Cat has bacteria in urine

[Pavel]

My cat 11 yo 8 lb had urine infection and got antibiotic (convenia shut) that has prolonged action ( 2 weeks). Next urine test showed he still has bacteria in urine and he got another antibiotic pills ( baytril 22.7 mg/day) during 2 weeks. After 3 weeks urine test shows that he stil has bacteria ( rare cocci) and vet prescribed him another antibiotic course ( baytril) for 2 weeks. I worry to give him antibiotic for almost 45 days. Any idea how it's possible do not kill bacteria with so strong medication during 1 month? (He also get small dose of methimazole because thyroid desease).