Project plan

Overview

Enterococcus faecium is a gram positive bacterium that is a frequent cause of bloodstream infections in hospitalized patients. Its acquired resistance to multiple antibiotics has led to a public health concern.

The project entails the analysis of transcriptomics data to determine the expression patterns of E.faecium in different mediums. In order to apply the transcriptomics data, the complete genomic sequence of the E745 E. faecium strain has been determined through a combination of short-read Illumina sequencing and long-read Pacific Biosciences and Oxford Nanopore sequencing.

Our goal is to identify which genes allow the proliferation of E. faecium in human blood.

Software and Analyses

Basic analyses:

• Genome assembly with PacBio reads.
• Genome assembly with Illumina and Nanopore reads.
• Assembly evaluation.
• Structural and functional annotation.
• Synteny comparison with a closely related genome.
• Reads preprocessing: trimming + quality check (before and after)
• RNA-Seq reads alignment against the assembled genome.
• Differential expression analysis between rich medium and heat-inactivated serum conditions.
• Plasmid identification.

Time plan

Analysis Step	Software	Input	Output	Time	Status	Deadline
Read Quality Control	Fast QC	FASTQ files	data quality report	10 min	Done	03.04
Reads preprocessing	Trimmomatic	FASTQ files	trimmed fasta files	50 min	Done	03.04
DNA assembly	Spades / Canu	FastQ files	assembly fasta file	2 h / 4,5 h	Done	11.04
Assembly evaluation	MUMmerplot / Quast	FastQ files	assembly evaluation report	5 min	Done	11.04
Annotation	Prokka	FastQ file	Annotation GFF file	5 min	Done	13.04
Aligner	BWA	FastQ files	BAM files	30 min	Done	14.04
Differential Expression	Htseq / DESeq	BAM / Gene count files	Gene count files	2 - 7 h	Done	19.04

Data management

.
└── genome analysis/
    ├── analysis/
    │   └── preprocessing/
    │       ├── trimmed/
    │       │   ├── trimmed_file1.fastq
    │       │   └── trimmed_file2.fastq
    │       ├── fastq_raw/
    │       │   └── report.txt
    │       └── fastq_trim/
    │           └── report.txt
    ├── code/
    │   ├── script1.sh
    │   └── script2.sh
    └── data/
        ├── metadata
        ├── raw_data/
        │   ├── genomics_data/
        │   │   ├── Illumina
        │   │   ├── Pacbio
        │   │   └── Nanopore
        │   └── transcriptomics_data/
        │       ├── RNA-Seq_BH
        │       ├── RNA-Seq_Serum
        │       ├── Tn-Seq_BHI
        │       ├── Tn-Seq_HSerum
        │       └── Tn-Seq_Serum
        └── trimmed_data

Original paper: RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum