PROTON PUMP inhibitors (PPIs), the commonly used medications for the treatment of heartburn and acid reflux, may also put you at risk for bone fractures and intestinal infections according to new research.

The drugs, which include over-the-counter Prilosec and prescription Nexium, Protonix, Prevacid and Aciphex, are among the most popular medications in the world with millions of people taking them on a daily basis. the PPIs work by blocking the production of acid in the stomach. Acid in the stomach is normal, but when that acid leaks into the esophagus or down into the small intestine, it can burn the tissue resulting in acid reflux or intestinal ulcers.

PPIs are very good at blocking the production of acid, and they are remarkably effective at relieving acid related symptoms. Surprisingly, blocking acid production in the stomach has little effect on digestion and the drugs generally have no major side effects. some people take PPIs for weeks, months or even years — taking them long after the acid-related symptoms have resolved.

But stomach acid was put there for a reason. It is the first line of defense against swallowed bacteria and other organisms, such as parasites. the highly acidic environment in the stomach kills most nasty bugs, protecting us against infections. the high acidity also helps with the digestion of certain nutrients, including calcium.

Blocking acid production and neutralizing the pH in the stomach allows bacteria to go unchecked downstream into the small bowel and colon. in America, this is rarely a problem because our food and water is clean and relatively bacteria free.

As PPI use increases, however, there is a new bacterium that is emerging as a threat. It is a rather benign sounding bug called Clostridium difficile, “C diff” for short. C diff infections can cause inflammation of the colon (colitis) that results in severe watery diarrhea and in some cases can cause severe abdominal pain, bloody diarrhea and fever. C diff infections are increasing the cause of fatal bowel infections.

C diff infection has been a known complication of antibiotic use for years. Antibiotics reduce the number of normal bacteria in the colon, allowing overgrowth of C diff. Hospitalized patients are particularly at risk, especially if they are on heavy does of antibiotics. New research shows that taking antibiotics and a PPI increases the risk even more. Altering the bowel flora with an antibiotic while at the same time eliminating the acid barrier in the upper intestinal tract appears to be a perfect storm for C diff infections.

Doctors are starting to see C diff infections in outpatients as well, some are just taking PPIs and have not had recent antibiotics.

All this has led the Food and Drug Administration to issue an alert last week regarding use of PPIs and the risk of C diff infections. along with avoiding unnecessary antibiotics, the FDA is recommending that “patients should use the lowest dose and shortest duration of PPI therapy appropriate to the condition being treated.” the FDA also urges patients to seek medical attention immediately if they experience watery diarrhea and abdominal pain that does not go away while taking a PPI.

C diff is not the only infection associated with PPIs. Other bowel infections such as salmonella and campylobacter are more common in patients taking PPIs, especially if they travel to areas where water and food is suspect. the less potent acid blocker medications called H2 blockers (Pepcid, Zantac, Tagamet, etc.) do not seem to incur the same risk of these infections.

Infection is not the only downside of PPIs. More data is suggesting that chronic use of PPIs increases risk of hip fractures and other bone fractures in older women. A new study utilizing data from the 80,000 women who have participated in the Nurses Health Study noted a 35 percent increased risk for hip fracture among regular PPI users. the risk of fracture increased with longer duration of use and return to normal after stopping the PPI for more than two years. the risk was particularly severe in women who smoke or previously smoked. Previous studies have shown association between PPIs and forearm and wrist fractures as well.

Last year, the FDA considered adding a warning to PPIs regarding the risk of osteoporosis. but decided against it because the “fracture risk with short-term, low-dose PPI use is unlikely. the available data show the patients at highest risk for fractures received high doses of prescription PPIs and/or used to PPI for one year or more.”

Despite the risk of PPIs, these drugs are incredibly effective in the treatment of acid reflux, gastritis, peptic ulcer disease and other acid-related stomach conditions.

It is safe to say that PPIs have revolutionized the treatment of these common conditions. however, like most good things, too much of it can be harmful. if you are taking a PPI, make sure that you take if for the shortest time needed — often one to two weeks is sufficient unless your doctor tells you otherwise. if your symptoms have resolved for several weeks, you may safely go off of the drug or step down to a less potent acid blocker such as an antacid or a calcium containing antacid.

Dr. Bill Elliott is assistant physician in chief for Kaiser Permanente’s Novato office and Petaluma. his column appears every third Monday.