In a discovery that challenges long-standing assumptions about necrotizing enterocolitis, a sudden and often fatal intestinal illness that affects premature infants, researchers at Washington University School of Medicine in St. Louis have identified previously unknown predictors for the disease.
While bacteria have been proposed as key drivers for the devastating disease, scientists have been unable to identify specific intestinal bacterial features that reliably predict the disease. In a new study, the researchers found within the gut microbiomes of babies that bacteria-infecting viruses and bacterial antibiotic resistance genes are additional harbingers of necrotizing enterocolitis.
The findings, published Sept. 16 in Gut, are the first to show that these biomarkers in stool can predict human disease risk up to eight days before clinical symptoms appear.
"The mortality rate for necrotizing enterocolitis has changed little since it was first described 65 years ago, and our ability to predict it has been virtually non-existent — until now," said Gautam Dantas, PhD , the Conan Professor of Laboratory and Genomic Medicine in the Department of Pathology & Immunology at WashU Medicine and co-corresponding author on the study. "By showing that bacteria-infecting gut viruses and bacterial drug resistance genes can accurately signal a baby's risk days in advance, we are offering clinicians a window of opportunity to intervene."
Viral dark matter
Necrotizing enterocolitis strikes a fragile and undeveloped gut lining. As inflammation flares, blood flow to the intestinal tissue is choked off, causing sections of the delicate intestine to swell, break down and die.
"With high mortality rates and severe long-term complications for survivors, the disease remains one of the most feared and challenging diagnoses in the neonatal intensive care unit," said co-corresponding author Barbara Warner, MD , the F. Sessions Cole, MD, Chair in Newborn Medicine and director of the Division of Newborn Medicine at WashU Medicine, who treats premature infants with necrotizing enterocolitis at St. Louis Children's Hospital.
For nearly two decades, Dantas and Warner have been collaborating with Phillip I. Tarr, MD , the Melvin E. Carnahan Professor of Pediatrics at WashU Medicine and co-corresponding author on the study, to better understand the gut ecosystem in preemie infants, focusing on harmful gut bacteria as the driver of necrotizing enterocolitis.
Sprinkled throughout the genomes of bacteria living in the gut is the genetic material of viruses. Rather than infecting human cells like the flu virus does, these viruses — called bacteriophages or phages — target bacteria, integrating their DNA into that of their bacterial host. Such integration can shuttle genes for antibiotic resistance or virulence between microbes, converting harmless bacteria into deadly, drug-resistant pathogens.
"When dealing with a disease as sudden and devastating as necrotizing enterocolitis, every day counts."Barbara Warner, MD, WashU Medicine
This viral dark matter within the bacterial genomes has been largely ignored, said Dantas. When Kailun Zhang, PhD, a postdoctoral research associate and first author on the study, joined the Dantas lab, she asked a simple question: What if this often-discarded phage information has an important role to play in necrotizing enterocolitis?
Zhang used advanced computer algorithms to dig into existing genetic data obtained from stool samples from 43 premature infants who developed necrotizing enterocolitis and 86 healthy preemies. The samples came from infants born between 23 and 33 weeks' gestation who spent time in the neonatal intensive care units at St. Louis Children's Hospital, Norton Children's Hospital in Louisville, Ky. or Oklahoma Children's Hospital OU Health. She pieced together phage genomic sequences and antibiotic resistance genes embedded inside gut bacterial genomic DNA and fed those genetic sequences into AI prediction models to identify premature infants at risk for necrotizing enterocolitis.
The analysis revealed that phage-bacterial interactions were an important early warning signal for early-onset necrotizing enterocolitis, which occurs in the first month of life. By tracking the genetic footprint of phages, the team's predictive models identified which premature infants would develop the disease up to eight days before physical symptoms appeared with approximately 75% accuracy.
"When dealing with a disease as sudden and devastating as necrotizing enterocolitis, every day counts," said Warner. "Improving predictive power will help clinicians intervene earlier than ever before with tried-and-true measures without having to wait years for new drugs to make a difference today."
The researchers also found that late-onset necrotizing enterocolitis, which strikes approximately six weeks or later after birth, appears to be biologically distinct from early-onset cases. They discovered that late-onset necrotizing enterocolitis is marked by the accumulation of antibiotic-resistance genes in gut bacteria, driven by cumulative antibiotic exposure during longer NICU stays. By tracking this gene buildup, the team could also predict late-onset necrotizing enterocolitis up to eight days before symptoms appeared with 83% accuracy.
"By showing that the phages that infect gut bacteria play an important role in disease, this computational approach opens doors to early diagnosis of other inflammatory illnesses, including inflammatory bowel disease, sepsis and drug-resistant bacterial infections, that plausibly involve phages or are precipitated by antibiotics," said Tarr. "Phage biology could also be within the causal pathway leading to necrotizing enterocolitis, and, if so, inform new approaches to interventions."
