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

被引:0
作者
Esser, Elisabeth [1 ,2 ]
Schulte, Eva C. [1 ,3 ,4 ,5 ,6 ]
Graf, Alexander [7 ]
Karollus, Alexander [2 ]
Smith, Nicholas H. [2 ]
Michler, Thomas [1 ,18 ]
Dvoretskii, Stefan [2 ]
Angelov, Angel [8 ]
Sonnabend, Michael [8 ]
Peter, Silke [8 ]
Engesser, Christina [8 ]
Radonic, Aleksandar [9 ]
Thuermer, Andrea [9 ]
von Kleist, Max [10 ,11 ]
Gebhardt, Friedemann [12 ]
da Costa, Clarissa Prazeres [12 ,13 ]
Busch, Dirk H. [12 ,13 ]
Muenchhoff, Maximilian [13 ,14 ,15 ]
Blum, Helmut [7 ]
Keppler, Oliver T. [13 ,14 ,15 ]
Gagneur, Julien [2 ,16 ,17 ]
Protzer, Ulrike [1 ,13 ]
机构
[1] Tech Univ Munich Helmholtz Munich, Inst Virol, Sch Med & Hlth, Munich, Germany
[2] Tech Univ Munich, Sch Computat Informat & Technol, Garching, Germany
[3] Ludwig Maximilians Univ Munchen, Univ Hosp, Dept Psychiat, Munich, Germany
[4] Ludwig Maximilians Univ Munchen, Univ Hosp, Inst Psychiat Phen & Genom, Munich, Germany
[5] Univ Bonn, Univ Hosp, Med Fac, Dept Psychiat, Bonn, Germany
[6] Univ Bonn, Univ Hosp, Inst Human Genet, Med Fac, Bonn, Germany
[7] Ludwig Maximilians Univ Munchen, Lab Funct Genome Anal, Gene Ctr, Munich, Germany
[8] Univ Tubingen, NGS Competence Ctr, Tubingen, Germany
[9] Robert Koch Inst RKI, Method Dev Res Infrastruct & IT MFI, Berlin, Germany
[10] Freie Univ FU Berlin, Dept Math & Comp Sci, Berlin, Germany
[11] Robert Koch Inst RKI, Project Grp, Berlin, Germany
[12] Tech Univ Munich, Inst Med Microbiol Immunol & Hyg, Sch Med, Munich, Germany
[13] German Ctr Infect Res DZ, Munich Partner Site, Munich, Germany
[14] Ludwig Maximilians Univ Munchen, Max Von Pettenkofer Inst, Fac Med, Munich, Germany
[15] Ludwig Maximilians Univ Munchen, Gene Ctr, Natl Reference Ctr Retroviruses, Virol,Fac Med, Munich, Germany
[16] Tech Univ Munich, Inst Human Genet, Sch Med & Hlth, Munich, Germany
[17] Helmholtz Ctr Munich, Computat Hlth Ctr, Neuherberg, Germany
[18] Ludwig Maximilians Univ Munchen, Inst Lab Med, Univ Hosp, Munich, Germany
关键词
COVID-19;
D O I
10.1038/s41598-024-56162-7
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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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页数:11
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