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| Status |
Public on Dec 09, 2022 |
| Title |
Characterization of Staphylococcus epidermidis clinical and commensal isolates transcriptome upon interaction with human blood |
| Organism |
Staphylococcus epidermidis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The release of cells from S. epidermidis biofilms formed on medical devices has been associated with the onset of bloodstream infections, resulting in increased morbidity and mortality rates. This has to do, in part, with the difficulty to accurately diagnose S. epidermidis bloodstream infections. S. epidermidis is a ubiquitous commensal of human skin and mucosa and, thus, a positive blood culture does not always represent an infection, possibly being the result of contamination during blood collection. As such, there is a high demand to find markers that can help clinicians to distinguish infection (clinical isolates) from contamination (commensal strains). With that in mind, several studies comparing phenotypic or genetic characteristics of clinical and commensal isolates have been performed over the years. However, because S. epidermidis virulence factors seem to be the same that confer its fitness as a commensal, we hypothesized that the ability of S. epidermidis strains to adapt to the host environment may not depend on a specific phenotypic and/or genetic makeup, but rather on the regulation of gene transcription. Thus, using RNA-Sequencing (RNA-seq), we characterized the transcriptome of commensal and clinical isolates in the context of infection to try to uncover differences and, thus, identify markers that could be used for the diagnostics. Several markers with the potential to discriminate between both groups were highlighted. Nevertheless, when the results obtained were confirmed in a wider collection of clinical and commensal isolates the discriminatory power of the genes initially identified was lost. Although we cannot rule out that the characterization of a larger collection of isolates would identify potential candidates, our transcriptomic data was not able to confirm our initial hypothesis, evidencing S. epidermidis opportunistic nature.
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| Overall design |
The transcriptome of the cells released from biofilms formed by three S. epidermidis clinical and three commensal isolates was characterized upon incubation with human blood for 2h at 37 oC and with agitation at 80 rpm. Each condition under test was analyzed once by RNA-seq, however, each sample analyzed was prepared by mixing total RNA from three independent assays.
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| Contributor(s) |
Brás S, França Â, Cerca N |
| Citation(s) |
36421239 |
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| Submission date |
Jul 03, 2021 |
| Last update date |
Dec 09, 2022 |
| Contact name |
Ângela França |
| E-mail(s) |
angelamosf@gmail.com
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| Organization name |
University of Minho
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| Department |
Biological Engineering
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| Street address |
Campus de Gualtar
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| City |
Braga |
| ZIP/Postal code |
4710-057 |
| Country |
Portugal |
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| Platforms (1) |
| GPL17893 |
Illumina MiSeq (Staphylococcus epidermidis) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA743573 |
| SRA |
SRP326836 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE179407_Strategy_1_RPKM_higher_than_1.txt.gz |
333 b |
(ftp)(http) |
TXT |
| GSE179407_Strategy_2_RPKM_higher_than_10000.txt.gz |
482 b |
(ftp)(http) |
TXT |
| GSE179407_Strategy_3_RPMK_higher_than_1.txt.gz |
2.6 Kb |
(ftp)(http) |
TXT |
| GSE179407_Strategy_3_RPMK_higher_than_10.txt.gz |
16.3 Kb |
(ftp)(http) |
TXT |
| GSE179407_Strategy_3_RPMK_higher_than_100.txt.gz |
19.9 Kb |
(ftp)(http) |
TXT |
| GSE179407_Strategy_3_RPMK_higher_than_1000.txt.gz |
3.8 Kb |
(ftp)(http) |
TXT |
| GSE179407_Strategy_3_RPMK_higher_than_5000.txt.gz |
480 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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