tetano
Editor, Senior Moderator
Elife
. 2022 Sep 13;11:e78427.
doi: 10.7554/eLife.78427. Online ahead of print.
Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study
Oliver Stirrup[SUP] 1 [/SUP], James Blackstone[SUP] 2 [/SUP], Fiona Mapp[SUP] 1 [/SUP], Alyson MacNeil[SUP] 3 [/SUP], Monica Panca[SUP] 3 [/SUP], Alison Holmes[SUP] 4 [/SUP], Nicholas Machin[SUP] 5 [/SUP], Gee Yen Shin[SUP] 6 [/SUP], Tabitha Mahungu[SUP] 7 [/SUP], Kordo Saeed[SUP] 8 [/SUP], Tranprit Saluja[SUP] 9 [/SUP], Yusri Taha[SUP] 10 [/SUP], Nikunj Mahida[SUP] 11 [/SUP], Cassie Pope[SUP] 12 [/SUP], Anu Chawla[SUP] 13 [/SUP], Maria-Teresa Cutino-Moguel[SUP] 14 [/SUP], Asif Tamuri[SUP] 15 [/SUP], Rachel Williams[SUP] 16 [/SUP], Alistair Darby[SUP] 17 [/SUP], David L Robertson[SUP] 18 [/SUP], Flavia Flaviani[SUP] 19 [/SUP], Eleni Nastouli[SUP] 6 [/SUP], Samuel Robson[SUP] 20 [/SUP], Darren Smith[SUP] 21 [/SUP], Kenneth Laing[SUP] 22 [/SUP], Irene Monahan[SUP] 22 [/SUP], Beatrix Kele[SUP] 14 [/SUP], Sam Haldenby[SUP] 17 [/SUP], Ryan George[SUP] 5 [/SUP], Matthew Bashton[SUP] 21 [/SUP], Adam A Witney[SUP] 22 [/SUP], Matthew Byott[SUP] 23 [/SUP], Francesc Coll[SUP] 24 [/SUP], Michael Chapman[SUP] 25 [/SUP], Sharon J Peacock[SUP] 26 [/SUP], COG‐UK HOCI Investigators; COVID‐19 Genomics UK (COG‐UK) Consortium; Joseph Hughes[SUP] 27 [/SUP], Gaia Nebbia[SUP] 28 [/SUP], David G Partridge[SUP] 29 [/SUP], Matthew Parker[SUP] 30 [/SUP], James Richard Price[SUP] 4 [/SUP], Christine Peters[SUP] 31 [/SUP], Sunando Roy[SUP] 32 [/SUP], Luke B Snell[SUP] 28 [/SUP], Thushan I de Silva[SUP] 33 [/SUP], Emma Thomson[SUP] 27 [/SUP], Paul Flowers[SUP] 34 [/SUP], Andrew Copas[SUP] 1 [/SUP], Judith Breuer[SUP] 32 [/SUP]
Affiliations
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.
Keywords: epidemiology; global health; human; infectious disease; microbiology.
. 2022 Sep 13;11:e78427.
doi: 10.7554/eLife.78427. Online ahead of print.
Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study
Oliver Stirrup[SUP] 1 [/SUP], James Blackstone[SUP] 2 [/SUP], Fiona Mapp[SUP] 1 [/SUP], Alyson MacNeil[SUP] 3 [/SUP], Monica Panca[SUP] 3 [/SUP], Alison Holmes[SUP] 4 [/SUP], Nicholas Machin[SUP] 5 [/SUP], Gee Yen Shin[SUP] 6 [/SUP], Tabitha Mahungu[SUP] 7 [/SUP], Kordo Saeed[SUP] 8 [/SUP], Tranprit Saluja[SUP] 9 [/SUP], Yusri Taha[SUP] 10 [/SUP], Nikunj Mahida[SUP] 11 [/SUP], Cassie Pope[SUP] 12 [/SUP], Anu Chawla[SUP] 13 [/SUP], Maria-Teresa Cutino-Moguel[SUP] 14 [/SUP], Asif Tamuri[SUP] 15 [/SUP], Rachel Williams[SUP] 16 [/SUP], Alistair Darby[SUP] 17 [/SUP], David L Robertson[SUP] 18 [/SUP], Flavia Flaviani[SUP] 19 [/SUP], Eleni Nastouli[SUP] 6 [/SUP], Samuel Robson[SUP] 20 [/SUP], Darren Smith[SUP] 21 [/SUP], Kenneth Laing[SUP] 22 [/SUP], Irene Monahan[SUP] 22 [/SUP], Beatrix Kele[SUP] 14 [/SUP], Sam Haldenby[SUP] 17 [/SUP], Ryan George[SUP] 5 [/SUP], Matthew Bashton[SUP] 21 [/SUP], Adam A Witney[SUP] 22 [/SUP], Matthew Byott[SUP] 23 [/SUP], Francesc Coll[SUP] 24 [/SUP], Michael Chapman[SUP] 25 [/SUP], Sharon J Peacock[SUP] 26 [/SUP], COG‐UK HOCI Investigators; COVID‐19 Genomics UK (COG‐UK) Consortium; Joseph Hughes[SUP] 27 [/SUP], Gaia Nebbia[SUP] 28 [/SUP], David G Partridge[SUP] 29 [/SUP], Matthew Parker[SUP] 30 [/SUP], James Richard Price[SUP] 4 [/SUP], Christine Peters[SUP] 31 [/SUP], Sunando Roy[SUP] 32 [/SUP], Luke B Snell[SUP] 28 [/SUP], Thushan I de Silva[SUP] 33 [/SUP], Emma Thomson[SUP] 27 [/SUP], Paul Flowers[SUP] 34 [/SUP], Andrew Copas[SUP] 1 [/SUP], Judith Breuer[SUP] 32 [/SUP]
Affiliations
- PMID: 36098502
- DOI: 10.7554/eLife.78427
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.
Keywords: epidemiology; global health; human; infectious disease; microbiology.