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Strains of Staph: Staphylococcus Aureus Classification Using Whole Genomes

Kim Austin

Lone Star College Montgomery Honors

What is Staphylococcus Aureus?

Pathogen associated with nosocomial diseases

Major Causal Agent of Disease

Most infections target skin or soft tissue

  • ~500,00 patients in the U.S. Hospitals contract a staph infection each year.

  • 85% of all invasive MRSA infections were from healthcare facilities with patients contracting infections after their stay ( two-thirds) and one-third while in the facility

Skin Abscess

Scalded Skin Syndrome

CDC: General Information about MRSA in Healthcare Settings.

Results

Mrsasurvivors.org

Carbuncle

Impetigo

Photos: Staph infection Resources.org

May become systemic if untreated

  • Toxic Shock Syndrome
  • Endocarditis
  • Osteomyelitis
  • Bacteremia
  • Meningitis
  • Sepsis
  • Necrotizing pneumonia
  • Necrotizing fasciitis aka "flesh eating disease

Endocarditis

Image from CDC.org

Visual Dot Plot Comparisons

Data

New Classification

Systems

Dot-Plots

Why Classify?

References

  • 144 Dot-plots were created, each one compares one strain of s. aureus to another.

Baron, S. (1996). Medical Microbiology 4th Edition. Galveston: University of Texas Medical Branch at Galveston.

  • Classifying bacteria by their entire genome will allow us to quickly identify the strain

  • The rapid identification of pathogenic bacteria will result in more effective treatment for patients as those practicing healthcare will be able to pair the specific bacteria to the medication needed.

Basic Local Alignment Search Tool. (n.d.). Retrieved March 20, 2015, from http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome

Methodology

Takuno's Phylogeny

Composite Image

CDC. (2013, September 16). General Information about MRSA in Healthcare Settings. Retrieved November 15, 2014, from CDC.gov: http://www.cdc.gov/mrsa/healthcare/index.html

Dealing with MRSA or Staph Infection Issues? (n.d.). Retrieved March 24, 2015, from http://www.staph-infection-resources.com/

National Center for Biotechnology Information. (n.d.). Retrieved September 14, 2014.

  • The speculative functions of the differing regions was identified using the Basic Local Alignment Search Tool or BLAST.

  • More than half of the sequence results were for hypothetical proteins with unknown function.

  • Vast amounts of genomic data are available, but there are not enough people to sort through it.

NIH News. (1999, May 27). Experimental Staph Vaccine Broadly Protective in Animal Studies. Retrieved November 10, 2014, from National Institute of Allergy and Infectious Diseases: http://web.archive.org/web/20070505050641/http://www3.niaid.nih.gov/news/newsreleases/1999/staph.htm

Col (Group A) Compared to MRSA (Group E)

Takuno et al. (2012). Population Genomics in Bacteria: A Case Study of Staphylococcus aureus

(n.d.). Retrieved March 13, 2015, from http://phil.cdc.gov/PHIL_Images/02122002/00007/PHIL_851_lores.jpg

Stoppler, M. C. (2014, July 11). Staph Infection (Staphylococcus aureus). Retrieved November 20, 2014, from Medicinenet.com: http://www.medicinenet.com/staph_infection/article.htm

Takuno analyzed genome-wide pattern of single

nucleotide polymorphisms (SNPS) to classify 12

strains of s. aureus into 5 groups: A, B, C, D, & E.

Takuno et al. (2012). Population Genomics in Bacteria: A Case Study of Staphylococcus aureus. Retrieved September 12, 2014.

Todar, K. P. (2012). Staphylococcus. Retrieved November 12, 2014, from Textbookofbacteriology.net: http://textbookofbacteriology.net/staph.html

Methodology

The purpose of this project was to test

this classification system by using a

whole genome analysis.

What is a Microbe? (n.d.). Retrieved March 30, 2015, from http://archives.microbeworld.org/microbes/

  • The genomes of 12 strains of s. aureus were downloaded from the National Center for Biotechnology Information (NCBI)

  • The program, UGENE, was used to analyze the sequences using dot-plots.

  • Dot-plots allow quick visual comparisons and discrimination between regions that are genetically similar and those that are different.

MRSA (Group E) compared to each of the 12 analyzed strains

Photoshop and GIMP were used to create a composite image by layering each dot-plot on one another

Thank You

Professor Ricky Johnson

Dr. Julie Harless

Lone Star Montgomery Honors College

Identification Methods

Classification Systems

Tests on Function

Classification systems used the rRNA in the

bacteria's ribosome as the changes were

infrequent and relatively easy to track.

Ribosomes are the sites at which information carried in the genetic code is converted into

protein molecules.

Mannitol Salts Agar:

Both S. Aureus and S. Epidermidis

can survive on the high-salt content

plate, but only S. Aureus can ferment

mannitol visible by the yellow color

change on the plate.

Mannitol Salts Agar

Coagulase Test:

S. aureus is coagulase positive. Coagulase allows the bacteria to isolate itself from the host's defenses by converting fibrinogen to fibrin to form a blood clot.

Credit: Major differences.com

Coagulase Test

S. Aureus is a facultative anerobe,

and can survive both with and

without oxygen.

Aerobic respiration

Gram Stain

  • The microscope was the first tool used to identify and classify bacteria.
  • Gram stains use a crystal violet dye that binds to the peptidoglycan layer in the cell wall of gram positive bacteria.
  • The purple color indicates that s. aureus is gram-positive

Gram stain from microbeworld.net

  • Staphylococcus comes from the Greek words staphyl meaning cluster and coccus meaning berry.
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