Pyelonephritis, following urinary tract infection, cystitis. Pyelonephritis is an infection of bacterial origin. It is caused by untreated or poorly treated cystitis. In the majority of cases, the germ comes from the bladder and goes up in the ureter to the kidney which it infects. This concerns infection of the pelvis (pyelitis) and that of the renal parenchyma (nephritis). These two structures play a role in the excretion of urine.