It would be foolish and dangerous to prescribe this as a preventative for infants. Remember that Brilacidin is an ANTIBIOTIC and taking this affects the microbiome by killing off certain bacteria, some of which may be beneficial. That's why many doctors tell you to take probiotics after you've taken antibiotics, to repopulate the good bacteria. The last thing any responsible physician would do is prescribe to a healthy child something like this that could have life-long adverse affects on the microbiome.

As far as your other questions -- that's what the targeted-release capsules are for. Some of them can survive the passage through the stomach and dissolve at the particular area of the intestinal tract that is the problem area -- at least in theory. This technology seems to be pretty advanced already. This is NOT microtablet technology, which is for a completely different application -- the ability to give patients different amounts of small-dose tablets, so that their doses can be fine-tuned for their individual cases (particularly important for psychoactive drugs or drugs with significant side effects, like Parkinson's disease drugs). What IPIX is working on is partnering with a company that can design capsules that dissolve at different points in the digestive system.
https://sensidose.se/en/technology-micro-tablets/

The UP clinical trial said that there was very little systemic absorption when Brilacidin was administered via enema. Whether Brilacidin is absorbed well through (deliberate) ingestion for dissolution in the stomach is something that will require a clinical trial, as it is as yet unknown.