A systematic outbreak investigation of SARS-CoV-2 transmission clusters in a tertiary academic care center

Matthias von Rotz; Richard Kuehl; Ana Durovic; Sandra Zingg; Anett Apitz; Fanny Wegner; Helena M B Seth-Smith; Tim Roloff; Karoline Leuzinger; Hans H Hirsch; Sabine Kuster; Manuel Battegay; Luigi Mariani; Stefan Schaeren; Stefano Bassetti; Florian Banderet-Uglioni; Adrian Egli; Sarah Tschudin-Sutter

doi:10.1186/s13756-023-01242-y

A systematic outbreak investigation of SARS-CoV-2 transmission clusters in a tertiary academic care center

Antimicrob Resist Infect Control. 2023 Apr 21;12(1):38. doi: 10.1186/s13756-023-01242-y.

Authors

Matthias von Rotz¹, Richard Kuehl¹, Ana Durovic², Sandra Zingg³, Anett Apitz⁴, Fanny Wegner^{5

6

7}, Helena M B Seth-Smith^{5

6

7}, Tim Roloff^{5

6

7}, Karoline Leuzinger^{8

9}, Hans H Hirsch^{1

8

9}, Sabine Kuster¹, Manuel Battegay¹, Luigi Mariani¹⁰, Stefan Schaeren¹¹, Stefano Bassetti¹², Florian Banderet-Uglioni⁴, Adrian Egli^{5

6

7}, Sarah Tschudin-Sutter¹³

Affiliations

¹ Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.
² Swiss Tropical and Public Health Institute, Basel, Switzerland.
³ Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland.
⁴ Employee Health Service, University Hospital Basel, Basel, Switzerland.
⁵ Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland.
⁶ Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
⁷ Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
⁸ Clinical Virology, Laboratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland.
⁹ Transplantation and Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland.
¹⁰ Department of Neurosurgery, University Hospital Basel, University of Basel, Basel, Switzerland.
¹¹ Department of Traumatology and Orthopedics, University Hospital Basel, University of Basel, Basel, Switzerland.
¹² Division of Internal Medicine, University Hospital Basel, University of Basel, Basel, Switzerland.
¹³ Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland. sarah.tschudin@usb.ch.

Abstract

Background: We sought to decipher transmission pathways in healthcare-associated infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within our hospital by epidemiological work-up and complementary whole genome sequencing (WGS). We report the findings of the four largest epidemiologic clusters of SARS-CoV-2 transmission occurring during the second wave of the pandemic from 11/2020 to 12/2020.

Methods: At the University Hospital Basel, Switzerland, systematic outbreak investigation is initiated at detection of any nosocomial case of SARS-CoV-2 infection, as confirmed by polymerase chain reaction, occurring more than five days after admission. Clusters of nosocomial infections, defined as the detection of at least two positive patients and/or healthcare workers (HCWs) within one week with an epidemiological link, were further investigated by WGS on respective strains.

Results: The four epidemiologic clusters included 40 patients and 60 HCWs. Sequencing data was available for 70% of all involved cases (28 patients and 42 HCWs), confirmed epidemiologically suspected in house transmission in 33 cases (47.1% of sequenced cases) and excluded transmission in the remaining 37 cases (52.9%). Among cases with identical strains, epidemiologic work-up suggested transmission mainly through a ward-based exposure (24/33, 72.7%), more commonly affecting HCWs (16/24, 66.7%) than patients (8/24, 33.3%), followed by transmission between patients (6/33, 18.2%), and among HCWs and patients (3/33, 9.1%, respectively two HCWs and one patient).

Conclusions: Phylogenetic analyses revealed important insights into transmission pathways supporting less than 50% of epidemiologically suspected SARS-CoV-2 transmissions. The remainder of cases most likely reflect community-acquired infection randomly detected by outbreak investigation. Notably, most transmissions occurred between HCWs, possibly indicating lower perception of the risk of infection during contacts among HCWs.

Keywords: COVID-19; Epidemiologic cluster; Nosocomial outbreaks; Outbreak investigation; SARS-CoV-2 cluster; Whole genome sequencing.

MeSH terms

COVID-19* / epidemiology
Cross Infection* / epidemiology
Disease Outbreaks
Humans
Phylogeny
SARS-CoV-2 / genetics
Tertiary Care Centers