Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
Identifieur interne : 000641 ( Ncbi/Checkpoint ); précédent : 000640; suivant : 000642Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
Auteurs : Joshua Quick ; Philip Ashton [Royaume-Uni] ; Szymon Calus ; Carole Chatt [Royaume-Uni] ; Savita Gossain [Royaume-Uni] ; Jeremy Hawker [Royaume-Uni] ; Satheesh Nair [Royaume-Uni] ; Keith Neal [Royaume-Uni] ; Kathy Nye [Royaume-Uni] ; Tansy Peters [Royaume-Uni] ; Elizabeth De Pinna [Royaume-Uni] ; Esther Robinson [Royaume-Uni] ; Keith Struthers [Royaume-Uni] ; Mark Webber ; Andrew Catto [Royaume-Uni] ; Timothy J. Dallman [Royaume-Uni] ; Peter Hawkey [Royaume-Uni] ; Nicholas J. LomanSource :
- Genome Biology [ 1474-7596 ] ; 2015.
Abstract
Foodborne outbreaks of
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
The online version of this article (doi:10.1186/s13059-015-0677-2) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13059-015-0677-2
PubMed: 26025440
PubMed Central: 4702336
Affiliations:
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PMC:4702336Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of <italic>Salmonella</italic>
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<author><name sortKey="Gossain, Savita" sort="Gossain, Savita" uniqKey="Gossain S" first="Savita" last="Gossain">Savita Gossain</name>
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<author><name sortKey="De Pinna, Elizabeth" sort="De Pinna, Elizabeth" uniqKey="De Pinna E" first="Elizabeth" last="De Pinna">Elizabeth De Pinna</name>
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<author><name sortKey="Hawkey, Peter" sort="Hawkey, Peter" uniqKey="Hawkey P" first="Peter" last="Hawkey">Peter Hawkey</name>
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</author>
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<series><title level="j">Genome Biology</title>
<idno type="ISSN">1474-7596</idno>
<idno type="eISSN">1474-760X</idno>
<imprint><date when="2015">2015</date>
</imprint>
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<profileDesc><textClass></textClass>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Foodborne outbreaks of <italic>Salmonella</italic>
remain a pressing public health concern. We recently detected a large outbreak of <italic>Salmonella enterica</italic>
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 <italic>Salmonella</italic>
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 <italic>Salmonella</italic>
.</p>
</sec>
<sec><title>Results</title>
<p>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.</p>
</sec>
<sec><title>Conclusions</title>
<p>Both approaches yielded reliable and actionable clinical information on the <italic>Salmonella</italic>
outbreak in less than half a day. The rapid availability of such information may facilitate more informed epidemiological investigations and influence infection control practices.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s13059-015-0677-2) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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</TEI>
<affiliations><list><country><li>Royaume-Uni</li>
</country>
<region><li>Angleterre</li>
<li>Grand Londres</li>
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</tree>
</affiliations>
</record>
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