If a dog has an infection then you shouldn't breed her until the infection is totally gone. Your vet can do cultures to determine when the infection is cleared. However, if the bacteria was introduced during the artificial insemination, then better sterilization and handling procedures need to be instituted during both the sperm harvesting and the actual AI. Douch of any kind can change the vaginal and uterine environment and possibly have an adverse effect on a potential litter. Uterine infections need to be treated with antibiotics early on in the infection.
If you are getting small litters from your females, then there are various things to check. First off, many dogs will reabsorb pups if under stress, sick, vaccinated and even dewormed, so you need to be sure your females are not under stress. You also need to not vaccinate them or deworm them if possible during the pregnancy. Also if females are interacting, the alpha female may be placing undue stress on the newly pregnant female leading to smaller litters. Keep these things in mind.
In addition, you need to be sure you are inseminating your female at the right time. If you are inseminating at home, then I would suggest at the vet's office and having testing done to ensure she is at the most fertile period of the heat cycle. In addition, you will want to have the male's sperm evaluated as well for mobility. All of these play a factor in how many pups are produced.
So I would first take your next female and male into the vet and have them evaluated. I would not douche them. Now you can use antibacterial wipes to keep the folds of the vulva clean and cut down on bacteria.
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