State-wide genomic epidemiology investigations of COVID-19 in healthcare workers in 2020 Victoria, Australia: Qualitative thematic analysis to provide insights for future pandemic preparedness

Anne E. Watt; Norelle L. Sherry; Patiyan Andersson; Courtney R. Lane; Sandra Johnson; Mathilda Wilmot; Kristy Horan; Michelle Sait; Susan A. Ballard; Christina Crachi; Dianne J. Beck; Caroline Marshall; Marion A. Kainer; Rhonda Stuart; Christian McGrath; Jason C. Kwong; Pauline Bass; Peter G. Kelley; Amy Crowe; Stephen Guy; Nenad Macesic; Karen Smith; Deborah A. Williamson; Torsten Seemann; Benjamin P. Howden

The Lancet Regional Health. Western Pacific (Aug 2022)

State-wide genomic epidemiology investigations of COVID-19 in healthcare workers in 2020 Victoria, Australia: Qualitative thematic analysis to provide insights for future pandemic preparedness

Anne E. Watt,
Norelle L. Sherry,
Patiyan Andersson,
Courtney R. Lane,
Sandra Johnson,
Mathilda Wilmot,
Kristy Horan,
Michelle Sait,
Susan A. Ballard,
Christina Crachi,
Dianne J. Beck,
Caroline Marshall,
Marion A. Kainer,
Rhonda Stuart,
Christian McGrath,
Jason C. Kwong,
Pauline Bass,
Peter G. Kelley,
Amy Crowe,
Stephen Guy,
Nenad Macesic,
Karen Smith,
Deborah A. Williamson,
Torsten Seemann,
Benjamin P. Howden

Affiliations

Anne E. Watt: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Norelle L. Sherry: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
Patiyan Andersson: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Courtney R. Lane: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Sandra Johnson: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Mathilda Wilmot: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Kristy Horan: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Michelle Sait: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Susan A. Ballard: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Christina Crachi: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Dianne J. Beck: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Caroline Marshall: Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Doherty Institute, Melbourne, Victoria, Australia
Marion A. Kainer: Department of Infectious Diseases, Western Health, Footscray, Victoria, Australia
Rhonda Stuart: Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia; South East Public Health Unit, Monash Health, Clayton, Victoria, Australia; Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
Christian McGrath: Department of Infectious Diseases, The Northern Hospital, Epping, Victoria, Australia
Jason C. Kwong: Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
Pauline Bass: Infection Prevention and Healthcare Epidemiology Department, Alfred Health, Prahran, Victoria, Australia
Peter G. Kelley: Department of Infectious Diseases, Peninsula Health, Frankston, Victoria, Australia
Amy Crowe: Department of Microbiology, St Vincent's Hospital Melbourne, Fitzroy, Victoria, Australia
Stephen Guy: Department of Infectious Diseases, Eastern Health, Box Hill, Victoria, Australia; Eastern Health Clinical School, Monash University, Victoria, Australia
Nenad Macesic: Department of Infectious Diseases, Epworth Hospital, Richmond, Victoria, Australia
Karen Smith: Centre for Research and Evaluation, Ambulance Victoria, Victoria, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Victoria, Australia
Deborah A. Williamson: Department of Infectious Diseases, The University of Melbourne at the Doherty Institute, Melbourne, Victoria, Australia; Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Torsten Seemann: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia; Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Benjamin P. Howden: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia; Corresponding author at: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, 792 Elizabeth St, Melbourne, Victoria 3000, Australia.

Journal volume & issue: Vol. 25
p. 100487

Abstract

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Summary: Background: COVID-19 has affected many healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiological investigations to identify HCW transmission dynamics and provide recommendations to optimise healthcare system preparedness for future outbreaks. Methods: Genome sequencing was attempted on all COVID-19 cases in Victoria, Australia. We combined genomic and epidemiologic data to investigate the source of HCW infections across multiple healthcare facilities (HCFs) in the state. Phylogenetic analysis and fine-scale hierarchical clustering were performed for the entire dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links. Findings: Between March-October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here, requested for hospital investigations. Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviours of patients that generated numerous secondary infections. Key limitations at the HCF level were identified. Interpretation: Genomic epidemiological analyses enhanced understanding of HCW infections, revealing unsuspected clusters and transmission networks. Combined analysis of all HCWs and patients in a HCF should be conducted, supported by high rates of sequencing coverage for all cases in the population. Established systems for integrated genomic epidemiological investigations in healthcare settings will improve HCW safety in future pandemics. Funding: The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.

Published in The Lancet Regional Health. Western Pacific

ISSN: 2666-6065 (Online)
Publisher: Elsevier
Country of publisher: United Kingdom
LCC subjects: Medicine: Public aspects of medicine
Website: https://www.thelancet.com/journals/lanwpc/home

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