Hi Sherrie,
It sounds like your vet may have been concerned about a pyelonephritis, or kidney infection and not just a run of the mill UTI, if it was as serious as described. I would suspect that they felt it possible when the bacteria was still present after the first 14 days, that there could have been a compliance issue where Stella may have been spitting out portions of the liquid Clavamox dose and was not getting the full dose each time. As you said, she was none too happy with it, as many cats may not be.
Fortunately, it sounds like the culture indicated that no antibiotic resistance to Clavamox was present, so it could still be used.
It’s hard to say if the tablet form was more effective because she was getting the full dose, or if the infection just took a longer time to clear. Pyelonephritis, if that’s what was present, can take longer courses of antibiotics than basic UTIs.
I don’t think it’s unreasonable to treat for two extra weeks, since you can’t always be 100% certain such a serious infection is gone from a urine sample alone. Sometimes, we recheck a culture again as well. I have treated similar types of infections longer too, as long as there’s a culture to back it up. There is a greater risk of bacterial resistance present if the Clavamox is stopped when there is still even a small population of that bacteria left. These remaining bacteria are the hardiest and most likely to develop resistance if they’re not killed. Probiotics can be helpful to counteract the effects of a longer antibiotic course on the rest of the body.
Two extra weeks is unlikely to impart antibiotic resistance in the same way that some kind of long-term prophylactic antibiotic use might, where an antibiotic is being used repeatedly at intervals for months or years to “prevent” an infection from occurring. That I certainly would not agree with, but I’d feel that’s different from extending an antibiotic course for 14 more days.