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Watt AE, Sherry NL, Andersson P, Lane CR, Johnson S, Wilmot M, Horan K, Sait M, Ballard SA, Crachi C, Beck DJ, Marshall C, Kainer MA, Stuart R, McGrath C, Kwong JC, Bass P, Kelley PG, Crowe A, Guy S, Macesic N, Smith K, Williamson DA, Seemann T, Howden BP. 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. THE LANCET REGIONAL HEALTH - WESTERN PACIFIC 2022; 25:100487. [PMID: 35677391 PMCID: PMC9168175 DOI: 10.1016/j.lanwpc.2022.100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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.
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Affiliation(s)
- 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.
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