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
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: G...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-08-01
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| Series: | The Lancet Regional Health. Western Pacific |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S266660652200102X |
| _version_ | 1828516772429430784 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Anne E. Watt |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T18:31:41Z |
| format | Article |
| id | doaj.art-807cadcdd2394ad3a56ff21ee1860436 |
| institution | Directory Open Access Journal |
| issn | 2666-6065 |
| language | English |
| last_indexed | 2024-12-11T18:31:41Z |
| publishDate | 2022-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | The Lancet Regional Health. Western Pacific |
| spelling | doaj.art-807cadcdd2394ad3a56ff21ee18604362022-12-22T00:54:53ZengElsevierThe Lancet Regional Health. Western Pacific2666-60652022-08-0125100487State-wide genomic epidemiology investigations of COVID-19 in healthcare workers in 2020 Victoria, Australia: Qualitative thematic analysis to provide insights for future pandemic preparednessAnne E. Watt0Norelle L. Sherry1Patiyan Andersson2Courtney R. Lane3Sandra Johnson4Mathilda Wilmot5Kristy Horan6Michelle Sait7Susan A. Ballard8Christina Crachi9Dianne J. Beck10Caroline Marshall11Marion A. Kainer12Rhonda Stuart13Christian McGrath14Jason C. Kwong15Pauline Bass16Peter G. Kelley17Amy Crowe18Stephen Guy19Nenad Macesic20Karen Smith21Deborah A. Williamson22Torsten Seemann23Benjamin P. Howden24Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological 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, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, AustraliaVictorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Doherty Institute, Melbourne, Victoria, AustraliaDepartment of Infectious Diseases, Western Health, Footscray, Victoria, AustraliaMonash 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, AustraliaDepartment of Infectious Diseases, The Northern Hospital, Epping, Victoria, AustraliaDepartment of Infectious Diseases, Austin Health, Heidelberg, Victoria, AustraliaInfection Prevention and Healthcare Epidemiology Department, Alfred Health, Prahran, Victoria, AustraliaDepartment of Infectious Diseases, Peninsula Health, Frankston, Victoria, AustraliaDepartment of Microbiology, St Vincent's Hospital Melbourne, Fitzroy, Victoria, AustraliaDepartment of Infectious Diseases, Eastern Health, Box Hill, Victoria, Australia; Eastern Health Clinical School, Monash University, Victoria, AustraliaDepartment of Infectious Diseases, Epworth Hospital, Richmond, Victoria, AustraliaCentre for Research and Evaluation, Ambulance Victoria, Victoria, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Victoria, AustraliaDepartment 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, AustraliaMicrobiological 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, AustraliaMicrobiological 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.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.http://www.sciencedirect.com/science/article/pii/S266660652200102XCovid-19Healthcare workersGenomic epidemiologyPandemic preparedness |
| spellingShingle | 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 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 Covid-19 Healthcare workers Genomic epidemiology Pandemic preparedness |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | Covid-19 Healthcare workers Genomic epidemiology Pandemic preparedness |
| url | http://www.sciencedirect.com/science/article/pii/S266660652200102X |
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