Journal Article
Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites
Maja Johanne Søndergaard Knudsen; Jose Alfredo Samaniego Castruita; Ingrid Maria Cecilia Rubin; Sarah Mollerup; Helle Krogh Johansen; Rasmus L. Marvig; Karen Leth Nielsen; Barbara Juliane Holzknecht; Morten Hoppe; Michael Kemp; Henrik Westh; Mette Pinholt
European Journal of Clinical Microbiology & Infectious Diseases · Vol. 44, Issue 6 · pp. 1425-1432 · 2025
Abstract
Background 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 (Tn 1549 ) insertion sites among vanB VREfm clones and identify emerging VREfm clones. Methods 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. Tn 1549 insertion sites were determined by in silico PCR. Nanopore sequencing was performed to assemble the regions surrounding Tn 1549 , which helped determine the insertion site locations. Results 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 Tn 1549 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 Tn 1549 on plasmids. No emerging clones were found. Results We have described the genomic epidemiology during the study period and identified ten chromosomal Tn 1549 insertion sites.