Cases of the contagious and deadly “superbug” known as CRE increased five-fold in community hospitals from 2008 to 2012 in the Southeastern U.S., according to a new study.

And while the actual number of patients discovered was low—305—the worry is that CRE infections are under-reported and threaten health care facilities nationwide, said one of the report’s authors. CRE is an antibiotic-resistant bacterium that usually strikes people in hospitals, nursing homes and other health centers.

“This is a wakeup call for hospitals on how to detect the disease,” said Dr. Joshua Thaden, one of the leading authors for the study published in the August issue of the medical journal, Infection Control and Hospital Epidemiology.

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“And the reason this is very serious is because of the high mortality rate (50 percent) of CRE,” Thaden explained. “The fact that we’re seeing an increase is concerning.”

The study was conducted at 25 community hospitals in North Carolina, South Carolina, Virginia, and Georgia from January 2008 through December 2012.

Adding to the concern is a report published last month that found another superbug, MRSA, at firehouses in Washington state.

Researchers at the University of Washington School of Public Health tested 33 firehouses for the presence of MRSA. The bug was found at 19 of those firehouses on ambulances, trucks and on kitchen surfaces.

Twelve crews reported having at least one member who had gotten an infection requiring medical care. No deaths have been reported.

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Dr. Allison Bartlett, an infectious disease specialist with La Rabida Children’s Hospital in Chicago, said it’s no surprise the bacteria was found where it was.

“Living in close quarters and a lack of frequent cleaning of high-touch surfaces likely all contribute to the high rates of bacterial contamination,” she said.

MRSA stands for Methicillin-resistant Staphylococcus aureus, and is another drug-resistant bacteria. It causes a range of illnesses, from skin and wound infections to pneumonia and bloodstream infections that can cause sepsis and death.

Anyone can get MRSA through direct contact with an infected wound or by sharing personal items, such as towels or razors, that have touched infected skin.

There are more than 80,000 cases of MRSA detected each year in the U.S., with a reported 11,285 deaths.

CRE, is the acronym for Carbapenem-resistant Enterobacteriaceae. Because the various strains of the bacteria are mostly resistant to antibiotics, it’s known as a superbug.

CRE can be transferred from a patient to the hands of the care provider, like a doctor or nurse, and from their hands to another patient. An estimated9,300 people in the U.S. are infected by CRE every year, resulting in around 600 deaths.

All in all, there are at least 2 million illnesses reported each year from the various superbugs, resulting in more than 23,000 deaths, according to the CDC.

Since most CRE cases—and even some MRSA infections—usually start in health care facilities, pressure has been mounting in hospitals to do a better job of tracking them, said Dr. Cristie Columbus, vice dean for Texas A&M College of Medicine.

“Many of them have adopted new laboratory guidelines for improving detection,” she said.

Columbus said that once infections have been detected, proper infection control, like patient isolation, needs to be implemented.

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Medical experts say that the overuse of antibiotics in humans and animals has led to the spread of superbugs.

That overuse is likely to continue in animals after a panel of the U.S. Second Court of Appeals ruled Thursday that the Food and Drug Administration does not have to consider banning the practice of feeding antibiotics to animals that are not sick.

The appeals court overturned two district court rulings in cases brought by the Natural Resources Defense Council and other groups. The suits sought to prompt the FDA to stop the routine use of certain antibiotics in healthy animals unless drug manufacturers proved the safety of such use.

Antibiotics are often used in livestock as a preventive measure. Eightypercent of all the antibiotics sold in the United States are used in livestock production.

There are calls for stronger antibiotics to deal with the superbug spread. However, that’s likely to just continue the vicious cycle of drug resistance, said Thaden, a Boston-based specialist in infectious disease.

“Developing new drugs is important, but the bacteria could end up resisting them as well,” he said.

—By CNBC’s Mark Koba