Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study.
Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study.
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DOI：
10.7554/elife.76854
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发表时间：
2022-07-19
期刊：
影响因子：
7.7
通讯作者：
Harbarth, Stephan
中科院分区：
文献类型：
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作者：
Abbas, Mohamed;Cori, Anne;Cordey, Samuel;Laubscher, Florian;Robalo Nunes, Tomas;Myall, Ashleigh;Salamun, Julien;Huber, Philippe;Zekry, Dina;Prendki, Virginie;Iten, Anne;Vieux, Laure;Sauvan, Valerie;Graf, Christophe E.;Harbarth, Stephan
关键词：
在老年环境中严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）的医院暴发中，关于传播链以及医护人员（HCW）和老年患者各自的作用仍存在不确定性。我们进行了一项回顾性队列研究，包括四个受疫情影响病房的2019年医院内冠状病毒病（COVID-19）患者，以及瑞士大学附属老年急症医院的所有SARS-CoV-2 RT-PCR阳性医护人员，该医院在2020年春季第一波大流行期间收治了COVID-19和非COVID-19患者。我们使用贝叶斯建模框架结合流行病学和基因测序数据，并重建了涉及患者和HCW的SARS-CoV-2的传播动力学，以确定谁感染了谁。我们根据病例类型（在专门的Covid-19聚集病房工作的医务工作者：HCWcovid;在发生疫情的非Covid-19病房工作的医务工作者：HCWexploit;医院内Covid-19患者：patientnoso）评估了一般传播模式，方法是在所有后树中推导出归因于每种病例类型的感染比例，并将其与随机预期进行比较。在研究期间（2020年3月1日至5月7日），我们纳入了180例SARS-CoV-2阳性病例：127名HCW（91名HCW covid，36名HCW爆发）和53名患者。患者的发病率为10%至19%，HCW为21%。我们估计，16例输入性事件的发生具有高置信度（4例患者，12例HCW），共同导致多达41例继发性病例;在另外6例病例（5例HCW，1例患者）中，输入性事件是可能的，后验概率在10%至50%之间。大多数患者间传播事件涉及患者共用病房（95.2%，95%可信区间[CrI] 84.2%-100%），与之相反的是那些共享一个房间（19.7%，95%CrI 6.7%-33.3%）。传播事件倾向于按病例类型聚集：病人被其他病人感染的可能性几乎是预期的两倍（观察：预期比率2.16，95%CrI 1.17-4.20，p=0.006）;同样，HCW爆发被其他HCW爆发感染的可能性是预期的两倍多（2.72，95%CrI 0.87-9.00，p=0.06）。HCWcovid感染者的比例与预期一样随机。我们发现HCW爆发中高传播者（≥2例继发病例）的比例比爆发后期的患者（28.6%对11.8%）更高，尽管这在统计学上并不显著。大多数进口事件与HCW有关。出乎意料的是，HCWcovid之间的传播比患者和HCW暴发之间的传播更有限。这一发现凸显了感染控制方面的差距，并提出了可能的改进领域，以限制医院内传播的程度。这项研究得到了瑞士国家科学基金会NRP 78资助计划（批准号4078P0_198363）的资助。
There is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in geriatric settings. We performed a retrospective cohort study including patients with nosocomial coronavirus disease 2019 (COVID-19) in four outbreak-affected wards, and all SARS-CoV-2 RT-PCR positive HCWs from a Swiss university-affiliated geriatric acute-care hospital that admitted both Covid-19 and non-Covid-19 patients during the first pandemic wave in Spring 2020. We combined epidemiological and genetic sequencing data using a Bayesian modelling framework, and reconstructed transmission dynamics of SARS-CoV-2 involving patients and HCWs, to determine who infected whom. We evaluated general transmission patterns according to case type (HCWs working in dedicated Covid-19 cohorting wards: HCWcovid; HCWs working in non-Covid-19 wards where outbreaks occurred: HCWoutbreak; patients with nosocomial Covid-19: patientnoso) by deriving the proportion of infections attributed to each case type across all posterior trees and comparing them to random expectations. During the study period (1 March to 7 May 2020), we included 180 SARS-CoV-2 positive cases: 127 HCWs (91 HCWcovid, 36 HCWoutbreak) and 53 patients. The attack rates ranged from 10% to 19% for patients, and 21% for HCWs. We estimated that 16 importation events occurred with high confidence (4 patients, 12 HCWs) that jointly led to up to 41 secondary cases; in six additional cases (5 HCWs, 1 patient), importation was possible with a posterior probability between 10% and 50%. Most patient-to-patient transmission events involved patients having shared a ward (95.2%, 95% credible interval [CrI] 84.2%–100%), in contrast to those having shared a room (19.7%, 95% CrI 6.7%–33.3%). Transmission events tended to cluster by case type: patientnoso were almost twice as likely to be infected by other patientnoso than expected (observed:expected ratio 2.16, 95% CrI 1.17–4.20, p=0.006); similarly, HCWoutbreak were more than twice as likely to be infected by other HCWoutbreak than expected (2.72, 95% CrI 0.87–9.00, p=0.06). The proportion of infectors being HCWcovid was as expected as random. We found a trend towards a greater proportion of high transmitters (≥2 secondary cases) among HCWoutbreak than patientnoso in the late phases (28.6% vs. 11.8%) of the outbreak, although this was not statistically significant. Most importation events were linked to HCW. Unexpectedly, transmission between HCWcovid was more limited than transmission between patients and HCWoutbreak. This finding highlights gaps in infection control and suggests the possible areas of improvements to limit the extent of nosocomial transmission. This study was supported by a grant from the Swiss National Science Foundation under the NRP78 funding scheme (Grant no. 4078P0_198363).