Rubin Ingrid Maria Cecilia, Karstensen Kasper Thystrup, Lindegaard Mikkel, Hegstad Kristin, Freitas Ana R, Hammerum Anette M, Roer Louise
Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark.
Microbiol Spectr. 2025 Sep 2;13(9):e0128925. doi: 10.1128/spectrum.01289-25. Epub 2025 Jul 31.
Since 2012, Denmark has seen a significant rise in vancomycin-resistant (VREfm) cases, mirroring trends in other countries, though exceptions occurred during the coronavirus disease 2019 (COVID-19) lockdown and between 2022 and 2023. This rise has been accompanied by ongoing changes in the endemic VREfm clones, reflecting the species' high genetic plasticity. VREfm rapidly acquires plasmids and mobile genetic elements, enriching it with putative virulence markers (PVMs), including surface proteins, pili, and factors encoding biofilm production and adhesion. L. Roer, H. Kaya, A.P. Tedim, C. Novias, et al. (Microbiol Spectr 12:e0372423, 2024, https://doi.org/10.1128/spectrum.03724-23) released a database of 27 PVMs for and . In this study, we examined 516 VREfm bloodstream isolates from 2015 to 2023, identifying eight new putative virulence genes added to the database, bringing the total to 35 PVMs. Using whole-genome sequencing (WGS) and single linkage clustering, we identified six dominant VREfm clusters: ST80-CT14 , ST117-CT24 , ST203-CT859 , ST1421-CT1134 , ST117-CT36 , and ST80-CT2406 . We observed significant differences in the distribution of PVMs, particularly in pilin, gene clusters (PGC-1, PGC-2, and PGC-4), genes involved in carbohydrate metabolism (e.g., , ), and biofilm production (e.g., , , ). These differences could explain variability in pathogenicity, metabolism, and adaptation to stress, contributing to shifts in endemic clones.IMPORTANCEThe newly developed and now updated database, VirulenceFinder, features 35 potential virulence markers for E. and E. , is highly scalable and provides a valuable tool for the in-depth analysis of closely related species using whole-genome sequencing (WGS) data. It holds considerable promise for a range of public health applications, such as hospital outbreak investigations, surveillance, and assessment of pathogenicity of bacterial species.
自2012年以来，丹麦耐万古霉素屎肠球菌（VREfm）病例显著增加，这与其他国家的趋势一致，不过在2019年冠状病毒病（COVID-19）封锁期间以及2022年至2023年期间出现了例外情况。这种增加伴随着地方性VREfm克隆的持续变化，反映了该物种高度的遗传可塑性。VREfm迅速获得质粒和可移动遗传元件，使其富含假定的毒力标记（PVMs），包括表面蛋白、菌毛以及编码生物膜产生和黏附的因子。L. Roer、H. Kaya、A.P. Tedim、C. Novias等人（《微生物学光谱》12：e0372423，2024，https://doi.org/10.1128/spectrum.03724 - 23）发布了一个包含27个针对屎肠球菌和粪肠球菌的PVMs的数据库。在本研究中，我们检查了2015年至2023年的516株VREfm血流分离株，确定了8个新的假定毒力基因被添加到数据库中，使PVMs总数达到35个。使用全基因组测序（WGS）和单连锁聚类，我们确定了6个主要的VREfm簇：ST80 - CT14、ST117 - CT24、ST203 - CT859、ST1421 - CT1134、ST117 - CT36和ST80 - CT2406。我们观察到PVMs的分布存在显著差异，特别是在菌毛、基因簇（PGC - 1、PGC - 2和PGC - 4）、参与碳水化合物代谢的基因（如、）以及生物膜产生相关基因（如、、）方面。这些差异可以解释致病性、代谢和对压力适应能力的变异性，导致地方性克隆的转变。重要性新开发并更新的数据库VirulenceFinder具有针对屎肠球菌和粪肠球菌的35个潜在毒力标记，具有高度可扩展性，为使用全基因组测序（WGS）数据深入分析密切相关物种提供了有价值的工具。它在一系列公共卫生应用中具有很大潜力，如医院暴发调查、监测以及评估细菌物种的致病性。
