Viability-Resolved Metagenomics Reveals Antagonistic Colonization Dynamics of Staphylococcus epidermidis Strains on...

Area of Science:

• Microbiology
• Neonatal Research
• Bioinformatics

Background:

• Preterm infants face high infection risks from skin microbes like coagulase-negative staphylococci (CoNS).
• Technical challenges in sequencing low-biomass skin swabs limit understanding of CoNS colonization in preterm infants.
• Strain-level analysis is crucial for understanding CoNS dynamics and preventing infections.

Purpose of the Study:

• To investigate the strain-level dynamics of the skin microbiome in preterm infants.
• To overcome technical barriers in sequencing low-biomass skin samples.
• To identify potential targets for preventing CoNS-related infections in neonates.

Main Methods:

• Studied microbiome from five skin sites and stool of four preterm infants over two months.
• Utilized propidium monoazide treatment to enrich for viable microbes.
• Employed metagenomic shotgun sequencing for species and strain resolution.

Main Results:

• Skin microbiomes overlapped across sites, dominated by Staphylococcus epidermidis and Staphylococcus capitis, distinct from stool.
• Skin microbial diversity increased over time despite antibiotic exposure.
• Identified antagonistic interactions between S. epidermidis strains ST2 and ST59, with differing colonization patterns and biofilm formation.

Conclusions:

• Viability treatment and shotgun sequencing enable strain-level insights into preterm infant skin colonization.
• Understanding CoNS strain dynamics can inform strategies to prevent neonatal infections.
• Antagonistic relationships between S. epidermidis strains influence colonization patterns on infant skin.