Surveillance and Characterization of Vancomycin-Resistant and Vancomycin-Variable Enterococci in a Hospital Setting

Abstract

Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple antibiotics. Methods: We conducted a point prevalence survey (PPS) to assess the prevalence of VRE and VVE colonization in hospitalized patients. Rectal swabs were collected from 160 patients and analyzed using molecular assays (MAs) and culture. Whole-genome sequencing (WGS) and core-genome multilocus sequence typing (cgMLST) were performed to identify the genetic diversity. Results: Of the 160 rectal swabs collected, 54 (33.7%) tested positive for the vanA and/or vanB genes. Culture-based methods identified 47 positive samples (29.3%); of these, 44 isolates were identified as E. faecium and 3 as E. faecalis. Based on the resistance profiles, 35 isolates (74.5%) were classified as VRE, while 12 (25.5%) were classified as VVE. WGS and cgMLST analyses identified seven clusters of E. faecium, with sequence type (ST) 80 being the most prevalent. Various resistance genes and virulence factors were identified, and this study also highlighted intra- and inter-ward transmission of VRE strains. Conclusions: Our findings underscore the potential for virulence and resistance of both the VRE and VVE strains, and they highlight the importance of effective infection control measures to prevent their spread. VVE in particular should be carefully monitored as they often escape detection. Integrating molecular data with clinical information will hopefully enhance our ability to predict and prevent future VRE infections.

Keywords: antimicrobial resistance; enterococci; hospital surveillance; vancomycin-resistant; vancomycin-variable; whole-genome sequencing.

Figure 1

Molecular analysis of AMR genes performed on VRE and VVE isolates. Panel (A): molecular characterization of vancomycin-resistant enterococci (VRE) isolates; and Panel (B): molecular characterization of vancomycin-variable enterococci (VVE) isolates.

Figure 2

Analysis of virulence determinants performed on 35 VRE and 12 VVE strains. A full list of the detected virulence genes can be found in Table S4. The width of each flow represents the number of isolates carrying a specific virulence gene, highlighting shared and unique profiles between the two groups. Figure created through SankeyMATIC (available at https://sankeymatic.com/, accessed on 16 April 2025).

Figure 3

Distribution of plasmids in 35 VRE and 12 VVE strains. Distribution of plasmids among vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) isolates. The width of each flow represents the number of isolates carrying a specific plasmid, highlighting shared and unique plasmid profiles between the two groups. Figure created through SankeyMATIC (available at https://sankeymatic.com/, accessed on 16 April 2025).

Figure 4

Resistance genes present in various plasmids carried by all the study isolates.

Figure 5

Distribution of the isolates by cluster type (CT) across hospital wards. W (1–5): W-1: Hepatology Unit, W-2: Viral Immunodeficiency Unit, W-3: Immune Systemic Infections Unit, W-4: Respiratory System Infectious Diseases Unit, W-5: High-Intensity Care Infectious Disease Unit; ICU: Intensive Care Unit.