Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study
Author:
Stirrup OliverORCID, Blackstone James, Mapp Fiona, MacNeil Alyson, Panca Monica, Holmes Alison, Machin Nicholas, Shin Gee Yen, Mahungu Tabitha, Saeed Kordo, Saluja Tranprit, Taha Yusri, Mahida Nikunj, Pope Cassie, Chawla Anu, Cutino-Moguel Maria-Teresa, Tamuri Asif, Williams Rachel, Darby Alistair, Robertson David, Flaviani Flavia, Nastouli Eleni, Robson Samuel, Smith Darren, Loose MatthewORCID, Laing Kenneth, Monahan Irene, Kele Beatrix, Haldenby Sam, George Ryan, Bashton Matthew, Witney Adam, Byott Matthew, Coll Francesc, Chapman Michael, Peacock Sharon, Hughes JosephORCID, Nebbia Gaia, Partridge David G, Parker Matthew, Price JamesORCID, Peters Christine, Roy Sunando, Snell Luke B, de Silva Thushan I, Thomson Emma, Flowers Paul, Copas Andrew, Breuer Judith, ,
Abstract
AbstractIntroductionViral 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.MethodsWe 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.ResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, 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 (IRR 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.ConclusionWhile 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.
Publisher
Cold Spring Harbor Laboratory
Reference32 articles.
1. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology 2. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study;The Lancet Infectious Diseases,2020 3. Lucey M , Macori G , Mullane N , Sutton-Fitzpatrick U , Gonzalez G , Coughlan S , et al. Whole-genome Sequencing to Track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission in Nosocomial Outbreaks. Clinical Infectious Diseases 2020. 4. Snell LB , Fisher CL , Taj U , Stirrup O , Merrick B , Alcolea-Medina A , et al. Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission. Clinical Microbiology and Infection 2021. 5. Nosocomial transmission and outbreaks of coronavirus disease 2019: the need to protect both patients and healthcare workers;Antimicrobial Resistance & Infection Control,2021
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