High-resolution genomic and molecular characterization of vancomycin-resistant enterococci from hospitalized patients in a tertiary care center in Riyadh, Saudi Arabia

Abstract

Vancomycin-resistant enterococci (VRE), particularly Enterococcus faecium, represent a significant nosocomial threat worldwide. In Saudi Arabia, limited genomic data exist to support phenotypic surveillance findings, impeding the understanding of resistance mechanisms, clonal diversity, and plasmid dynamics. To investigate the genomic and phenotypic characteristics of vancomycin-resistant E. faecium and E. faecalis clinical isolates from a tertiary care center in Riyadh, Saudi Arabia, and to assess antimicrobial resistance genes, virulence factors, sequence types, and plasmid replicons. Seventy-five VRE isolates were collected between 2017 and 2019 and subjected to antimicrobial susceptibility testing per CLSI guidelines. The whole genome sequencing (WGS) was performed using the Illumina MiSeq platform. Species identification, MLST/cgMLST typing, resistome, virulome, and plasmidome analyses were conducted using established bioinformatics pipelines (e.g., CARD, VFDB, PlasmidFinder, pyMLST). Among 75 isolates, 50 E. faecium and 6 E. faecalis passed WGS quality thresholds. E. faecium isolates showed high resistance to vancomycin (100%), ciprofloxacin (98%), and ampicillin (96%), while linezolid retained activity (98% susceptible). The vanA gene was detected in 93.9% of E. faecium isolates; other resistance determinants included tet(M), erm(B), and liaR/liaS mutations associated with daptomycin non-susceptibility. MLST revealed multiple STs, including ST136, ST102, and ST252, with no dominant clone, supporting polyclonality. Plasmid analysis identified 20 replicon types, predominantly rep11a, rep2, and repUS15, some co-associated with AMR genes. Virulence profiling showed enrichment of bopD, acm, and cpsA/uppS genes. E. faecalis isolates exhibited limited resistance and no clonal clustering. This is the most comprehensive genomic study of VRE from Saudi Arabia to date. Our findings reveal a diverse, polyclonal population of E. faecium harboring high-risk resistance and virulence determinants disseminated via plasmids. These data underscore the need for routine genomic surveillance to guide infection control and antimicrobial stewardship.