Bacteria have gotten a lot of press in the last few years, in part because we’re rapidly learning just how powerful they can be. Researchers have recently learned that premature babies are already infected with drug-resistant bacteria. The results of their study were published in the journal Nature Microbiology.

You have microbes all over your body, inside and out. The name for your personal collection of bacteria, fungi, and viruses is the microbiome. A healthy microbiome is balanced and diverse, and helps keep your body running.

As you’ve probably heard, some bacteria species are better for you than others. Scientists and doctors are particularly worried about drug-resistant bacteria—species that have evolved a resistance to antibiotics. It’s a sort of arms race in which humans attempt to develop drugs faster than bacteria develop resistance to them.

A large part of the problem is our overuse of antibiotics. The more antibiotics we ingest, the more our bacteria can adjust and learn to overcome them. And we’re ingesting a lot of antibiotics. Public health officials worry about what they call “nightmare bacteria,” which infect more than 2 million Americans each year. 

Among the infected are some of our most vulnerable: preterm babies. Researchers collected more than 400 fecal samples from 84 preemies in the Neonatal Intensive Care Unit (NICU) at St. Louis Children’s Hospital. They found that the babies’ gut microbiomes were dominated by drug-resistant bacteria, including Escherichia coli (E. coli), Klebsiella, and Enterobacter. Sequencing the DNA of these bacteria revealed 794 different genes that boost antibiotic resistance. Of those genes, 79 percent had never before been associated with antibiotic resistance. 

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How and why were these babies infected so quickly and so thoroughly? Drugs. Current medical protocol for premature infants often involves giving them a number of antibiotics, regardless of whether or not the babies actually have bacterial infections. The medicine is supposed to keep them safe, but it may be having the opposite effect; the babies who had been given the most medication were the ones with the least-diverse gut bacteria. Taken as a whole, the premature babies studied had 10 times less bacterial diversity than babies born at term.

The prevalence of harmful bacteria in their bellies could explain why preemies are so often sick. 

"Our study demonstrates that even well-studied bacteria—the ones that we know cause disease or their close relatives—have many genes associated with antibiotic resistance that have not been characterized before," senior author Gautam Dantas said in a press statement. "Premature babies do not always get bacterial infections that need treatment, but we have known for a long time that they are at higher risk for infection than babies born full term. Now, we know that preterm-infant guts are attracting exactly the wrong kinds of bacteria."

"Extremely preterm infants often have multiple medical problems, with symptoms of prematurity overlapping with other conditions like infection," added co-author Barbara B. Warner. "The conventional wisdom has been antibiotics can't hurt and they might help. But our new study demonstrates that wide-scale use of antibiotics in this population does not come without cost." 

Dantas envisions a shift from outright antibiotics to aiming for drugs that disable the bacteria's disease-causing properties. "If we can stop these bacteria from producing toxins, rather than kill them outright, we won't see the same selection pressure," he said. "We don't necessarily need to kill these bacteria; we just need to stop them from killing us."