Few people check into a hospital expecting to come down with a severe case of diarrhea while undergoing care for an entirely unrelated problem. And even fewer expect to die of the hospital-acquired intestinal infection that causes the watery stools. Yet for approximately 14,000 Americans each year, that is exactly what happens. The culprit is a strain of a spore-forming bacterium known as Clostridium difficile, or C. diff—in particular, a relatively recent strain that has grown more virulent and resistant to drugs.

The new strain of C. diff, called NAP1, emerged in the mid-2000s, and is at least in part responsible for skyrocketing infection rates in hospitals throughout the U.S. In 1993 fewer than 100,000 hospital stays were associated with C. diff either as a primary diagnosis upon admission or as a secondary diagnosis after admission, according to the Agency for Healthcare Research and Quality. By 2009, that number had climbed to 336,600, with about 9.1 percent of those stays ending in death at the hospital (versus 2.1 percent of all inpatient hospitalizations). NAP1, which produces far more of the illness-causing toxin than other C. diff strains, is also refractory to many once-effective antibiotics; when treatment is stopped, the illness recurs.

Even though deaths from NAP1 are on the rise, many hospitals fail to take simple and inexpensive measures to prevent infection. A recent survey from the Association for Professionals in Infection Control and Epidemiology (APIC) of 1,087 hospitals revealed inadequate implementation of cleaning strategies known to prevent hospital-acquired C. diff infections, such as daily wipe-downs of commonly touched surfaces with bleach, washing hands with soap and water, and limiting antibiotic use. All hospitals surveyed are taking measures to reduce C. diff infections, but their responses vary widely.

Part of the problem is a lack of data about how C. diff spreads, says Jennie Mayfield, clinical epidemiologist at Barnes-Jewish Hospital/Washington University School of Medicine, St. Louis, and president-elect of the 14,000-member APIC. The bacterium somehow eludes the methods of isolating and culturing that have made headway in unraveling the spread of other common hospital pathogens such as MRSA (methicillin-resistant Staphylococcus aureus) and VRE (vancomycin-resistant Enterococcus), rates of which have both gone down in recent years. C. diff is notoriously difficult to isolate (one reason behind its name), making it nearly impossible to track its path through hospitals. “We don’t even know if patients on the same nursing unit are getting infected with the same strains,” says Mayfield. “We can assume it, but we don’t really know.”

The survey, says Mayfield, reflects that uncertainty, beginning with basic hand washing. Alcohol gels and foams don’t remove the spores so are an inadequate defense against spreading the germ. Only soap and water can rinse spores away. “If everybody washed their hands like they’re supposed to, there would be hardly any transmission of this stuff,” says Deverick Anderson, associate professor of medicine and chair of antibiotic stewardship at Duke University. However, only 77 percent of survey respondents had a policy of promoting soap-and-water hand washing when caring for C. diff–infected patients, and only 10 percent had policies requiring sick patients to wash their hands with soap and water.

The survey also showed a variation in how hospitals clean patients’ rooms. C. diff spores live on surfaces like bedrails, bedpans, and doorknobs for several months, and are usually placed on those surfaces by the unwashed hands of caregivers who have handled materials soiled by infected patients. When uninfected patients touch those surfaces, they unknowingly collect spores and can then ingest them, allowing C. diff to germinate in the gut and release bowel-harming toxins. Frequent wipe-downs of highly touched surfaces with bleach, the only common disinfectant that kills C. diff spores, are a surefire way to eradicate the bacteria from patient rooms. But according to the APIC survey, only 67 percent of respondents have a firm daily-bleaching policy in place at their facilities.

Just as crucial as the wipe-downs, says Mayfield, is the integration of objective measures of room cleanliness. “In the past, it’s usually been housekeeping supervisors walking around, eyeballing rooms,” says Mayfield of the way cleanliness has usually been evaluated. “It’s just visual observation, it’s subjective.”

Now, tools are available to check for the presence of organic matter on a given surface. One device uses swabs to check cleaned surfaces for the presence of ATP, the energy storehouse of the cell, an indicator of biological life forms. With another, a fluid that glows under ultraviolet light is dabbed randomly throughout a room. If those dabbed areas glow after cleaning, the surface has not been properly cleaned. But according to the APIC survey, these tools are not being integrated broadly. “What’s surprising to me is that we have an objective way of measuring the effectiveness,” says Mayfield, who notes that 64 percent of respondents are still doing subjective observation of room-cleaning practices.

Cutting down on erroneous use of antibiotics is a confirmed preventive measure. “That, to me, remains the key potential intervention for decreasing C. diff,” says Anderson. Yet again, the APIC survey showed a wide variation in practices. Antibiotics have always been associated with C. diff infections. But whereas the illness used to occur most often in patients taking clindamycin and amoxicillin, this latest strain is associated with some of the most commonly used antibiotics, such as ciprofloxacin and levofloxacin. Yet just 60 percent of survey respondents have instituted antimicrobial stewardship programs to prevent overuse of these medications.

The survey also showed a wide variety in isolation practices, with major differences in when infected patients, who are mostly aged 65 or older and mostly come to hospitals from nursing homes, were put into isolation and the duration of their stay.

As the cost of treating patients with C. diff infections rises and the high death rate continues, health officials are beginning to sound the alarm bells. In January of this year, the Centers for Medicare and Medicaid Services began requiring hospitals to report C. diff events in order to receive reimbursement for care (a C. diff illness raises the cost of care by about $2,400 per patient, according to one study, cited by the Centers for Disease Control and Prevention (CDC) among others). And new C. diff­-killing technologies—such as vaporized hydrogen peroxide and ultraviolet light—are being tested to see if they do a better job of eradicating the bacteria compared with standard cleaning practices. At Duke, Anderson is leading a nine-hospital study, funded by the CDC, comparing bleach plus UV light versus bleach alone, with results expected by mid-2014.

Basic science to learn exactly how C. diff spreads is vital, Mayfield says, to shaping strategies to stop it. The bacterium may be hiding out in unrecognized places in the hospital, for example. In addition, its increased presence outside of the hospital indicates some other factor at play in its spread. “We’re not going to tolerate deviance from best practices,” says Mayfield, “but we are still at the point with this organism where we are not even sure what the best practices are.”