Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii
Abstract Background: Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Diagnostic advantages lie in the ability to detect unsuspected, uncultivatable, or very slow-growing organisms. Objective: To evaluate...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Cambridge University Press
2021-01-01
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| Series: | Antimicrobial Stewardship & Healthcare Epidemiology |
| Online Access: | https://www.cambridge.org/core/product/identifier/S2732494X21002333/type/journal_article |
| _version_ | 1811157244608249856 |
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| author | Thomas M. Elliott Patrick N. Harris Leah W. Roberts Michelle Doidge Trish Hurst Krispin Hajkowicz Brian Forde David L. Paterson Louisa G. Gordon |
| author_facet | Thomas M. Elliott Patrick N. Harris Leah W. Roberts Michelle Doidge Trish Hurst Krispin Hajkowicz Brian Forde David L. Paterson Louisa G. Gordon |
| author_sort | Thomas M. Elliott |
| collection | DOAJ |
| description |
Abstract
Background:
Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Diagnostic advantages lie in the ability to detect unsuspected, uncultivatable, or very slow-growing organisms.
Objective:
To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital.
Design:
Cost-effectiveness study.
Setting:
Intensive care unit and burn unit of large metropolitan hospital.
Patients:
Simulated intensive care unit and burn unit patients.
Methods:
We built a complex simulation model to estimate pathogen transmission, associated hospital costs, and quality-adjusted life years (QALYs) during a 32-month outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB). Model parameters were determined using microbiology surveillance data, genome sequencing results, hospital admission databases, and local clinical knowledge. The model was calibrated to the actual pathogen spread within the intensive care unit and burn unit (scenario 1) and compared with early use of WGS (scenario 2) and early use of WGS and metagenomics (scenario 3) to determine their respective cost-effectiveness. Sensitivity analyses were performed to address model uncertainty.
Results:
On average compared with scenario 1, scenario 2 resulted in 14 fewer patients with CRAB, 59 additional QALYs, and $75,099 cost savings. Scenario 3, compared with scenario 1, resulted in 18 fewer patients with CRAB, 74 additional QALYs, and $93,822 in hospital cost savings. The likelihoods that scenario 2 and scenario 3 were cost-effective were 57% and 60%, respectively.
Conclusions:
The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes.
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| first_indexed | 2024-04-10T05:03:57Z |
| format | Article |
| id | doaj.art-a534bbbda1f648a4adbf02e718f87ad9 |
| institution | Directory Open Access Journal |
| issn | 2732-494X |
| language | English |
| last_indexed | 2024-04-10T05:03:57Z |
| publishDate | 2021-01-01 |
| publisher | Cambridge University Press |
| record_format | Article |
| series | Antimicrobial Stewardship & Healthcare Epidemiology |
| spelling | doaj.art-a534bbbda1f648a4adbf02e718f87ad92023-03-09T12:27:47ZengCambridge University PressAntimicrobial Stewardship & Healthcare Epidemiology2732-494X2021-01-01110.1017/ash.2021.233Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumanniiThomas M. Elliott0https://orcid.org/0000-0002-7702-7688Patrick N. Harris1https://orcid.org/0000-0002-2895-0345Leah W. Roberts2https://orcid.org/0000-0002-1024-0564Michelle Doidge3Trish Hurst4Krispin Hajkowicz5Brian Forde6https://orcid.org/0000-0002-2264-4785David L. Paterson7Louisa G. Gordon8https://orcid.org/0000-0002-3159-4249QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, AustraliaThe University of Queensland, Centre for Clinical Research, Herston, Brisbane, Queensland, Australia Central Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Brisbane, Queensland, AustraliaSchool of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United KingdomInfectious Diseases Unit, Royal Brisbane and Womens’ Hospital, Herston, Brisbane, Queensland, AustraliaInfectious Diseases Unit, Royal Brisbane and Womens’ Hospital, Herston, Brisbane, Queensland, AustraliaCentral Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Brisbane, Queensland, Australia Infectious Diseases Unit, Royal Brisbane and Womens’ Hospital, Herston, Brisbane, Queensland, AustraliaThe University of Queensland, Centre for Clinical Research, Herston, Brisbane, Queensland, Australia School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, AustraliaThe University of Queensland, Centre for Clinical Research, Herston, Brisbane, Queensland, AustraliaQIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia The University of Queensland, School of Public Health, Brisbane, Queensland, Australia Queensland University of Technology, School of Nursing, Kelvin Grove, Brisbane, Queensland, Australia Abstract Background: Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Diagnostic advantages lie in the ability to detect unsuspected, uncultivatable, or very slow-growing organisms. Objective: To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital. Design: Cost-effectiveness study. Setting: Intensive care unit and burn unit of large metropolitan hospital. Patients: Simulated intensive care unit and burn unit patients. Methods: We built a complex simulation model to estimate pathogen transmission, associated hospital costs, and quality-adjusted life years (QALYs) during a 32-month outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB). Model parameters were determined using microbiology surveillance data, genome sequencing results, hospital admission databases, and local clinical knowledge. The model was calibrated to the actual pathogen spread within the intensive care unit and burn unit (scenario 1) and compared with early use of WGS (scenario 2) and early use of WGS and metagenomics (scenario 3) to determine their respective cost-effectiveness. Sensitivity analyses were performed to address model uncertainty. Results: On average compared with scenario 1, scenario 2 resulted in 14 fewer patients with CRAB, 59 additional QALYs, and $75,099 cost savings. Scenario 3, compared with scenario 1, resulted in 18 fewer patients with CRAB, 74 additional QALYs, and $93,822 in hospital cost savings. The likelihoods that scenario 2 and scenario 3 were cost-effective were 57% and 60%, respectively. Conclusions: The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes. https://www.cambridge.org/core/product/identifier/S2732494X21002333/type/journal_article |
| spellingShingle | Thomas M. Elliott Patrick N. Harris Leah W. Roberts Michelle Doidge Trish Hurst Krispin Hajkowicz Brian Forde David L. Paterson Louisa G. Gordon Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii Antimicrobial Stewardship & Healthcare Epidemiology |
| title | Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii |
| title_full | Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii |
| title_fullStr | Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii |
| title_full_unstemmed | Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii |
| title_short | Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii |
| title_sort | cost effectiveness analysis of whole genome sequencing during an outbreak of carbapenem resistant acinetobacter baumannii |
| url | https://www.cambridge.org/core/product/identifier/S2732494X21002333/type/journal_article |
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