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Alina Orozco edited this page May 27, 2019 · 4 revisions

Welcome to my GenomeAnalysis wiki!

Background

Enterococci are typically commensal bacterium in the human gut, such that most live in the gastrointestinal tract and derive sustenance from the the body without doing any harm. However, some species can cause infection, including Enterococcus faecium, which has been identified as a major cause of bloodstream infections in immunocompromised hospitalized patients. [1]

Antibiotic resistance from Gram-positive to Gram-negative infections is a growing concern in the medical and health community [2]. E. faecium is among those microorganisms that has recently acquired resistance to multiple antibiotics, including to common treatments such as the glycopeptide vancomycin [1]. This research aims to characterize the genetic mechanisms of the growth and survival of the vancomycin-resistant E. faecium bacterium in the bloodstream.

This study aims to identify genes that allow​ E. faecium to grow in human blood by comparing the transcriptome expression profile of E.faecium E745 in rich medium(Brain Heart Infusion medium) to that of the profile in human serum(Serum) with RNA-seq. The transposon mutant library with Tn-seq was then used to identify the genes specifically required for growth.

Motivation

The goal of this project is to verify and recreate the analysis carried out by Zhang et. al [1] for educational purposes as well as potentially revealing new insight into previous research.

Wiki and Repository

Wiki pages:

  • Project Plan
  • Methods for replication
  • Analysis Interpretation

The script files used for these processes is included within the code folder in the GenomeAnalysis repository. Some result files used for interpretation are included within the folder analysis in the same repository.

Citations:

  1. Zhang X, de Maat V, Guzmán Prieto AM, Prajsnar TK, Bayjanov JR, de Been M, Rogers MRC, Bonten MJM, Mesnage S, Willems RJL, van Schaik W (2017) RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum BMC Genomics. 2017 Nov 21;18(1):893. doi: 10.1186/s12864-017-4299-9.

  2. de Kraker ME1, Davey PG, Grundmann H; BURDEN study group.(2011) Mortality and hospital stay associated with resistant Staphylococcus aureus and Escherichia coli bacteremia: estimating the burden of antibiotic resistance in Europe.PLoS Med. 2011 Oct;8(10):e1001104. doi: 10.1371/journal.pmed.1001104. Epub 2011 Oct 11.

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