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Unexpected details regarding nosocomial transmission revealed by whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2)

Part of: SARS-CoV-2/COVID-19

Published online by Cambridge University Press:  20 August 2021

Sofia Myhrman Open the ORCID record for Sofia Myhrman [Opens in a new window] ,
Josefin Olausson ,
Johan Ringlander ,
Linéa Gustavsson ,
Hedvig E. Jakobsson ,
Martina Sansone  and
Johan Westin
Sofia Myhrman*
Affiliation:
Department of Clinical Microbiology, Infection Control Unit, Region Vastra Gotaland, Sahlgrenska University Hospital, Gothenburg, Sweden
Josefin Olausson
Affiliation:
Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
Johan Ringlander
Affiliation:
Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
Linéa Gustavsson
Affiliation:
Department of Geriatric Medicine, Region Vastra Gotaland, Sahlgrenska University Hospital, Gothenburg, Sweden
Hedvig E. Jakobsson
Affiliation:
Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
Martina Sansone
Affiliation:
Department of Clinical Microbiology, Infection Control Unit, Region Vastra Gotaland, Sahlgrenska University Hospital, Gothenburg, Sweden Department of Infectious Diseases, Region Vastra Gotaland, Sahlgrenska University Hospital, Gothenburg, Sweden
Johan Westin
Affiliation:
Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden Department of Infectious Diseases, Region Vastra Gotaland, Sahlgrenska University Hospital, Gothenburg, Sweden
*
Author for correspondence: Sofia Myhrman, E-mail: [email protected]
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Abstract

Objective:

Effective infection prevention and control (IPC) measures are key for protecting patients from nosocomial infections and require knowledge of transmission mechanisms in different settings. We performed a detailed outbreak analysis of the transmission and outcome of coronavirus disease 2019 (COVID-19) in a geriatric ward by combining whole-genome sequencing (WGS) with epidemiological data.

Design:

Retrospective cohort study.

Setting:

Tertiary-care hospital.

Participants:

Patients and healthcare workers (HCWs) from the ward with a nasopharyngeal sample (NPS) positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA during the outbreak period.

Methods:

Patient data regarding clinical characteristics, exposure and outcome were collected retrospectively from medical records. Stored NPSs from 32 patients and 15 HCWs were selected for WGS and phylogenetic analysis.

Results:

The median patient age was 84 years and 17 (53%) of 32 were male. Also, 14 patients (44%) died within 30 days of sampling. Viral loads were significantly higher among the deceased. WGS was successful in 28 (88%) of 32 patient samples and 14 (93%) of 15 HCW samples. Moreover, 3 separate viral clades were identified: 1 clade and 2 subclades among both patient and HCW samples. Integrated epidemiological and genetic analyses revealed 6 probable transmission events between patients and supported hospital-acquired COVID-19 among 25 of 32 patients.

Conclusions:

WGS provided an insight into the outbreak dynamics and true extent of nosocomial COVID-19. The extensive transmission between patients and HCWs indicated that current IPC measures were insufficient. We recommend increased use of WGS in outbreak investigations to identify otherwise unknown transmission links and to evaluate IPC measures.

Type
Original Article
Information
Infection Control & Hospital Epidemiology , Volume 43 , Issue 10 , October 2022 , pp. 1403 - 1407
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Copyright
© The Author(s), 2021. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America

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Footnotes

a

Authors of equal contribution.

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