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RNA sequencing of S. simiae CCM 7213T, S. capitis SK14 and S. epidermidis RP62A strains

ABSTRACT: RNA sequencing of S. simiae CCM 7213T, S. capitis SK14 and S. epidermidis RP62A strains

PROVIDER: PRJNA601089 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10883624_1.fastq.gz	Fastqsanger.gz
	SRR10883624_2.fastq.gz	Fastqsanger.gz
	SRR10883625_1.fastq.gz	Fastqsanger.gz
	SRR10883625_2.fastq.gz	Fastqsanger.gz
	SRR10883626_1.fastq.gz	Fastqsanger.gz

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RNA sequencing of S. simiae CCM 7213T, S. capitis SK14 and S. epidermidis RP62A strains

Project description:The goal of our study was to perform RNA sequencing of whole transcripts to determine and compare the real length of 3’UTRs among closely-related staphylococcal species. We found that most of the mRNAs encoding orthologous genes in staphylococcal species have 3’UTRs with different lengths in addition to sequence variation.

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Project description: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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