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Background  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 .    Results  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.    Conclusions  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.    Electronic supplementary material  The online version of this article (doi:10.1186/s13059-015-0677-2) contains supplementary material, which is available to authorized users.

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella