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

• DOI: 10.1186/s13059-015-0677-2
• Publication Date: 2015-05-29T11:09:03Z
• 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
• Keywords: Cross Infection/epidemiology; Cross Infection; 0303 health sciences; Research; 610; Salmonella Infections/epidemiology; Sequence Analysis, DNA; Salmonella enteritidis/classification; Disease Outbreaks; 3. Good health; DNA/methods; Hospitalization; 03 medical and health sciences; SDG 3 - Good Health and Well-being; Salmonella enteritidis; Salmonella Infections; Humans; Sequence Analysis

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 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.