COVID-19 Hospital-Acquired Infections Among Patients in Victorian Health Services - March 2021 COVID-19 Hospital-Acquired Infections Among Patients in Victorian Health Services (25 January 2020-15 November 2020) Final Report OFFICIAL COVID-19 Hospital-Acquired Infections Among Patients in Victorian Health Services - March 2021 To receive this document in another format, phone +61 (03) 9096 0000, using the National Relay Service 13 36 77 if required, or email [email protected]. Authorised and published by the Victorian Government, 1 Treasury Place, Melbourne. © State of Victoria, Australia, Department of Health, April 2021. Suggested citation: Veale, H. J.1, Dale, K. 1, Ampt, F. 1,10, Kalman, T. 1, Kaufman, C. 1, Gibson, E. 1,6,9, Carville, K. 1,5, Harper, C.1,12, Ahmed, H. 1, Pehm, M. 1,13, Bull, A. 2, Brett, J. 2, Worth, L. 2, Sherry, N. L. 3,11, Leeb, K. 1, Cheng, A.1,7,8, Rowe., S. L. 1 (2021). COVID-19 Hospital-Acquired Infections Among Patients in Victorian Health Services (25 January 2020- 15 November 2020). Victorian Department of Health. * Authors Veale and Dale contributed equally to this report. This work was guided by the COVID-19 Hospital-Acquired Infections Working Group: Prof Brett Sutton1 Prof Allen Cheng1, 7, 8 Nicola Quin1 Ben Fielding1 Kira Leeb1 Dr Frances Ampt1, 10 Stacey Rowe1 Tali Kalman1 Hilary Veale1 Kylie Carville1,5 Claire Boardman1,7 Judy Sutherland1 Dr Ann Bull2 Judy Brett2 A/Prof Leon Worth2 Dr Norelle Sherry3,11 Angela Nolan4 Affiliations: 1 Victorian Department of Health, Melbourne, Australia 2 Victorian Healthcare Associated Infections Surveillance System, Melbourne, Australia 3 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne 4 St Vincent’s Hospital, Melbourne, Australia 5 Doherty Institute for Immunity and Infection, Melbourne, Australia 6 Geelong Centre for Emerging Infectious Disease, Geelong, Australia 7 Monash University, Melbourne, Australia 8 Alfred Health, Melbourne, Australia 9 Deakin University, Geelong, Australia 10 Burnet Institute, Melbourne, Australia 11 Austin Health, Melbourne, Australia 12 Queensland University of Technology, Queensland, Australia 13 The Royal Women’s Hospital, Melbourne, Australia OFFICIAL COVID-19 Hospital-Acquired Infections Among Patients in Victorian Health Services - March 2021 Contents Abbreviations & Acronyms ........................................................................................................................ 5 Key Findings ............................................................................................................................................. 6 Introduction................................................................................................................................................ 7 Purpose ..................................................................................................................................................... 8 Methods..................................................................................................................................................... 8 Results .................................................................................................................................................... 12 Acquisition in hospitalised COVID-19 patients .................................................................................... 12 Characteristics and outcomes of patients with C19-HAIs ................................................................... 16 Hospitals with C19-HAIs ..................................................................................................................... 18 Genomic analysis of C19-HAI patients ............................................................................................... 22 Key strengths, challenges and lessons learnt ..................................................................................... 27 Case study 1: The risk of ‘unrecognised cases’...................................................................................... 34 Case study 2: PPE use is not always perfect ......................................................................................... 35 Discussion ............................................................................................................................................... 36 Acknowledgements ................................................................................................................................. 41 References .............................................................................................................................................. 42 Appendix 1: Definitions of C19-HAI diagnosed during hospital stay....................................................... 45 Appendix 2: Definitions of C19-HAI diagnosed post-discharge .............................................................. 46 Appendix 3: Facilitated discussion attendee brief ................................................................................... 48 Appendix 4: Victorian Hospitals with C19-HAIs ...................................................................................... 52 OFFICIAL COVID-19 Hospital-Acquired Infections Among Patients in Victorian Health Services - March 2021 List of figures Figure 1: Selection process for patients with definite and probable C19-HAIs ........................................... 13 Figure 2: Timeline of COVID-19 cases in Victoria (25 January 2020- 15 November 2020), stratified by hospitalisation and healthcare acquisition .................................................................................................. 15 Figure 3: Age distribution of COVID- 19 cases, by hospitalisation and C19-HAI status ............................ 16 Figure 4: Prevalence of COVID-19 infections per 100,000 people/km2 and location of hospitals with C19- HAIs in metropolitan Melbourne .................................................................................................................. 20 Figure 5: C19-HAI cases by genomic cluster and hospital ......................................................................... 24 List of tables Table 1: Results of assessment process for patients with C19-HAIs diagnosed between 25 January 2020 and 15 November 2020 ............................................................................................................................... 14 Table 2: C19-HAIs by hospitalisation status and timing of diagnosis ......................................................... 14 Table 3: Demographic characteristics and outcomes of patients with C19-HAIs and patients hospitalised with community-acquired COVID-19; number (column per cent) unless specified .................................... 17 Table 4: Definite and probable C19-HAIs in patients, by hospital and health service (25 January to 15 November 2020; ordered by number of C19-HAI cases per health service). ............................................. 19 Table 5: Definite and probable C19-HAIs, by Department of Health region and hospital type, 25 January 2020 to 15 November 2020......................................................................................................................... 20 Table 6: Characteristics of hospitals unaffected, affected and highly affected by C19-HAIs, Victoria 2020; median (range) unless specified ................................................................................................................. 21 Table 7: Genomic clustering for C19-HAI patients, by hospital (25 January to 15 November 2020) ......... 23 Table 8: Examples of possible chains of transmission for C19-HAI patients ............................................. 25 Table 9: Patient factors relevant to C19-HAIs............................................................................................. 27 Table 10: Infrastructure limitations relevant to C19-HAIs ........................................................................... 29 Table 11: Resource/technology factors relevant to C19-HAIs .................................................................... 30 Table 12: Staff factors ................................................................................................................................. 31 Table 13: Broader pandemic, social and political context ........................................................................... 32 Table 14: Summary of instrumental strategies and 'lessons learnt' by participating health services ......... 33 Table 15: Summary of suggestions by health services for improvement in State responses .................... 33 OFFICIAL COVID-19 Hospital-Acquired Infections Among Patients in Victorian Health Services - March 2021 Abbreviations & Acronyms AGB Aerosol Generating Behaviours AV Ambulance Victoria C19-HAI COVID-19 Hospital- Acquired Infections CALD Culturally and Linguistically Diverse CHO Chief Health Officer COVID-19 Coronavirus Disease 2019 (viral disease caused by SARS-CoV-2) CQV COVID-19 Quarantine Victoria The department Department of Health ICD International Classification of Disease IPC Infection Prevention and Control ICU Intensive Care Unit HEPA High- Efficiency Particle Air Filters HH Hand Hygiene IQR Inter- Quartile Range HSIMT Health Services Incident Management Team MDU- PHL Microbiological Diagnostic Unit Public Health Laboratory N/A Not Applicable MET