AI is certainly the cleanest way to proceed when mating animals. It has the lowest risk of infection. AI isn't actually that difficult to do but I can understand you prefering a natural breeding.
I'd ask to see a vet report on vet stationary about the infection though.
As the stallion was withdrawing I don't see any easy way fecal contamination could occur at that point. If she did it during the mount that would be different. With the open reproductive tract contamination could come from her surroudings too - is her normal barn space clean?
I would sugget doing the enema and cleaning the stallion and the mare to ensure no bacterial contamination from the breeding. Ask your vet about what product would be best.
From this site
www.equinescienceupdate.co.uk/mannos.htm
I found this to consider too
"Mannose may be useful for treating uterine infections
Bacterial infections of the uterus are a common cause of infertility in mares. Infections caused by Streptococcus zooepidemicus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae account for the majority of cases. Some strains of these bacteria have developed resistance to multiple antibiotics. The number of resistant strains continues to rise, as does the number of antimicrobials to which they are resistant. This can make treatment very difficult.
Although work goes on to produce new antibiotics, development of resistance by bacteria may outpace the ability to develop new antibiotics. Because of this, additional methods of combatting infection have been sought.
In order for bacteria to infect epithelial cells such as those lining the mare`s reproductive tract, they must first adhere to the surface of the cells. They do this by attaching to certain sugars within the cell wall glycoprotein . Each species of bacteria attaches to a particular sugar. Dr Sheryl King, and her colleagues at the Southern Illinois University, investigated the ability of specific sugars to prevent bacteria adhering to the uterine lining (endometrium). They collected samples of endometrium from healthy, in season, mares. They prepared small slices of the endometrium and incubated them for 30 minutes at 4ºC with suspensions of E. coli, P. aeruginosa, S. zooepidemicus, with or without additional sugars. The sugars they used were mannose, N-acetyl-D-glucosamine, N-acetyl-D-galactosamine, glucose, galactose, and N-acetyl-neuraminic acid. They examined the tissue preparations under the microscope measured the percentage of endometrial cells which had bacteria attached to them. "We found that mannose significantly inhibited adhesion of all three species of bacteria, (although it did not completely prevent bacterial adhesion)" reports Dr King. A concentration of 75mg/ml of mannose was needed to inhibit adhesion of P. aeruginosa; while concentrations as low as 0.4mg/ml inhibited adhesion of E. coli . Mannose concentrations between 3.13mg/ml and 25mg/ml caused significant inhibition of adhesion of S. zooepidemicus. N-acetyl-D-galactosamine inhibited adhesion of E. coli and P. aeruginosa only. The other sugars had no effect.
Further research has shown that mannose does not adversely affect sperm motility, morphology or fertilizing ability, when used as a component of semen extender. Dr King concludes that mannose and N-acetyl-D-galactosamine may interfere with adhesion and subsequent colonisation of the endometrium in mares by Streptococcus zooepidemicus, Pseudomonas aeruginosa and Klebsiella pneumoniae. She suggests that in mares with uterine infections, use of sugars to competitively displace bacteria from their attachment sites on cells may provide an adjunct to antibiotic treatment. "We feel that using mannose in horse breeding practices could decrease costs, increase efficiency and make a long-term positive contribution to animal and human health maintenance."
for more details see:
Use of specific sugars to inhibit bacterial adherence to equine endometrium in vitro. Sheryl S King, Deena A Young, Lynn G Nequin, Elaine M Carnevale.American Journal of Veterinary Research, (2000) 61, (4), 446-449."
Hope this helps you!
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