A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital

Lis Marbjerg; Caroline Louise Stougaard; Sophie Amalie Grønhøj Sørensen; Amalie Vørs Thomsen; Lis Wang; Lise Andersen; Thomas Emil Andersen; Birgitte Kallipolitis; Michael Kemp

doi:10.3389/fmed.2021.733676

A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital

Lis Marbjerg
, Caroline Louise Stougaard
, Sophie Amalie Grønhøj Sørensen
, Amalie Vørs Thomsen
, Lis Wang
, Lise Andersen
, Thomas Emil Andersen
, Birgitte Kallipolitis
, Michael Kemp^*

^*Corresponding author for this work

University of Southern Denmark

Research output: Contribution to journal › Journal article › Research › peer-review

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Abstract

A new easy-to-use online bioinformatic tool analyzing whole genome sequences of healthcare associated bacteria was used by a local infection control unit to retrospectively map genetic relationship of isolates of E. faecium carrying resistance genes to vancomycin in a hospital. Three clusters of isolates were detected over a period of 5 years, suggesting transmission between patients. Individual relatedness between isolates within each cluster was established by SNP analyses provided by the system. Genetic antimicrobial resistance mechanisms to antibiotics other than vancomycin were identified. The results suggest that the system is suited for hospital surveillance of E. faecium carrying resistance genes to vancomycin in settings with access to next Generation Sequencing without bioinformatic expertise for interpretation of the genome sequences.

Original language	English
Article number	733676
Journal	Frontiers in Medicine
Volume	8
Number of pages	6
ISSN	2296-858X
DOIs	https://doi.org/10.3389/fmed.2021.733676
Publication status	Published - 27. Oct 2021

Bibliographical note

Publisher Copyright:
Copyright © 2021 Marbjerg, Stougaard, Sørensen, Thomsen, Wang, Andersen, Andersen, Kallipolitis and Kemp.

Funding

Statens Serum Institut, Copenhagen, Denmark is thanked for sharing genome sequence data.

Keywords

bioinformatics
genomic epidemiology
infection control
surveillance
vancomycin resistant enterococci
whole genome sequencing

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10.3389/fmed.2021.733676Licence: CC BY

Open Access VersionFinal published version, 1.28 MBLicence: CC BY

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Marbjerg, L., Stougaard, C. L., Sørensen, S. A. G., Thomsen, A. V., Wang, L., Andersen, L., Andersen, T. E., Kallipolitis, B., & Kemp, M. (2021). A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital. Frontiers in Medicine, 8, Article 733676. https://doi.org/10.3389/fmed.2021.733676

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title = "A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital",

abstract = "A new easy-to-use online bioinformatic tool analyzing whole genome sequences of healthcare associated bacteria was used by a local infection control unit to retrospectively map genetic relationship of isolates of E. faecium carrying resistance genes to vancomycin in a hospital. Three clusters of isolates were detected over a period of 5 years, suggesting transmission between patients. Individual relatedness between isolates within each cluster was established by SNP analyses provided by the system. Genetic antimicrobial resistance mechanisms to antibiotics other than vancomycin were identified. The results suggest that the system is suited for hospital surveillance of E. faecium carrying resistance genes to vancomycin in settings with access to next Generation Sequencing without bioinformatic expertise for interpretation of the genome sequences.",

keywords = "bioinformatics, genomic epidemiology, infection control, surveillance, vancomycin resistant enterococci, whole genome sequencing",

author = "Lis Marbjerg and Stougaard, \{Caroline Louise\} and S{\o}rensen, \{Sophie Amalie Gr{\o}nh{\o}j\} and Thomsen, \{Amalie V{\o}rs\} and Lis Wang and Lise Andersen and Andersen, \{Thomas Emil\} and Birgitte Kallipolitis and Michael Kemp",

note = "Publisher Copyright: Copyright {\textcopyright} 2021 Marbjerg, Stougaard, S{\o}rensen, Thomsen, Wang, Andersen, Andersen, Kallipolitis and Kemp.",

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day = "27",

doi = "10.3389/fmed.2021.733676",

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A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital. / Marbjerg, Lis; Stougaard, Caroline Louise; Sørensen, Sophie Amalie Grønhøj et al.
In: Frontiers in Medicine, Vol. 8, 733676, 27.10.2021.

Research output: Contribution to journal › Journal article › Research › peer-review

TY - JOUR

T1 - A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital

AU - Marbjerg, Lis

AU - Stougaard, Caroline Louise

AU - Sørensen, Sophie Amalie Grønhøj

AU - Thomsen, Amalie Vørs

AU - Wang, Lis

AU - Andersen, Lise

AU - Andersen, Thomas Emil

AU - Kallipolitis, Birgitte

AU - Kemp, Michael

PY - 2021/10/27

Y1 - 2021/10/27

N2 - A new easy-to-use online bioinformatic tool analyzing whole genome sequences of healthcare associated bacteria was used by a local infection control unit to retrospectively map genetic relationship of isolates of E. faecium carrying resistance genes to vancomycin in a hospital. Three clusters of isolates were detected over a period of 5 years, suggesting transmission between patients. Individual relatedness between isolates within each cluster was established by SNP analyses provided by the system. Genetic antimicrobial resistance mechanisms to antibiotics other than vancomycin were identified. The results suggest that the system is suited for hospital surveillance of E. faecium carrying resistance genes to vancomycin in settings with access to next Generation Sequencing without bioinformatic expertise for interpretation of the genome sequences.

AB - A new easy-to-use online bioinformatic tool analyzing whole genome sequences of healthcare associated bacteria was used by a local infection control unit to retrospectively map genetic relationship of isolates of E. faecium carrying resistance genes to vancomycin in a hospital. Three clusters of isolates were detected over a period of 5 years, suggesting transmission between patients. Individual relatedness between isolates within each cluster was established by SNP analyses provided by the system. Genetic antimicrobial resistance mechanisms to antibiotics other than vancomycin were identified. The results suggest that the system is suited for hospital surveillance of E. faecium carrying resistance genes to vancomycin in settings with access to next Generation Sequencing without bioinformatic expertise for interpretation of the genome sequences.

KW - bioinformatics

KW - genomic epidemiology

KW - infection control

KW - surveillance

KW - vancomycin resistant enterococci

KW - whole genome sequencing

U2 - 10.3389/fmed.2021.733676

DO - 10.3389/fmed.2021.733676

M3 - Journal article

C2 - 34778297

AN - SCOPUS:85118776683

SN - 2296-858X

VL - 8

JO - Frontiers in Medicine

JF - Frontiers in Medicine

M1 - 733676

ER -

A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital

Abstract

Bibliographical note

Funding

Keywords

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