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Preemies’ gut bacteria reveal vast scope of antibiotic resistance

A new study of gut bacteria in premature infants reveals the vast scope of the problem of antibiotic resistance and gives new insight into the extreme vulnerability of these young patients, according to researchers at Washington University School of Medicine in St. Louis.

The study appears online March 7 in the journal Nature Microbiology.

The gut microbiome has emerged in recent years as a vital player in human health, affecting factors as diverse as nutritional status, bone development and immune function. The new study shows that the microbes colonizing the gastrointestinal tracts of babies born prematurely are not health-promoting or even benign organisms, but close relatives of bacteria known to cause hospital-acquired infections, including Escherichia coli (E. coli), Klebsiella and Enterobacter.

The researchers sequenced all of the DNA in the bacterial communities living in the preterm babies’ guts. Using new techniques they developed, the investigators identified almost 800 genes in these bacterial communities that confer resistance to antibiotics. They noted that about 80 percent of these genes had not previously been associated with antibiotic resistance.

“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,” said senior author Gautam Dantas, PhD, associate professor of pathology and immunology. “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.”

Because of this increased risk of infection, almost all preterm infants cared for in neonatal intensive care units (NICUs) receive antibiotics in the first two days of life, regardless of their health status. And a majority of those receive many more days of treatment.

“Extremely preterm infants often have multiple medical problems, with symptoms of prematurity overlapping with other conditions like infection,” said co-author Barbara B. Warner, MD, a professor of pediatrics and neonatologist at St. Louis Children’s Hospital. “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.”

The study included babies cared for in the NICU of St. Louis Children’s Hospital, where the investigators collected 401 fecal samples from 84 preterm infants over the first three months of life. By sequencing all of the bacterial DNA in these fecal samples, the investigators identified resistance genes to 16 different antibiotics. The babies that received antibiotics only in the first few days of life served as a comparison group to the babies that received antibiotics early plus subsequent treatments later. On average, the babies that continued receiving antibiotics had a total of 21 days of treatment. All babies were born before 33 weeks’ gestation.