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

doi:10.1007/s10096-025-05091-y

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

^*Corresponding author for this work

Clinical Microbiology

Research output: Contribution to journal › Article › Research › peer-review

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 (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.

Original language	English
Pages (from-to)	1425-1432
Number of pages	8
Journal	European Journal of Clinical Microbiology and Infectious Diseases
Volume	44
Issue number	6
Early online date	1 Apr 2025
DOIs	https://doi.org/10.1007/s10096-025-05091-y
Publication status	Published - Jun 2025

Keywords

Carbon-Oxygen Ligases/genetics
Denmark/epidemiology
Genome, Bacterial
Bacterial Proteins/genetics
Molecular Epidemiology
Humans
Enterococcus faecium/genetics
Vancomycin-Resistant Enterococci/genetics
DNA Transposable Elements
Gram-Positive Bacterial Infections/epidemiology
Transposon insertion sites
Vancomycin-resistant Enterococci
Vre
vanB
vancomycin-resistant Enterococcus faecium
Tn1549

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Knudsen, M. J. S., Castruita, J. A. S., Rubin, I. M. C., Mollerup, S., Johansen, H. K., Marvig, R. L., Nielsen, K. L., Holzknecht, B. J., Hoppe, M., Kemp, M., Westh, H., & Pinholt, M. (2025). Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites. European Journal of Clinical Microbiology and Infectious Diseases, 44(6), 1425-1432. https://doi.org/10.1007/s10096-025-05091-y

Knudsen, Maja Johanne Søndergaard ; Castruita, Jose Alfredo Samaniego ; Rubin, Ingrid Maria Cecilia et al. / Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites. In: European Journal of Clinical Microbiology and Infectious Diseases. 2025 ; Vol. 44, No. 6. pp. 1425-1432.

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title = "Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites",

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 (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, M{\"u}nster, 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.",

keywords = "Carbon-Oxygen Ligases/genetics, Denmark/epidemiology, Genome, Bacterial, Bacterial Proteins/genetics, Molecular Epidemiology, Humans, Enterococcus faecium/genetics, Vancomycin-Resistant Enterococci/genetics, DNA Transposable Elements, Gram-Positive Bacterial Infections/epidemiology, Transposon insertion sites, Vancomycin-resistant Enterococci, Vre, vanB, vancomycin-resistant Enterococcus faecium, Tn1549",

author = "Knudsen, \{Maja Johanne S{\o}ndergaard\} and Castruita, \{Jose Alfredo Samaniego\} and Rubin, \{Ingrid Maria Cecilia\} and Sarah Mollerup and Johansen, \{Helle Krogh\} and Marvig, \{Rasmus L\} and Nielsen, \{Karen Leth\} and Holzknecht, \{Barbara Juliane\} and Morten Hoppe and Michael Kemp and Henrik Westh and Mette Pinholt",

note = "{\textcopyright} 2025. The Author(s).",

year = "2025",

month = jun,

doi = "10.1007/s10096-025-05091-y",

language = "English",

volume = "44",

pages = "1425--1432",

journal = "European Journal of Clinical Microbiology and Infectious Diseases",

issn = "0934-9723",

publisher = "Springer Science and Business Media Deutschland GmbH",

number = "6",

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Knudsen, MJS, Castruita, JAS, Rubin, IMC, Mollerup, S, Johansen, HK, Marvig, RL, Nielsen, KL, Holzknecht, BJ, Hoppe, M, Kemp, M, Westh, H & Pinholt, M 2025, 'Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites', European Journal of Clinical Microbiology and Infectious Diseases, vol. 44, no. 6, pp. 1425-1432. https://doi.org/10.1007/s10096-025-05091-y

Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites. / Knudsen, Maja Johanne Søndergaard; Castruita, Jose Alfredo Samaniego; Rubin, Ingrid Maria Cecilia et al.
In: European Journal of Clinical Microbiology and Infectious Diseases, Vol. 44, No. 6, 06.2025, p. 1425-1432.

Research output: Contribution to journal › Article › Research › peer-review

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

PY - 2025/6

Y1 - 2025/6

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 - Carbon-Oxygen Ligases/genetics

KW - Denmark/epidemiology

KW - Genome, Bacterial

KW - Bacterial Proteins/genetics

KW - Molecular Epidemiology

KW - Humans

KW - Enterococcus faecium/genetics

KW - Vancomycin-Resistant Enterococci/genetics

KW - DNA Transposable Elements

KW - Gram-Positive Bacterial Infections/epidemiology

KW - Transposon insertion sites

KW - Vancomycin-resistant Enterococci

KW - Vre

KW - vanB

KW - vancomycin-resistant Enterococcus faecium

KW - Tn1549

U2 - 10.1007/s10096-025-05091-y

DO - 10.1007/s10096-025-05091-y

M3 - Article

C2 - 40167959

SN - 0934-9723

VL - 44

SP - 1425

EP - 1432

JO - European Journal of Clinical Microbiology and Infectious Diseases

JF - European Journal of Clinical Microbiology and Infectious Diseases

IS - 6

ER -

Knudsen MJS, Castruita JAS, Rubin IMC, Mollerup S, Johansen HK, Marvig RL et al. Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites. European Journal of Clinical Microbiology and Infectious Diseases. 2025 Jun;44(6):1425-1432. Epub 2025 Apr 1. doi: 10.1007/s10096-025-05091-y

Genomic epidemiology of vancomycin-resistant Enterococcus faecium in Eastern Denmark from 2020 to 2022, and identification of vanB Tn1549 insertion sites

Abstract

Keywords

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