Abstract 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 …

In this study we investigated the use of both the MiSeq and the MinION to provide clinically
relevant information during an ongoing local hospital outbreak of Salmonella enterica
Serovar Enteritidis. During the outbreak we sequenced 16 isolates using a 6 hour MiSeq
'draft sequencing'protocol we developed to quickly rule isolates in or out of the outbreak.
Later we sequenced two isolates on the MinION, one known to be from