Knudsen Maja Johanne Søndergaard, Castruita Jose Alfredo Samaniego, Rubin Ingrid Maria Cecilia, Mollerup Sarah, Johansen Helle Krogh, Marvig Rasmus L, Nielsen Karen Leth, Holzknecht Barbara Juliane, Hoppe Morten, Kemp Michael, Westh Henrik, Pinholt Mette
Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark.
Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark.
Eur J Clin Microbiol Infect Dis. 2025 Jun;44(6):1425-1432. doi: 10.1007/s10096-025-05091-y. Epub 2025 Apr 1.
We aimed to describe the genomic epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) in Eastern Denmark from 2020 to 2022, identify and characterise the vanB Transposon 1549 (Tn1549) insertion sites among vanB VREfm clones and identify emerging VREfm clones.
We analysed all VREfm from our routine diagnostic sequencing during the study period. Using the Seqsphere + v.8.2.0 software (Ridom GmbH, Münster, Germany, ( http://www.ridom.de/seqsphere ), minimum spanning trees were created to visualise clusters. Tn1549 insertion sites were determined by in silico PCR. Nanopore sequencing was performed to assemble the regions surrounding Tn1549, which helped determine the insertion site locations.
We included 2,437 isolates in the study. A total of 463 isolates carried vanA, 1,963 isolates carried vanB, and 11 isolates carried both genes. Of all isolates carrying vanB, 254 isolates had the Tn1549 inserted in the araA2 gene, 1,604 in the sir2 gene, and 116 in neither the araA2 nor sir2 genes. We identified eight chromosomal insertion sites other than in the araA2 and sir2 genes. Three isolates carried the Tn1549 on plasmids. No emerging clones were found.
We have described the genomic epidemiology during the study period and identified ten chromosomal Tn1549 insertion sites.
我们旨在描述2020年至2022年丹麦东部耐万古霉素屎肠球菌（VREfm）的基因组流行病学，鉴定并表征vanB型VREfm克隆中Tn1549转座子的插入位点，以及识别新出现的VREfm克隆。
我们分析了研究期间常规诊断测序得到的所有VREfm。使用Seqsphere + v.8.2.0软件（德国明斯特的Ridom GmbH公司，( http://www.ridom.de/seqsphere )）创建最小生成树以可视化聚类。通过计算机PCR确定Tn1549的插入位点。进行纳米孔测序以组装Tn1549周围的区域，这有助于确定插入位点的位置。
我们在研究中纳入了2437株分离株。共有463株分离株携带vanA基因，1963株携带vanB基因，11株同时携带这两个基因。在所有携带vanB的分离株中，254株的Tn1549插入到araA2基因中，1604株插入到sir2基因中，116株在araA2基因和sir2基因中均未插入。我们在araA2基因和sir2基因之外还鉴定出了八个染色体插入位点。三株分离株的Tn1549位于质粒上。未发现新出现的克隆。
我们描述了研究期间的基因组流行病学，并鉴定出了十个染色体Tn1549插入位点。
