Early-life skin microbiota in hospitalized preterm and full-term infants

Abstract

Background: The infant skin microbiota may serve as a reservoir of bacteria that contribute to neonatal infections and stimulate local and systemic immune development. The objectives of our study were to characterize the skin microbiota of preterm and full-term infants during their birth hospitalization and describe its relationship to the microbiota of other body sites and the hospital environment.

Results: We conducted a cross-sectional study of 129 infants, including 40 preterm and 89 full-term infants. Samples were collected from five sites: the forehead and posterior auricular scalp (skin upper body); the periumbilical region, inguinal folds, and upper thighs (skin lower body); the oral cavity; the infant's immediate environment; and stool. Staphylococcus, Streptococcus, Enterococcus, and enteric Gram-negative bacteria including Escherichia and Enterobacter dominated the skin microbiota. The preterm infant microbiota at multiple sites had lower alpha diversity and greater enrichment with Staphylococcus and Escherichia than the microbiota of comparable sites in full-term infants. The community structure was highly variable among individuals but differed significantly by body site, postnatal age, and gestational age. Source tracking indicated that each body site both contributed to and received microbiota from other body sites and the hospital environment.

Conclusion: The skin microbiota of preterm and full-term infants varied across individuals, by body site, and by the infant's developmental stage. The skin harbored many organisms that are common pathogens in hospitalized infants. Bacterial source tracking suggests that microbiota are commonly exchanged across body sites and the hospital environment as microbial communities mature in infancy.

Keywords: Cutaneous; Escherichia; Microbiome; Neonatal intensive care unit; Neonate; Staphylococcus.

Conflict of interest statement

Ethics approval and consent to participate

The study was approved by the Duke Institutional Review Board (Pro00045553), and written informed consent was obtained from parents.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1

The relative abundance of bacterial genera at the level of phylum (a) and genus (b) for each body site. The lowest taxonomic classification is given for OTUs that were unable to be assigned a genus-level taxonomic classification

Fig. 2

Principal coordinate analysis (PCoA) of generalized UniFrac distances. Each dot represents a sample and each color indicates a body site: stool (blue), skin upper body (green), skin lower body (red), and oral cavity (purple). The distribution of samples by body site is shown along the first and second axes of the PCoA plot. Along the first axis (PC1), the sample distribution differed significantly between the stool and skin upper body (p = 0.0048), the stool and oral cavity (p < 0.0001), skin upper body and skin lower body (p = 0.0049), skin upper body and oral cavity (p = 0.0049), and skin-lower body and oral cavity (p < 0.0001), but not between the stool and skin lower body (p = 0.1842; p values determined by pairwise Wilcoxon rank sum tests with Benjamini-Hochberg correction). Along the second axis (PC2), the oral samples differed from the skin upper body (p < 0.0001) and skin lower body (p < 0.0001), but other sites were not significantly different

Fig. 3

Comparison of the preterm and full-term infant microbiota across body sites. a The mean proportion (per sample) of the top OTUs within each body site in preterm and full-term infants. b Intra-individual generalized UniFrac distances between body sites in preterm and full-term infants. Between-site distances were greater in full-term infants than preterm infants (median 0.75 vs 0.70, p = 0.006). c Shannon diversity across body sites and gestational age groups. Alpha diversity was significantly lower among oral samples than the stool, skin upper body, and skin lower body (p values determined by pairwise Wilcoxon rank sum tests with Benjamini-Hochberg correction). Shannon diversity did not differ significantly across the other body sites. Alpha diversity was lower in the skin among preterm infants compared to the full-term infants. *p < 0.05, **p < 0.01

Fig. 4

Source tracking of microbiota across body sites. The mean proportion of microbiota within each site (“sink”) attributable to each source are shown among intraindividual (a) and interindividual (b) sink-source pairs. Intraindividual relationships between sites are further depicted (c), with the weight of arrows between sites showing the relative contribution of each source