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Should Antibiotics Be Taken Preventively?

When I saw John's ziplock full of military-prescribed doxy, I wondered how many other soldiers were taking the same precautions.
Sean Locke / Stocksy

In April, I vacationed with a friend in Myanmar, the southeast Asian country once known as Burma that recently emerged from a military dictatorship. In Yangon, the country’s biggest city and former capital, we had a beer with a member of the American military who was there working at the embassy—let’s call him John. We were in the middle of Thingyan, the raucous annual festival in which everyone throws water at everyone else while walking down the street (or while hanging out of the backs of pickup trucks).


This was great fun for my friend and me—cultural immersion and all that—but John said he and other Americans living there were often less enthusiastic. The water is barely treated, he said, and lots of people end up getting conjunctivitis or digestive illnesses when that bacteria-filled water enters their noses and mouths. That's why he was on a constant low dose of an oral antibiotic, he said. He told me the military hands them out. Later, I saw that he had a ziplock bag of orange pills, with the word “doxycycline” written on it in Sharpie.

The image made my science journalist senses tingle. That can’t be good for you, right?

Long-term use of antibiotics can be harmful—at least for most people, says James J. Collins, professor of biological engineering at MIT. “The general understanding is that antibiotics only affect bacterial cells, and that’s false,” he says. “It’s correct that antibiotics at clinical doses do not kill human cells,” but that doesn’t mean they don’t affect human cells at all. One thing antibiotics do is affect the function of the mitochondria, a structure found in most human cells (and those of many other organisms) that converts carbohydrates into energy, synthesizes proteins, and signals cell growth and death. Mitochondria, in short, are really important for the body to function properly.

Antibiotics limit how well mitochondria can function. According to a study done by Collins’ lab in 2013, “clinically relevant” doses of antibiotics threw off cells’ mitochondria, causing them to produce a byproduct usually reserved for killing off cells and putting them in a state called oxidative stress. At high levels, oxidants can cause inflammation, other studies have shown. Over time that can increase a person’s likelihood of developing chronic diseases like arthritis or metabolic conditions like diabetes. Oxidants also cause mutations in cells and may over time make mutations happen faster, increasing the likelihood that one could cause cancer.


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Antibiotics also eviscerate the microbiome, the colonies of bacteria that live in and on the body that do things like help people digest food, kill off potential pathogens, and regulate mood. Microbiota are made up of some helpful bacteria, some harmless, and some that under different circumstances could make us sick. Antibiotics could alter the composition of the microbiome, especially the one in our guts, Collins says. A cleared-out microbiome means that there are free niches that could be taken over by those disease-causing bacteria, such as C. diff.

Killing off the friendly microbes also causes others to mutate more quickly. That, Collins says, can cause the remaining bacteria to become resistant not only to the antibiotic being used, but also to other antibiotics. Those resistant bugs could spread to other people, which could make them sick and with few options for treatment. One type of bacteria that causes pneumonia and bronchitis has already shown resistance to doxycycline. There are people for whom preventative antibiotics aren’t a bad idea, Collins notes. People who have suppressed immune systems might benefit, he says, “but not a healthy soldier.”

So I wondered, is John the only one with a ziplock of doxy in his room, or are there other soldiers like him, as mandated by military policy?

According to Kevin Dwyer, the chief of media relations for the Defense Health Agency—which is in charge of making sure service members across the Army, Navy, and Air Force receive high-quality and up-to-date medical care—there are likely many military personnel on doxycycline in Myanmar and beyond, but not for the reason John gave. “There is no DoD [Department of Defense] policy for the practice of giving doxycycline prophylactically for food- and waterborne diseases in the setting described. However, doxycycline is an approved and recommended medication for the prevention of malaria in endemic regions of Myanmar,” Dwyer tells me.

Geographic combatant command establishes which preventative measures to take for a particular region based on recommendations from agencies like the World Health Organization and the Centers for Disease Control and Prevention (CDC), so even though the CDC does not consider malaria a risk in the state of Yangon, it recommends medications on a national or regional scale. Malarone is the antimalarial of choice in Myanmar, but doxycycline is a “recommended alternative.”

The CDC lists no limit on how long patients can take doxycycline safely. But some people don’t like to take it because of its lengthy list of side effects, including sensitivity to sun (not exactly ideal if you’re out in it all the time) and nausea. To understand whether doxycycline in particular would have a different effect on the body than other antibiotics, I reached out to the CDC since researchers there have published several studies on the use of the drug as an antimalarial. A spokesperson replied that biochemical differences between antibiotics mean that each works a little differently and will have different effects on the body. So it’s not clear whether doxy’s long-term effects would differ much from those that Collins describes.

Collins admits there’s a lot that we don’t know about the long-term effects of antibiotics, including some of their fundamental effects on pathogens (especially at the site of infection), the microbiome, and human cells. “There is much to be discovered as to what these magic bullets are doing, both the positive and negative,” Collins says. And what does he wish that more people knew about antibiotics? “They come with a potential for harm. One should be careful about taking them. They’re not candy.”

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