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Whole-genome enrichment and sequencing of Chlamydia trachomatisdirectly from clinical samples

Overview of attention for article published in BMC Infectious Diseases, November 2014
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (61st percentile)
  • Good Attention Score compared to outputs of the same age and source (65th percentile)

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4 tweeters

Citations

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43 Dimensions

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47 Mendeley
Title
Whole-genome enrichment and sequencing of Chlamydia trachomatisdirectly from clinical samples
Published in
BMC Infectious Diseases, November 2014
DOI 10.1186/s12879-014-0591-3
Pubmed ID
Authors

Mette T Christiansen, Amanda C Brown, Samit Kundu, Helena J Tutill, Rachel Williams, Julianne R Brown, Jolyon Holdstock, Martin J Holland, Simon Stevenson, Jayshree Dave, CY William Tong, Katja Einer-Jensen, Daniel P Depledge, Judith Breuer

Abstract

Background Chlamydia trachomatis is a pathogen of worldwide importance, causing more than 100 million cases of sexually transmitted infections annually. Whole-genome sequencing is a powerful high resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The objective of this study was to perform whole-genome enrichment and sequencing of C. trachomatis directly from clinical samples.Methods C. trachomatis positive samples comprising seven vaginal swabs and three urine samples were sequenced without prior in vitro culture in addition to nine cultured C. trachomatis samples, representing different serovars. A custom capture RNA bait set, that captures all known diversity amongst C. trachomatis genomes, was used in a whole-genome enrichment step during library preparation to enrich for C. trachomatis DNA. All samples were sequenced on the MiSeq platform.ResultsFull length C. trachomatis genomes (>95-100% coverage of a reference genome) were successfully generated for eight of ten clinical samples and for all cultured samples. The proportion of reads mapping to C. trachomatis and the mean read depth across each genome were strongly linked to the number of bacterial copies within the original sample. Phylogenetic analysis confirmed the known population structure and the data showed potential for identification of minority variants and mutations associated with antimicrobial resistance. The sensitivity of the method was >10-fold higher than other reported methodologies.ConclusionsThe combination of whole-genome enrichment and deep sequencing has proven to be a non-mutagenic approach, capturing all known variation found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 47 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Sweden 1 2%
Unknown 46 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 16 34%
Student > Ph. D. Student 8 17%
Student > Master 7 15%
Lecturer > Senior Lecturer 3 6%
Student > Postgraduate 3 6%
Other 9 19%
Unknown 1 2%
Readers by discipline Count As %
Agricultural and Biological Sciences 20 43%
Biochemistry, Genetics and Molecular Biology 12 26%
Immunology and Microbiology 5 11%
Medicine and Dentistry 5 11%
Nursing and Health Professions 1 2%
Other 2 4%
Unknown 2 4%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 25 September 2015.
All research outputs
#2,349,670
of 6,399,176 outputs
Outputs from BMC Infectious Diseases
#1,073
of 2,976 outputs
Outputs of similar age
#57,414
of 155,813 outputs
Outputs of similar age from BMC Infectious Diseases
#56
of 184 outputs
Altmetric has tracked 6,399,176 research outputs across all sources so far. This one has received more attention than most of these and is in the 61st percentile.
So far Altmetric has tracked 2,976 research outputs from this source. They receive a mean Attention Score of 3.3. This one has gotten more attention than average, scoring higher than 60% 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 155,813 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 61% of its contemporaries.
We're also able to compare this research output to 184 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 65% of its contemporaries.