Stirrup, Oliver, Blackstone, James, Mapp, Fiona, MacNeil, Alyson, Panca, Monica, Holmes, Alison 
ORCID: 0000-0001-5554-5743, Machin, Nicholas, Shin, Gee Yen, Mahungu, Tabitha, Saeed, Kordo et al (show 39 more authors)
(2022)
Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.
ELIFE, 11.
e78427-.
|
Text
Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection Mu.pdf - Published version Download (2MB) | Preview |
Abstract
<h4>Background</h4>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.<h4>Methods</h4>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' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated.<h4>Results</h4>A total of 2170 HOCI cases were recorded from October 2020 to 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<i>=</i>0.14) or rapid (0.85, 0.48-1.50; p<i>=</i>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.<h4>Conclusions</h4>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.<h4>Funding</h4>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.<h4>Clinical trial number</h4>NCT04405934.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | COVID-19, viral genomics, hospital-acquired infection, healthcare-associated infection, infection prevention, molecular epidemiology, infection control, Human |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 10 Jan 2023 16:20 |
| Last Modified: | 28 Jan 2023 19:45 |
| DOI: | 10.7554/eLife.78427 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3166972 |
Dimensions
Dimensions
