Co-carriage of diverse vancomycin-resistant Enterococcus faecium ST80-lineages by 70% of patients in an Irish hospital

Nicole L Kavanagh; Peter M Kinnevey; Grainne I Brennan; Brian O'Connell; Richard V Goering; David C Coleman

doi:10.1093/jacamr/dlaf065

Co-carriage of diverse vancomycin-resistant Enterococcus faecium ST80-lineages by 70% of patients in an Irish hospital

JAC Antimicrob Resist. 2025 Apr 29;7(3):dlaf065. doi: 10.1093/jacamr/dlaf065. eCollection 2025 Jun.

Authors

Nicole L Kavanagh¹, Peter M Kinnevey¹, Grainne I Brennan^{2

3}, Brian O'Connell^{2

3}, Richard V Goering⁴, David C Coleman¹

Affiliations

¹ Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Lincoln Place, Dublin D02 F859, Ireland.
² Department of Clinical Microbiology, St. James's Hospital, Dublin, Ireland.
³ National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland.
⁴ Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, USA.

Abstract

Background: Vancomycin-resistant Enterococcus faecium (VREfm) are significant nosocomial pathogens. Irish VREfm comprise diverse vanA-encoding ST80-complex type (CT) lineages. Recent studies indicate that within-patient VREfm diversity could confound surveillance. This study investigated the intra-host VREfm genetic diversity among colonized Irish hospital patients.

Methods: Rectal VREfm (n = 150) from 10 patients (15 isolates each) were investigated by WGS, core-genome MLST and split k-mer (SKA)-SNP analysis. Plasmids and vanA-transposons from 39 VREfm representative of CTs identified were resolved by hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequences. Plasmid relatedness was assessed based on Mash distances. Thirty vancomycin-susceptible E. faecium (VSEfm) from four VREfm-positive patients were also investigated.

Results: All isolates were clade A1 and most were ST80 (VREfm, 147/150; VSEfm, 25/30). Seventy-percent of patients (7/10) harboured either two (n = 4), three (n = 2) or four (n = 1) VREfm CTs. Individual patient isolate pairs from different CTs differed significantly (median SKA-SNPs 2933), but differences were minimal between isolate pairs of the same CT (median SKA-SNPs 0). In total, 193 plasmids were identified in 39 VREfm investigated. Near-identical plasmids (≥99.5% average nucleotide identity) were identified in divergent CTs from multiple patients. Most VREfm (28/39, 72%) harboured vanA on closely related transferable, linear plasmids. Divergent CTs within individual patients harboured either indistinguishable vanA-transposons or vanA-transposons with distinct organizational iterations. Four VSEfm from different CTs investigated harboured similar plasmids to VREfm.

Conclusion: VREfm within-host diversity is highly prevalent in Irish hospital patients, which complicates surveillance. Linear plasmids play an important role in the emergence of Irish VREfm.