Well, they're saying both. The popular idea was that in healthy people, urine (and by association, the bladder) was devoid of bacteria because studies (or who knows, maybe just one study) were not able to culture anything. But they tried culturing urine in various ways and found multitudes of bacteria in healthy urine.

They're also saying that after they were able to successfully culture bacteria from urine, some strains seem more common in people with certain bladder conditions, raising the possibility that there is connection with the condition, such as "overactive bladder". If H. pylori bacteria can cause ulcers, it's not a stretch to believe that certain bladder problems can also have a bacterial cause.