The germ, resistant to some antibiotics, has become a regular menace in hospitals and nursing homes. The study found it played a role in nearly 300,000 hospitalizations in 2005, more than double the number in 2000.
The infection, Clostridium difficile, is found in the colon and can cause diarrhea and a more serious intestinal condition known as colitis. It is spread by spores in feces. But the spores are difficult to kill with most conventional household cleaners or antibacterial soap.
C-diff, as it's known, has grown resistant to certain antibiotics that work against other colon bacteria. The result: When patients take those antibiotics, competing bacteria die off and C-diff explodes.
"It's getting more frequent and harder to treat, but I should say, still treatable," said CBS News medical correspondent Dr. Jon LaPook. "What happens is your colon is filled with trillions of bacteria but they're in balance. If you take antibiotics, sometimes it throws the bacteria out of whack.
"This is spread in hospitals from room to room by doctors and nurses who can spread it from patient to patient," LaPook added.
This virulent strain of C-diff was rarely seen before 2000.
"The nature of this infection is changing. It's more severe," said Dr. L. Clifford McDonald, a Centers for Disease Control and Prevention expert who was not part of the study.
There are other factors that play into the rise of C-diff cases as well, including a larger number of patients who are older and sicker. "And there may be some overuse and inappropriate use of antibiotics," said Dr. Marya Zilberberg, a University of Massachusetts researcher and lead author of the study.
The Zilberberg study was based on a sample of more than 36 million annual discharges from non-governmental U.S. hospitals. That data was used to generate the study's national estimates.
The research is being published in the June issue of Emerging Infectious Diseases, a CDC publication.
Using other scientists' estimates, the study concluded that 2.3 percent of the cases in 2004 were fatal - about 5,500 deaths. That was nearly double the percentage of C-diff-related cases that ended in death in 2000.
Many of the people who died had other health problems. The study did not try to determine if Clostridium difficile was the main cause of death in each case, Zilberberg said.
But earlier research concluded the infection is the underlying cause of thousands of deaths annually, and the problem is getting worse.
C-diff has become an acute health concern in Canada, where it was blamed for 260 deaths at seven Ontario hospitals recently, and 2,000 deaths in Quebec since 2002.
The Association for Professionals in Infection Control and Epidemiology is currently working with U.S. hospitals to study prevalence of the infection and what infection control measures seem to work best.
"This is not a time for alarm, but more a time for educating health professionals to understand this particular pathogen," said Kathy Warye, chief executive of the Washington, D.C.-based association.