Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals

Monica Panca; James Blackstone; Oliver Stirrup; Maria-Teresa Cutino-Moguel; Luke Blagdon Snell; Emma C Thomson; Christine Peters; Gaia Nebbia; Alison H. Holmes; Anu Chawla; Nicholas Machin; Yusri Taha; Tabitha W Mahungu; Tranprit Saluja; Thushan I de Silva; Kordo Saeed; Cassie F Pope; Gee Yee Shin; Rachel Williams; Alistair Darby; Darren L. Smith; Matthew Loose; Samuel C Robson; Kenneth Laing; David G Partridge; James Richard Price; Judith Breuer

doi:10.1016/j.jhin.2023.06.005

Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals

Monica Panca, James Blackstone, Oliver Stirrup, Maria-Teresa Cutino-Moguel, Luke Blagdon Snell, Emma C Thomson, Christine Peters, Gaia Nebbia, Alison H. Holmes, Anu Chawla, Nicholas Machin, Yusri Taha, Tabitha W Mahungu, Tranprit Saluja, Thushan I de Silva, Kordo Saeed, Cassie F Pope, Gee Yee Shin, Rachel Williams, Alistair DarbyDarren L. Smith, Matthew Loose, Samuel C Robson, Kenneth Laing, David G Partridge, James Richard Price, Judith Breuer

King's College London

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

Abstract

Background: The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole-genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals. Aim: To estimate the cost implications of using the information from the sequencing reporting tool (SRT), used to determine likelihood of nosocomial infection in IPC practice. Methods: A micro-costing approach for SARS-CoV-2 WGS was conducted. Data on IPC management resource use and costs were collected from interviews with IPC teams from 14 participating sites and used to assign cost estimates for IPC activities as collected in the trial. Activities included IPC-specific actions following a suspicion of healthcare-associated infection (HAI) or outbreak, as well as changes to practice following the return of data via SRT. Findings: The mean per-sample costs of SARS-CoV-2 sequencing were estimated at £77.10 for rapid and £66.94 for longer turnaround phases. Over the three-month interventional phases, the total management costs of IPC-defined HAIs and outbreak events across the sites were estimated at £225,070 and £416,447, respectively. The main cost drivers were bed-days lost due to ward closures because of outbreaks, followed by outbreak meetings and bed-days lost due to cohorting contacts. Actioning SRTs, the cost of HAIs increased by £5,178 due to unidentified cases and the cost of outbreaks decreased by £11,246 as SRTs excluded hospital outbreaks. Conclusion: Although SARS-CoV-2 WGS adds to the total IPC management cost, additional information provided could balance out the additional cost, depending on identified design improvements and effective deployment.

Original language	English
Pages (from-to)	23-32
Number of pages	10
Journal	Journal of Hospital Infection
Volume	139
Early online date	10 Jun 2023
DOIs	https://doi.org/10.1016/j.jhin.2023.06.005
Publication status	Published - Sept 2023

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Panca, M., Blackstone, J., Stirrup, O., Cutino-Moguel, M-T., Snell, L. B., Thomson, E. C., Peters, C., Nebbia, G., Holmes, A. H., Chawla, A., Machin, N., Taha, Y., Mahungu, T. W., Saluja, T., de Silva, T. I., Saeed, K., Pope, C. F., Shin, G. Y., Williams, R., ... Breuer, J. (2023). Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals. Journal of Hospital Infection, 139, 23-32. https://doi.org/10.1016/j.jhin.2023.06.005

@article{ebd497e14ebf4b71bc67491af79b7353,

title = "Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals",

abstract = "Background: The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole-genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals. Aim: To estimate the cost implications of using the information from the sequencing reporting tool (SRT), used to determine likelihood of nosocomial infection in IPC practice. Methods: A micro-costing approach for SARS-CoV-2 WGS was conducted. Data on IPC management resource use and costs were collected from interviews with IPC teams from 14 participating sites and used to assign cost estimates for IPC activities as collected in the trial. Activities included IPC-specific actions following a suspicion of healthcare-associated infection (HAI) or outbreak, as well as changes to practice following the return of data via SRT. Findings: The mean per-sample costs of SARS-CoV-2 sequencing were estimated at £77.10 for rapid and £66.94 for longer turnaround phases. Over the three-month interventional phases, the total management costs of IPC-defined HAIs and outbreak events across the sites were estimated at £225,070 and £416,447, respectively. The main cost drivers were bed-days lost due to ward closures because of outbreaks, followed by outbreak meetings and bed-days lost due to cohorting contacts. Actioning SRTs, the cost of HAIs increased by £5,178 due to unidentified cases and the cost of outbreaks decreased by £11,246 as SRTs excluded hospital outbreaks. Conclusion: Although SARS-CoV-2 WGS adds to the total IPC management cost, additional information provided could balance out the additional cost, depending on identified design improvements and effective deployment.",

author = "Monica Panca and James Blackstone and Oliver Stirrup and Maria-Teresa Cutino-Moguel and Snell, {Luke Blagdon} and Thomson, {Emma C} and Christine Peters and Gaia Nebbia and Holmes, {Alison H.} and Anu Chawla and Nicholas Machin and Yusri Taha and Mahungu, {Tabitha W} and Tranprit Saluja and {de Silva}, {Thushan I} and Kordo Saeed and Pope, {Cassie F} and Shin, {Gee Yee} and Rachel Williams and Alistair Darby and Smith, {Darren L.} and Matthew Loose and Robson, {Samuel C} and Kenneth Laing and Partridge, {David G} and Price, {James Richard} and Judith Breuer",

note = "Funding Information: Members of different teams who provided data:, Infection Prevention and Control: M. Cummins (Barts Health NHS Trust, London, UK); G. Mollett, A. Marek (NHS Greater Glasgow and Clyde, Glasgow, UK); C. Beviz, H. Mitchell (Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK); B. Taylor, D. Lankstead (Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK); K. Wylie (Manchester University NHS Foundation Trust, Manchester, UK); A. Cobb (Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK); E. Baxter (Nottingham University Hospitals NHS Trust, Nottingham, UK); D. Thomlinson (City Hospital, Birmingham, UK); L. Hail (University College London Hospitals NHS Foundation Trust, London, UK). Income, Contracting and Costing: D. Jaramillo (Barts Health NHS Trust, London, UK); J. Haughney (NHS Greater Glasgow and Clyde, Glasgow, UK); S. Mookerjee (Imperial College Healthcare NHS Trust, London, UK); P. Dudley, C. Wilson (Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK); J. Field (Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK). Laboratories: A. Da Silva Filipe, D. Macpherson, D. Mair (NHS Greater Glasgow and Clyde, Glasgow, UK); C. McCann (Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK); J. Schutter (University of Sheffield, Sheffield, UK); K. Laing (St George's University Hospitals NHS Foundation Trust, London, UK); A. Beckett (Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK); S. Glaysher (Portsmouth Hospitals University NHS Trust, Portsmouth, UK); K.F. Cook, C. Fearn, S. Goudarzi, H. Dent, H. Paul (School of Pharmacy and Biomedical Science & School of Biological Sciences, University of Portsmouth, Portsmouth, UK). K. Saeed would like to thank M. Connell, B. James and other colleagues in the Costing/Central Management Accounting Team at University Hospital Southampton as well as J. Brookes, S. Dailly, S. Jeremiah, J. Prieto, C. Holmes, T. Julius, A. Elliott, P. Doherty, K. Chandler, D. Court, S. Aplin and other colleagues in infection prevention at University Hospital Southampton for all their support during those challenging times and providing some of the interviews and costing calculations for the study. Funding Information: The study was funded by UK Research and Innovation and the Wellcome Trust through the COG-UK Consortium grant. J. Breuer receives funding from the National Institute for Health Research UCL/UCLH Biomedical Research Centre. Publisher Copyright: {\textcopyright} 2023 The Authors",

year = "2023",

month = sep,

doi = "10.1016/j.jhin.2023.06.005",

language = "English",

volume = "139",

pages = "23--32",

journal = "Journal of Hospital Infection",

issn = "0195-6701",

publisher = "W.B. Saunders Ltd",

}

Panca, M, Blackstone, J, Stirrup, O, Cutino-Moguel, M-T, Snell, LB, Thomson, EC, Peters, C, Nebbia, G, Holmes, AH, Chawla, A, Machin, N, Taha, Y, Mahungu, TW, Saluja, T, de Silva, TI, Saeed, K, Pope, CF, Shin, GY, Williams, R, Darby, A, Smith, DL, Loose, M, Robson, SC, Laing, K, Partridge, DG, Price, JR & Breuer, J 2023, 'Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals', Journal of Hospital Infection, vol. 139, pp. 23-32. https://doi.org/10.1016/j.jhin.2023.06.005

TY - JOUR

T1 - Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals

AU - Panca, Monica

AU - Blackstone, James

AU - Stirrup, Oliver

AU - Cutino-Moguel, Maria-Teresa

AU - Snell, Luke Blagdon

AU - Thomson, Emma C

AU - Peters, Christine

AU - Nebbia, Gaia

AU - Holmes, Alison H.

AU - Chawla, Anu

AU - Machin, Nicholas

AU - Taha, Yusri

AU - Mahungu, Tabitha W

AU - Saluja, Tranprit

AU - de Silva, Thushan I

AU - Saeed, Kordo

AU - Pope, Cassie F

AU - Shin, Gee Yee

AU - Williams, Rachel

AU - Darby, Alistair

AU - Smith, Darren L.

AU - Loose, Matthew

AU - Robson, Samuel C

AU - Laing, Kenneth

AU - Partridge, David G

AU - Price, James Richard

AU - Breuer, Judith

N1 - Funding Information: Members of different teams who provided data:, Infection Prevention and Control: M. Cummins (Barts Health NHS Trust, London, UK); G. Mollett, A. Marek (NHS Greater Glasgow and Clyde, Glasgow, UK); C. Beviz, H. Mitchell (Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK); B. Taylor, D. Lankstead (Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK); K. Wylie (Manchester University NHS Foundation Trust, Manchester, UK); A. Cobb (Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK); E. Baxter (Nottingham University Hospitals NHS Trust, Nottingham, UK); D. Thomlinson (City Hospital, Birmingham, UK); L. Hail (University College London Hospitals NHS Foundation Trust, London, UK). Income, Contracting and Costing: D. Jaramillo (Barts Health NHS Trust, London, UK); J. Haughney (NHS Greater Glasgow and Clyde, Glasgow, UK); S. Mookerjee (Imperial College Healthcare NHS Trust, London, UK); P. Dudley, C. Wilson (Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK); J. Field (Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK). Laboratories: A. Da Silva Filipe, D. Macpherson, D. Mair (NHS Greater Glasgow and Clyde, Glasgow, UK); C. McCann (Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK); J. Schutter (University of Sheffield, Sheffield, UK); K. Laing (St George's University Hospitals NHS Foundation Trust, London, UK); A. Beckett (Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK); S. Glaysher (Portsmouth Hospitals University NHS Trust, Portsmouth, UK); K.F. Cook, C. Fearn, S. Goudarzi, H. Dent, H. Paul (School of Pharmacy and Biomedical Science & School of Biological Sciences, University of Portsmouth, Portsmouth, UK). K. Saeed would like to thank M. Connell, B. James and other colleagues in the Costing/Central Management Accounting Team at University Hospital Southampton as well as J. Brookes, S. Dailly, S. Jeremiah, J. Prieto, C. Holmes, T. Julius, A. Elliott, P. Doherty, K. Chandler, D. Court, S. Aplin and other colleagues in infection prevention at University Hospital Southampton for all their support during those challenging times and providing some of the interviews and costing calculations for the study. Funding Information: The study was funded by UK Research and Innovation and the Wellcome Trust through the COG-UK Consortium grant. J. Breuer receives funding from the National Institute for Health Research UCL/UCLH Biomedical Research Centre. Publisher Copyright: © 2023 The Authors

PY - 2023/9

Y1 - 2023/9

N2 - Background: The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole-genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals. Aim: To estimate the cost implications of using the information from the sequencing reporting tool (SRT), used to determine likelihood of nosocomial infection in IPC practice. Methods: A micro-costing approach for SARS-CoV-2 WGS was conducted. Data on IPC management resource use and costs were collected from interviews with IPC teams from 14 participating sites and used to assign cost estimates for IPC activities as collected in the trial. Activities included IPC-specific actions following a suspicion of healthcare-associated infection (HAI) or outbreak, as well as changes to practice following the return of data via SRT. Findings: The mean per-sample costs of SARS-CoV-2 sequencing were estimated at £77.10 for rapid and £66.94 for longer turnaround phases. Over the three-month interventional phases, the total management costs of IPC-defined HAIs and outbreak events across the sites were estimated at £225,070 and £416,447, respectively. The main cost drivers were bed-days lost due to ward closures because of outbreaks, followed by outbreak meetings and bed-days lost due to cohorting contacts. Actioning SRTs, the cost of HAIs increased by £5,178 due to unidentified cases and the cost of outbreaks decreased by £11,246 as SRTs excluded hospital outbreaks. Conclusion: Although SARS-CoV-2 WGS adds to the total IPC management cost, additional information provided could balance out the additional cost, depending on identified design improvements and effective deployment.

AB - Background: The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole-genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals. Aim: To estimate the cost implications of using the information from the sequencing reporting tool (SRT), used to determine likelihood of nosocomial infection in IPC practice. Methods: A micro-costing approach for SARS-CoV-2 WGS was conducted. Data on IPC management resource use and costs were collected from interviews with IPC teams from 14 participating sites and used to assign cost estimates for IPC activities as collected in the trial. Activities included IPC-specific actions following a suspicion of healthcare-associated infection (HAI) or outbreak, as well as changes to practice following the return of data via SRT. Findings: The mean per-sample costs of SARS-CoV-2 sequencing were estimated at £77.10 for rapid and £66.94 for longer turnaround phases. Over the three-month interventional phases, the total management costs of IPC-defined HAIs and outbreak events across the sites were estimated at £225,070 and £416,447, respectively. The main cost drivers were bed-days lost due to ward closures because of outbreaks, followed by outbreak meetings and bed-days lost due to cohorting contacts. Actioning SRTs, the cost of HAIs increased by £5,178 due to unidentified cases and the cost of outbreaks decreased by £11,246 as SRTs excluded hospital outbreaks. Conclusion: Although SARS-CoV-2 WGS adds to the total IPC management cost, additional information provided could balance out the additional cost, depending on identified design improvements and effective deployment.

UR - http://www.scopus.com/inward/record.url?scp=85164669287&partnerID=8YFLogxK

U2 - 10.1016/j.jhin.2023.06.005

DO - 10.1016/j.jhin.2023.06.005

M3 - Article

SN - 0195-6701

VL - 139

SP - 23

EP - 32

JO - Journal of Hospital Infection

JF - Journal of Hospital Infection

ER -

Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals

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