快速 SARS-CoV-2 基因组测序在支持医院获得性 COVID-19 感染的感染控制中的有效性：多中心前瞻性研究。

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.

机构信息

Institute for Global Health, University College London, London, United Kingdom.

The Comprehensive Clinical Trials Unit, University College London, London, United Kingdom.

出版信息

Elife. 2022 Sep 13;11:e78427. doi: 10.7554/eLife.78427.

BACKGROUND

Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.

METHODS

We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated.

RESULTS

A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p0.14) or rapid (0.85, 0.48-1.50; p0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.

CONCLUSIONS

While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.

FUNDING

COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute.

CLINICAL TRIAL NUMBER

NCT04405934.

背景

对 SARS-CoV-2 的病毒测序已被用于暴发调查，但支持在医院环境中常规用于感染预防和控制（IPC）的证据有限。

方法

我们在 14 家英国急性医院信托机构进行了一项前瞻性非随机试验，对测序进行了研究。各研究点均有为期 4 周的基线数据收集期，随后进行干预期，包括使用序列报告工具（SRT）进行 8 周的“快速”（<48 小时）和 4 周的“较长周转时间”（5-10 天）测序。收集所有医院获得性 COVID-19 感染（HOCI；入院后≥48 小时检测到）的数据。评估测序干预对 IPC 知识和行动以及可能/确定的医院获得性感染（HAI）发病率的影响。

结果

2020 年 10 月至 2021 年 4 月期间共记录了 2170 例 HOCI 病例，对应于卫生服务极度紧张的时期，干预期间共返回了 650/1320 例（49.2%）的序列报告。我们没有发现较长周转时间（发病率比 1.60，95%CI 0.85-3.01；p0.14）或快速（0.85，0.48-1.50；p0.54）干预阶段的 HAI 每周发病率有统计学意义的变化与基线阶段相比。然而，在快速和较长周转时间阶段，分别有 7.8%和 7.4%的所有 HOCI 病例以及报告返回的病例改变了 IPC 实践。在一项“按方案”敏感性分析中，当 SRT 报告在 5 天内返回时，20.7%的 HOCI 病例对 IPC 措施产生了影响。由于病例数量和资源有限，大多数站点都无法有效应对测序结果。