Elliott Thomas M, Harris Patrick N, Roberts Leah W, Doidge Michelle, Hurst Trish, Hajkowicz Krispin, Forde Brian, Paterson David L, Gordon Louisa G
QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
The University of Queensland, Centre for Clinical Research, Herston, Brisbane, Queensland, Australia.
Antimicrob Steward Healthc Epidemiol. 2021 Dec 13;1(1):e62. doi: 10.1017/ash.2021.233. eCollection 2021.
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 (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.
全基因组测序（WGS）鸟枪法宏基因组学（宏基因组学）试图直接从样本中对整个遗传内容进行测序。其诊断优势在于能够检测出未被怀疑、无法培养或生长非常缓慢的生物体。
评估在一家大型都市医院中使用WGS和宏基因组学进行疫情管理的临床和经济效果。
成本效益研究。
大型都市医院的重症监护病房和烧伤病房。
模拟的重症监护病房和烧伤病房患者。
我们构建了一个复杂的模拟模型，以估计耐碳青霉烯类鲍曼不动杆菌（CRAB）爆发的32个月期间病原体传播情况、相关医院成本以及质量调整生命年（QALY）。模型参数通过微生物监测数据、基因组测序结果、医院入院数据库和当地临床知识来确定。该模型针对重症监护病房和烧伤病房内实际的病原体传播情况进行了校准（情景1），并与早期使用WGS（情景2）以及早期使用WGS和宏基因组学（情景3）进行比较，以确定它们各自的成本效益。进行了敏感性分析以解决模型的不确定性问题。
与情景1相比，情景2平均导致CRAB患者减少14例，QALY增加59个，成本节省75,099美元。与情景1相比，情景3导致CRAB患者减少18例，QALY增加74个，医院成本节省93,822美元。情景2和情景3具有成本效益的可能性分别为57%和60%。
预计在感染控制过程中使用WGS和宏基因组学将产生良好的经济和临床效果。
