Annika Sobkowiak (Münster / DE), Alina Oelgemöller (Münster / DE), Natalie Scherff (Münster / DE), Franziska Schuler (Münster / DE), Vera Schwierzeck (Münster / DE), Vincent van Almsick (Münster / DE), Alexander Mellmann (Münster / DE)
Introduction: The prevalence of vancomycin resistant Enterococcus faecium (VREfm) is increasing worldwide and the management of nosocomial outbreaks has become a challenge in infection control. Using whole genome sequencing (WGS), we investigated potential VREfm outbreak clusters including vanA plasmid clusters.
Methods: VREfm were collected as part of routine hospital surveillance in a one-year period (2022) and sequenced with a PacBio® Sequel IIe system. After de novo assembly, the WGS datasets were further analysis using MOB-Suite v.3.1.8 and NCBI AMRFinder Plus v.3.11.26 to characterize plasmids and to extract resistance genes. We used Ridom SeqSphere+ v.9.0.1 software, we extracted cgMLST allelic profiles and compared plasmids via a Mash based approach. Transmission clusters (0 alleles distance/ Mash distance ≤0.001) were further evaluated based on patient records and infection control evaluation.
Results: Of the 232 VREfm isolates analysed, 122 vanA and 111 vanB carrying isolates were identified. While vanA was exclusively plasmid-encoded, vanB was only found within the chromosome. The predominant sequence types (ST) were 80 (47% of all VREfm) and 117 (47%). 102 vanA were found in ST80 and 101 vanB in ST117. Based on cgMLST, 13 clusters with 2 to 17 isolates were identified, which harboured a vanA plasmid. In 7 clusters we could find an epidemiological link, indicating a nosocomial transmission.
In addition, we found 9 plasmid clusters via mash. The size of the vanA plasmids in the biggest cluster varied between 22 and 39 kb; the replication type was characterized as rep_889 alone or together with rep_1763 and predicted as non‑mobilizable. In every plasmid, the vanA genes associated with transposable elements such as IS1216E.
Summary: The analyses of VREfm sequencing data provides a comprehensive overview of the van gene distribution and the variation of plasmids harbouring a vanA locus. Our results suggests that other mobile genetic elements rather than plasmids play a role in the spread of vancomycin resistance in VREfm. In the future, analysis of plasmid clusters could be used as part of outbreak investigations or to study the epidemiology of VREfm.