With cystitis, cyst- refers to the bladder, and -itis refers to inflammation, therefore cystitis describes an inflamed bladder, which is usually the result of a bacterial infection, but also can result from fungal infections, chemical irritants, foreign bodies like kidney stones, as well as trauma.
Now a urinary tract infection, or UTI, is any infection of the urinary tract, which includes the upper portion of the tract—the kidneys and ureters, and the lower portion of the tract—the bladder and urethra.
So cystitis, when it’s caused by an infection, is a type of lower UTI.
Lower UTIs are almost always caused by an ascending infection, where bacteria typically moves from the rectal area to the urethra and then migrate up the urethra and into the bladder.
Having said that, on rare occasions, a descending infection can happen as well where bacteria starts in the blood or lymph and then goes to the kidney and makes its way down to the bladder and urethra.
Normally, urine is sterile, meaning bacteria doesn’t live there; the composition of urine, which has a high urea concentration and low pH, helps keep bacteria from setting up camp.
Also, though, the unidirectional flow in the act of urinating also helps to keep bacteria from invading the urethra and bladder.
Some bacteria, though, are better surviving in and resisting these conditions, and can stick to and colonize the bladder mucosa.