Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates

Area of Science:

• Microbiology
• Genomics
• Neonatal Health

Background:

• Infants are colonized by diverse bacterial strains with significant health implications.
• Metagenomics shows strain differences, but within-strain gene content evolution is less understood.

Purpose of the Study:

• Investigate the rate, mechanisms, and phenotypic consequences of gene content diversification within Staphylococcus epidermidis strains in newborns.

Main Methods:

• Whole-genome sequencing and phenotyping of over 600 Staphylococcus epidermidis isolates from newborns.
• Long-read Nanopore sequencing to map genomic architecture of structural variants.

Main Results:

• Observed rapid gene gain and loss events within S. epidermidis strains, exceeding point mutation rates.
• Identified variations in the methicillin resistance gene (mecA) and SCCmec island, impacting antibiotic resistance.
• Structural variants evolved rapidly, leading to patient-specific genomic diversity.

Conclusions:

• Gene content diversification, not just single-nucleotide polymorphisms, is a primary driver of S. epidermidis evolution in newborns.
• Rapid structural variant evolution contributes to phenotypic diversity and antibiotic resistance within strains.