The urinary tract is a single structure. It fills up with urine from the renal pelvis to the urethra. Most cases of acute pyelonephritis occur when pathogens enter the bladder by ascending from the urethra.
Streptococci, Lactobacilli, and Staphylococcus are usually present between the vaginal entry and the distal portion of the urethra. In women with a predisposition to cystitis; enterobacteria(a pathogen found in the intestines) is present in the vaginal opening, the distal part of the urethra and the skin surrounding it.
The reason for this is uncertain. Among some of the causes for this change is the abnormal microflora of the perineum after antibiotic treatment. Although infections of the external genital organs, and contraceptives( particularly, vaginal diaphragms and spermicides), also add to this condition.
Because the urethra alternately compresses and relaxes during intercourse; It's possible that a small number of bacteria enters the bladder from the vulva.
The virulence of the pathogen determins the plausibility of developing cystitis, so does the number of infiltrating bacteria and the environment of local and general defense mechanisms.
Bacteria that has penetrated the bladder, quickly disappear due to leaching from the urine, its antimicrobial qualities and that of the bladder mucosa. The bladder's wall contains neutrophils capable of phagocytosis. Urine has a bacteriostatic and bactericidal effect due to its high level of urea and high osmolality.