Genomic Characterization of Antibiotic-Resistant Enterococcus Spp. Strains in Clinical Settings of Yichang, China

Objective: Antimicrobial-resistant Enterococcus species are important causes of hospital-acquired infections, yet genomic surveillance data from Yichang, China, are lacking. Methods: Between February 2023 and December 2024, 150 antibiotic-resistant Enterococcus isolates were collected from five hospitals in Yichang. Antimicrobial susceptibility testing was performed according to CLSI standards. Fifty-nine representative isolates underwent whole-genome sequencing for species identification, multilocus sequence typing (MLST), antimicrobial resistance (AMR) gene detection, virulence profiling, and phylogenetic analysis. Results: E. faecalis (46.7%) and E. faecium (42.7%) were the predominant species, mainly isolated from urine specimens. High multidrug resistance rates were observed, particularly in E. faecium , which showed extensive resistance to β-lactams and fluoroquinolones. MLST analysis identified E. faecium ST78 and E. faecalis ST16 as the dominant clones, both corresponding to internationally reported epidemic lineages. Importantly, two novel E. faecalis sequence types were identified, each resulting from single-nucleotide substitutions in housekeeping genes, indicating ongoing local genetic evolution. Resistome analysis revealed enrichment of vancomycin, tetracycline, aminoglycoside, and lincosamide resistance genes in Yichang isolates compared with reference genomes. In addition, E. faecalis carried a broader repertoire of resistance and virulence genes than E. faecium . Conclusion: Our findings demonstrate that whole-genome sequencing is not only a powerful tool for characterizing dominant epidemic clones but also an effective strategy for surveillance of atypical and emerging Enterococcus species. The detection of two novel sequence types and region-specific resistance patterns highlights the value of genomic monitoring in guiding infection-control policies, antimicrobial stewardship, and early warning of multidrug-resistant strain dissemination in hospital settings. Keywords: antimicrobial-resistant Enterococcus , whole-genome sequencing, multilocus sequence typing, resistance gene, virulence gene