is right in suspecting infection arising in the ureter
Usually any kind of abnormalities in renal physiology can cause frequent and reccurent urinary tract infection
Urine test may be negative for microorganism since there is a minimum requiered level of bacteria's are needed for a positive result.
Urine results may not be correlated with the level of symptoms experienced and this is particularly true for women.
So she needs to take antibiotics when there is signs of UTI.
Also consult your urologist for further course of action.