Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15
Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15
复制标题
DOI：
10.3201/eid2403.171499
复制
发表时间：
2018-03-01
影响因子：
11.8
通讯作者：
Hanage, William P.
中科院分区：
文献类型：
--
作者：
MacFadden, Derek R.;McGeer, Allison;Hanage, William P.
目前机构流感暴发的临床定义是否充分尚不清楚。我们对加拿大多伦多 2014-15 流感季节期间发生的机构流感暴发进行了回顾性基因组测序和流行病学分析。我们对长期护理机构 38 个报告的机构暴发病例中每一个最早提交的 2 个甲型 H3N2 流感阳性样本进行了测序。基因组测序显示，使用当前临床定义确定的大多数爆发对都高度相关。监测样本的纳入表明，暴发源可能是来自更广泛的流行谱系的传入。使用大多数基因组和血凝素特异性基因进行的成对距离分析能够确定区分爆发对内和爆发对之间的阈值；曲线下面积范围为0.93-0.95。用于定义长期护理机构中流感爆发的常规基因组测序不太可能显着增加当前的临床定义。测序可能被证明对于调查疫情传入来源最有用。
Adequacy of the current clinical definition of institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic analysis of institutional influenza outbreaks that occurred during the 2014-15 influenza season in Toronto, Canada. We sequenced the 2 earliest submitted samples positive for influenza A(H3N2) from each of 38 reported institutional outbreaks in long-term care facilities. Genome sequencing showed most outbreak pairs identified by using the current clinical definition were highly related. Inclusion of surveillance samples demonstrated that outbreak sources were likely introductions from broader circulating lineages. Pairwise distance analysis using majority genome and hemagglutinin-specific genes enabled identification of thresholds for discrimination of within and between outbreak pairs; the area under the curve ranged 0.93-0.95. Routine genome sequencing for defining influenza outbreaks in long-term care facilities is unlikely to add significantly to the current clinical definition. Sequencing may prove most useful for investigating sources of outbreak introductions.