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


Date: 14th January 2015 | Source: Genome Biology

Authors: Joshua Quick, Philip Ashton, Szymon Calus, Carole Chatt, Savita Gossain, Jeremy Hawker, Satheesh Nair, Keith Neal, Kathy Nye, Tansy Peters, Elizabeth De Pinna, Esther Robinson, Keith Struthers, Mark Webber, Andrew Catto, Timothy J. Dallman, Peter Hawkey, Nicholas J. Loman.

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. 

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