What Causes Relapsing Of Fever And Urine Infection?

My father 63 yers old had UTI, Symptoms were onset fever 101-103 F nausea very weak, After admitted in local hospital Dr prescribe Amikacin Sulphate 500 Mg injection IV After 7 days treatment he was released from hospital. But after 7 days fever relapsed after urine culture it was showed E.coli ifection relapsed then a our Dr. Advised Gatifloxacin 400 mg daily for 5 days and Nitrofurantoin 100 mg twaice a daly for 6 days after completion of Gatifloxacin. after this fever was over and he was completely recover. but after 15 days of completion medication fver was relapsed again with 101-103 F with nausea, chills . but no burning sensation, or frequently urge of urination was seen. After Urine R/E it was reveled that puss cell 30-35 hpf/ml, sedimentation present a few epithelial cells are present, others ware negative SG 1080 pH 6.5 colour pale yellow and slightly hazy. DR. then gave him Amikanic sulphate 500mg for 7 days with nitrofurantoin 100mg twice a daily for 14 days. Now my father is completely recover. a day before yesterday he completed antibiotic course of nitrofurantoin. Yesterday a Urine RE shows puss cell 2-3 /hpf pH 6.5 and a few epithelial cells are present. My question is after a long time antibiotic course how it is possible that present of puss in urine? is it means that he is not completely cure? please give me a suggestion.