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Esser E, Schulte EC, Graf A, Karollus A, Smith NH, Michler T, Dvoretskii S, Angelov A, Sonnabend M, Peter S, Engesser C, Radonic A, Thürmer A, von Kleist M, Gebhardt F, da Costa CP, Busch DH, Muenchhoff M, Blum H, Keppler OT, Gagneur J, Protzer U. Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events. Sci Rep 2024; 14:5768. [PMID: 38459123 PMCID: PMC10923895 DOI: 10.1038/s41598-024-56162-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/02/2024] [Indexed: 03/10/2024] Open
Abstract
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.
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Affiliation(s)
- Elisabeth Esser
- 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
- 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
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Alexander Karollus
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Nicholas H Smith
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Thomas Michler
- 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
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Angel Angelov
- NGS Competence Center, University of Tübingen, Tübingen, Germany
| | | | - Silke Peter
- NGS Competence Center, University of Tübingen, Tübingen, Germany
| | | | - Aleksandar Radonic
- Method development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), Berlin, Germany
| | - Andrea Thürmer
- Method development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität (FU) Berlin, Berlin, Germany
- Project Groups, Robert-Koch Institute (RKI), Berlin, Germany
| | - Friedemann Gebhardt
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Clarissa Prazeres da Costa
- 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
- 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
- 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
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Oliver T Keppler
- 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
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Institute of Human Genetics, School of Medicine & Health, Technical University of Munich, Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
| | - Ulrike Protzer
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany.
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Eggers O, Renschler FA, Michalek LA, Wackler N, Walter E, Smollich F, Klein K, Sonnabend MS, Egle V, Angelov A, Engesser C, Borisova M, Mayer C, Schütz M, Bohn E. YgfB increases β-lactam resistance in Pseudomonas aeruginosa by counteracting AlpA-mediated ampDh3 expression. Commun Biol 2023; 6:254. [PMID: 36894667 PMCID: PMC9998450 DOI: 10.1038/s42003-023-04609-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
YgfB-mediated β-lactam resistance was recently identified in multi drug resistant Pseudomonas aeruginosa. We show that YgfB upregulates expression of the β-lactamase AmpC by repressing the function of the regulator of the programmed cell death pathway AlpA. In response to DNA damage, the antiterminator AlpA induces expression of the alpBCDE autolysis genes and of the peptidoglycan amidase AmpDh3. YgfB interacts with AlpA and represses the ampDh3 expression. Thus, YgfB indirectly prevents AmpDh3 from reducing the levels of cell wall-derived 1,6-anhydro-N-acetylmuramyl-peptides, required to induce the transcriptional activator AmpR in promoting the ampC expression and β-lactam resistance. Ciprofloxacin-mediated DNA damage induces AlpA-dependent production of AmpDh3 as previously shown, which should reduce β-lactam resistance. YgfB, however, counteracts the β-lactam enhancing activity of ciprofloxacin by repressing ampDh3 expression and lowering the benefits of this drug combination. Altogether, YgfB represents an additional player in the complex regulatory network of AmpC regulation.
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Affiliation(s)
- Ole Eggers
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Fabian A Renschler
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Lydia Anita Michalek
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Noelle Wackler
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Elias Walter
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Fabian Smollich
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Kristina Klein
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Michael S Sonnabend
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institute for Medical Microbiology and Hygiene, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Valentin Egle
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
- Cluster of Excellence "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
| | - Angel Angelov
- NGS Competence Center Tübingen (NCCT), Institute for Medical Microbiology and Hygiene, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Christina Engesser
- NGS Competence Center Tübingen (NCCT), Institute for Medical Microbiology and Hygiene, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Marina Borisova
- Cluster of Excellence "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
- Department of Biology, Organismic Interactions/Glycobiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Christoph Mayer
- Cluster of Excellence "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
- Department of Biology, Organismic Interactions/Glycobiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Monika Schütz
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Erwin Bohn
- Institute for Medical Microbiology and Hygiene, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
- Cluster of Excellence "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany.
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