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This is most likely a recurring Urinary tract infection.
You are absolutely correct to be concerned, Not only can recurring infections damage your baby's urinary tract but her immune system as well.
UTI's must be treated with an effective broad spectrum antibiotic like Clavamox or clidimycin and for a long enough duration so all bacteria is eradicated. If not, they will refluorish, stronger and more resistant and reinfect her. In addition, the bacteria can become tolerant of the same anibiotic so the medication should be varied for best results.
If this becomes more frequent, your baby should not eat dry food. Canned only so she gets adequate fluid. She should also be encouraged to drink as much as possible to keep the kidneys and bladder flushed. You can give her one daily drop of unsweetened (only) cranberry juice. That will reduce the PH of her urine and make her bladder inhospitable to UTI bacteria.
It is also possible these events may be triggered by stones or crystals, you may want to consider low ash, low magnesium food or even a renal diet if she would eat it.
Please let me know if you still have questions and how your baby is feeling. I will be happy to help in any way possible.
Has she been treated with these antibiotics:
Conclusions and Clinical Relevance-Most nonenteric E coli infections in dogs involve the urinary tract. Amikacin, gentamicin, norfloxacin, and enrofloxacin have the highest efficacy against canine E coli isolates. For E coli isolates from dogs, in vitro susceptibility to commonly used antimicrobial agents has remained fairly stable during the past decade. (J Am Vet Med Assoc 2001;218:381-384)
Here is the entire link:
The problem may be that she was not treated for a long enough period to effectively kill all bacterium, so after the meds were stopped, the ecoli reflourished stronger than ever and reinfected her.
I understand you do not want her on antibiotics for extended period but the meds have to be continued until her urine tests negative for two full weeks. Then she should be completely free of it.
Please let me know if you still have questions.