Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10400.18/7641 |
Resumo: | Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities. |
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Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical StrainAnti-Bacterial AgentsBacterial ProteinsComputational BiologyDrug Resistance, MicrobialEnterococcus faecalisGenome, BacterialGenotypeGram-Positive Bacterial InfectionsHumansMicrobial Sensitivity TestsMolecular Sequence AnnotationPhylogenySpectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationStress, PhysiologicalVancomycinVancomycin-Resistant EnterococciProteomeTranscriptomeMultiomicsAntibiotic ResistanceProteomicsTranscriptomicsEnterococcusTranslational ResearchBiomarkersResistência aos AntimicrobianosAntibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities.L.P. was granted a PhD fellowship by Fundação para a Ciência e a Tecnologia and European Social Fund (SFRH/BD/81307/2011). This work was supported by the Associate Laboratory for Green Chemistry-LAQV, which is financed by national funds from Fundação para a Ciência e a Tecnologia/ MCTES (UID/QUI/50006/2019). This research is also a result of the GenomePT project (POCI-01-0145-FEDER- 022184), supported by COMPETE 2020—Operational Programme for Competitiveness and Internationalisation, Lisboa Portugal Regional Operational Programme (Lisboa, 2020), Algarve Portugal Regional Operational Programme (CRESC Algarve, 2020), under the PORTUGAL 2020 Partnership Agreement, through the EuropeanRegionalDevelopment Fund, andbyFundação para a Ciência e a Tecnologia.Work performed in University of La Rioja was supported by project SAF2016- 76571-R of Agencia Estatal de Investigatio´n and FEDER.Mary Ann LiebertRepositório Científico do Instituto Nacional de SaúdePinto, LuísTorres, CarmenGil, ConchaSantos, Hugo M.Capelo, José LuísBorges, VítorGomes, João PauloSilva, CatarinaVieira, LuísPoeta, PatríciaIgrejas, Gilberto2021-04-05T17:20:22Z2020-022020-02-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.18/7641engOMICS. 2020 Feb;24(2):81-95. doi: 10.1089/omi.2019.0164.1536-231010.1089/omi.2019.0164info:eu-repo/semantics/embargoedAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-20T15:42:07Zoai:repositorio.insa.pt:10400.18/7641Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:42:16.861579Repositório 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 |
Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain |
title |
Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain |
spellingShingle |
Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain Pinto, Luís Anti-Bacterial Agents Bacterial Proteins Computational Biology Drug Resistance, Microbial Enterococcus faecalis Genome, Bacterial Genotype Gram-Positive Bacterial Infections Humans Microbial Sensitivity Tests Molecular Sequence Annotation Phylogeny Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Stress, Physiological Vancomycin Vancomycin-Resistant Enterococci Proteome Transcriptome Multiomics Antibiotic Resistance Proteomics Transcriptomics Enterococcus Translational Research Biomarkers Resistência aos Antimicrobianos |
title_short |
Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain |
title_full |
Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain |
title_fullStr |
Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain |
title_full_unstemmed |
Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain |
title_sort |
Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain |
author |
Pinto, Luís |
author_facet |
Pinto, Luís Torres, Carmen Gil, Concha Santos, Hugo M. Capelo, José Luís Borges, Vítor Gomes, João Paulo Silva, Catarina Vieira, Luís Poeta, Patrícia Igrejas, Gilberto |
author_role |
author |
author2 |
Torres, Carmen Gil, Concha Santos, Hugo M. Capelo, José Luís Borges, Vítor Gomes, João Paulo Silva, Catarina Vieira, Luís Poeta, Patrícia Igrejas, Gilberto |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório Científico do Instituto Nacional de Saúde |
dc.contributor.author.fl_str_mv |
Pinto, Luís Torres, Carmen Gil, Concha Santos, Hugo M. Capelo, José Luís Borges, Vítor Gomes, João Paulo Silva, Catarina Vieira, Luís Poeta, Patrícia Igrejas, Gilberto |
dc.subject.por.fl_str_mv |
Anti-Bacterial Agents Bacterial Proteins Computational Biology Drug Resistance, Microbial Enterococcus faecalis Genome, Bacterial Genotype Gram-Positive Bacterial Infections Humans Microbial Sensitivity Tests Molecular Sequence Annotation Phylogeny Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Stress, Physiological Vancomycin Vancomycin-Resistant Enterococci Proteome Transcriptome Multiomics Antibiotic Resistance Proteomics Transcriptomics Enterococcus Translational Research Biomarkers Resistência aos Antimicrobianos |
topic |
Anti-Bacterial Agents Bacterial Proteins Computational Biology Drug Resistance, Microbial Enterococcus faecalis Genome, Bacterial Genotype Gram-Positive Bacterial Infections Humans Microbial Sensitivity Tests Molecular Sequence Annotation Phylogeny Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Stress, Physiological Vancomycin Vancomycin-Resistant Enterococci Proteome Transcriptome Multiomics Antibiotic Resistance Proteomics Transcriptomics Enterococcus Translational Research Biomarkers Resistência aos Antimicrobianos |
description |
Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-02 2020-02-01T00:00:00Z 2021-04-05T17:20:22Z |
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 |
http://hdl.handle.net/10400.18/7641 |
url |
http://hdl.handle.net/10400.18/7641 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
OMICS. 2020 Feb;24(2):81-95. doi: 10.1089/omi.2019.0164. 1536-2310 10.1089/omi.2019.0164 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/embargoedAccess |
eu_rights_str_mv |
embargoedAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Mary Ann Liebert |
publisher.none.fl_str_mv |
Mary Ann Liebert |
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 |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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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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