Stirrup, O;
Blackstone, J;
Mapp, F;
MacNeil, A;
Panca, M;
Holmes, A;
Machin, N;
Shin, GY;
Mahungu, T;
Saeed, K;
et al.
Stirrup, O; Blackstone, J; Mapp, F; MacNeil, A; Panca, M; Holmes, A; Machin, N; Shin, GY; Mahungu, T; Saeed, K; Saluja, T; Taha, Y; Mahida, N; Pope, C; Chawla, A; Cutino-Moguel, M-T; Tamuri, A; Williams, R; Darby, A; Robertson, DL; Flaviani, F; Nastouli, E; Robson, S; Smith, D; Laing, K; Monahan, I; Kele, B; Haldenby, S; George, R; Bashton, M; Witney, AA; Byott, M; Coll, F; Chapman, M; Peacock, SJ; COG‐UK HOCI Investigators; COVID‐19 Genomics UK (COG‐UK) Consortium; Hughes, J; Nebbia, G; Partridge, DG; Parker, M; Price, JR; Peters, C; Roy, S; Snell, LB; de Silva, TI; Thomson, E; Flowers, P; Copas, A; Breuer, J
(2022)
Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study.
Elife, 11.
ISSN 2050-084X
https://doi.org/10.7554/eLife.78427
SGUL Authors: Laing, Kenneth Witney, Adam Austin
Abstract
Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48h) and 4 weeks of 'longer-turnaround' (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected ≥48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. Results: A total of 2170 HOCI cases were recorded from October 2020-April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources. Conclusion: While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days. Funding: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute. Clinical trial number: ClinicalTrials.gov Identifier: NCT04405934.
Item Type: |
Article
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Additional Information: |
Copyright Stirrup et al. This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use and redistribution provided that the original author and source are credited. |
Keywords: |
epidemiology, global health, human, infectious disease, microbiology, COG‐UK HOCI Investigators, COVID‐19 Genomics UK (COG‐UK) Consortium, epidemiology, global health, human, infectious disease, microbiology, 0601 Biochemistry and Cell Biology |
SGUL Research Institute / Research Centre: |
Academic Structure > Infection and Immunity Research Institute (INII) |
Journal or Publication Title: |
Elife |
ISSN: |
2050-084X |
Language: |
eng |
Dates: |
Date | Event |
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25 October 2022 | Published | 13 September 2022 | Published Online | 25 August 2022 | Accepted |
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Publisher License: |
Creative Commons: Attribution 4.0 |
Projects: |
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PubMed ID: |
36098502 |
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Go to PubMed abstract |
URI: |
https://openaccess.sgul.ac.uk/id/eprint/114881 |
Publisher's version: |
https://doi.org/10.7554/eLife.78427 |
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