A Randomized Controlled Trial Investigating if Antibiotic Use in the First 48 Hours of Life Adversely Impacts the Preterm Infant Microbiome
Phase: NA
Conditions: Premature Birth of Newborn, Enterocolitis, Necrotizing
Sponsor: University of Chicago

 
 
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University of Chicago Medical Center Research Protocol 
Principal Investigator:  
Erika C. Claud, MD – Pediatrics/Neonatology &    
 
 
 
 
 
 
 
Medicine/Gastroenterology 
Other Investigators:  
Nicole E.G. Grady, MD – Pediatrics/Neonatology 
 
 
 
 
Allison H. Bartlett, MD – Pediatrics/Infections Diseases 
 
Study Title: Antibiotic stewardship and protection of the developing preterm infant 
microbiome 
 
ABSTRACT: 
Fear of early-onset sepsis (EOS) has led to nearly universal initiation of empiric antibiotics 
at birth in preterm infants. While the risk of morbidity and mortality from EOS is high, the 
frequency is low at 0.98 per 1000 live births (Stoll et al 2011). Evidence shows that there 
are significant risks involved with prolonged antibiotic therapy, including necrotizing 
enterocolitis, invasive fungal infection, and even death. Furthermore, antibiotics alter the 
microbiome, which is increasingly being recognized as a key determinant of health and 
disease. The development of the microbiome begins at birth; the very time empiric 
antibiotics are begun in the majority of preterm infants. We hypothesize that antibiotic 
stewardship principles can be used to limit empiric antibiotic use at birth in preterm 
infants, thus leading to protection of the developing microbiome and improved clinical 
outcomes. 
I. 
Aim and Hypotheses  
Preterm infants are frequently started on empiric antibiotics at birth due to the risk of 
early onset sepsis (EOS). While the risk of morbidity and mortality from EOS is high, the 
frequency is low at 0.98 per 1000 live births (Stoll et al 2011). There are risks involved 
with antibiotic therapy including disseminated fungal infection, neonatal necrotizing 
enterocolitis, and alteration of the gastrointestinal microbiome (Nash et al 2009). We 
hypothesize that antibiotic stewardship principles can be used to limit empiric antibiotic 
use at birth in preterm infants, thus leading to protection of the developing microbiome 
and improved clinical outcomes. 
Aim 1: Implement an antibiotic stewardship program to limit initial empiric antibiotic 
administration in a pilot study group of 30 preterm patients, 28-34 weeks gestation. 
Aim 2: Evaluate outcomes in infants who do, or do not, receive empiric antibiotics at 
birth. Blood culture results, clinical outcomes, length of stay, total days of antibiotics 
received during NICU admission, and microbiome development from birth until 
hospital discharge will be examined. 

 
 
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II.   
Background and Rationale 
A.    Background: 
Greater than 12% of infants in the United States are born premature and may begin their 
lives within the neonatal intensive care unit (Matthews et al).   Within this population, the 
evaluation and treatment for early-onset sepsis (EOS) is an ongoing controversy.  EOS 
remains the leading cause of morbidity and mortality in neonates with a rate of 0.98 per 
1000 live births (Stoll et al).  Infants admitted to NICUs are frequently started on empiric 
antibiotics due to the risk of EOS. Although the CDC has released algorithms for the 
evaluation of EOS for all newborns, without a lower gestational age limit indicated to which 
they apply, clinical experience has shown that nearly all premature infants receive empiric 
antibiotics (Verani et al 2010).  Recent algorithms by the AAPs Committee on the Fetus & 
Newborn recommend discontinuing empiric therapy at 48 hours with negative cultures in 
preterm infants (Polin et al 2012).  However, although it has been shown that discontinuing 
antibiotics when cultures are negative in asymptomatic ELBW infants does not 
compromise clinical outcomes, they often receive prolonged antibiotic treatment courses 
(Cordero & Ayers 2003).  Furthermore, Kuppala et al (2011), studied very low birth weight 
(VLBW) infants, and found that within their population, 16% did not receive empiric 
antibiotics.  For those who were treated, each day of initial empiric antibiotic therapy 
significantly increased the odds of developing late-onset sepsis (LOS), NEC or death, and for 
infants who had received any initial empiric antibiotic exposure, the number needed to 
harm was 3.  
Within our unit, there were 794 admissions in 2014.  Of these, 196 were within our study’s 
target age range of 28-34 6/7 weeks of gestation at birth.  While there were no positive 
blood cultures at birth within this gestational age range, only 6 of these 196 patients did 
not receive empiric antibiotics at birth.   Additionally, of the 190 that were treated, 43 were 
treated beyond the standard 48-hour rule-out-sepsis recommendations.   
Recently, there has been a growing body literature describing the effects of antibiotics on 
the gastrointestinal microbiome. In a study of 26 patients in 2009, Tanaka et al. found that 
the neonates that has received either oral or intravenous antibiotics during the first 4 days 
of life had less gut microbial diversity, as well as an attenuation in colonization with 
Bifidobacterium and an increase in colonization with Enterococcus.  Additionally, a study by 
Fouhy et al showed that infants exposed to the empiric antibiotics ampicillin and 
gentamicin shortly after birth tend to develop microbiomes with higher proportions of 
Proteobacteria, Actinobacteria, and Lactobacillus than the unexposed infants for up to a 
month following the treatment course. 
These changes within the microbiome may be especially important within the premature 
population, where Wang et al (2009) found that infants who developed necrotizing 
enterocolitis (NEC) had significantly more days of antibiotics prior to disease onset, as well 

 
 
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as differences in their gastrointestinal microbiome, having less microbial diversity and an 
increased abundance of Gammaproteobacter. Similarly, Cotton et al (2009) has also shown 
that prolonged antibiotic therapy (>5 days) was associated with increased odds of NEC or 
death.  In earlier studies, Cotton et al (2006) linked prolonged broad spectrum antibiotic 
therapy with increased risk for invasive fungal infections.  Beyond the immediate neonatal 
timeframe, gastrointestinal microbial dysbiosis has also been linked to multiple diseases 
affecting long term health, including inflammatory bowel disease (IBD), obesity, asthma 
and atopy (Arietta et al 2014).   
Due to the effects of the microbiome health and disease, as well as growing concerns for 
antibiotic resistance, there has been a growing recognition for the need for antimicrobial 
stewardship. According to the Infections Diseases Society of America (IDSA), antimicrobial 
stewardship includes interventions targeted toward the improvement and monitoring of 
appropriate antimicrobial use by selecting the most optimal drug regimen, including the 
type of drug used, the dose, the duration of therapy and the route of administration.  While 
studies have found that, in general, antibiotic stewardship is not commonly used within 
pediatric hospitals (Hersh et al 2009), Comer Children’s Hospital has a strong, 
multidisciplinary antimicrobial stewardship team with an active presence within the NICU. 
These collaborations are necessary to promote proper and safe use of antibiotics, as 
Grohskoph et al  (2005) found that as many as 47% if infants within NICUs were on at least 
one antibiotic, and Clark et al (2006) found that antibiotics are the most prescribed 
medications within NICUs.  Within our NICU at Comer, 30-40% of patients are on at least 
one antibiotic on a given day (Nash et al 2014).  While there is less published literature on 
the presence of antibiotic resistant organisms (AROs) within NICUs, de Man et al (2000) 
found that infants treated with cefotaxime as initial empiric therapy were 18 times as likely 
to grow resistant organisms. 
Limiting initial empiric antibiotic therapy is one way to promote healthy gastrointestinal 
microbiome development, as well as limit the presence of AROs.  While there is little data 
supporting the withholding of initial antibiotics in neonates, the administration of empiric 
antibiotics has been questioned for decades.  In 1961, William Blanc questioned the safety 
of empiric antibiotics, stating “The diagnosis of congenital and early neonatal infections is 
difficult, and the systemic prophylactic administration of antibiotics is potentially harmful.  
Its dangers have to be weighed against the risk of infection.”   More recently, Tagare et al 
(2010) found that in low risk preterm neonates there was no evidence that routine empiric 
antibiotic use had a protective effect in clinical sepsis, further questioning the immediate 
use of antibiotics at birth. 
 
B. Rationale: 
Evaluation and treatment for EOS is an ongoing controversy in neonatology. While the risk 
of morbidity and mortality from EOS is high, the frequency is low at 0.98 per 1000 live 
births (Stoll et al 2011). Although the CDC has released algorithms for the evaluation of 
EOS for all newborns, there are no specific algorithms for preterm infants, and clinical 

 
 
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experience has shown that nearly all premature infants receive empiric antibiotics (Verani 
et al 2010). Recently, there has been growing literature on the detrimental effects of 
antibiotics on the development of the gastrointestinal microbiome. Important in the 
premature population, Wang et al (2009) found that infants who developed NEC had 
significantly more days of antibiotics prior to disease onset, as well as differences in their 
microbiome. Cotton et al (2009) has also shown that prolonged antibiotic therapy (>5 
days) was associated with increased odds of NEC or death. Additionally, the microbiome 
has been linked with long-term health outcomes, such as asthma, obesity and IBD.  With 
this growing body of evidence suggesting potential harm associated with empiric antibiotic 
exposure by preventing healthy microbialization, and the growing numbers of infections 
with antibiotic resistant organisms (Bizzarro & Gallagher 2007), it is critical to develop 
guidelines to limit antibiotic use in premature infants, and study the effect on clinical 
outcomes and the microbiome development. 
III.  
Research Plan  
Methods: 
Through literature review and expert input, inclusion and exclusion criteria for 
randomization have been developed and reviewed to allow preterm infants, with a low risk 
of infection, to be closely observed and monitored, rather than receive routine empiric 
antibiotics on admission to the NICU. 
 
Inclusion Criteria for randomization: 
1) Infant must be born between the gestational ages of 28 0/7 weeks and 34 
6/7 weeks  
-AND- 
2) Infant must be considered to have a low risk of infection by one of the 
following criteria: 
a. Delivered for maternal indications (Cesarean section or induction 
of labor for maternal health, including HELLP, pre-eclampsia, 
placental abruption, history of IUFD/abruption, multiple gestation 
requiring preterm delivery, etc) 
-OR- 
b. Delivered due to preterm labor to a mother without the diagnosis 
of chorioamnionitis/maternal fever or prolonged rupture of 
membranes >18 hours 
 
Exclusion Criteria: 
1) Signs of clinical illness within the first 3 hours of life (Escobar et al 2014): 
a. 5-minute Apgar <5 
b. Requiring vasoactive drugs 
c. Seizures 
d. Significant respiratory distress requiring supplemental oxygen 
>40% 
2) I:T Ratio of >0.2 on initial CBC 
3) Congenital anomalies, including renal anomalies requiring serum 
antibiotic level monitoring.  

 
 
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30 patients who meet inclusion criteria will be enrolled for randomization.  Parents of 
infants that may be eligible will be consented prior to the birth if the infant.  If the infant 
meets the inclusion criteria at the time of birth, they will be randomized into one of the 
study groups.  Parents who consent will be notified whether or not their child met 
inclusion criteria and were randomized in the study.  They can choose to withdraw their 
child from the study at any time. 
 
If infants are not determined to be low-risk at the time of birth, and do not meet the 
inclusion criteria for randomization, they will remain in the study for stool sample analysis 
and data collection.  Their medical management will be ordered by the primary care team, 
including the possible administration for antibiotics at birth.   
 
The study design will be a randomized, double-blinded study where all consented infants 
who meet the inclusion criteria will undergo a standard limited sepsis evaluation at birth, 
consisting of a blood culture and complete blood count with differential, as recommended 
in the CDC guidelines for prevention of GBS sepsis. Following evaluation, infants will be 
randomized.  The control group of infants will receive current standard of care empiric 
antibiotic coverage with ampicillin and gentamicin.  The infants in the intervention group 
will receive placebo at the same dosing intervals of the routine antibiotic coverage.  
Antibiotics, or placebo, will be discontinued after 48 hours, at which time the blood culture 
would be reported as negative at 48 hours, consistent with the standard of care rule out 
sepsis evaluation.  Each treatment group, control and intervention, will have 15 study 
participants.  We will further aim to have half in each treatment group to be under the 
gestational age of 32 weeks and half older than 32 weeks.  Multiples will be randomized to 
the same treatment group.  We will consent up to 80 patients in order to have 30 that will 
meet randomization criteria. 
 
If at any time during the initial 48 hour trial period an infant shows clinical signs of sepsis, 
as defined below, or the initial blood culture becomes positive, the infant will be un-
blinded.  Repeat evaluation will be performed, and antibiotics will either be initiated for 
those in the intervention group, or appropriately broadened, per the discretion of the 
medical team, for those already receiving antibiotics.  These patients will remain in the 
study for intention-to-treat analysis 
 
Signs of clinical sepsis for which to unblind infant from the study and repeat 
evaluation (Hofer et al 2012, Bekhof et al 2013) 
 
 
-Temperature Instability (Rectal, >38.5C, <36.0C or >1.5C change in 3 hours) 
 
-Increased respiratory support of more than 20% increase in oxygen 
 
-Pale/dusky skin tones 
 
-Prolonged capillary refill time 
 
-Lethargy 
 
-Development of Seizures 
 
-Requiring vasoactive medications for cardiovascular support 
 
-Other signs of illness per the discretion of the managing team 
 

 
 
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Throughout their entire hospitalization, all infants will receive routine neonatal care per 
the medical team managing the patient.   
 
During the entire hospitalization of the patients, daily stool samples will be collected from 
the infant diaper as available from spontaneous defecation, for analysis of the fetal 
microbiota through 16S rRNA gene-based analysis, as previously described by Wang, et al 
(2009).  Through this stool analysis, the development of the fetal microbiome from birth 
through discharge will be examined and compared between the infants who do, or do not, 
receive empiric antibiotics at birth.  Some of the stool samples will also be shared with the 
investigators at the University of Guelph in Ontario, Canada for further analysis, including 
identification of certain metabolites and antibiotic levels.  The samples that are sent will be 
deidentified.  Parents may be contacted when the infants are 18 months of life to answer a 
short health questionnaire about hospitalizations and chronic illnesses, as well as to 
provide stool samples for further analysis to determine if the differences persist once they 
are outside of the hospital environment.  All supplies for stool samples and return postage 
will be provided to the parents.  Parents will receive a small monetary compensation ($15 
gift card) for returning the questionnaire and stool sample.   
 
In addition to analyzing the microbiome, blood culture results, clinical outcomes (chronic 
lung disease, retinopathy of prematurity, intraventricular hemorrhage, death, NEC), length 
of stay, initiation and type of feeds, feeding tolerance and total days of antibiotic use will be 
examined through review of the EMR.   
 
Monitoring: 
 
The study team will report all events in accordance with IRB policies and procedures. 
Events not meeting reporting criteria will be provided at the time of continuing review. 
 
All enrolled infants will be continuously monitored for signs of infection during the first 48 
hours of life, as well as through the remainder of their hospitalization due to their 
admission in an ICU setting.  Because of the small size of this pilot study, if there is any 
adverse event or safety concern, it will be immediately analyzed.   
 
In addition, we will meet to evaluate for adverse events and safety for every 3 patients that 
are enrolled into the randomization portion of the study (weekly may be impractical due to 
the varied response in consent among our patient population - there may be many weeks 
without new study participants).  This will result in 10 meetings throughout the course of 
the pilot study.  We will also invite the NICU's medical director to participate in these 
meetings to ensure patient safety. 
 
We will not be performing an interim efficacy analysis.  This is due to the small sample size 
and single site design, as well as their prematurity of our study population which requires 
prolonged hospitalization.  The study subjects will be continuously and closely monitored 
due to their gestational age and hospitalization within an intensive care setting.  If at any 
time a patient becomes ill during the initial 48 hours, they will become unblinded.  If it is a 

 
 
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repeated pattern that only those patients who are receiving placebo are becoming ill, the 
safety of the study will be reevaluated by the study team.  
 
If three patients from this group develop sepsis in the first 48 hours, the trial will end. 
 
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