| 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. |
X Demographics
The data shown below were collected from the profiles of 4 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Spain | 1 | 25% |
| Unknown | 3 | 75% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 4 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 78 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Sweden | 1 | 1% |
| Unknown | 77 | 99% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 22 | 28% |
| Student > Ph. D. Student | 10 | 13% |
| Student > Master | 9 | 12% |
| Student > Bachelor | 6 | 8% |
| Student > Doctoral Student | 4 | 5% |
| Other | 15 | 19% |
| Unknown | 12 | 15% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 21 | 27% |
| Biochemistry, Genetics and Molecular Biology | 18 | 23% |
| Immunology and Microbiology | 10 | 13% |
| Medicine and Dentistry | 5 | 6% |
| Nursing and Health Professions | 3 | 4% |
| Other | 8 | 10% |
| Unknown | 13 | 17% |
Attention Score in Context
This research output has an Altmetric Attention Score of 3. 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
#12,906,172
of 22,770,070 outputs
Outputs from BMC Infectious Diseases
#2,991
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Outputs of similar age
#117,245
of 258,738 outputs
Outputs of similar age from BMC Infectious Diseases
#61
of 190 outputs
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