Background Aberrations in the preterm microbiome following antibiotic therapy have been reported in previous studies. The objective of this study was to probe potential underlying mechanisms between this observation and susceptibility to adverse prematurity-related outcomes. Results Metagenomic shotgun sequencing was performed on 133 stool and 253 skin samples collected at 1 and 3 weeks of age from 68 infants born at <36 weeks postmenstrual age and birth weight <2000 g. After accounting for gestational age and maternal antibiotics, the distribution of organisms in all samples and the corresponding metabolic pathway abundance were compared between infants exposed to postnatal antibiotics and antibiotics-naïve infants. In antibiotic-naïve infants, gestational and postnatal age imparted similar trajectories on maturation of the microbial community and associated metabolic functional capacity, with postnatal age exerting greater contribution. Antibiotic exposure was associated with reversal in maturation trajectory from the first week to the third week of age (p< 0.001). Butyrate-producing genera, including Clostridium and Blautia, were significantly more abundant in antibiotic-naïve neonates at 3 weeks postnatal age. Correspondingly, metabolic pathways required for short-chain fatty acid synthesis were significantly increased in antibiotic-naïve infants, but not in antibiotic-exposed neonates, at 3 weeks after birth. Conclusions Early brief antibiotic exposure markedly disrupts developmental trajectory of the neonatal microbiome and its corresponding functional capacity. Our findings may provide a mechanistic explanation for the known associations between antibiotic use and adverse outcomes in preterm infants.

Background: Aberrations in the preterm microbiome following antibiotic therapy have been reported in previous studies. The objective of this study was to probe potential underlying mechanisms between this observation and susceptibility to adverse prematurity-related outcomes. Results: Metagenomic shotgun sequencing was performed on 132 fecal and 264 skin samples collected at 1 and 3 weeks of age from 68 infants born at <36 weeks postmenstrual age and birth weight <2000 g. After accounting for gestational age and maternal antibiotics, the distribution of organisms in all samples and the corresponding metabolic pathway abundance were compared between infants exposed to postnatal antibiotics and antibiotics-naïve infants. In antibiotic-naïve infants, gestational and postnatal age imparted similar trajectories on maturation of the microbial community and associated metabolic functional capacity, with postnatal age exerting greater contribution. Antibiotic exposure was associated with reversal in maturation trajectory from the first week to the third week of age (p< 0.001). Butyrate producing genera, including Clostridium and Blautia were significantly more abundant in antibiotic-naïve neonates at 3 weeks postnatal age. Correspondingly, metabolic pathways required for short chain fatty acid synthesis were significantly increased in the antibiotic-naïve infants, but not in antibiotic-exposed neonates, at three weeks after birth. Conclusions: Early brief antibiotic exposure markedly disrupts developmental trajectory of the neonatal microbiome and its corresponding functional capacity. Our findings may provide a mechanistic explanation for the known associations between antibiotic use and adverse outcomes in preterm infants.

Background: Aberrations in the preterm microbiome following antibiotic therapy have been reported in previous studies. The objective of this study was to probe potential underlying mechanisms between this observation and susceptibility to adverse prematurity-related outcomes. Results: Metagenomic shotgun sequencing was performed on 133 stool and 253 skin samples collected at 1 and 3 weeks of age from 68 infants born at <36 weeks postmenstrual age and birth weight <2000 g. After accounting for gestational age and maternal antibiotics, the distribution of organisms in all samples and the corresponding metabolic pathway abundance were compared between infants exposed to postnatal antibiotics and antibiotics-naïve infants. In antibiotic-naïve infants, gestational and postnatal age imparted similar trajectories on maturation of the microbial community and associated metabolic functional capacity, with postnatal age exerting greater contribution. Antibiotic exposure was associated with reversal in maturation trajectory from the first week to the third week of age (p< 0.001). Butyrate producing genera, including Clostridium and Blautia were significantly more abundant in antibiotic-naïve neonates at 3 weeks postnatal age. Correspondingly, metabolic pathways required for short chain fatty acid synthesis were significantly increased in antibiotic-naïve infants, but not in antibiotic-exposed neonates, at three weeks after birth. Conclusions: Early brief antibiotic exposure markedly disrupts developmental trajectory of the neonatal microbiome and its corresponding functional capacity. Our findings may provide a mechanistic explanation for the known associations between antibiotic use and adverse outcomes in preterm infants.

Background Staphylococcus aureus colonization in infants in the neonatal intensive care unit (NICU) often leads to repeated infections and severe disease. Methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) infections are major causes of NICU outbreaks. Current national practice in NICUs utilizes nare swab surveillance for S. aureus. We hypothesize that infants colonized in the stool with S. aureus may go unrecognized particularly when nare swab negative, allowing for a transmission reservoir. While it is unclear why some S. aureus nare carriers are also stool colonized, isolates tend to have clonality. A true prevalence of S. aureus fecal carriage is not well understood and variable.MethodsAvailable stool samples were prospectively collected from 42 of 55 infants admitted in a level IV NICU on a single day, per Cincinnati Children’s institutional review board approval. Nare swab results were obtained from electronic medical records. DNA was isolated from stool and shotgun metagenomic sequencing was performed via Hiseq Illuminex 2500. The presence of S. aureus and MRSA were defined as having >100 sequencing reads and a mecA DNA read fraction ratio >40 per stool sample, respectively.ResultsOf the 42 stool samples sequenced, 33 were S. aureus (15 MSSA, 18 MRSA) positive. All infants with nare positive MSSA (n = 9) were colonized in the stool with a 93% and 100% sensitivity and specificity, respectively. While infants with nare positive MRSA (n = 10) were stool colonized with 100% and 83% sensitivity and specificity, respectively. Three nare positive infants with MRSA had S.a. in the stool but lacked the presence of mecA. When comparing clinical nare swabs to stool metagenomic surveillance, sensitivities were 60% for MSSA and 56% for MRSA.ConclusionInfant colonization of S. aureus in the NICU remains a major problem despite current national surveillance and isolation practices. We found that nare swab surveillance for S. aureus in infants significantly underestimated colonization rates when compared with shotgun metagenomics of stool. These results suggest that nare swabs alone may not have adequate sensitivity and the implementation of stool surveillance should be considered to augment current practices. Future study is necessary to understand how the S. aureus stool reservoir contributes to transmissionDisclosures All authors: No reported disclosures.