Micro 10-11

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Taxonomy

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Taxonomy: The science of characterizing and naming organisms in order to arrange them into hierarchical groups (Taxa). Organisms with similar properties are grouped together and separated from ones that are different.

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Taxonomy can be viewed as three separate but interrelated areas:

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Identification: process of characterizing and isolate ( a population of cells descended from a single cell, pure culture) to determine the group(taxon) to which belongs.

Classification: process of arranging organisms into similar or related groups, primarily to it easier to identify them for study.

Nomenclature: System of assigning names.

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taxonomic hierarchy:.

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Taxonomic classification categories are arranged in hierarchical order with the species being the basic unit

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Taxonomic range

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Taxonomic ranks:

Kingdom,Phylum, Class, Order, Family, Genus, Species ( basic)

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Gram stain 1

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Gram Stain:

Distinguish between gram+ and gram bacteria.

In clinical lab, the gram stain is generally not sensitive or specific enough to Dx the cause of most infections, but still is an extremely useful tool.

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Gram stain 2

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The gram reaction is used for identifying the shape and arrangement of the bacteria cells, and if the organism is a pure culture or not.

Most imp bacteria cannot be identified by the Gram stain. Ex Streptococcus pyogenes (strep throat) can not distinguish microscopically from the normal microbiota. Also, a Gram stain from a stool specimen cannot distinguish salmonella from E. coli. Generally these microorganism must be isolated in pure culture and tested for more accuracy.

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Gram stain 3

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In certain cases gram stain gives enough info that can lead an appropriate Tx. Ex gram stain from sputum that shows numerous WBCs and gram + diplococci is highly suggestive for streptococcus pneumoniae ( pneumoniae). Other ex: the presence of Gram – diplococci clustered in WBCs in a urethral sample from a man may be considered Dx gonorrhea ( Neisseria gonorrhoeae) Dx possible to make because Neisseria gonorrhoeae is the only gram – diplococci clustered in WBCS found in a male urethra secretion

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Culture characteristics:

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Colony morphology can give initial clues to identify microorganisms. Ex: colonies of bacterium serratia marcescens are often red when incubated at 22*C due to production the red pigment.

The bacterium Pseudomonas aeruginosa often produces a soluble greenish pigment, which discolors the growth medium. In addition also this bacterium has a distinguish fruit odo

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Biochemical test 1

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A variety of biochemical tests that can be used to determine an isolate`s metabolic capabilities. Some of the test are quite rapid because they detect the presence of enzymes already in bacterial colony.

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Biochemical test 2

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The easiest one and fasted is catalase, an enzyme that many organisms produce to protect themselves against hydrogen peroxide. Is done in a petri dish and the breakdown of the hydrogen peroxide forms O2 and H2O. the O2 can be observed as bubbles in the reagent. Most bacteria that grows in the presence of O2 care called catalase positive. (exceptions: Lactic acids bacteria such as members of the Streptococcus.)

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Biochemical test 3

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Most biochemical test rely on chemical indicator that changes color when compound is degraded.

Test that needs to be tested or for the purpose of fermentation of sugar, they are placed in growth medium containing sugar and a pH indicator. If organism ferments sugar, acid is produced which lower pH resulting in color change. An an inverted tube traps the gas emitted.

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Biochemical test 4

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Urease degrades urea enzyme producing CO@ and ammonia. The container must have a pH indicator as well.

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Biochemical test notes

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The basic strategy for identifying bacteria based on their biochemical test relies on a dichotomous key; a serie of alternatives choices that lead to the identification of an organism.

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Biochemical test notes 2

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Each test requires an incubation period.

H pylori can be detected by the breath test. Bacteria breaks urea ( by its urease) and release CO2 which escapes through the airway. Several hours after drink the solution pt exhales in a balloon, the air is testes for CO2.

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Phage typing 1

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Strains of a given species may differ in their susceptibility to bacteriophages. Bacteriophages, or phages, are viruses that infect bacteria, often lysing them.

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Phage typing 2

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The organism's susceptibility to a particular phage can easily be determined:

1- the culture of the organism is inoculated in molten.

2- agar nutrient cooled and poured onto the surface of an agar plate creating a uniform layer of cells.

3- drops of different types of bacteriophages are placed on the surface of the agar.

During the incubation, the bacteria multiply forming a fog or visible cells. The strain shows a clear area in the place where the bacteriophage is located.

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Antibiograms

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Antimicrobial susceptibility patterns, or antibiograms that can distinguish different strains. As with phage typing, this method has largely been replaced by molecular techniques. To determine the antibiogram, a culture is uniformly inoculated onto the surface of nutrient agar. Paper discs containing different antibiotics or other antimicrobial meds are then placed on the agar. After incubation, clear areas will be visible around discs of antimicrobials that inhibit or kill the organism.

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Staphylococcus aureus

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Gram positive, a coccus. Causes: MRSA, Toxic shock syndrome, Food poisoning, Endocarditis, Sepsis

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Streptococcus pyogene

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Gram positive, coccus. Causes: Strep throat, Glomerulone- phritis, Cellulitis, Erysipelas

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Treponema Pallidum

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Spirochete, gram negative. Causes: Syphilis

yaws

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H. Pylori

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Rod shape, gram negative. Causes: Peptic ulcers, Gastritis, Stomach Cancer.

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E. Coli

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Rod shape, gram negative. Causes: UTI

Kidney failure

Enterocolitis

Meningitis

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Clostridium tetani

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Rod, gram positive. Causes: tetanus

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Clostridium perfringens

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Rod, gram positive. Causes: Food poisoning

Gastroenteritis

Cholecystitis

Gas gangrene

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Pseudomona aeruginosa

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Rod, gram negative. Causes: UTI

Respiratory infection

Soft tissue infection

Osteomyelitis