Abstract
Background: There is a growing move to provide care for premature infants in a single family, private room neonatal intensive care unit (NICU) in place of the traditional shared space, open bay NICU. The resultant effect on the developing neonatal microbiota is unknown.Study Design: Stool and groin skin swabs were collected from infants in a shared-space NICU (old NICU) and a single-family room NICU (new NICU) on the same hospital campus. Metagenomic sequencing was performed and data analyzed by CosmosID bioinformatics software package.Results: There were no significant differences between the cohorts in gestational age, length of stay, and delivery mode; infants in the old NICU received significantly more antibiotics (p = 0.03). Differentially abundant antimicrobial resistance genes and virulence associated genes were found between the cohorts in stool and skin, with more differentially abundant antimicrobial resistance genes in the new NICU. The entire bacterial microbiota analyzed to the genus level significantly differed between cohorts in skin (p = 0.0001) but not in stool samples. There was no difference in alpha diversity between the two cohorts. DNA viruses and fungi were detected but did not differ between cohorts.Conclusion: Differences were seen in the resistome and virulome between the two cohorts with more differentially abundant antimicrobial resistance genes in the new NICU. This highlights the influence that different NICU environments can have on the neonatal microbiota. Whether the differences were due to the new NICU being a single-family NICU or located in a newly constructed building warrants exploration. Long term health outcomes from the differences observed must be followed longitudinally.
Highlights
The human intestinal microbiota undergoes rapid dynamic changes in the first few months to years of life and these changes are hypothesized to shape future health (Yatsunenko et al, 2012)
There was a significantly greater amount of antibiotic use during neonatal intensive care unit (NICU) stay in the old NICU, compared with the new NICU (12/14 infants in old NICU vs. 8 /18 infants in new NICU, p = 0.03)
Analysis of the specific classes of antibiotics used showed more 3rd generation cephalosporin use in the old NICU compared with the new NICU (4/14 infants in old NICU vs. 0/18 infants in new NICU, p = 0.03)
Summary
The human intestinal microbiota undergoes rapid dynamic changes in the first few months to years of life and these changes are hypothesized to shape future health (Yatsunenko et al, 2012). Infants born prematurely and in the neonatal intensive care unit (NICU) are vulnerable and have been shown to exhibit aberrant microbiota development, including harboring high levels of antimicrobial resistance genes (Costello et al, 2013; La Rosa et al, 2014; Gibson et al, 2016; Gasparrini et al, 2016). Premature infants are at risk of developing conditions associated with microbiota dysbiosis, both in the NICU, such as life threatening necrotizing enterocolitis (Pammi et al, 2017a), and later in life (Boyle et al, 2012). The resultant effect on the developing neonatal microbiota is unknown
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