There is no reason for that "unpleasant side effect" to EVER happen. The reason antibiotics cause diarrhea is that they kill off the beneficial gastrointestinal tract flora as well as the bothersome bacteria. Which means your GI tract simply doesn't work (or as well). EVERY doctor who prescribes antibiotics should recommend that their patients either eat "active culture yogurt", or go down to the local health food store and buy a bottle of acidophius capsules.
If you take antibiotics long enough WITHOUT the acidophilus, you risk an explosive growth of candida-type fungi, which can REALLY do "bad things" to your body. It happened to me, and it literally took YEARS to fully recover.
That is a common reason but not the only reason. Sometimes oral antibiotics can cause diarrhea in fewer than 24 hours and that has nothing to do with killing the beneficial bacteria. Of course, your suggestion to take a supplement is a good one.
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On the duration of the antibiotic course, I know that my wife's stubborn sinus infections aren't knocked out by fewer than 15-20 days of treatment. A shorter course such as ten days will cause an improvement, but the infection bounces right back.
I forgot to mention that my dad had an episode similar to yours and never did fully get over it (for decades). It wasn't possible to go to the drugstore then and purchase acidophilus and I'm not sure if varieties of yogurt were common. There was buttermilk. Not known if Candida/yeast was involved.