Multiomics substrates of resistance to emerging pathogens? Transcriptome and proteome profile of a vancomycin-resistant enterococcus faecalis clinical strain

Luís Pinto, Carmen Torres, Concha Gil, Hugo M. Santos, José Luís Capelo, Vítor Borges, João Paulo Gomes, Catarina Silva, Luís Vieira, Patrícia Poeta, Gilberto Igrejas

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)81-95
Number of pages15
JournalOMICS A Journal of Integrative Biology
Volume24
Issue number2
DOIs
Publication statusPublished - Feb 2020

Keywords

  • antibiotic resistance
  • biomarkers
  • Enterococcus
  • multiomics
  • proteomics
  • transcriptomics
  • translational research

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