Hi and thanks for the query, Normally, the treatment of pyelonephritis, depending on the drug after two weeks as you describe should be sufficient. However, with some resistant and atypical strains, this might take some longer. An important aspect in the management of pyelonephritis, especially in a patient with other risk factors, or in case its a recurrent phenomenon, is an active search to identify the causative organism. Urine cultures and antibiotic sensitivity tests to prescribe the appropriate anti biotic to tackle the particular germ in question could be very useful. This not only aids in diagnosis, but in measuring the efficacy of the treatment when completed. Ultrasound images of the kidney could also help, because in some patients, renal abscesses, especially when symptoms persist should be actively sought for. Suggest you consult a nephrologist. thanks and best regards, Bain LE, MD.