Epidemiological and Genomic analysis of a Sydney Hospital COVID-19 Outbreak

  1. Elaine Tennant
  2. Melanie Figtree
  3. Jo Tallon
  4. Rowena A Bull
  5. Malinna Yeang
  6. Ira W Deveson
  7. James M Ferguson
  8. Thiruni Adikari
  9. Edward C Holmes
  10. Sebastiaan Van Hal
  11. Jillian M Hammond
  12. Igor Stevanovski
  13. Katerina Mitsakos
  14. Drew Hilditch-Roberts
  15. William Rawlinson
  16. Bernard Hudson

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Abstract

Australia’s early COVID-19 experience involved clusters in northern Sydney, including hospital and aged-care facility (ACF) outbreaks. We explore transmission dynamics, drivers and outcomes of a metropolitan hospital COVID-19 outbreak that occurred in the context of established local community transmission. A retrospective cohort analysis is presented, with integration of viral genome sequencing, clinical and epidemiological data. We demonstrate using genomic epidemiology that the hospital outbreak (n=23) was linked to a concurrent outbreak at a local aged care facility, but was phylogenetically distinct from other community clusters. Thirty day survival was 50% for hospitalised patients (an elderly cohort with significant comorbidities) and 100% for staff. Staff who acquired infection were unable to attend work for a median of 26.5 days (range 14-191); an additional 140 staff were furloughed for quarantine. Transmission from index cases showed a wide dispersion (mean 3.5 persons infected for every patient case and 0.6 persons infected for every staff case). One patient, who received regular nebulised medication prior to their diagnosis being known, acted as an apparent superspreader. No secondary transmissions occurred from isolated cases or contacts who were quarantined prior to becoming infectious. This analysis elaborates the wide-ranging impacts on patients and staff of nosocomial COVID-19 transmission and highlights the utility of genomic analysis as an adjunct to traditional epidemiological investigations. Delayed case recognition resulted in nosocomial transmission but once recognised, prompt action by the outbreak management team and isolation with contact and droplet (without airborne) precautions were sufficient to prevent transmission within this cohort. Our findings support current PPE recommendations in Australia but demonstrate the risk of administering nebulised medications when COVID-19 is circulating locally.

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  1. ScreenIT

    SciScore for 10.1101/2021.02.17.21251943: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: Research approval was granted by NSLHD Human Research Ethics Committee (HREC) (2020/STE01571).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study has several limitations. The OMT were required to gather epidemiological data rapidly. Accordingly, there may have been gaps in the collected information, due to ascertainment and recall bias. Review of the outbreak management underlines the siloed nature of our healthcare system, with allied professions being managed through very separate streams; this can present a barrier to rapid infection control actions. An OMT should incorporate cross-discipline membership to produce equivalent contact tracing and communication efforts across medical, nursing, allied health and corporate services. A further challenge is the rapid bed movement of patients and the lack of a clear formal mechanism for identifying contacts between patients that are unrelated to bed residence. Despite the OMT’s efforts, infection and transmission events may have been missed. Ongoing serological studies performed in NSLHD and other jurisdictions may enhance our understanding. In summary, we describe a hospital outbreak of COVID-19 linked to a community ACF cluster and which had substantial impacts on both patients and staff. Our results add weight to the recommendation that nebulisers should not be used in patients suspected to have COVID-19. Our study also illustrates that tackling viral outbreaks requires a sophisticated, detailed approach in which multidisciplinary team members must collaborate closely to achieve success. These principles will serve us well for tackling the COVID-19 pandemic in ...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.02.17.21251943 on medRxiv