Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events.

Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
08 Mar 2024
Historique:
received: 30 08 2023
accepted: 02 03 2024
medline: 9 3 2024
pubmed: 9 3 2024
entrez: 8 3 2024
Statut: epublish

Résumé

The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can contribute to deciphering nosocomial SARS-CoV-2 transmission 926 SARS-CoV-2 viral genomes from 622 staff members and patients were collected between February 2020 and January 2021 at a university hospital in Munich, Germany, and analysed along with the place of work, duration of hospital stay, and ward transfers. Bioinformatically defined transmission clusters inferred from viral genome sequencing were compared to those inferred from interview-based contact tracing. An additional dataset collected at the same time at another university hospital in the same city was used to account for multiple independent introductions. Clustering analysis of 619 viral genomes generated 19 clusters ranging from 3 to 31 individuals. Sequencing-based transmission clusters showed little overlap with those based on contact tracing data. The viral genomes were significantly more closely related to each other than comparable genomes collected simultaneously at other hospitals in the same city (n = 829), suggesting nosocomial transmission. Longitudinal sampling from individual patients suggested possible cross-infection events during the hospital stay in 19.2% of individuals (14 of 73 individuals). Clustering analysis of SARS-CoV-2 whole genome sequences can reveal cryptic transmission events missed by classical, interview-based contact tracing, helping to decipher in-hospital transmissions. These results, in line with other studies, advocate for viral genome sequencing as a pathogen transmission surveillance tool in hospitals.

Identifiants

DOI: 10.1038/s41598-024-56162-7 PMID: 38459123
pubmed: 38459123
doi: 10.1038/s41598-024-56162-7
pii: 10.1038/s41598-024-56162-7
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

5768

Subventions

Organisme : Federal German Ministry of Education and Science (BMBF)
ID : 01KI2016
Organisme : Bavarian Ministry of Science and Culture
ID : FOR-COVID consortium
Organisme : Bavarian Ministry of Science and Culture
ID : FOR-COVID consortium
Organisme : Bavarian Ministry of Science and Culture
ID : FOR-COVID consortium

Informations de copyright

© 2024. The Author(s).

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Auteurs

Elisabeth Esser (E)

Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany.
School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.

Eva C Schulte (EC)

Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany.
Department of Psychiatry, University Hospital, LMU Munich, Munich, Germany.
Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Munich, Germany.
Department of Psychiatry, University Hospital, Medical Faculty, University of Bonn, Bonn, Germany.
Institute of Human Genetics, University Hospital, Medical Faculty, University of Bonn, Bonn, Germany.

Alexander Graf (A)

Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany.

Alexander Karollus (A)

School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.

Nicholas H Smith (NH)

School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.

Thomas Michler (T)

Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany.
Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany.

Stefan Dvoretskii (S)

School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.

Angel Angelov (A)

NGS Competence Center, University of Tübingen, Tübingen, Germany.

Michael Sonnabend (M)

NGS Competence Center, University of Tübingen, Tübingen, Germany.

Silke Peter (S)

NGS Competence Center, University of Tübingen, Tübingen, Germany.

Christina Engesser (C)

NGS Competence Center, University of Tübingen, Tübingen, Germany.

Aleksandar Radonic (A)

Method development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), Berlin, Germany.

Andrea Thürmer (A)

Method development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), Berlin, Germany.

Max von Kleist (M)

Department of Mathematics and Computer Science, Freie Universität (FU) Berlin, Berlin, Germany.
Project Groups, Robert-Koch Institute (RKI), Berlin, Germany.

Friedemann Gebhardt (F)

Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany.

Clarissa Prazeres da Costa (CP)

Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany.
German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany.

Dirk H Busch (DH)

Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany.
German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany.

Maximilian Muenchhoff (M)

German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany.
Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU Munich, Munich, Germany.

Helmut Blum (H)

Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany.

Oliver T Keppler (OT)

German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany.
Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU Munich, Munich, Germany.

Julien Gagneur (J)

School of Computation, Information and Technology, Technical University of Munich, Garching, Germany. gagneur@in.tum.de.
Institute of Human Genetics, School of Medicine & Health, Technical University of Munich, Munich, Germany. gagneur@in.tum.de.
Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany. gagneur@in.tum.de.

Ulrike Protzer (U)

Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany. protzer@tum.de.
German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany. protzer@tum.de.

Classifications MeSH