HI, I am not a doctor but a patient that suffers with a similar problem!
Sadly this is not uncommon. I have a similar problem but have a defect in my kidneys called MSK, that increases my infections and kidney stones. The problem is most of our current culture methods are based on 100 year old techniques that are based on colony count or number of bacteria etc.. Though these methods are great for the standard acute infections, doctors are now realizing that they do not work for those of us with low level chronic or in some cases biofilm infections. IN this case only
a small amount of the bacteria actually slough off in the urine from time to time, so
catching them is tough and usually since the bacteria are in there own little fortress
in the kidneys, when they do it is of not insignificant numbers to show up as infection on cultures.
If there is not defect etc in the kidney give these bacteria a safe haven then usually long term low level infections should prevent your daughters problems etc. If these are verified by ultrasound etc. that makes me wonder if there is some minor scarring etc. in her kidney or if they can just seem the inflammation. As a patient myself,. I would encourage you to get copies of her tests and read the reports too.
I can send you some links to info on biofilms if you pm me we are not to post them here. Or you can goggle biofilm or complicated urinary tract infection.
I am very interested in biofilm information due to having what I am told is chronic bladder infection in the wall of my bladder 'follicular cystitis' as well as IC and I am in constant pain that is getting worse.
Many thanks for any help you can give me