As long as the pathogen lives on in dental biofilm, antibiotics might have a hard time reaching it - some forms of biofilm are not really penetrated by antibiotics (one reason why H Pylori is so hard to get rid of). From there it can just spread again when the round is finished.

It’s not even clear that this strain only builds biofilm in the oral cavity. Biofilm in the GI tract has just recently become a field of interest.