Most antibiotics are derived from microorganisms themselves, which have been using said compounds in battle for millions of years. We start using them carte-blanche in the course of one-hundred years, and they all develop immunity. Not too shocking, considering they evolved the substances in the first place.
The synthetic antibiotics (Carbapenem) tend to be more effective, yet far more expensive than the microorganism-derived compounds (Penicillin). Still, bacterial evolution outpaces our development rate.
Clostridium difficile is a common enteric pathogen normally kept in check by healthy colon flora (like what's found in yogurt). Patients who are on long-term antibiotics kill off their healthy flora, leaving only the antibiotic-resistant C diff behind.
The C diff then multiply, colonizing and conquering your whole colon, and producing two toxins. Toxin A will cause severe diarrhea, while Toxin B will dissolve the cells of your colon, eventually causing perforation and death.
As the article states, stool transplants have been effective in 'invading' the C diff colon with normal healthy flora, which then fight off the C diff and colonize the patient. Still damned gross...and it means the lab needs to test the transplant stool to ensure it is healthy enough for transfer (don't want to give the patient a new infection).
And yes, I'm working stool and urine bench this week.