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

doi:10.1016/j.jhin.2023.06.005

. 2023 Sep:139:23-32.

doi: 10.1016/j.jhin.2023.06.005. Epub 2023 Jun 10.

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

M Panca¹, J Blackstone², O Stirrup³, M-T Cutino-Moguel⁴, E Thomson⁵, C Peters⁶, L B Snell⁷, G Nebbia⁷, A Holmes⁸, A Chawla⁹, N Machin¹⁰, Y Taha¹¹, T Mahungu¹², T Saluja¹³, T I de Silva¹⁴, K Saeed¹⁵, C Pope¹⁶, G Y Shin¹⁷, R Williams¹⁸, A Darby¹⁹, D L Smith²⁰, M Loose²¹, S C Robson²², K Laing²³, D G Partridge²⁴, J R Price⁸, J Breuer²⁵

Affiliations

¹ Comprehensive Clinical Trials Unit, Institute of Clinical Trials and Methodology, UCL, London, UK. Electronic address: m.panca@ucl.ac.uk.
² Comprehensive Clinical Trials Unit, Institute of Clinical Trials and Methodology, UCL, London, UK.
³ Institute for Global Health, UCL, London, UK.
⁴ Barts Health NHS Trust, London, UK.
⁵ MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
⁶ NHS Greater Glasgow and Clyde, Glasgow, UK.
⁷ Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK.
⁸ Imperial College Healthcare NHS Trust, London, UK.
⁹ Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK.
¹⁰ Manchester University NHS Foundation Trust, Manchester, UK.
¹¹ Departments of Virology and Infectious Diseases, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK.
¹² Royal Free NHS Foundation Trust, London, UK.
¹³ Sandwell and West Birmingham NHS Trust, UK.
¹⁴ Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK.
¹⁵ University Hospital Southampton NHS Foundation Trust, Southampton, UK.
¹⁶ St George's University Hospitals NHS Foundation Trust, London, UK; Institute for Infection and Immunity, St George's University of London, London, UK.
¹⁷ University College London Hospitals NHS Foundation Trust, London, UK.
¹⁸ Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK.
¹⁹ Centre for Genomic Research, University of Liverpool, Liverpool, UK.
²⁰ Department of Applied Sciences, Northumbria University, Newcastle, UK.
²¹ School of Life Sciences, University of Nottingham, Nottingham, UK.
²² Centre for Enzyme Innovation & School of Pharmacy and Biomedical Science, University of Portsmouth, Portsmouth, UK.
²³ Institute for Infection and Immunity, St George's University of London, London, UK.
²⁴ Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.
²⁵ Department of Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, UCL, London, UK.

PMID: 37308063
PMCID: PMC10257337
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

M Panca et al. J Hosp Infect. 2023 Sep.

. 2023 Sep:139:23-32.

doi: 10.1016/j.jhin.2023.06.005. Epub 2023 Jun 10.

Authors

Affiliations

¹ Comprehensive Clinical Trials Unit, Institute of Clinical Trials and Methodology, UCL, London, UK. Electronic address: m.panca@ucl.ac.uk.
² Comprehensive Clinical Trials Unit, Institute of Clinical Trials and Methodology, UCL, London, UK.
³ Institute for Global Health, UCL, London, UK.
⁴ Barts Health NHS Trust, London, UK.
⁵ MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
⁶ NHS Greater Glasgow and Clyde, Glasgow, UK.
⁷ Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK.
⁸ Imperial College Healthcare NHS Trust, London, UK.
⁹ Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK.
¹⁰ Manchester University NHS Foundation Trust, Manchester, UK.
¹¹ Departments of Virology and Infectious Diseases, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK.
¹² Royal Free NHS Foundation Trust, London, UK.
¹³ Sandwell and West Birmingham NHS Trust, UK.
¹⁴ Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK.
¹⁵ University Hospital Southampton NHS Foundation Trust, Southampton, UK.
¹⁶ St George's University Hospitals NHS Foundation Trust, London, UK; Institute for Infection and Immunity, St George's University of London, London, UK.
¹⁷ University College London Hospitals NHS Foundation Trust, London, UK.
¹⁸ Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK.
¹⁹ Centre for Genomic Research, University of Liverpool, Liverpool, UK.
²⁰ Department of Applied Sciences, Northumbria University, Newcastle, UK.
²¹ School of Life Sciences, University of Nottingham, Nottingham, UK.
²² Centre for Enzyme Innovation & School of Pharmacy and Biomedical Science, University of Portsmouth, Portsmouth, UK.
²³ Institute for Infection and Immunity, St George's University of London, London, UK.
²⁴ Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.
²⁵ Department of Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, UCL, London, UK.

PMID: 37308063
PMCID: PMC10257337
DOI: 10.1016/j.jhin.2023.06.005

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.

Keywords: COVID-19; Cost; Healthcare-associated infection; Infection prevention and control; Micro-costing; SARS-CoV-2.

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References

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[1] Bhattacharya A., Collin S.M., Stimson J., Thelwall S., Nsonwu O., Gerver S., et al. Healthcare-associated COVID-19 in England: A national data linkage study. J Infect. 2021;83:565–572. doi: 10.1016/j.jinf.2021.08.039. - DOI - PMC - PubMed

[2] Bhattacharya A., Collin S.M., Stimson J., Thelwall S., Nsonwu O., Gerver S., et al. Healthcare-associated COVID-19 in England: A national data linkage study. J Infect. 2021;83:565–572. doi: 10.1016/j.jinf.2021.08.039. - DOI - PMC - PubMed

[3] Ngandu N.K., Mmotsa T.M., Dassaye R., Thabetha A., Odendaal W., Langdown N., Ndwandwe D. Hospital acquired COVID-19 infections amongst patients before the rollout of COVID-19 vaccinations, a scoping review. BMC Infect Dis. 2022;22:140. doi: 10.1186/s12879-022-07128-5. - DOI - PMC - PubMed

[4] Ngandu N.K., Mmotsa T.M., Dassaye R., Thabetha A., Odendaal W., Langdown N., Ndwandwe D. Hospital acquired COVID-19 infections amongst patients before the rollout of COVID-19 vaccinations, a scoping review. BMC Infect Dis. 2022;22:140. doi: 10.1186/s12879-022-07128-5. - DOI - PMC - PubMed

[5] Ajayi B., Trompeter A.J., Umarji S., Saha P., Arnander M., Lui D.F. Catching the second wave: clinical characteristics and nosocomial infection rates in major trauma and orthopaedic patients during the COVID-19 pandemic. Bone Jt Open. 2021;2:661–670. doi: 10.1302/2633-1462.28. - DOI - PMC - PubMed

[6] Ajayi B., Trompeter A.J., Umarji S., Saha P., Arnander M., Lui D.F. Catching the second wave: clinical characteristics and nosocomial infection rates in major trauma and orthopaedic patients during the COVID-19 pandemic. Bone Jt Open. 2021;2:661–670. doi: 10.1302/2633-1462.28. - DOI - PMC - PubMed

[7] Collins AS. Preventing Health Care–Associated Infections. In: Hughes RG, editor. Patient Safety and Quality: An Evidence-Based Handbook for Nurses. Rockville (MD): Agency for Healthcare Research and Quality (US); 2008 Apr. Chapter 41. - PubMed

[8] Collins AS. Preventing Health Care–Associated Infections. In: Hughes RG, editor. Patient Safety and Quality: An Evidence-Based Handbook for Nurses. Rockville (MD): Agency for Healthcare Research and Quality (US); 2008 Apr. Chapter 41. - PubMed

[9] Manoukian S., Stewart S., Graves N., Mason M., Robertson C., Kennedy S., et al. Bed-days and costs associated with the inpatient burden of healthcare-associated infection in the UK. Journal of Hospital Infection. 2021;114:43–50. doi: 10.1016/j.jhin.2020.12.027. - DOI - PubMed

[10] Manoukian S., Stewart S., Graves N., Mason M., Robertson C., Kennedy S., et al. Bed-days and costs associated with the inpatient burden of healthcare-associated infection in the UK. Journal of Hospital Infection. 2021;114:43–50. doi: 10.1016/j.jhin.2020.12.027. - DOI - PubMed

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

Affiliations

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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Abstract

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