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

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. Hospita...

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Bibliographic Details
Published in:Genome Biology Vol. 16; no. 1; p. 114
Main Authors: Quick, Joshua, Ashton, Philip, Calus, Szymon, Chatt, Carole, Gossain, Savita, Hawker, Jeremy, Nair, Satheesh, Neal, Keith, Nye, Kathy, Peters, Tansy, De Pinna, Elizabeth, Robinson, Esther, Struthers, Keith, Webber, Mark, Catto, Andrew, Dallman, Timothy J, Hawkey, Peter, Loman, Nicholas J
Format: Journal Article
Language:English
Published: England BioMed Central 30-05-2015
Subjects:
Bioinformatics
Cross Infection - epidemiology
Cross Infection - microbiology
Disease control
Disease Outbreaks
DNA sequencing
Epidemiology
Food contamination & poisoning
Foodborne diseases
Genomes
Hospitalization
Hospitals
Humans
Laboratories
Outbreaks
Patients
Phages
Phylogenetics
Phylogeny
Public health
Salmonella
Salmonella enterica
Salmonella enteritidis - classification
Salmonella enteritidis - genetics
Salmonella enteritidis - isolation & purification
Salmonella Infections - epidemiology
Salmonella Infections - microbiology
Sequence Analysis, DNA - methods
Surveillance
Tuberculosis
United Kingdom > UK
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Summary: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.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-015-0677-2