{
  "abstract": "Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause of healthcare-associated infections, yet outbreak analysis remains challenging, particularly for prevalent lineages. One of the most striking examples is the Sequence Type (ST) 117/Complex Type (CT) 71/vanB lineage, whose rapid expansion across Germany coincided with a sharp rise in VRE prevalence observed around 2019. Defining reliable genomic thresholds remains particularly difficult, as current core-genome Multi-Locus Sequence Typing (cgMLST) cutoffs are based largely on expert consensus or limited case series. Here, we evaluate the discriminatory performance of cgMLST and split k-mer analysis (SKA) for resolving relatedness within ST117/CT71 and investigate whether low core-genome diversity represents a lineage-specific trait or a population-wide property of E. faecium. While cgMLST captures the overall population structure of ST117/CT71, SKA provided higher resolution, distinguishing isolates identical by cgMLST. Analysis of 2,505 genomes showed that ST117/CT71 does not exhibit reduced allelic variability compared with other hospital-adapted lineages, suggesting that limited core-genome diversity is a broader population characteristic. Complementary transposon analyses further identified two temporally distinct ST117/CT71 sublineages carrying different Tn1549-like structures. To assess allelic variation within confirmed transmission events, we analyzed 138 outbreak clusters from 96 hospitals. Outbreak-associated isolates showed sharply compressed allelic differences (median = 1), with 90% of pairwise comparisons falling within [≤]9 alleles. Thus, the commonly applied [≤]20-allele threshold risks overestimating genomic relatedness and grouping unrelated isolates. Based on these data, we propose lowering the cgMLST alert threshold to [≤]9 alleles for initial cluster detection of local outbreaks, followed by confirmatory high-resolution analyses such as SKA.",
  "abstract_shown": true,
  "affiliations": [
    "Robert Koch Institut"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "R. E. Weber"
    },
    {
      "name": "G. Werner"
    },
    {
      "name": "J. K. Bender"
    },
    {
      "name": "B. Haldemann"
    },
    {
      "name": "O. Drechsel"
    },
    {
      "affs": [
        0
      ],
      "name": "M. A. Fischer"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3y31j5h9n76bx.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.11.10.765572",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.11.10.765572v1.full",
  "id": "3y31j5h9n76bx",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.11.10.765572v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.11.10.765572v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-10",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/3y31j5h9n76bx.ris",
  "sources": [
    {
      "first_seen": "2026-11-12T12:21:44Z",
      "native_id": "10.64898/2026.11.10.765572",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.11.10.765572v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Rise and Fall of a Superbug: Analyzing the epidemic success of a distinct clone of vancomycin-resistant Enterococcus faecium ST117/CT71 in Germany, 2017 - 2024.",
  "title_text": "Rise and Fall of a Superbug: Analyzing the epidemic success of a distinct clone of vancomycin-resistant Enterococcus faecium ST117/CT71 in Germany, 2017 - 2024.",
  "type": "preprint",
  "updated_at": "2026-11-13T00:23:44Z",
  "url": "https://research.draconitic.com/paper/3y31j5h9n76bx",
  "venue": "bioRxiv",
  "versions": []
}