TY - JOUR
T1 - Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites
AU - Knudsen, Maja Johanne Søndergaard
AU - Castruita, Jose Alfredo Samaniego
AU - Rubin, Ingrid Maria Cecilia
AU - Mollerup, Sarah
AU - Johansen, Helle Krogh
AU - Marvig, Rasmus L
AU - Nielsen, Karen Leth
AU - Holzknecht, Barbara Juliane
AU - Hoppe, Morten
AU - Kemp, Michael
AU - Westh, Henrik
AU - Pinholt, Mette
N1 - © 2025. The Author(s).
PY - 2025/2/27
Y1 - 2025/2/27
N2 - 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 (Tn1549) 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. 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.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 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.RESULTS: We have described the genomic epidemiology during the study period and identified ten chromosomal Tn1549 insertion sites.
AB - 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 (Tn1549) 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. 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.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 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.RESULTS: We have described the genomic epidemiology during the study period and identified ten chromosomal Tn1549 insertion sites.
KW - Bacterial Proteins/genetics
KW - Carbon-Oxygen Ligases/genetics
KW - DNA Transposable Elements
KW - Denmark/epidemiology
KW - Enterococcus faecium/genetics
KW - Genome, Bacterial
KW - Gram-Positive Bacterial Infections/epidemiology
KW - Humans
KW - Molecular Epidemiology
KW - Vancomycin-Resistant Enterococci/genetics
UR - http://www.scopus.com/inward/record.url?scp=105001639482&partnerID=8YFLogxK
U2 - 10.1007/s10096-025-05091-y
DO - 10.1007/s10096-025-05091-y
M3 - Journal article
C2 - 40167959
SN - 0934-9723
VL - 44
SP - 1425
EP - 1432
JO - European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
JF - European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
IS - 6
ER -