Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study

Oliver Stirrup; James Blackstone; Fiona Mapp; Alyson Macneil; Monica Panca; Alison Holmes; Nicholas Machin; Gee Yen Shin; Tabitha Mahungu; Kordo Saeed; Tranprit Saluja; Yusri Taha; Nikunj Mahida; Cassie Pope; Anu Chawla; Maria-Teresa Cutino-Moguel; Asif Tamuri; Rachel Williams; Alistair Darby; David L. Robertson; Flavia Flaviani; Eleni Nastouli; Samuel Robson; Darren Smith; Matthew Loose; Kenneth Laing; Irene Monahan; Beatrix Kele; Sam Haldenby; Ryan George; Matthew Bashton; Adam A. Witney; Matthew Byott; Francesc Coll; Michael Chapman; Sharon J. Peacock; Joseph Hughes; Gaia Nebbia; David G. Partridge; Matthew Parker; James Richard Price; Christine Peters; Sunando Roy; Luke B. Snell; Thushan I. de Silva; Emma Thomson; Paul Flowers; Andrew Copas; Judith Breuer

doi:10.7554/eLife.78427

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study

Oliver Stirrup, James Blackstone, Fiona Mapp, Alyson Macneil, Monica Panca, Alison Holmes, Nicholas Machin, Gee Yen Shin, Tabitha Mahungu, Kordo Saeed, Tranprit Saluja, Yusri Taha, Nikunj Mahida, Cassie Pope, Anu Chawla, Maria-Teresa Cutino-Moguel, Asif Tamuri, Rachel Williams, Alistair Darby, David L. RobertsonFlavia Flaviani, Eleni Nastouli, Samuel Robson, Darren Smith, Matthew Loose, Kenneth Laing, Irene Monahan, Beatrix Kele, Sam Haldenby, Ryan George, Matthew Bashton, Adam A. Witney, Matthew Byott, Francesc Coll, Michael Chapman, Sharon J. Peacock, Joseph Hughes, Gaia Nebbia, David G. Partridge, Matthew Parker, James Richard Price, Christine Peters, Sunando Roy, Luke B. Snell, Thushan I. de Silva, Emma Thomson, Paul Flowers, Andrew Copas, Judith Breuer

Research output: Contribution to journal › Article › peer-review

50 Downloads (Pure)

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’ (

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.

Original language	English
Article number	e78427
Number of pages	31
Journal	eLife
Volume	11
DOIs	https://doi.org/10.7554/eLife.78427
Publication status	Published - 13 Sept 2022

Keywords

UKRI
MRC

Access to Document

10.7554/eLife.78427Licence: CC BY

Effectiveness of rapid SARS-CoV-2 genomeFinal published version, 2.1 MBLicence: CC BY

10 Citations
1 Article

Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK
COG-UK Consortium, Robson, S., Cook, K. F., Glaysher, S., Beckett, A. H., Goudarzi, S., Fearn, C. P. S., Loveson, K. F., Elliott, S., Wyllie, S., Lloyd, A., Bicknell, K., Lumley, S. & Chauhan, A., 20 Jan 2023, In: Frontiers in Cellular and Infection Microbiology. 12, 20 p., 1066390.
Research output: Contribution to journal › Article › peer-review

Open Access
File
83 Downloads (Pure)

Dataset: GISAID EpiCov SARS-CoV-2 Whole Genome Sequencing Database
Robson, S. (Creator), GISAID, 18 Nov 2020
https://www.epicov.org/epi3/frontend#3bd481
Dataset
COVID-19 Genomics UK (COG-UK) consortium
Robson, S. (Creator), NCBI, 29 Apr 2020
https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB37886
Dataset

Cite this

Stirrup, O., Blackstone, J., Mapp, F., Macneil, A., Panca, M., Holmes, A., Machin, N., Shin, G. Y., Mahungu, T., Saeed, K., Saluja, T., Taha, Y., Mahida, N., Pope, C., Chawla, A., Cutino-Moguel, M.-T., Tamuri, A., Williams, R., Darby, A., ... Breuer, J. (2022). Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study. eLife, 11, Article e78427. https://doi.org/10.7554/eLife.78427

@article{ad5bfda4edf849ce91226f29ca347356,

title = "Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study",

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 {\textquoteleft}rapid{\textquoteright} (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 {\textquoteleft}per-protocol{\textquoteright} 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.",

keywords = "UKRI, MRC",

author = "Oliver Stirrup and James Blackstone and Fiona Mapp and Alyson Macneil and Monica Panca and Alison Holmes and Nicholas Machin and Shin, {Gee Yen} and Tabitha Mahungu and Kordo Saeed and Tranprit Saluja and Yusri Taha and Nikunj Mahida and Cassie Pope and Anu Chawla and Maria-Teresa Cutino-Moguel and Asif Tamuri and Rachel Williams and Alistair Darby and Robertson, {David L.} and Flavia Flaviani and Eleni Nastouli and Samuel Robson and Darren Smith and Matthew Loose and Kenneth Laing and Irene Monahan and Beatrix Kele and Sam Haldenby and Ryan George and Matthew Bashton and Witney, {Adam A.} and Matthew Byott and Francesc Coll and Michael Chapman and Peacock, {Sharon J.} and Joseph Hughes and Gaia Nebbia and Partridge, {David G.} and Matthew Parker and Price, {James Richard} and Christine Peters and Sunando Roy and Snell, {Luke B.} and {de Silva}, {Thushan I.} and Emma Thomson and Paul Flowers and Andrew Copas and Judith Breuer",

year = "2022",

month = sep,

day = "13",

doi = "10.7554/eLife.78427",

language = "English",

volume = "11",

journal = "eLife",

issn = "2050-084X",

publisher = "eLife Sciences Publication",

}

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, Loose, M, Laing, K, Monahan, I, Kele, B, Haldenby, S, George, R, Bashton, M, Witney, AA, Byott, M, Coll, F, Chapman, M, Peacock, SJ, 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: Multicentre, prospective study', eLife, vol. 11, e78427. https://doi.org/10.7554/eLife.78427

TY - JOUR

T1 - Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study

AU - Stirrup, Oliver

AU - Blackstone, James

AU - Mapp, Fiona

AU - Macneil, Alyson

AU - Panca, Monica

AU - Holmes, Alison

AU - Machin, Nicholas

AU - Shin, Gee Yen

AU - Mahungu, Tabitha

AU - Saeed, Kordo

AU - Saluja, Tranprit

AU - Taha, Yusri

AU - Mahida, Nikunj

AU - Pope, Cassie

AU - Chawla, Anu

AU - Cutino-Moguel, Maria-Teresa

AU - Tamuri, Asif

AU - Williams, Rachel

AU - Darby, Alistair

AU - Robertson, David L.

AU - Flaviani, Flavia

AU - Nastouli, Eleni

AU - Robson, Samuel

AU - Smith, Darren

AU - Loose, Matthew

AU - Laing, Kenneth

AU - Monahan, Irene

AU - Kele, Beatrix

AU - Haldenby, Sam

AU - George, Ryan

AU - Bashton, Matthew

AU - Witney, Adam A.

AU - Byott, Matthew

AU - Coll, Francesc

AU - Chapman, Michael

AU - Peacock, Sharon J.

AU - Hughes, Joseph

AU - Nebbia, Gaia

AU - Partridge, David G.

AU - Parker, Matthew

AU - Price, James Richard

AU - Peters, Christine

AU - Roy, Sunando

AU - Snell, Luke B.

AU - de Silva, Thushan I.

AU - Thomson, Emma

AU - Flowers, Paul

AU - Copas, Andrew

AU - Breuer, Judith

PY - 2022/9/13

Y1 - 2022/9/13

N2 - 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’ (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.

AB - 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’ (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.

KW - UKRI

KW - MRC

UR - https://elifesciences.org/articles/78427

U2 - 10.7554/eLife.78427

DO - 10.7554/eLife.78427

M3 - Article

SN - 2050-084X

VL - 11

JO - eLife

JF - eLife

M1 - e78427

ER -

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study

Abstract

Keywords

Access to Document

Fingerprint

Research output

Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK

Datasets

Dataset: GISAID EpiCov SARS-CoV-2 Whole Genome Sequencing Database

COVID-19 Genomics UK (COG-UK) consortium

Cite this