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Genome Biol. 2015 May 30;16:114. doi: 10.1186/s13059-015-0677-2.

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

Author information

1
Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. j.quick@bham.ac.uk.
2
NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK. j.quick@bham.ac.uk.
3
Public Health England, Colindale, London, UK. philip.ashton@phe.gov.uk.
4
Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. s.t.calus@bham.ac.uk.
5
NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK. s.t.calus@bham.ac.uk.
6
Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK. carol.chatt@phe.gov.uk.
7
Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK. savita.gossain@heartofengland.nhs.uk.
8
Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK. Jeremy.Hawker@phe.gov.uk.
9
Public Health England, Colindale, London, UK. satheesh.nair@phe.gov.uk.
10
Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK. Keith.Neal@phe.gov.uk.
11
Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK. Kathy.Nye@phe.gov.uk.
12
Public Health England, Colindale, London, UK. Tansy.Peters@phe.gov.uk.
13
Public Health England, Colindale, London, UK. Elizabeth.DePinna@phe.gov.uk.
14
Department of Microbiology, University of Warwick, Warwick, UK. E.R.Robinson@warwick.ac.uk.
15
Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK. keith.struthers@uhcw.nhs.uk.
16
NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK. m.a.webber@bham.ac.uk.
17
Medical Directorate, Heart of England NHS Trust, Birmingham, UK. andrew.catto@heartofengland.nhs.uk.
18
Public Health England, Colindale, London, UK. Tim.Dallman@phe.gov.uk.
19
Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. peter.hawkey@heartofengland.nhs.uk.
20
Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK. peter.hawkey@heartofengland.nhs.uk.
21
Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. n.j.loman@bham.ac.uk.

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.

PMID:
26025440
PMCID:
PMC4702336
DOI:
10.1186/s13059-015-0677-2
[Indexed for MEDLINE]
Free PMC Article

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