Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://hdl.handle.net/1822/80668 |
Resumo: | Bloodstream infections caused by Staphylococcus epidermidis are often misdiagnosed since no diagnostic marker found so far can unequivocally discriminate true infection from sample contamination. While attempts have been made to find genomic and/or phenotypic differences between invasive and commensal isolates, possible changes in the transcriptome of these isolates under in vivo-mimicking conditions have not been investigated. Herein, we characterized the transcriptome, by RNA sequencing, of three clinical and three commensal isolates after 2 h of exposure to whole human blood. Bioinformatics analysis was used to rank the genes with the highest potential to distinguish invasive from commensal isolates and among the ten genes identified as candidates, the gene SERP2441 showed the highest potential. A collection of 56 clinical and commensal isolates was then used to validate, by quantitative PCR, the discriminative power of the selected genes. A significant variation was observed among isolates, and the discriminative power of the selected genes was lost, undermining their potential use as markers. Nevertheless, future studies should include an RNA sequencing characterization of a larger collection of isolates, as well as a wider range of conditions to increase the chances of finding further candidate markers for the diagnosis of bloodstream infections caused by S. epidermidis. |
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Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infectionsbloodstream infection diagnosiscommensal isolatesclinical isolatesex vivo human blood modelRNA sequencingmolecular diagnosis markersScience & TechnologyBloodstream infections caused by Staphylococcus epidermidis are often misdiagnosed since no diagnostic marker found so far can unequivocally discriminate true infection from sample contamination. While attempts have been made to find genomic and/or phenotypic differences between invasive and commensal isolates, possible changes in the transcriptome of these isolates under in vivo-mimicking conditions have not been investigated. Herein, we characterized the transcriptome, by RNA sequencing, of three clinical and three commensal isolates after 2 h of exposure to whole human blood. Bioinformatics analysis was used to rank the genes with the highest potential to distinguish invasive from commensal isolates and among the ten genes identified as candidates, the gene SERP2441 showed the highest potential. A collection of 56 clinical and commensal isolates was then used to validate, by quantitative PCR, the discriminative power of the selected genes. A significant variation was observed among isolates, and the discriminative power of the selected genes was lost, undermining their potential use as markers. Nevertheless, future studies should include an RNA sequencing characterization of a larger collection of isolates, as well as a wider range of conditions to increase the chances of finding further candidate markers for the diagnosis of bloodstream infections caused by S. epidermidis.This work was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of the unit [UIDB/04469/2020]. S.B. was supported by a fellowship granted by a Doctoral Advanced Training [NORTE-69-2015-15] funded by the European Social Fund under the scope of NORTE2020.info:eu-repo/semantics/publishedVersionMultidisciplinary Digital Publishing Institute (MDPI)Universidade do MinhoBrás, SusanaFrança, Ângela Maria Oliveira Sousa2022-11-112022-11-11T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/1822/80668engBrás, S.; França, A. Transcriptome Mining to Identify Molecular Markers for the Diagnosis of Staphylococcus epidermidis Bloodstream Infections. Antibiotics 2022, 11, 1596. https://doi.org/10.3390/antibiotics111115962079-63822079-638210.3390/antibiotics11111596https://www.mdpi.com/2079-6382/11/11/1596info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:49:52Zoai:repositorium.sdum.uminho.pt:1822/80668Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:48:27.596499Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections |
title |
Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections |
spellingShingle |
Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections Brás, Susana bloodstream infection diagnosis commensal isolates clinical isolates ex vivo human blood model RNA sequencing molecular diagnosis markers Science & Technology |
title_short |
Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections |
title_full |
Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections |
title_fullStr |
Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections |
title_full_unstemmed |
Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections |
title_sort |
Transcriptome mining to identify molecular markers for the diagnosis of Staphylococcus epidermidis bloodstream infections |
author |
Brás, Susana |
author_facet |
Brás, Susana França, Ângela Maria Oliveira Sousa |
author_role |
author |
author2 |
França, Ângela Maria Oliveira Sousa |
author2_role |
author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Brás, Susana França, Ângela Maria Oliveira Sousa |
dc.subject.por.fl_str_mv |
bloodstream infection diagnosis commensal isolates clinical isolates ex vivo human blood model RNA sequencing molecular diagnosis markers Science & Technology |
topic |
bloodstream infection diagnosis commensal isolates clinical isolates ex vivo human blood model RNA sequencing molecular diagnosis markers Science & Technology |
description |
Bloodstream infections caused by Staphylococcus epidermidis are often misdiagnosed since no diagnostic marker found so far can unequivocally discriminate true infection from sample contamination. While attempts have been made to find genomic and/or phenotypic differences between invasive and commensal isolates, possible changes in the transcriptome of these isolates under in vivo-mimicking conditions have not been investigated. Herein, we characterized the transcriptome, by RNA sequencing, of three clinical and three commensal isolates after 2 h of exposure to whole human blood. Bioinformatics analysis was used to rank the genes with the highest potential to distinguish invasive from commensal isolates and among the ten genes identified as candidates, the gene SERP2441 showed the highest potential. A collection of 56 clinical and commensal isolates was then used to validate, by quantitative PCR, the discriminative power of the selected genes. A significant variation was observed among isolates, and the discriminative power of the selected genes was lost, undermining their potential use as markers. Nevertheless, future studies should include an RNA sequencing characterization of a larger collection of isolates, as well as a wider range of conditions to increase the chances of finding further candidate markers for the diagnosis of bloodstream infections caused by S. epidermidis. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-11-11 2022-11-11T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://hdl.handle.net/1822/80668 |
url |
https://hdl.handle.net/1822/80668 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Brás, S.; França, A. Transcriptome Mining to Identify Molecular Markers for the Diagnosis of Staphylococcus epidermidis Bloodstream Infections. Antibiotics 2022, 11, 1596. https://doi.org/10.3390/antibiotics11111596 2079-6382 2079-6382 10.3390/antibiotics11111596 https://www.mdpi.com/2079-6382/11/11/1596 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Multidisciplinary Digital Publishing Institute (MDPI) |
publisher.none.fl_str_mv |
Multidisciplinary Digital Publishing Institute (MDPI) |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799133062921977857 |