metronidazole. Faecal transfaunation is a frequently used technique in chronic C. difficile infections in humans with excellent outcomes. The technique may well play a role in these cases but with a dearth of clinical research in the equine patient its use is anecdotal at best.

The prognosis of these cases is dependant on the severity of the clinical signs, duration of signs prior to instigation of therapy and, frequently, availability of finances.


Salmonella is a Gram-negative, facultative anaerobe with multiple subspecies and thousands of serotypes. S. enterica var. typhimurium is considered the most pathogenic serotype and is associated with a higher case fatality than the other serotypes. Many other serotypes will infect horses leading to clinical disease of varying severity.

Diagnosis of salmonellosis can be made using either culture or polymerase chain reaction (PCR). The former will allow typing of the bacteria but can take up to 72 hours to confirm the diagnosis. The latter will confirm the presence of the bacteria and has been shown to be as sensitive as culture with a rapid turnaround making it helpful in acute cases of diarrhoea (Pusterla et al, 2010). Due to the variable pathogenicity of each serotype it is advisable to type any positive results. When trying to confirm a negative diagnosis, it is recommended that multiple samples are taken, ideally three to five samples on consecutive days that are then submitted for either culture or PCR.

Many horses will be carriers of the bacteria with the suspected prevalence in the normal population ranging from 2 to 20 percent, with the lower end being more likely. Shedding from carriers will increase when hospitalised, colicking or during exceptionally hot periods. Increased duration of starvation prior to anaesthesia has also been linked with increased shedding of the bacteria. The increased susceptibility of some patients to Salmonella is not well defined but appears to occur with antibiotic administration, surgery, pre-existing GI disease and diet changes (Kim et al, 2001).

Salmonella primarily affects the caecum and proximal colon in adults, leading to an enterocolitis with limited systemic translocation, although in foals it is frequently associated with septicaemia. Salmonella is an intracellular pathogen with uptake into the epithelial cells of the GI tract being required for pathogenesis. Once within the cells, it will cause a severe inflammatory response and increased secretion of fluids into the lumen of the GI tract. Another cytotoxin leads to morphological damage of the cells and altered permeability of the epithelium, allowing translocation of bacteria as well as ongoing inflammation and mucosal damage.

Just as for clostridiosis, the signs can vary dramatically from a non-clinical carrier to a fulminant, fatal diarrhoea with SIRS and multi-organ failure. Acute enterocolitis is characterised by severe fibrinonecrotic typhlocolitis, intestinal oedema and intramural thrombosis. There will also be severe ulceration of the mucosa. Horses will often present with fever, anorexia and colic, which will then progress to diarrhoea and associated signs of sepsis and shock.

Treatment is mostly symptomatic with requirement for fluid therapy and plasma transfusions. Oral treatment with di-tri-octahedral smectite is recommended. Antimicrobial therapy, as with all diarrhoea, is controversial and should be based on the clinical impression of the case. The author regularly uses gentamicin to reduce the possible risk of translocation and subsequent septicaemia.

Thankfully, Salmonella remains a rare infectious agent in the UK, but it should be tested for in any acute onset diarrhoea with clinically ill horses.


Equine coronavirus (ECoV) is a betacoronavirus that has been shown to be associated with outbreaks of diarrhoea, anorexia, lethargy, pyrexia and even neurological signs in the USA and Japan. Recently, ECoV was found to be present in the UK equine population at a rate of 2.6 percent of samples that were submitted for symptoms consistent with coronavirus (Bryan et al, 2018) or other infectious diarrhoeas.

Diagnosis is based on qPCR of faeces with clinically affected horses shedding the virus for up to 11 days during infection. qPCR is a highly sensitive diagnostic method with faecal ELISA no longer being an appropriate method due to the poor sensitivity. Haematologically, there will be a marked leucopenia due to a pancytopenia and frequently signs of hypovolaemia. Those patients showing neurological deficits also have hyperammonaemia.

Treatment of these cases is symptomatic and, due to the viral nature of the disease, antibiotics should only be considered if there is concern regarding translocation of bacteria due to increased GI permeability. Many of these horses will require plasma to alleviate the hypoalbuminaemia.


Due to the high level of anthelmintic use in the UK, GI disease associated with large strongyles is rare and therefore only cyathostomins will be discussed. With an ever-increasing resistance to anthelmintics being seen in the UK equine population (Matthews, 2014), it is imperative that targeted protocols with appropriate anthelmintic choice are performed, which requires the input of the veterinary surgeon and knowledge of the property and horses present. Recent studies have assessed the resistance of cyathostomins to multiple drugs in both England and Scotland where every property had resistance to fenbendazole, 70 percent of studs had resistance to pyrantel and 17 percent of liveries in England had resistance to pyrantel (0 percent in Scotland) as well as some evidence of reduced efficacy of ivermectin (Molento et al, 2012).

During the life cycle, the L3 larvae is ingested orally and will then penetrate the epithelial cells of the caecum and colon. Following penetration, the larvae will become encysted in a fibrous capsule where they will gradually mature to an L4 stage. The encysted stage can be as short as six weeks or can be prolonged over several years. When L4 larvae emerge, they enter the lumen of the intestine to continue the reproductive cycle. The mass emergence of the encysted population during late winter or spring is associated with the most severe clinical signs and disease. That said, just the presence of the encysted cyathostomins leads to an inflammatory response in the local area, leading to further fibrosis, oedema, haemorrhage and occasionally ulceration. These changes alone can lead to altered permeability of the intestine.

Clinical signs are again on a spectrum ranging from lethargy and weight loss to severe diarrhoea, hypoalbuminaemia and death. It is more frequently seen in younger horses, particularly under the age of five, but can, theoretically, be seen in any age of horse. It should be noted that there is an increased susceptibility seen in aged horses, particularly those affected by pituitary pars intermedia dysfunction.

Diagnosis is based on clinical signs, haematological/biochemical changes and ultrasonography as the mass emergence of encysted larvae is not associated with egg production. Haematological and biochemical analysis is essential as there will often be a marked hypoalbuminaemia, neutrophilia and inflammatory marker elevation. Ultrasonography of the abdomen will likely show a thickening of the colon and caecum, but this is not pathognomonic of the disease.

Luminal cyathostomins are relatively easy to kill with most anthelmintics but the encysted cyathostomins are a challenge. Moxidectin is the most efficacious of treatments whilst ivermectin maintains some activity against encysted cyathostomins and therefore the former is used in most clinical cases. If the disease is severe then concurrent treatment with glucocorticoids is recommended and supportive care should be considered including plasma transfusions. It should be noted that in some severe cases, the damage to the intestinal mucosa is irreparable and treatment can therefore fail.


If an infectious aetiology is considered likely in any case of diarrhoea, strict biosecurity measures should be put in place to protect not only the other horses but also any humans, due to the zoonotic potential of the clostridial diseases and Salmonella. As such, all horses should be isolated with separate equipment used to muck out and clean the horse and ideally a different muckheap. When in hospital, it is recommended that any bedding is destroyed as clinical waste to reduce the risk of spread.

All personnel entering the stable should wear personal protective equipment including overalls, boot covers and gloves. When transitioning out of the stable these garments should be removed carefully (if overtly contaminated washed immediately), and then feet should be dipped in disinfectant and hands washed prior to leaving the area. It should be noted that alcohol gels alone are not suitable for reducing the spread of clostridial spores and therefore should not be relied upon. Foot dips can be made with either bleach or products such as Virkon. The former must be changed as soon as there is any gross contamination as organic material deactivates bleach.

When the horse is no longer shedding the infectious agent, it is advisable to strip the stable of all bedding, wash down the stable and walls to remove organic material and clean with a product such as Virkon. Clostridial spores and Salmonella are highly resistant to cleaning but in undertaking a simple protocol, the number of spores or bacteria contaminating the stable will be reduced dramatically.

If the affected horse has been in a field, the field should ideally be left empty for as long as possible. UV light will kill the spores and bacteria but, with limited extended periods of strong sunshine, this is impossible to quantify in the UK.


Infectious diarrhoea, although not common in the UK, can frequently be fatal and therefore must be considered in any diarrhoea case. C. difficile appears to be the most common in the author’s experience both clinically and in the faecal samples seen in the laboratory at Liphook Equine Hospital. Salmonella thankfully is infrequent in samples submitted to the laboratory but must be considered a possible aetiology in all cases.


Kim, L. M., Morley, P. S., Traub-Dargatz, J. L., Salman, M. D. and Gentry-Weeks, C.


Factors associated with Salmonella shedding among equine colic patients at a veterinary teaching hospital. Journal of the American Veterinary Medical Association, 218, 740-748

Lawler, J. B., Hassel, D. M., Magnuson, R. J., Hill, A. E., McCue, P. M. and Traub-Dargatz, J. L.


Adsorptive effects of di-tri-octahedral smectite on Clostridium perfringens alpha, beta, and beta-2 exotoxins and equine colostral antibodies. American Journal of Veterinary Research, 69, 233-239.

Matthews, J. B.


Anthelmintic resistance in equine nematodes. International Journal for Parasitology: Drugs and Drug Resistance, 4, 310-315.

Molento, M. B., Nielsen, M. K. and Kaplan, R. M.


Resistance to avermectin/milbemycin anthelmintics in equine cyathostomins–current situation. Veterinary Parasitology, 185, 16-24.

Pusterla, N., Byrne, B. A., Hodzic, E., Mapes, S., Jang, S. S. and Magdesian, K. G.


Use of quantitative real-time PCR for the detection of Salmonella spp. in fecal samples from horses at a veterinary teaching hospital. The Veterinary Journal, 186, 252-255.

Tillotson, K., Traub-Dargatz, J. L., Dickinson, C. E., Ellis, R. P., Morley, P. S., Hyatt, D. R., Magnuson, R. J., Riddle, W. T., Bolte, D. and Salman, M. D.


Population-based study of fecal shedding of Clostridium perfringens in broodmares and foals. Journal of the American Veterinary Medical Association, 220, 342-348.

Jamie Prutton

Jamie Prutton, BSc (Hons), BVSc, DipACVIM, DipECEIM, MRCVS, completed an internship at Rossdales Equine Hospital before starting an internal medicine residency at UC Davis. He holds Diplomate status from the American College of Veterinary Internal Medicine and has been practising at Liphook Equine Hospital since 2015.

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