Antibiotic Dysbiosis in Preterm Infants

Study Overview
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Brief Summary
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Prolonged antibiotic use in preterm neonates has significant consequences on the developing intestinal microbiome, metabolome and host response, predisposing the neonate to various major morbidities, including necrotizing enterocolitis (NEC), late-onset sepsis, bronchopulmonary dysplasia (BPD), and mortality. The hypothesis is that early and prolonged antibiotic use in preterm neonates has significant consequences on the developing intestinal microbiome, metabolome and host response, predisposing the neonate to various major morbidities. It is possible that the effect of this widespread antibiotic use outweighs the potential benefits. This study will randomize preterm infants born at less than 33 weeks gestation to either pre-emptive antibiotics or no-pre-emptive antibiotics. The purpose of this research is to evaluate the risks and benefits of current practice to determine optimal levels of antibiotic use that protects the babies from infection with minimal effect on the microbiome and subsequent adverse outcomes related to overuse of antibiotics.

Detailed Description
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A majority of preterm very low birthweight (VLBW) infants are exposed to antibiotics. Surveys from large databases in the US show that the rate of culture proven bacteremia in these infants at birth is only between 1-2 percent. Antibiotic use, especially when repeated, induces a perturbation (dysbiosis) in gut microbiota that may not recover to the basal state. Antibiotic use increases the risk of subsequent disease and adverse outcomes. The dependence of the developing immune system on the intestinal microbiota is supported by emerging evidence from studies in animals demonstrating decreased resistance to subsequent disease with early exposure to antibiotics. A retrospective review of 50,0261 neonates across 127 neonatal intensive care units (NICUs) from California showed a forty-fold variation in NICU antibiotic prescribing practice with similar burdens of proven infection and mortality. A large number of preterm infants are thus subjected to a potentially harmful course of antibiotics that provides no clear benefit. There remains a major gap in our understanding of antibiotic-related intestinal microbial dysbiosis and how this may result in disease. There will be two aims. In the first aim, a prospective, randomized pilot study, will test the effects of pre-emptive postnatal antibiotics on the microbiome, metabolome and inflammatory responses in the neonate during the NICU course. The second aim will assess the effects of pre-emptive postnatal antibiotics on adverse outcomes in the neonate while in the NICU. The hypothesis is that higher antibiotic use will not be associated with decreased early onset sepsis and in fact, will be associated with increased adverse outcomes including retinopathy of prematurity, necrotizing enterocolitis, spontaneous ileal perforation, late onset sepsis, chronic lung disease, bronchopulmonary dysplasia, intraventricular hemorrhage, periventricular leukomalacia, and mortality.

Official Title
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Antibiotic Effects on the Developing Microbiome, Metabolome and Morbidities in Preterm Neonates

Conditions
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Enterocolitis, Necrotizing, Bacteremia, Bronchopulmonary Dysplasia, Intraventricular Hemorrhage, Periventricular Leukomalacia, Chronic Lung Disease, Ileal Perforation

Intervention / Treatment
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* Drug: Antibiotic
* Other: Gastric fluid
* Other: Breast milk
* Other: Stool samples
* Drug: Antibiotics - pre-emptive


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: All infants less than 33 weeks gestation. Exclusion Criteria: Infants who are non-viable at birth.

Ages Eligible for Study
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Minimum Age: 23 Weeks
Maximum Age: 33 Weeks

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Design Details

Primary Purpose: Treatment
Allocation: Randomized
Intervention Model: Crossover Assignment
Masking: None (Open Label)


Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Other: Antibiotics Control<br>These neonates have a clinical indication to receive antibiotics, such as maternal chorioamnionitis with fetal tachycardia. The standard of care antibiotics include Ampicillin and Gentamicin or Cefotaxime and as part of standard of care blood tests such as complete blood cell counts, blood cultures, and C-reactive proteins will be performed. Study interventions will include the collection of samples for the following: breast milk, gastric fluid and stool samples for analysis of the microbiome and metabolome. | Drug: Antibiotic<br>* Babies that are assigned to antibiotics receive therapy based on the clinical team's discretion.<br>* Other names: Ampicillin or Gentamicin or Cefotaxime;Other: Gastric fluid<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using gastric aspirate.<br>* Other names: Gastric aspirate;Other: Breast milk<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using mother's breast milk.<br>Other: Stool samples<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using infant's stool.<br>|
| Other: No Antibiotics Control<br>These neonates show no signs of respiratory distress(RDS) or have no indications of maternal chorioamnionitis. Antibiotics is not indicated for this group as standard of care. Study interventions will include the collection of samples for the following: breast milk, gastric fluid and stool samples for analysis of the microbiome and metabolome, along with standard of care complete blood counts, blood cultures, and C-reactive proteins. | Other: Gastric fluid<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using gastric aspirate.<br>* Other names: Gastric aspirate;Other: Breast milk<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using mother's breast milk.<br>Other: Stool samples<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using infant's stool.<br>|
| Other: Randomized to pre-emptive antibiotics<br>This group will be randomized to receive standard of care antibiotics which include Ampicillin and Gentamicin or Cefotaxime. Standard of care blood tests such as complete blood cell counts, blood cultures, and C-reactive proteins will be performed. Study interventions will include the collection of samples for the following: breast milk, gastric fluid and stool samples for analysis of the microbiome and metabolome. | Other: Gastric fluid<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using gastric aspirate.<br>* Other names: Gastric aspirate;Other: Breast milk<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using mother's breast milk.<br>Other: Stool samples<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using infant's stool.<br>Drug: Antibiotics - pre-emptive<br>* Babies that are randomized to antibiotics receive therapy based on the clinical team's discretion.<br>* Other names: Ampicillin or Gentamicin or Cefotaxime;|
| Other: Randomized to no pre-emptive antibiotics<br>This group will be randomized not to receive standard of care antibiotics. Study interventions will include the collection of samples for the following: breast milk, gastric fluid and stool samples for analysis of the microbiome and metabolome, along with standard of care complete blood counts, blood cultures, and C-reactive proteins. | Other: Gastric fluid<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using gastric aspirate.<br>* Other names: Gastric aspirate;Other: Breast milk<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using mother's breast milk.<br>Other: Stool samples<br>* Microbiome, metabolome, and inflammatory mediators will be evaluated using infant's stool.<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Rates of composite morbidities and mortality, including necrotizing enterocolitis(NEC), late onset sepsis (LOS), bronchopulmonary dysplasia (BPD) and death | Enrolled subjects' medical record will be reviewed to determine the association between antibiotic administration and the components of the composite outcome | Until discharge from the NICU, up to 1 year | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Rates of bacteremia | Enrolled subjects' medical record will be reviewed to determine the association between antibiotic administration and the development of bacteremia after the first week of life. | Until discharge from the NICU, up to 1 year | 
| Microbiota 16s ribosomal ribonucleic acid (rRNA) metagenomic sequencing | Pacific BioSciences or Illumina sequencing will be done and the data analyzed using metagenomics Rapid Annotation using Subsystem Technology (MG-RAST). | Until discharge from the NICU, up to 1 year | 
| Microbial diversity analysis | Microbial diversity is assessed using Chao1, Shannon, and ordination methods implemented using a software program called phyloseq package in R.42 Chao1 estimates the species richness for each sample, while the Shannon Index scores richness and abundance, though is not sufficient in assessing overall microbiome differences. Detrended Correspondence Analysis (DCA), a multivariate statistical method, will be applied to detect overall microbiome differences. Adonis methods were used to attribute additional variables' contribution to microbial variance. | Until discharge from the NICU, up to 1 year | 
| Calprotectin (microgram per gram) levels in stool | Calprotectin levels will be analyzed using an ELISA kit. | Until discharge from the NICU, up to 1 year | 
| Metabolomic analysis (microMol per gram) in gastric aspirate, stool, and breast milk | Metabolites as biomarkers of microbial-host metabolism will be identified by nuclear magnetic resonance and mass spectrometry. Levels of vitamins(microMol per gram), polyphenols(microMol per gram), cholesterol (microMol per gram), and short chain fatty acids(microMol per gram) will be measured. | Until discharge from the NICU, up to 1 year | 
| S1000A12 (microgram per gram) in stool | S1000A12 levels will be analyzed using an ELISA kit. | Until discharge from the NICU, up to 1 year | 
| Intraleukin-6 (micrograms per gram) in stool | Intraleukin-6 values will be assessed using multiplex technologies. | Until discharge from the NICU, up to 1 year | 
| Intraleukin-8 (micrograms per gram) in stool | Intraleukin-8 values will be assessed using multiplex technologies. | Until discharge from the NICU, up to 1 year | 
| Intraleukin-10 (micrograms per gram) in stool | Intraleukin-10 values will be assessed using multiplex technologies. | Until discharge from the NICU, up to 1 year | 
| Rates of bronchopulmonary dysplasia (BPD) | Enrolled subjects' medical record will be reviewed to determine the association between antibiotic administration and diagnosis of BPD. | Until discharge from the NICU, up to 1 year | 
| Rates of spontaneous ileal perforation | Enrolled subjects' medical record will be reviewed to determine the association between antibiotic administration and spontaneous ileal perforation | Until discharge from the NICU, up to 1 year | 
| Rates of intraventricular hemorrhage | Enrolled subjects' medical record will be reviewed to determine the association between antibiotic administration and intraventricular hemorrhage | Until discharge from the NICU, up to 1 year | 
| Rates of necrotizing enterocolitis (NEC) | Enrolled subjects' medical record will be reviewed to determine the association between antibiotic administration and intraventricular hemorrhage | Until discharge from the NICU, up to 1 year | 
| Rates of retinopathy of prematurity | Enrolled subjects' medical record will be reviewed to determine the association | Until discharge from the NICU, up to 1 year | 
| Rates of periventricular leukomalacia | Enrolled subjects' medical record will be reviewed to determine the association | Until discharge from the NICU, up to 1 year |