The urinary tract (which consists of the kidneys, the ureters, the urinary bladder and the urethra) is sterile and is free from any bacteria or other organims.  On the other hand, the gastointestinal tract usually contains organisms, like Escherichia coli (E. coli), which passes out in large numbers in the faces. Under normal circumstances, they do not cause any harm in the intestine, but they are extremely harmful to the urinary tract when they enter the urethral orifice which is adjacent to the anal canal. 
This may occur especially when improper washing / cleaning is done after each defecation. The area outside the anal orifice remains contaminated with E. coli.  Urinary tract infections are more common in women since the anal canal lies closer to the urethral orifice in women and it is easier for the bacteria, including E. coli to migrate from the anal canal into the urethra, especially in women.  Moreover, the urethra is very short in women (only an inch long), so that the bacteria can reach the bladder and sterile urine quickly.. On the other hand, the urethra in males is longer, and is much further away from the anus or anal orifice, and therefore the chances of infection from the anus to the urethra are significantly reduced.  However, infections in the urinary tract may also be caused by bacterial infections in the bloodstream, usually from a serious infection in another part of the body.  These bacteria may also cause damage to various parts of the urinary tract including both the bladder and kidney. Urinary tract infections are also frequently caused by a catheter which is sometimes inserted into the bladder in hospitalized patients or in patient who are severely debilitated, also ccontributing to the increased risk of urinary tract infections.

As soon as the bacteria reach the urinary bladder, they start multiplying in the urine, which happens to be an excellent medium for their growth. Chances of the growth of these organisms become much more in any part of the urinary tract, e.g. the kidneys, the ureters, etc., when there is some obstruction in the urinary flow.   For example, a stone, a stricture or some congenital abnormality ( like horseshoe kidneys, etc.) which does not allow the free passage of urine from the kidneys to the urinary bladder / urethra, allows for stagnation of  the urine, increasing the possiblity of bacterial growth and infection.

This collection/stagnation of urine facilitates the growth or multiplication of bacteria. If the obstruction is in either part of the ureter, the infection/ growth of the organisms will occur above the obstruction in the ureter and in the kidneys of the side involved. However, if the obstruction is much lower down, say in the urethra, as a result of an enlarged prostate, in males, which is a common occurrence, the growth/infection will be in the urinary bladder, and may, in advanced cases, go higher up, in both the ureters and in both the kidneys as well.

In the urinary bladder, the organisms cause marked inflammation in which case pus cells are formed, which are passed out into the urine. Once the urinary bladder is infected, and the patient is not careful, and does not take proper antibiotics or is only partially treated, the infection may extend up to the kidneys through the ureters. The infection of the urinary bladder is called cystitis, and once the bacterial infection reaches the kidneys, it is called pyelonephritis.

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