Genomic-based characterization of Enterococcus spp.: an emerging pathogen isolated from human gut

Area of Science:

• Microbiology
• Genomics
• Probiotics

Background:

• Enterococci are common gut microbes with probiotic potential due to enterocin production.
• Concerns exist regarding Enterococci as probiotics due to transferable virulence factors and antibiotic resistance genes.
• These traits can transform Enterococci into opportunistic pathogens, raising safety issues for probiotic use.

Purpose of the Study:

• To investigate the presence of antibiotic resistance and virulence genes in Enterococcus species isolated from the human gut.
• To assess the potential of these isolates as opportunistic pathogens using whole-genome sequencing.

Main Methods:

• Isolation and culturing of four human-origin Enterococcus species (E. faecalis, E. casseliflavus, E. gallinarum).
• Whole-genome sequencing (WGS) using Oxford Nanopore MinION technology.
• Analysis of WGS data using epi2me, Comprehensive Antibiotic Resistance Database (CARD), and RAST software for gene identification.

Main Results:

• Detection of resistance determinants for clinically significant antibiotics, including vancomycin.
• Identification of functional virulence factor genes within the studied Enterococcus strains.
• Comparative genomics using G-view server revealed shared and unique genetic elements.

Conclusions:

• Genomic analysis confirmed E. faecalis, E. casseliflavus, and E. gallinarum strains as opportunistic pathogens.
• All isolates exhibited vancomycin resistance genes, which were phenotypically expressed.
• Bacteriocin resistance genes were identified in E. casseliflavus and E. gallinarum strains.