Antibiotics or antimicrobial drugs are effective medications for the treatment of bacterial infections in horses.

Common equine infections requiring antibiotics include infected skin wounds and abscesses, pneumonia, infectious diarrhea, cellulitis, peritonitis and more.

Many antibiotics have broad-spectrum action meaning they act against many different bacteria. Others more specifically target certain bacterial strains. Your veterinarian can determine which antibiotic is appropriate for your horse given their medical situation.

These drugs are not without risks, and they can have adverse effects on horse health when given without veterinary oversight.

Misuse and overuse of antimicrobials are common problems in the equine industry. This has contributed to growing antibiotic resistance whereby bacteria undergo changes that make them impervious to existing antibiotics.

As a horse owner, it is important to understand how antibiotics work, when they should be used and how to properly administer them to your horse.

This article will review antibiotic use in horses, types of equine antibiotics, and how to limit the associated risks for your horse.

Antibiotics for Horses

If you’re a long-time horse owner, chances are you have given your horse some form of equine antibiotic before. You may even have a leftover bottle of oral antibiotics in your feed room.

But reaching for antibiotics every time your horse scrapes his leg can have unintended consequences. These medications must be used carefully to maximize their benefits and minimize risks.

Antibiotic drugs treat bacterial infections in animals by killing bacteria or preventing them from multiplying so the horse’s immune response can beat the infection. [1][14]

Infections occur when harmful microorganisms invade and reproduce in your horse’s body. While beneficial probiotic bacteria help your horse stay healthy, exposure to pathogenic bacteria can lead to disease. [1]

Antibiotics combat pathogenic bacteria, but they can also disrupt the good microorganisms that are a part of the horse’s natural microbiome, potentially causing diarrhea or gut issues. This is one risk of antibiotic use in horses. [12]

Mad About Horses
Join Dr. Chris Mortensen, PhD on an exciting adventure into the story of the horse and learn how we can make the world a better place for all equines.
Apple Podcasts Spotify Youtube
Mad Barn - Equine Nutrition Consultants

How Antibiotics Work in Horses

Your horse is exposed to a wide variety of microorganisms in its environment. Most environmental bacteria are harmless, but some are disease-causing pathogens. [13]

Your horse has several natural defenses against pathogenic bacteria, including the good bacteria that populate the gastrointestinal tract. Skin also acts as a structural defense and the immune system fights against bacteria that enter the body. [2]

While the immune system can neutralize many bacterial infections in a healthy horse, severe infections may require medical intervention with antibiotics. [14]

Mechanisms of Action

In general, antibiotics work by disrupting biological processes in bacteria to impair their ability to function and replicate.

Antibiotics are able to selectively target bacteria and not animal cells because bacteria have different cell structures and metabolic functions. Antimicrobial medications have fatal consequences for microbes without damaging surrounding tissue. [15]

Some antibiotics work by deforming the bacterial cell wall, interfering with metabolic processes, targeting DNA function, or preventing energy production. [3]

Different antibiotics have different mechanisms of action targeting classes of bacteria responsible for the infection. Strategic selection is vital as not all antibiotics are equally effective. [3]

Treating Horses with Antibiotics

Several forms of antibiotics are administered to horses by veterinarians. [1] Systemic antibiotic treatments circulate throughout the entire body while local antibiotics only affect the area in which they are applied.

Systemic therapy is often necessary for infectious diseases but has a greater risk of disrupting the gut microbiome. [17]

This type of antibiotic includes oral and injectable medications. Oral antibiotics are simple for horse owners to administer, but veterinarians prefer intravenous antibiotics for immediate delivery in cases of severe infection. [1]

Horse owners are likely familiar with topical antibiotics, such as triple antibiotic ointment. Topical administration delivers antibiotic medicine directly to the affected tissues, most commonly the skin. [18]

Veterinarians can also use intra-articular administration of local antibiotics to treat affected joints. [19]

When to Use Antibiotics for Horses

Veterinary use of antibiotics in horses and other animals spans nearly a century. These medications have changed history: many once-fatal diseases are now treatable thanks to antibiotics. [20]

There are many cases when your veterinarian might recommend antibiotic treatment, but horse owners are often prone to overusing and misusing these drugs.

Successful antibiotic treatment depends on correct drug selection, dosing, time course and administration. [1] It is always recommended to consult a veterinarian before giving your horse any medicine.

The Equine Veterinarian’s Role

Depending on the situation, your vet may be able to use cultures to identify pathogenic bacteria and determine which antibiotics will work best. Alternatively, when time is of the essence, they can make educated recommendations based on your horse’s clinical signs. [6]

Most importantly, veterinarians can determine if your horse needs antibiotics in the first place or if these medications might not be necessary.

Sometimes, antibiotics cause more harm than good. The antimicrobial drug that worked for your horse last time may not be the best choice for his current infection. [17]

Veterinarians prescribe antibiotics for precise lengths of time and according to specific schedules. Not following instructions can interfere with therapeutic efficacy. [14]

Even if your horse’s condition improves within a few days of treatment, completing the entire treatment course is vital to prevent antibiotic resistance. [5]

Always follow manufacturer instructions regarding how and when to administer the drug. If your vet recommends dosing twice a day, try to administer the antibiotics 12 hours apart to ensure the drug reaches therapeutic levels in your horse’s body. [1]

Equine Infectious Diseases

Horses with a weakened immune system due to age, stress, chronic disease, immunosuppressive medications, or malnutrition are most susceptible to infectious diseases. But even healthy horses can get sick unexpectedly. [14]

Signs of internal illness include reduced appetite, diarrhea, lethargy, weight loss, poor coat quality, abnormal vital signs, fever, and unusual behaviors. [6]

Horse owners often sense when something is off with their horse and subtle changes can provide early clues about health concerns. If you suspect your horse is unwell, contact your veterinarian immediately.

Early diagnosis can help avoid unnecessary antibiotic use. Bacterial infections that don’t improve after three days may require antibiotics to resolve. [6]

Bacterial Infections

Examples of bacterial infections in horses include tetanus, strangles, Potomac horse fever, botulism, anthrax, lymphangitis, and cellulitis.

Viral Infections

Many equine infectious diseases involve viral infections, which don’t respond to antibiotics. Adult horses with a cough or nasal discharge often have viral infections. [6]

Vaccines are also available to protect against some of these viral conditions. [14]

Infected Wounds

Infection is often the main concern for equine wound care. A compromised skin barrier allows pathogenic bacteria from the environment to invade your horse’s body. [14]

Severe cuts, scrapes, gashes, and puncture wounds have a significant risk of infection. [21]

These injuries require veterinary evaluation to determine the appropriate treatment. If your veterinarian believes an infection is likely, they may prescribe antibiotics.

Lacerations near joints are particularly concerning, as joint infections can be life-threatening to horses and require aggressive early treatment. Treat any sign of an infected joint as an emergency. [19]

However, minor wounds often heal on their own without complications. Owners can help reduce the risk of infection by keeping the area clean of debris, allowing drainage, and applying local antiseptic. [7]

Signs of Infection

Signs of infection include heat, swelling, abnormal odor, red skin, yellow discharge, and tenderness. Talk to your veterinarian if your horse has a minor wound with signs of infection. [21]

Infected leg wounds can cause cellulitis, a bacterial infection of the soft connective tissues. This condition involves a sudden onset of extreme swelling that makes the limb look like a stovepipe. [8]

Chronic cases of cellulitis can lead to lymphangitis, so prompt treatment is critical. [8]

When Antibiotics Aren’t Necessary

While antibiotics are effective for some bacterial infections, these medications don’t always improve recovery times.

For example, abscesses caused by strangles might be part of an effective immune response to the disease. [22]

Hoof abscesses also rarely need antibiotics. Many abscesses improve with drainage, bandaging, and appropriate management. [9]

Many cases of fever involving minor respiratory symptoms are viral infections that should resolve independently. [6] Most superficial skin wounds heal without antibiotics when kept clean.

Common Antibiotics for Horses

Veterinarians will use clinical history and laboratory results to choose the best antibiotic for your horse.

There are fewer safe and effective classes of antibiotics for horses compared to other species. The limited options makes proper antibiotic selection critical for treating horses and preventing antibiotic resistance. [25]

You should never give your horse an antibiotic prescribed for your other pets without veterinary approval. [1]

Here are several of the most common antibiotics used for horses.


Sulfonamides are broad-spectrum antibiotics that stop various bacteria from multiplying by interfering with DNA synthesis. [23]

This category includes sulfamethoxazole-trimethoprim, a popular oral antibiotic used to treat infections in minor wounds. Horse owners know this antibiotic as SMZ.


Penicillin is one of the first antibiotics ever discovered and belongs to a class of antibiotics called beta lactams. This family of drugs kills gram-positive bacteria by damaging the cell wall. Examples include penicillin, ampicillin, and amoxicillin. [24]

Veterinarians frequently administer penicillin as injections because of poor absorption from the gut. Penicillin is a popular treatment choice for streptococcal infections in horses. [24]


Tetracyclines limit bacterial growth by targeting protein synthesis. This drug class includes doxycycline and minocycline, popular treatment options for Lyme disease in horses. [26]


Metronidazole breaks apart bacterial DNA and is a preferred treatment for anaerobic bacterial infections. Anaerobic bacteria grow in the absence of oxygen. [27]

Abscesses, soft tissue infections, respiratory infections, and deep puncture wound infections often involve anaerobic bacteria. [27]


Chloramphenicol is another broad-spectrum antibiotic used for various infections, including anaerobic infections. [28]

Horse owners generally administer this antibiotic orally or as an ophthalmic solution. You should always handle chloramphenicol with gloves as it can cause aplastic anemia in humans. [28]


This category of antibiotics inhibit protein synthesis, ultimately causing damage to the cell membrane and other structures. They are most effective against gram-negative bacteria but have some limited activity against gram-positive bacteria. They are often combined with penicillin to target a wider range of microbes. [33]

Commonly used aminoglycosides in equine medicine are:

  • Gentamicin: Commonly given intravenously and may also be infused into the uterus to treat uterine infections in mares struggling to conceive. [1][29]
  • Amikacin: Commonly used to treat orthopedic infections such as septic arthritis and uterine infections in mares [34]
  • Neomycin: A component of the triple antibiotic ointment known as Neo Poly Bac which also contains the antibitoics polymyxin and bacitracin. This is commonly used to treat eye infections such as bacterial keratitis [18][35]
  • Streptomycin: Once used as a treatment for leptospirosis, it is currently infrequently used due to concerns about adverse reactions [36]
  • Kanamycin: Can be used for intramuscular, intramammary and subcutaneous administration in horses [37]


Macrolides are a category of antibiotics that interfere with protein synthesis and target a wider spectrum of microbes than penicillin. [3]

Examples of macrolides include erythromycin, azithromycin and clarithromycin. Erythomycin or clarithromycin are commonly used in combination with the antibiotic rifampicin to target Rhodococcus equi. This pathogen is often responsible for pneumonia in foals. [38]

Erythromycin is not commonly used in older horses due to concerns about antibiotic-induced colitis. [39]


Enrofloxacin and marbofloxacin are fluoroquinolones used in equine medicine. These inhibit DNA synthesis to impair the ability for bacterial cells to replicate. These antibiotics are effective against intestinal aerobic pathogens but less so against anaerobes. [40]

Quinolones are not recommended for growing horses as they can damage the cartilage in young animals. [30]

Treatment Options for Common Infections

The following is a list of common infectious conditions in horses, the bacterial species involved and the recommended antibiotic treatment. [32]

Bacterial endocarditis

  • Organisms: Pasteurella spp., Actinobacillus spp., Streptococcus spp.
  • Primary: Penicillin with Gentamicin or Enrofloxacin
  • Alternative: Rifampin plus antibiotic selected based on lab culture results


  • Organisms: Mannheimia haemolytica, Actinomyces spp., Klebsiella spp., Streptococcus spp.
  • Primary: Chloramphenicol or Trimethoprim-sulfa
  • Alternative: Ceftriaxone


  • Organisms: Clostridium tetani
  • Primary: Metronidazole or Penicillin

Acute Diarrhea

  • Organisms: Neorickettsia risticii, Salmonella spp., Clostridium spp., Aeromonas spp., Lawsonia intracellularis, Escherichia coli, Actinobacillus spp.
  • Primary: Determine based on diagnosis; (i.e. oxytetracycline, metronidazole)
  • Alternative: Penicillin, Gentamicin, Metronidazole

Peritonitis (primary)

  • Organisms: Actinobacillus equuli, Escherichia coli, Staphylococcus spp., Streptococcus spp., Bacteroides fragilis, Clostridium spp.
  • Primary: Penicillin and/or Gentamicin
  • Alternative: Trimethoprim-sulfa

Peritonitis (secondary)

  • Organisms: Rhodococcus equi
  • Primary: Penicillin with Metronidazole and Gentamicin or Enrofloxacin
  • Alternativ: Chloramphenicol


  • Organisms: Staphylococcus aureus, Streptococcus spp.
  • Primary: Trimethoprim-sulfa or Penicillin and Gentamicin
  • Alternative: Oxytetracycline or Doxycycline

Septic arthritis

  • Organisms: Streptococcus zooepidemicus, Escherichia coli, Actinobacillus spp., Staphylococcus spp., Salmonella spp.
  • Primary: Chloramphenicol
  • Alternative: Penicillin, Gentamicin and/or Metronidazole


  • Organisms: Rhodococcus equi, Streptococcus zooepidemicus, Streptococcus equi, Actinobacillus spp., Pseudomonas aeruginosa
  • Primary: Clarithromycin and Rifampin (for R. equi), Penicillin or Ceftiofur
  • Alternative: Doxycycline and Rifampin (for R. equi), Penicillin and Gentamicin

Prophylaxis for surgery

  • Primary: Penicillin (with or without Gentamicin)


  • Organisms: Streptococcus equi zooepidemicus, Escherichia coli, Actinobacillus spp., Klebsiella spp., Enterobacter spp., Staphylococcus aureus, Pasteurella spp., Bacteroides spp., Clostridium spp.
  • Primary: Penicillin and/or Gentamicin and/or Metronidazole
  • Alternative: Chloramphenicol


  • Organisms: Streptococcus spp.
  • Primary: Penicillin
  • Alternative: Trimethoprim-sulfa


  • Organisms: Streptococcus equi subsp. Equi
  • Primary: Penicillin
  • Alternative: Trimethoprim-sulfa

Wounds (contaminated)

  • Primary: Trimethoprim-sulfa (on limbs), Penicillin, Gentamicin and Metronidazole (with open fracture), Penicillin and Gentamicin (involving joints)
  • Alternative: Trimethoprim-sulfa, Oxytetracycline, Doxycycline, Metronidazole

Antibiotic Risks for Horses

Caution is recommended whenever giving antibiotics to your horse. Any antibiotic treatment involves some risk of side effects for equine patients. Horses can also have allergic reactions to some medications. [17]

Horse owners can limit the risk of complications by following dosing instructions, choosing the right antibiotic for their horse’s condition, and only using antibiotics under veterinary supervision. [25]

Antibiotic Resistance in Horses

Due to growing antibiotic resistance, bacterial infections are harder to treat in nearly all species. [5]

This resistance occurs when bacteria evolve in response to antibiotic use. Resistant bacteria are more likely to survive and reproduce, leading to the rise of so-called “superbugs“. [12]

Antibiotic resistance presents a health threat to the entire equine population. [1] Reducing the unnecessary use of antibiotics is the best way to combat antibiotic resistance.

Underdosing also promotes resistance, so always administer the complete dosing regimen. [5]

Antibiotic-Induced Colitis

Horses have a large colon home to trillions of probiotic bacteria that play a role in digestion, nutrient synthesis and immune function. [16]

While antibiotics target pathogenic bacteria, they may also affect populations of good bacteria. [4]

Horses given antibiotics can experience gut dysbiosis in which the microbiome becomes disrupted.

Symptoms include digestive upset, colic, and mild diarrhea. Monitor your horse closely for any signs of gut discomfort or stool changes. [10]

Gut dysbiosis can also interfere with fibre fermentation in the hindgut and cause inflammation. In severe cases, colitis (inflammation in the colon) can be life-threatening. [10]

Caring for Your Horse After Antibiotics

Horse owners can mitigate the potential adverse effects of antibiotics on the equine gut with appropriate management and feeding practices. [17]

To support your horse’s gut health, feed a forage-based diet, ensure they drink plenty of water and give your horse adequate turnout.

You can also support your horse’s gut microflora with digestive health supplements, including probiotics and prebiotics. [16]

Probiotics for Horses on Antibiotics

Probiotics are beneficial microbes naturally found in the gastrointestinal tract. Probiotic supplements are especially beneficial for horses during and after a course of antibiotics.

Also called direct-fed microbials, probiotics deliver live bacteria to the equine digestive tract. [11]

Research suggests these supplements may limit the overgrowth of harmful bacteria, support the rebound of healthy microbiota, and reduce the risk of diarrhea. [11]

Discuss probiotics with your veterinarian to ensure that you choose an appropriate supplement for your horse. [31]

Choosing the Best Equine Probiotic

Equine probiotic formulas often contain lactic acid-producing bacteria, yeast cultures, and prebiotics. [11]

Choose a probiotic for your horse with a high concentration of multiple strains of beneficial bacteria. Mad Barn’s Optimum Probiotic is a 5-strain pure probiotic supplement containing 20 billion CFUs per serving.

Horses recovering after antibiotic therapy may benefit from advanced digestive support including higher concentrations of probiotics, prebiotics, digestive enzymes, and nucleotides.

For additional support, feed our comprehensive Optimum Digestive Health supplement. [31]

Optimum Digestive Health

5 stars
4 stars
3 stars
2 stars
1 star

Learn More

  • Prebiotics, probiotics & enzymes
  • Support hindgut development
  • Combats harmful toxins in feed
  • Complete GI tract coverage


  • Antibiotics are generally considered safe when given according to veterinary and manufacturer instructions.
  • Different classes of antibiotics target different types of pathogenic bacteria.
  • Veterinary oversight is critical for determining when antibiotics are necessary.
  • Overuse of antibiotics contributes to antibiotic resistance, a significant health concern.
  • Antibiotics can cause digestive issues by disrupting good bacteria in the horse’s gastrointestinal tract.
  • Probiotics can help support digestive health in horses recovering from antibiotic treatment.

Is Your Horse's Diet Missing Anything?

Identify gaps in your horse's nutrition program to optimize their well-being.


  1. Haggett, E. et al. Overview of the use of antimicrobials for the treatment of bacterial infections in horses. Equine Vet Ed. 2010
  2. Perkins, G. et al. The development of equine immunity: Current knowledge on immunology in the young horse. Equine Vet J. 2014.
  3. Etebu, E. et al. Antibiotics: Classification and mechanisms of action with emphasis on molecular perspectives. Int J of Appl Microbiol and Biotech Research.
  4. Costa, M. et al. Changes in equine fecal microbiota associated with the use of systemic antimicrobial drugs. BMC Vet Research. 2015.
  5. Roberts, J. et al. Antibiotic resistance–What’s dosing got to do with it? Critic Care Med. 2008.
  6. Desmettre, P. Diagnosis and Prevention of Equine Infectious Diseases: Present Status, Potential, and Challenges for the Future. Adv in Vet Med. 1999.
  7. Freeman, S. et al. BEVA primary care clinical guidelines: Wound management in the horse. Equine Vet J. 2020.
  8. Braid, H. et al. A cross-sectional survey of the diagnosis and treatment of distal limb cellulitis in horses by veterinary surgeons in the United Kingdom. Equine Vet Ed. 2021.
  9. Redding, W. et al. Septic Diseases Associated with the Hoof Complex: Abscesses, Puncture Wounds, and Infection of the Lateral Cartilage. Vet Clinics of North Amer: Equine Pract. 2012.
  10. Baverud, V. Clostridium difficile associated with acute colitis in mature horses treated with antibiotics. Equine Vet J. 2010.
  11. Schoster, A. et al. Probiotic Use in Horses – What is the Evidence for Their Clinical Efficacy? J of Vet Internal Med. 2014.
  12. Baquero, F. Evolution of antibiotic resistance. Trends in Ecol and Evol. 1997.
  13. Scholter, M. et al. The use of immunological methods to detect and identify bacteria in the environment. Biotech Adv. 1995.
  14. Giguere, S. et al. Equine Immunity to Bacteria. Vet Clin North Am Equine Pract. 2000.
  15. Falkow, S. et al. The Interaction of Bacteria with Mammalian Cells. Annual Review Cell Biol. 1992.
  16. Venable, E. et al. Role of the gut microbiota in equine health and disease. Animal Frontiers. 2016.
  17. Khusro, A. et al. Adverse Effect of Antibiotics Administration on Horse Health: An Overview. J Equine Vet Sci. 2021.
  18. Jones, R. et al. Contemporary antimicrobial activity of triple antibiotic ointment: a multiphased study of recent clinical isolates in the United States and Australia. Diag Microbiol and Infect Disease. 2006.
  19. Pezzanite, L. et al. Intra-articular administration of antibiotics in horses: Justifications, risks, reconsideration of use and outcomes. Equine Vet J. 2021.
  20. Aminov, R. A brief history of the antibiotic era: lessons learned and challenges for the future. Front Microbiol. 2010.
  21. Orsini, J. et al. Management of severely infected wounds in the equine patient. Clin Techniq Equine Pract. 2004.
  22. Timoney, J. Strangles. Vet Clin North Am Equine Pract. 1993.
  23. Duijkeren, E. et al. Trimethoprim/sulfonamide combinations in the horse: a review. J Vet Pharm and Therap. 1994.
  24. Love, D. et al. Serum concentrations of penicillin in the horse after administration of a variety of penicillin preparations. Equine Vet J. 1983.
  25. Baggot, J. et al. Antimicrobial selection and dosage in the treatment of equine bacterial infections. Equine Vet J. 1987.
  26. Chang, Y. et al. Antibiotic treatment of experimentally Borrelia burgdorferi-infected ponies. Vet Microbiol. 2005.
  27. Tally, F. et al. Antimicrobial activity of metronidazole in anaerobic bacteria. Antimicrob Agents and Chemother. 1978.
  28. Estell, K. et al. Pharmacokinetics of multiple doses of chloramphenicol in fed adult horses. Vet J. 2020.
  29. Durham, A. An evaluation of serum gentamicin concentrations and bacterial susceptibility to gentamicin in equine practice. J Vet Intern Med. 2018.
  30. Beluche, L. et al. In vitro dose-dependent effects of enrofloxacin on equine articular cartilage. Am J Ver Res. 1999.
  31. Collinet, A. et al. Multidimensional Approach for Investigating the Effects of an Antibiotic-Probiotic Combination on the Equine Hindgut Ecosystem and Microbial Fibrolysis. Front Microbiol. 2021.
  32. Suggested Treatment Options By Condition [Equine]. OSU VMC Antimicrobial Use Guidelines. 2020.
  33. Krause, K.M. et al. Aminoglycosides: An Overview. Cold Spring Harb Perspect Med. 2016.
  34. Dahan, R. et al. Pharmacokinetics of regional limb perfusion using a combination
    of amikacin and penicillin in standing horses
    . Can Vet J. 2019.
  35. Scott, E.M. et al. Evaluation of the bacterial ocular surface microbiome in clinically normal horses before and after treatment with topical neomycin-polymyxin-bacitracin. PLoS One. 2019.
  36. Verma, A. et al. Leptospirosis in Horses. Vet Microbiol. 2013.
  37. EMEA Committee for Veterinary Medicinal Products: Kanamycin Summary Report. EMEA. 1999.
  38. Buckley, T. et al. Resistance studies of erythromycin and rifampin for Rhodococcus equi over a 10-year period. Ir Vet J. 2007.
  39. Gustafsson, A. et al. The association of erythromycin ethylsuccinate with acute colitis in horses in Sweden. Equine Vet J. 1997.
  40. Edlund, C. and Nord, C.E. Effect of quinolones on intestinal ecology. Drugs. 1999.