Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection : Multicentre, prospective study
© 2022, Stirrup et al..
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' (<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.
Results: 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=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.
Conclusions: 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: NCT04405934.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2022 |
|---|---|
| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:11 |
|---|---|
| Enthalten in: |
eLife - 11(2022) vom: 13. Sept. |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Stirrup, Oliver [VerfasserIn] |
|---|
| Links: |
|---|
| Anmerkungen: |
Date Completed 27.10.2022 Date Revised 02.08.2023 published: Electronic ClinicalTrials.gov: NCT04405934 Citation Status MEDLINE |
|---|
| doi: |
10.7554/eLife.78427 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM346153972 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM346153972 | ||
| 003 | DE-627 | ||
| 005 | 20231226030737.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2022 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.7554/eLife.78427 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1153.xml |
| 035 | |a (DE-627)NLM346153972 | ||
| 035 | |a (NLM)36098502 | ||
| 035 | |a (PII)e78427 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Stirrup, Oliver |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection |b Multicentre, prospective study |
| 264 | 1 | |c 2022 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 27.10.2022 | ||
| 500 | |a Date Revised 02.08.2023 | ||
| 500 | |a published: Electronic | ||
| 500 | |a ClinicalTrials.gov: NCT04405934 | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2022, Stirrup et al. | ||
| 520 | |a 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 | ||
| 520 | |a 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' (<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 | ||
| 520 | |a Results: 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=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 | ||
| 520 | |a Conclusions: 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 | ||
| 520 | |a 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 | ||
| 520 | |a Clinical trial number: NCT04405934 | ||
| 650 | 4 | |a Multicenter Study | |
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a COVID-19 | |
| 650 | 4 | |a epidemiology | |
| 650 | 4 | |a global health | |
| 650 | 4 | |a healthcare-associated infection | |
| 650 | 4 | |a hospital-acquired infection | |
| 650 | 4 | |a human | |
| 650 | 4 | |a infection control | |
| 650 | 4 | |a infection prevention | |
| 650 | 4 | |a infectious disease | |
| 650 | 4 | |a microbiology | |
| 650 | 4 | |a molecular epidemiology | |
| 650 | 4 | |a viral genomics | |
| 700 | 1 | |a Blackstone, James |e verfasserin |4 aut | |
| 700 | 1 | |a Mapp, Fiona |e verfasserin |4 aut | |
| 700 | 1 | |a MacNeil, Alyson |e verfasserin |4 aut | |
| 700 | 1 | |a Panca, Monica |e verfasserin |4 aut | |
| 700 | 1 | |a Holmes, Alison |e verfasserin |4 aut | |
| 700 | 1 | |a Machin, Nicholas |e verfasserin |4 aut | |
| 700 | 1 | |a Shin, Gee Yen |e verfasserin |4 aut | |
| 700 | 1 | |a Mahungu, Tabitha |e verfasserin |4 aut | |
| 700 | 1 | |a Saeed, Kordo |e verfasserin |4 aut | |
| 700 | 1 | |a Saluja, Tranprit |e verfasserin |4 aut | |
| 700 | 1 | |a Taha, Yusri |e verfasserin |4 aut | |
| 700 | 1 | |a Mahida, Nikunj |e verfasserin |4 aut | |
| 700 | 1 | |a Pope, Cassie |e verfasserin |4 aut | |
| 700 | 1 | |a Chawla, Anu |e verfasserin |4 aut | |
| 700 | 1 | |a Cutino-Moguel, Maria-Teresa |e verfasserin |4 aut | |
| 700 | 1 | |a Tamuri, Asif |e verfasserin |4 aut | |
| 700 | 1 | |a Williams, Rachel |e verfasserin |4 aut | |
| 700 | 1 | |a Darby, Alistair |e verfasserin |4 aut | |
| 700 | 1 | |a Robertson, David L |e verfasserin |4 aut | |
| 700 | 1 | |a Flaviani, Flavia |e verfasserin |4 aut | |
| 700 | 1 | |a Nastouli, Eleni |e verfasserin |4 aut | |
| 700 | 1 | |a Robson, Samuel |e verfasserin |4 aut | |
| 700 | 1 | |a Smith, Darren |e verfasserin |4 aut | |
| 700 | 1 | |a Loose, Matthew |e verfasserin |4 aut | |
| 700 | 1 | |a Laing, Kenneth |e verfasserin |4 aut | |
| 700 | 1 | |a Monahan, Irene |e verfasserin |4 aut | |
| 700 | 1 | |a Kele, Beatrix |e verfasserin |4 aut | |
| 700 | 1 | |a Haldenby, Sam |e verfasserin |4 aut | |
| 700 | 1 | |a George, Ryan |e verfasserin |4 aut | |
| 700 | 1 | |a Bashton, Matthew |e verfasserin |4 aut | |
| 700 | 1 | |a Witney, Adam A |e verfasserin |4 aut | |
| 700 | 1 | |a Byott, Matthew |e verfasserin |4 aut | |
| 700 | 1 | |a Coll, Francesc |e verfasserin |4 aut | |
| 700 | 1 | |a Chapman, Michael |e verfasserin |4 aut | |
| 700 | 1 | |a Peacock, Sharon J |e verfasserin |4 aut | |
| 700 | 0 | |a COG-UK HOCI Investigators |e verfasserin |4 aut | |
| 700 | 0 | |a COVID-19 Genomics UK (COG-UK) consortium |e verfasserin |4 aut | |
| 700 | 1 | |a Hughes, Joseph |e verfasserin |4 aut | |
| 700 | 1 | |a Nebbia, Gaia |e verfasserin |4 aut | |
| 700 | 1 | |a Partridge, David G |e verfasserin |4 aut | |
| 700 | 1 | |a Parker, Matthew |e verfasserin |4 aut | |
| 700 | 1 | |a Price, James Richard |e verfasserin |4 aut | |
| 700 | 1 | |a Peters, Christine |e verfasserin |4 aut | |
| 700 | 1 | |a Roy, Sunando |e verfasserin |4 aut | |
| 700 | 1 | |a Snell, Luke B |e verfasserin |4 aut | |
| 700 | 1 | |a de Silva, Thushan I |e verfasserin |4 aut | |
| 700 | 1 | |a Thomson, Emma |e verfasserin |4 aut | |
| 700 | 1 | |a Flowers, Paul |e verfasserin |4 aut | |
| 700 | 1 | |a Copas, Andrew |e verfasserin |4 aut | |
| 700 | 1 | |a Breuer, Judith |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t eLife |d 2012 |g 11(2022) vom: 13. Sept. |w (DE-627)NLM221831460 |x 2050-084X |7 nnns |
| 773 | 1 | 8 | |g volume:11 |g year:2022 |g day:13 |g month:09 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.7554/eLife.78427 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 11 |j 2022 |b 13 |c 09 | ||