Equine endometritis: causes, diagnosis and what the vet does next
Endometritis is inflammation of the lining of the mare's uterus, and it is the most common reason a mare fails to conceive or loses an early pregnancy. It comes in two forms: the clinical form with fluid and discharge, and the subclinical form with no outward sign at all. The subclinical form is the one that costs breeders seasons, because the standard swab culture finds only about 34 % of infected mares (Nielsen 2005). This page collects what is known, with sources, and links to the detailed pages on each part.
The hidden form goes by several names in the veterinary literature: subclinical endometritis, latent uterine infection, dormant endometritis. Breeders usually do not name the condition at all; they say the mare is barren, empty, or simply a problem mare. This page uses the terms side by side so that each reader finds what they are looking for.
What is equine endometritis?
Endometritis is the uterus reacting to something it should clear: bacteria or fungi after mating or foaling, semen and debris after insemination, or urine and air in a mare with poor conformation. A healthy mare clears this within a day or two. A susceptible mare does not, and the inflammation persists, damages the lining and prevents an embryo from surviving.
Veterinarians distinguish four overlapping situations:
| Form | What it means | What the owner sees |
|---|---|---|
| Persistent mating-induced endometritis | The normal reaction to semen does not resolve within 48 hours | Fluid on the ultrasound after covering |
| Clinical endometritis | Active infection with inflammation | Discharge, fluid, sometimes a short cycle |
| Subclinical endometritis | Infection or inflammation without visible signs | Nothing, except a mare that does not get in foal |
| Chronic degenerative endometritis (endometrosis) | Scarring of the lining after repeated inflammation | Repeated early pregnancy loss, poor biopsy grade |
The dormant form of subclinical endometritis is the one bActivate was developed for: bacteria that have stopped growing, sit 300 to 500 micrometres deep in the lining (Petersen 2009) and do not show on a swab.
How common is it?
A German analysis of 28,887 uterine samples found potentially pathogenic bacteria or fungi in 25.9 % of them; among the positive cultures, 79.7 % were beta-haemolytic streptococci, above all Streptococcus equi subspecies zooepidemicus (Köhne 2024). Among problem mares, mares that stay empty after several cycles, the published activation series found a hidden infection in 47 to 87 %: 47 % (30 of 64) at Hagyard Equine Medical Institute, 84 % (16 of 19) at Kildangan Stud, 87 % in the Copenhagen study of 2025.
Read more: Bacteria in the mare's uterus: the German study and Streptococcus zooepidemicus in horses.
What causes it?
- Streptococcus equi subsp. zooepidemicus is the dominant organism. It can switch into a dormant persister state inside the endometrium, where it neither grows on a culture plate nor responds to antibiotics (Petersen 2015).
- E. coli, Klebsiella, Pseudomonas and Staphylococcus aureus make up most of the rest of the bacterial findings; Candida and other yeasts are rarer and often follow repeated antibiotic treatment (Köhne 2024).
- Susceptibility matters as much as the organism: age, parity, poor perineal conformation, delayed uterine clearance and previous infections all make a mare less able to clear what a healthy mare clears on her own.
Read more: Biofilm in the mare's uterus: why breaking it up is not enough.
What are the signs?
In the clinical form: vaginal discharge, fluid in the uterus on ultrasound, a short interval between heats, sometimes a mare that "does not look right" after covering. In the subclinical form there is often nothing to see. The signs are then in the breeding record: two or more well-timed covers with proven semen without a pregnancy, an early loss before day 40, fluid after covering, or a clean swab in a mare that still stays empty. An older mare, from about 10 years, or a mare with several foals is more often affected than a young maiden mare, because the lining clears infection less well with age and parity.
Read more: Ultrasound of the empty mare: what the vet sees and Is my mare a candidate?
How is it diagnosed?
No single test finds everything. The vet usually combines them.
| Method | What it finds | Limit |
|---|---|---|
| Ultrasound | Fluid, oedema, cysts | Does not identify the organism |
| Swab culture | Bacteria on the surface of the lining | Found 34 % of infected mares in a direct comparison |
| Cytology | Inflammatory cells | Inflammation without the organism |
| Biopsy culture | Bacteria deeper in the lining | Found 82 % in the same comparison; invasive |
| Activation culture (bActivate) | Dormant bacteria that start growing again | Diagnostic only; a positive result still needs an antibiogram |
In the peer-reviewed activation study, Streptococcus zooepidemicus grew in 64 % of mares (16 of 25) after activation and in 8 % (1 of 12) after a control flush with saline (Petersen 2015). bActivate is a culture medium, not a treatment: it makes dormant bacteria visible to the standard culture so the vet can choose an antibiotic from the antibiogram.
Read more: Swab culture vs bActivate, Why a clean swab does not rule out infection and What is bActivate?
How is it treated?
Treatment is the veterinarian's decision, after culture and antibiogram. For streptococci, penicillin remained effective in 99.5 % of isolates in the German analysis; multidrug resistance was found in 3.1 % of isolates (Köhne 2024). Uterine lavage removes fluid and debris and supports the mare's own clearance, and is often combined with drugs that help the uterus contract. Antibiotics given without a culture are the one thing every source advises against: they select resistant organisms and, in the dormant form, do not reach the bacteria at all.
Read more: Uterine lavage in the mare: when and why, Positive activation culture: what happens next and How to use bActivate.
What does it cost to leave it?
A mare that stays empty costs a year of keep without a foal, plus stud fee, semen and vet work for every further cycle. In the Hagyard series of 64 problem mares, 83 % (53 of 64) were pregnant after targeted treatment and 70 % of those with a known outcome (32 of 46) foaled; the study had no placebo group, so the figures describe the whole pathway of diagnosis and treatment, not one product. Historically, problem mares foaled at 15 to 50 % against 80 to 85 % in the general population (Bosh 2009).
Read more: Saving time and money: the economics of a hidden infection and Studies and effect.
Sources
- Nielsen JM. Endometritis in the mare: A diagnostic study comparing cultures from swab and biopsy. Theriogenology 2005;64(3):510-518. doi.org/10.1016/j.theriogenology.2005.05.034
- Petersen MR, Nielsen JM, Lehn-Jensen H, Bojesen AM. Streptococcus equi subspecies zooepidemicus resides deep in the chronically infected endometrium of mares. Clinical Theriogenology 2009;1(1):393-409. clinicaltheriogenology.net
- Petersen MR, Skive B, Christoffersen M, Lu K, Nielsen JM, Troedsson MHT, Bojesen AM. Activation of persistent Streptococcus equi subspecies zooepidemicus in mares with subclinical endometritis. Veterinary Microbiology 2015;179(1-2):119-125. PMID 26123371. doi.org/10.1016/j.vetmic.2015.06.006, full text on ResearchGate
- Petersen MR, Bojesen AM. Field study at Hagyard Equine Medical Institute: 64 problem mares. Clinical Theriogenology 2014;6(3):313-314 (congress abstract, no placebo group). therio.org (PDF)
- Kildangan Stud series: 19 mares, 84 % activation-positive, 89 % pregnancy of bred mares. J Equine Vet Sci 2018;66:117 (congress abstract). doi.org/10.1016/j.jevs.2018.05.162
- Köhne M et al. Frequency of potentially pathogenic bacterial and fungal isolates among 28,887 endometrial samples from mares. J Equine Vet Sci 2024;133:105008. doi.org/10.1016/j.jevs.2024.105008
- Bosh KA, Powell D, Shelton B, Zent WW. Reproductive performance measures among Thoroughbred mares in central Kentucky. Equine Veterinary Journal 2009;41(9):883-888. doi.org/10.2746/042516409X456068
FAQ
Frequently asked questions about equine endometritis
Short answers; the sources are on this page.
Can a mare have endometritis with a clean swab?
Yes. In a direct comparison, swab culture found 34 % of infected mares and biopsy culture 82 % (Nielsen 2005). Dormant bacteria deep in the lining do not reach the swab and do not grow on the plate.
Is subclinical endometritis contagious?
Streptococcus zooepidemicus lives on healthy horses and is an opportunist rather than a contagious disease of the uterus. The risk is the individual mare's inability to clear it, not spread between mares.
How long after covering should fluid be gone?
A healthy mare clears semen and inflammatory fluid within about 48 hours. Fluid that persists beyond that is the classic sign of delayed uterine clearance and should be discussed with the vet before the next cover.
Does bActivate treat endometritis?
No. bActivate is a diagnostic culture medium. It activates dormant bacteria so they grow in the standard culture and can be identified and tested for antibiotic sensitivity. The treatment that follows is prescribed by the veterinarian.
When should a breeder ask for the activation culture?
When a mare stays empty after two or more well-timed covers with proven semen, after an early loss, with fluid on the ultrasound, or with a clean swab and still no pregnancy. The mares in the published series had been empty for at least three cycles.
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