What other options?
What other options are you talking about? The usual response is a course of antibiotics but the complications is that we are breeding antibiotic resistant bugs. The article pointed out that the species of bacteria has developed immunity and can cause problems from diarrhea to death.
The problem is that the results are clinical experiments and not the full research to confirm if this treatment is effective. I think that the super bugs are only dangerous because they developed immunity to antibacterial drugs that kill off their competition. The super bugs may be easily killed by other bacteria that are beneficial to health.