Staphylococcus aureus

Data Downloaded from EBI:

https://www.ebi.ac.uk/ena/data/view/PRJEB21460

-Would not let me right click and copy the file 1 ans file 2 on my mac.

Project Focus:

I will be researching Staphylococcus aureus and how this bacteria is related to and if it actually causes endocarditis. I will be looking at a study that showed this infection as a health-care associated infection and comparing it to infections outside of a hospital setting. I will be using this paper for research: https://jamanetwork.com/journals/jama/fullarticle/201122 along with others. I will be looking at whole-genome sequencing of bloodstream S. Aureus.

Endocarditis Strains 1-4

Strain 1: SAMEA104137068

https://www.ebi.ac.uk/ena/data/view/PRJEB21460

  • File 1: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR201/007/ERR2013967/ERR2013967_1.fastq.gz
  • File 2: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR201/007/ERR2013967/ERR2013967_2.fastq.gz

Strain 2: SAMEA104137069

https://www.ebi.ac.uk/ena/data/view/SAMEA104137069

  • File 1: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR201/008/ERR2013968/ERR2013968_1.fastq.gz
  • File 2: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR201/008/ERR2013968/ERR2013968_2.fastq.gz

Strain 3: SAMEA104137070

https://www.ebi.ac.uk/ena/data/view/SAMEA104137070

  • File 1: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR201/009/ERR2013969/ERR2013969_1.fastq.gz
  • File 2: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR201/009/ERR2013969/ERR2013969_2.fastq.gz

Strain 4: SAMEA104137071

https://www.ebi.ac.uk/ena/data/view/SAMEA104137071

  • File 1: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR201/000/ERR2013970/ERR2013970_1.fastq.gz
  • File 2: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR201/000/ERR2013970/ERR2013970_2.fastq.gz

 

Human-To-Bovine (https://www.ncbi.nlm.nih.gov/pubmed/23505465/)

CC8 Strains 5-7

Strain 5: SAMN06320931

https://www.ebi.ac.uk/ena/data/view/SRR5244799

  • File 1: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR524/009/SRR5244799/SRR5244799_1.fastq.gz
  • File 2: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR524/009/SRR5244799/SRR5244799_2.fastq.gz

Strain 6: SAMN06320930

https://www.ebi.ac.uk/ena/data/view/SRR5244800

  • File 1: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR524/000/SRR5244800/SRR5244800_1.fastq.gz
  • File 2: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR524/000/SRR5244800/SRR5244800_2.fastq.gz

Strain 7: SAMN06320904

https://www.ebi.ac.uk/ena/data/view/SRR5244826

  • File 1: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR524/006/SRR5244826/SRR5244826_1.fastq.gz
  • File 2: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR524/006/SRR5244826/SRR5244826_2.fastq.gz

 

Poster Content

Background:

  • S. aureus is a member of the normal flora in the body, is a coccal (round) shaped bacteria that is Gram-Positive
  • Found in the Resp. tract, nose, and skin
  • Strains are not always pathogenic, if they are they are the common cause of skin infections, abscesses and resp infections.
  • The isolates can cause invasive disease, but it is unknown if some isolates are more likely to cause severe infections then others (EBI reference)
  • Pathogenic strains promote infections by producing virulence factors such as protein toxins and the expression of a cell-surface protein that binds and inactivates antibodies
  • Common antibiotic resistant strain of S. aureus is MRSA
  • No approved vaccine
  • 20-30% of the human population are long term carriers
  • S. aureus is most common causes of bacteria and infective Endocarditis
  • Leading cause of bloodstream infections
  • W/o antibiotics=fatality rate of 80%, With= 15-50% depending on age and health

https://en.wikipedia.org/wiki/Staphylococcus_aureus (Reference to info above)

Reference Genome:

ASM900v1 Ref-1

ASM958v1 Ref-2

ASM964v1 Ref-3 (didn’t download yet)

 

 

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