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

Overview of attention for article published in Genome Biology, May 2015
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (98th percentile)
  • High Attention Score compared to outputs of the same age and source (93rd percentile)

Mentioned by

news
2 news outlets
blogs
3 blogs
twitter
128 X users
patent
1 patent
facebook
2 Facebook pages
googleplus
1 Google+ user

Citations

dimensions_citation
270 Dimensions

Readers on

mendeley
564 Mendeley
citeulike
1 CiteULike
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Title
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
Published in
Genome Biology, May 2015
DOI 10.1186/s13059-015-0677-2
Pubmed ID
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

Abstract

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 minutes. Using a novel streaming phylogenetic placement method samples can be assigned to a serotype in 40 minutes 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.

X Demographics

X Demographics

The data shown below were collected from the profiles of 128 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 564 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 6 1%
United States 4 <1%
Brazil 3 <1%
Netherlands 2 <1%
India 1 <1%
Germany 1 <1%
Portugal 1 <1%
New Zealand 1 <1%
Argentina 1 <1%
Other 6 1%
Unknown 538 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 112 20%
Researcher 110 20%
Student > Master 84 15%
Student > Bachelor 62 11%
Other 27 5%
Other 95 17%
Unknown 74 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 171 30%
Biochemistry, Genetics and Molecular Biology 144 26%
Medicine and Dentistry 42 7%
Immunology and Microbiology 30 5%
Computer Science 24 4%
Other 64 11%
Unknown 89 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 114. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 24 November 2022.
All research outputs
#366,885
of 25,405,598 outputs
Outputs from Genome Biology
#175
of 4,471 outputs
Outputs of similar age
#3,884
of 280,724 outputs
Outputs of similar age from Genome Biology
#5
of 65 outputs
Altmetric has tracked 25,405,598 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 98th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,471 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. This one has done particularly well, scoring higher than 96% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 280,724 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 98% of its contemporaries.
We're also able to compare this research output to 65 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 93% of its contemporaries.