Why a Clean Swab Does Not Rule Out Infection in a Problem Mare

Many breeders know the pattern. The mare returns a clean uterine swab, the vet clears her for breeding, she is covered, and she still does not get in foal. It is easy to conclude that infection is not the issue. Often it is, and the swab simply missed it.

The swab catches only about a third of infections

In a peer-reviewed study, Danish veterinarian Jesper Møller Nielsen compared bacterial culture from a uterine swab against culture from a uterine biopsy, using inflammatory cells in the tissue as the reference for infection. The swab detected only 34 percent of infected mares. A biopsy detected 82 percent. A standard swab misses roughly two out of three infected mares (Nielsen, Theriogenology 2005).

Why the swab misses so much

A swab samples only the surface of the lining, and only a small patch of it. In the problem mare the infection is often not on the surface. Imaging research has shown that Streptococcus zooepidemicus, the bacterium most often behind infectious endometritis, can reside deep inside chronically infected endometrium, well below what a swab reaches (Petersen et al. 2009). A swab cannot find bacteria it never touches.

Even a better sample is not the whole answer

A biopsy or a uterine flush reaches more than a swab, and for many infections that is enough. But the problem mare has a second issue: some bacteria are dormant. They have shut down their metabolism and are not multiplying, and every culture method, swab, flush or biopsy, depends on bacteria growing on a plate. Dormant bacteria do not grow, so all three miss them. In a controlled study, activating the dormant bacteria first raised the share that could be cultured from 8 percent to 64 percent (Petersen et al. 2015).

When activation makes even a swab work

This points to when activation is worth doing. The swab's weakness is the hidden, low-grade infection: when little is growing, there is little to find. Activation changes that. When bActivate brings the dormant bacteria back into active growth, the infection becomes florid. Within about 48 hours, mares that looked completely clean often show discharge and fluid, and a large amount of bacteria can be recovered.

Hagyard's field study captured this directly: the team took a uterine swab before bActivate and again 24 hours after. Before activation, a swab finds little on a hidden infection, in line with the 34 percent sensitivity Nielsen reported. After activation, a swab detected dormant Streptococcus zooepidemicus in 47 percent of these problem mares (Petersen and Bojesen 2014). At Kildangan Stud, where a uterine flush was used after activation, the activation-positive rate reached 84 percent (internal clinical data, M. Osborne, 19 mares). The infection goes from undetectable to detectable once the dormant bacteria are woken, and a flush, which samples more of the uterus than a swab, finds even more of it.

What to do instead

Two practical points follow. A biopsy or a low-volume flush is a more reliable sample than a surface swab. And where a dormant infection is suspected, the bacteria must be brought back into an active state before any culture can find them. bActivate is a diagnostic growth medium that reactivates dormant Streptococcus zooepidemicus so a culture can identify it and the veterinarian can treat accordingly.

What this means for your problem mare

A clean swab is reassuring, but in a mare that keeps failing to conceive it is not proof that the uterus is clear. If your mare has normal cycles and clean swabs and still does not get in foal, a hidden or dormant infection is a likely explanation. It is worth asking your veterinarian about a biopsy or flush and, where indicated, activation before the next culture. You can hear Professor Anders Miki Bojesen and Dr. Morten Ronn Petersen discuss this on the bActivate podcast, or review the clinical evidence.

Frequently asked questions

Can a mare have a uterine infection even if her swab is clean?
Yes. A standard swab culture detects only about 34% of infected mares, against 82% for a biopsy culture (Nielsen, Theriogenology 2005). The bacteria most often responsible sit deep in the uterine lining and can be dormant, so they never reach the swab and do not grow on the plate.

How accurate is a uterine swab culture in mares?
It finds roughly one infected mare in three. The swab samples a small patch of the surface, while the infection often sits deeper in the tissue. A clean swab narrows the search but does not end it.

Which test finds the infections a swab misses?
A biopsy or a low-volume lavage samples far more of the uterus than a swab. For dormant bacteria, no culture method is enough on its own, because culture depends on growth. Activation before culture revealed the bacteria in 64% of treated mares versus 8% of controls (Veterinary Microbiology, 2015).

My mare's swab is clean but she is still not in foal. What now?
Ask your veterinarian about a biopsy or lavage instead of another surface swab, and about activation before the next culture. An estimated 70 to 80% of mares still open at the end of the season carry a hidden infection that standard culture misses.

Written by the Bojesen & Petersen Biotech ApS team. Medical oversight: Prof. Anders Miki Bojesen DVM PhD (University of Copenhagen) and Dr. Morten Ronn Petersen DVM PhD Dipl. ACT.