Abstract
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. To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital. Cost-effectiveness study. Intensive care unit and burn unit of large metropolitan hospital. Simulated intensive care unit and burn unit patients. 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. 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. The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes.
Highlights
Whole-genome sequencing (WGS) shotgun metagenomics attempts to sequence the entire genetic content straight from the sample
Active transmission of 17 cases of sequence type (ST) 1050 (ST1050) carbapenem-resistant A. baumannii (CRAB) were identified between May and August 2016; 6 cases were identified between December 2016 and August 2017; and 8 cases were identified between May and August 2018 (Fig. 1).[16]
In scenario 1, the infection control team detected on average 30 (IQR, 3–39) patients with CRAB, accrued total hospital costs of AU$1,608,571 (US$1,093,828) (IQR, AU$1,421,564, AU $1,677,308; US$966,664, US$1,140,569) and 6,578 quality-adjusted life years (QALYs) (IQR, 6,476, 6,707) (Table 2). This compares with Scenario 2 outcomes of 14 fewer patients with CRAB, 59 additional QALYs and AU $75,099 (US$51,067) cost savings
Summary
Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Objective: To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital. Setting: Intensive care unit and burn unit of large metropolitan hospital. 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). 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. 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. Conclusions: The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes. (Received 16 August 2021; accepted 25 October 2021)
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