Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Enterococcus faecium is a common gut bacterium.
• It has emerged as a significant nosocomial pathogen due to antibiotic resistance and virulence factors.
• Understanding its genome dynamics is crucial for combating infections.

Purpose of the Study:

• To describe the genome dynamics of multidrug-resistant Enterococcus faecium during asymptomatic gut colonization.
• To investigate evolutionary rates and genetic variation within E. faecium strains.
• To identify mechanisms contributing to its adaptability and pathogenicity.

Main Methods:

• Whole-genome sequencing of 96 multidrug-resistant E. faecium strains from five patients.
• Analysis of isolates collected over extended periods (15 months to 6.5 years).
• Estimation of evolutionary rates and detailed analysis of accessory genome variations.

Main Results:

• Ninety-five isolates belonged to the clinically relevant E. faecium clade A1.
• Evidence of concurrent colonization by multiple lineages and inter-patient strain transfer.
• Significant genomic variation observed due to gene gain/loss, prophage acquisition, and insertion sequence element activity.

Conclusions:

• The E. faecium genome exhibits high dynamism during asymptomatic gut colonization.
• Genomic flexibility, driven by horizontal gene transfer and recombination, generates diversity.
• This adaptability supports its role as a successful and evolving nosocomial pathogen.