Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction.
Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction.
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SARS-COV-2在康复诊所的爆炸性医学院爆发：爆发重建的基因组学的局限性。
DOI：
10.1016/j.jhin.2021.07.013
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发表时间：
2021-11
期刊：
影响因子：
--
通讯作者：
Harbarth S
中科院分区：
文献类型：
--
作者：
Abbas M;Robalo Nunes T;Cori A;Cordey S;Laubscher F;Baggio S;Jombart T;Iten A;Vieux L;Teixeira D;Perez M;Pittet D;Frangos E;Graf CE;Zingg W;Harbarth S
尽管采取了常规的感染控制措施，但严重急性呼吸综合征冠状病毒-2(SARS-CoV-2)在医院内的暴发仍很频繁。使用先进的基因组和统计技术进行了暴发调查，以重建可能的传播链，并评估医护人员在SARS-CoV-2传播中的作用。对一所大学附属康复诊所发生的SARS-CoV-2院内暴发疫情进行了调查，涉及患者和医务工作者，病原体全基因组序列(WGS)覆盖率很高。从流行病学数据(RT)估计随时间变化的繁殖数，并使用最大似然系统发育来评估病原体的遗传多样性。将基因组和流行病学数据结合到贝叶斯框架中以模拟传播的方向性，并进行病例对照研究以调查患者院内感染SARS-CoV-2的危险因素。疫情从2020年3月14日持续到4月12日，涉及37名患者(31名WGS)和39名雇员(31名WGS)，其中37人是卫生工作者。峰值RT估计在2.2到3.6之间。系统进化树显示了非常有限的遗传多样性，62个分离物中有60个(96.7%)形成了一大群相同的基因组。尽管在重建的传播事件中产生了不确定性，但分析表明，卫生工作者(其中一例是指示病例)在交叉传播中发挥了重要作用，鉴于卫生工作者病例的数量(46.7%)，可归因于卫生工作者的感染(P<；2.2e-16)的比例(70.7%)比预期的要大得多。考虑到感染患者[79.0%；95%可信区间(CI)78.5~79.5%]和虚弱患者(临床虚弱评定量表评分5；82.3%；95%可信区间81.8~83.4%)，来自医务工作者的超额传播率较高。此外，虚弱的患者比其他患者发生医院内新冠肺炎的风险更大(调整后的优势比为6.94，95%可信区间为2.13-22.57)。这份疫情报告强调了卫生工作者在卫生保健环境中SARS-CoV-2传播动态中的重要作用。病原体基因组中有限的遗传多样性阻碍了个体传播事件的重建，导致对谁感染谁的不确定性很大。然而，这项研究表明，尽管存在这种不确定性，但可以观察到显著的传播模式。
Nosocomial outbreaks of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are frequent despite implementation of conventional infection control measures. An outbreak investigation was undertaken using advanced genomic and statistical techniques to reconstruct likely transmission chains and assess the role of healthcare workers (HCWs) in SARS-CoV-2 transmission. A nosocomial SARS-CoV-2 outbreak in a university-affiliated rehabilitation clinic was investigated, involving patients and HCWs, with high coverage of pathogen whole-genome sequences (WGS). The time-varying reproduction number from epidemiological data (Rt) was estimated, and maximum likelihood phylogeny was used to assess genetic diversity of the pathogen. Genomic and epidemiological data were combined into a Bayesian framework to model the directionality of transmission, and a case–control study was performed to investigate risk factors for nosocomial SARS-CoV-2 acquisition in patients. The outbreak lasted from 14th March to 12th April 2020, and involved 37 patients (31 with WGS) and 39 employees (31 with WGS), 37 of whom were HCWs. Peak Rt was estimated to be between 2.2 and 3.6. The phylogenetic tree showed very limited genetic diversity, with 60 of 62 (96.7%) isolates forming one large cluster of identical genomes. Despite the resulting uncertainty in reconstructed transmission events, the analyses suggest that HCWs (one of whom was the index case) played an essential role in cross-transmission, with a significantly greater fraction of infections (P<2.2e-16) attributable to HCWs (70.7%) than expected given the number of HCW cases (46.7%). The excess of transmission from HCWs was higher when considering infection of patients [79.0%; 95% confidence interval (CI) 78.5–79.5%] and frail patients (Clinical Frailty Scale score >5; 82.3%; 95% CI 81.8–83.4%). Furthermore, frail patients were found to be at greater risk for nosocomial COVID-19 than other patients (adjusted odds ratio 6.94, 95% CI 2.13–22.57). This outbreak report highlights the essential role of HCWs in SARS-CoV-2 transmission dynamics in healthcare settings. Limited genetic diversity in pathogen genomes hampered the reconstruction of individual transmission events, resulting in substantial uncertainty in who infected whom. However, this study shows that despite such uncertainty, significant transmission patterns can be observed.
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DOI：
10.1093/cid/ciab281
发表时间：
2021-09-15
期刊：
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
影响因子：
--
作者：
Braun KM;Moreno GK;Buys A;Somsen ED;Bobholz M;Accola MA;Anderson L;Rehrauer WM;Baker DA;Safdar N;Lepak AJ;O'Connor DH;Friedrich TC
通讯作者：
Friedrich TC
影响因子：
5.5
作者：
Abbas M;Robalo Nunes T;Martischang R;Zingg W;Iten A;Pittet D;Harbarth S
通讯作者：
Harbarth S
影响因子：
33.9
作者：
Dora, Amy, V;Winnett, Alexander;Goetz, Matthew B.
通讯作者：
Goetz, Matthew B.
影响因子：
33.9
作者：
Taylor, Joanne;Carter, Rosalind J.;Lynfield, Ruth
通讯作者：
Lynfield, Ruth
影响因子：
3
作者：
Campbell F;Didelot X;Fitzjohn R;Ferguson N;Cori A;Jombart T
通讯作者：
Jombart T