Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.
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DOI：
10.1186/s13059-015-0677-2
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发表时间：
2015-05-30
期刊：
影响因子：
12.3
通讯作者：
Loman NJ
中科院分区：
文献类型：
--
作者：
Quick J;Ashton P;Calus S;Chatt C;Gossain S;Hawker J;Nair S;Neal K;Nye K;Peters T;De Pinna E;Robinson E;Struthers K;Webber M;Catto A;Dallman TJ;Hawkey P;Loman NJ
沙门氏菌的食源性爆发仍然是一个紧迫的公共卫生问题。我们最近检测到肠道沙门氏菌血清型肠道噬菌体14b型的大爆发，影响了我们医院的30多名患者。这次疫情与社区、国家和欧洲范围的病例有关。沙门氏菌的医院患者处于高风险状态，需要快速反应。我们最初使用Illumina MiSeq上的一种新的快速方案通过全基因组测序来调查这次疫情;然后我们将这些数据与来自监测测序的全基因组数据进行整合，从而将疫情置于全国范围内。此外，我们还研究了新发布的测序技术（来自Oxford Nanopore Technologies的MinION）在医院沙门氏菌爆发管理中的潜力。我们证明，与标准测序方案相比，快速MiSeq测序可以减少回答时间，而不会对结果产生影响。我们第一次证明，MinION可以在真实的时间内和DNA文库加载后的几分钟内获得临床相关信息。MinION测序允许在20分钟内确定物种水平。使用一种新的流式系统发育定位方法，样品可以在40分钟内分配到一个血清型，并确定在不到2小时的爆发的一部分。这两种方法在不到半天的时间内就产生了关于沙门氏菌爆发的可靠和可操作的临床信息。迅速提供这类信息可能有助于更知情的流行病学调查，并影响感染控制做法。本文的在线版本（doi：10.1186/s13059 - 015 - 0677 - 2）包含补充材料，可供授权用户使用。
Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patients with Salmonella are at high risk, and require a rapid response. We initially investigated this outbreak by whole-genome sequencing using a novel rapid protocol on the Illumina MiSeq; we then integrated these data with whole-genome data from surveillance sequencing, thereby placing the outbreak in a national context. Additionally, we investigated the potential of a newly released sequencing technology, the MinION from Oxford Nanopore Technologies, in the management of a hospital outbreak of Salmonella. We demonstrate that rapid MiSeq sequencing can reduce the time to answer compared to the standard sequencing protocol with no impact on the results. We show, for the first time, that the MinION can acquire clinically relevant information in real time and within minutes of a DNA library being loaded. MinION sequencing permits confident assignment to species level within 20 min. Using a novel streaming phylogenetic placement method samples can be assigned to a serotype in 40 min and determined to be part of the outbreak in less than 2 h. Both approaches yielded reliable and actionable clinical information on the Salmonella outbreak in less than half a day. The rapid availability of such information may facilitate more informed epidemiological investigations and influence infection control practices. The online version of this article (doi:10.1186/s13059-015-0677-2) contains supplementary material, which is available to authorized users.