Discovering The Genetic and Microbial Basis of Adverse Outcomes in Premature Babies

Questioning Common Practice 

Neonatologists routinely face the challenge of caring for extremely low birth weight babies (<28 weeks’ gestation) at risk for the lethal bloodstream infections causing sepsis and necrotizing enterocolitis, or NEC. Currently, the most common practice is to give these infants empiric antibiotics at birth and for the next two to three days as clinicians await microbiology results. However, there are no data to support or refute this practice, and numerous studies have shown that >95% of extremely low birthweight infants receiving empiric antibiotics do not have early onset sepsis. In some cases, antibiotics may actually disrupt the delicate gut microbiome and increase the riskof infection. The challenge is to determine which infants can safely avoid antibiotics and whether antibiotics interact with genetic and microbial risk factors to increase the risk of severe diseases.

Identifying Determinants of Adverse Outcomes

The NICU Antibiotics and Outcomes, or NANO trial, is an NIH/NICHD-funded multicenter randomized controlled trial. Mike Morowitz, MD, with the Universityof Pittsburgh Medical Center Children’s Hospital, is the trial’s principal investigator.¹ The NANO trial challenges whether empiric antibiotics at birth may increase the risk of adverse outcomes, such as NEC in extremely low birth weight infants. The Children’s Mercy Kansas City Level IV NICU is one of 14 sites participating in this study. Though the NANO trial includes funding to collect both genomic and microbial specimens from these babies, it does not include funding to perform the genomic and microbial analysis of them.

Venkatesh Sampath, MBBS, MRCPCh, neonatologist and Medical Director of the Donald Thibeault Lung and Immunology Laboratories at Children’s Mercy, recognized the importance of genetic and microbial analysis to the NANO trial. In a separate grant, March of Dimes is funding a three-year study that will provide for genomic and microbial analysis to supplement the NANO trial’s core clinical activities. The goal of the March of Dimes trial is to identify genomic and microbiome determinants of adverse outcomes among infants enrolled in the NANO trial.²

Dr. Sampath has previously demonstrated that deleterious mutations in the toll-like receptor (TLR) family of innate immune genes impact susceptibility to NEC and sepsis. He will lead the genomic aspect of this work, while Dr. Morowitz will focus on profiling the infant gut microbiome.

“This March of Dimes study gives us aunique opportunity to confirm some of thegenetic data we have regarding NEC andsepsis, identify new genetic risk factors,and determine how these genetic riskfactors interact with the gut microbiomeand early antibiotic use to increase the riskof NEC and sepsis.” – Dr. Sampath

Sequencing Genetic Samples 

The hypothesis for the March of Dimes-funded study is to test whether specific TLR gene mutations in extremely low birth weight infants increase vulnerability to late onset sepsis and NED by amplifyingthe consequences of antibiotic-induced gut dysbiosis. During the pilot phase of the study, Dr. Sampath is conducting exome sequencing for 350 specimens previously collected from infants in the Children’s Mercy NICU and other centers, and that have been held in a biorepository. Collection of 20 out of an anticipated 300 DNA samples from infants participating in the NANO trial also will be completed during this phase, as well as initial analyses of TLR-related exome sequences for 10 infants.The sequencing will be performed in conjunction with the Children’s Mercy Genomic Medicine Center, led by Tomi Pastinen, MD, PhD, Director, and Emily Farrow, PhD, CGC, Director, Laboratory Operations. Dr. Sampath’s ongoing NIH-funded study³ has identified the SIGIRR gene as a potential risk factor for NEC, and this study will seek to detect other possible genetic targets. Over the course of the March of Dimes study, genetic samples from additional neonates recruited into the NANO trial will be added to the biorepository, and will be sequenced.

Exploring Genetic and Microbial Connections

Dr. Sampath already is working on the pilot portion of this trial, exome sequencing 350 babies for specific TLR genetic mutations. Upon approval from March of Dimes, he will continue analyzing these DNA samples.

The goal for the March of Dimes-funded study is for Children’s Mercy to complete genetic analyses for morethan 700 babies, while Dr. Morowitz and his team analyze the microbiome of these infants. Their work will result in one of the most far-reaching studies in neonatology exploring the genetic and microbial connections to NEC and sepsis in extremely low birth weight babies.

Determining Which Infants Antibiotics May Help

Dr. Sampath is working to understand why some preterminfants develop NEC and some do not by identifying pathogenic TLR pathway variants via exome sequencing.This data will be used to study the relationship between genetic risk factors, the gut microbiome and antibiotics.The results may aid in the development of genetic and microbiome tools to screen infants at risk for NEC and sepsis in the NICU, instituting precision measures to help physicians determine which infants are at highest risk for these life-threatening complications and may benefit from avoidance of antibiotics or altering the microbiome using probiotics and other therapies.