Jawetz Chapter 3-4- Classification

Differentiate identification from classification.

1. Identification

• Practical use of a classification scheme

• Isolate and distinguish from the complex flora

• Verify authenticity and special properties in clinical setting

• Isolate causative disease agent

  2.Classification

• Categorization into taxonomic groups

Which are the most useful taxonomic ranks in microbiology?

Family, genus, species

____________ is used to discriminate characteristics below the species level

Subtyping

Give examples of selective media.

Sodium azide, bile salts, colistin, nalidixic acid

What is the limitation of using and applying numerical taxonomy in classifying bacteria?

It’s a static system that does not consider evolution, only general traits

The ________________ is a system that uses numerical taxonomy based on unweighted biochemical characteristics to identify a wide range of medically important microorganisms.

Analytical Profile Index (API)

Give examples of nucleic-acid based taxonomy methods.

• Plasmid Analysis

• Restriction Endonuclease Analysis

• Genomic Analysis

• Repetitive Sequence Analysis

• Ribosomal RNA Sequencing

• Ribotyping

Give examples of species that can be detected through biochemical test that determines carbohydrate breakdown.

Escherichia spp.

What does the Voges-Proskauer (VP) test detect?

Acetoin, a product of glucose fermentation via the butylene glycol pathway.

Name at least three VP-positive bacteria.

• Enterobacter aerogenes

• Klebsiella pneumoniae

• Serratia marcescens

Is Escherichia coli VP positive or negative?

VP negative (uses mixed acid fermentation instead).

Which Gram-positive spore-former is VP positive?

Bacillus cereus

Which biotype of Vibrio cholerae is VP positive?

El Tor biotype

How does the Voges-Proskauer test work?

Voges-Proskauer is highly related to glucose fermentation, and the following test has the following steps:

1.You grow the bacteria in a sugar-rich liquid (usually glucose broth).

2.Add special chemicals (α-naphthol and KOH) after incubation.

3.If acetoin is present, the chemicals react and turn the liquid red or pink — that means it's VP positive.

4.If it stays yellow or copper, it's VP negative.

Acetoin, which is also called ___________, is a ___________ (positive/neutral/negative) compound detected in the Voges-Proskauer test.

acetylmethylcarbinol; neutral

What happens during the ONPG test?

ONPG test is highly related to the lactose fermentation pathway. Displayed below are the steps of how it is performed:

1.A small amount of bacteria is added to a tube containing ONPG and sometimes a broth or buffer.

2.The mixture is incubated (usually at 35–37°C) for a few hours (or up to 24 hours).

3.If the bacteria produce β-galactosidase, the ONPG is broken down, and the liquid turns yellow.

The ONPG in ONPG test stands for ______________ which acts like a “fake _______”

ortho-nitrophenyl-β-D-galactopyranoside, lactose

It is used to differentiate Staphylococcus aureus from other, less pathogenic staphylococci.

Coagulase test

This test is particularly useful in differentiation of staphylococci (positive) from streptococci (negative), but it also has taxonomic application to Gram-negative bacteria

Catalase test

The amino acids usually tested in the decarboxylase test are ________, ___________, and ___________

lysine, ornithine, arginine

Proteinase is the same as __________

protease

Describe the Southern Blot procedure

The enzyme _________ breaks down urea into two molecules of ammonia and one molecule of CO₂, raising the pH of the medium. This increase in pH changes the color of the test medium to _________, indicating a positive result; otherwise, the color is _________ in a negative result. This test can help differentiate P. vulgaris from other enteric rods.

Urease; bright pink (fuchsia); yellow/orange

The oxidase test detects the ____ component of the cytochrome–oxidase complex. A positive reaction causes the reagent to change from clear to _________ when oxidized. This test is useful for distinguishing Pseudomonas aeruginosa (oxidase ____) from E. coli (oxidase ____).

c; purple (or dark blue); +; -

The nitrate reduction test detects a bacterium's ability to reduce ________ to nitrites or nitrogen gas. This test is commonly used in __________ to detect the presence of Gram-negative rods that may be causing _________.

nitrates; urinalysis; urinary tract infections (UTIs)

In the citrate utilization test, bacteria that can use _________ as their sole carbon source will grow on the agar medium. This growth usually causes the medium to turn from green to _________ due to an increase in pH. Bacteria such as _________ are examples of citrate-positive organisms.

sodium citrate; blue; Klebsiella pneumoniae

The ability of some bacteria to produce hydrogen sulfide (H₂S) from amino acids or other sulfur-containing compounds is detected by the formation of a __________ color, due to the reaction of H₂S with heavy metals like iron. This test is useful in distinguishing between ________________.

black; Gram-negative rods

The indole test detects an organism’s ability to break down __________ into indole. A positive result is indicated by a __________ color after the addition of a benzaldehyde reagent, while a negative result shows __________ color change.

tryptophan; red; no

Review the fundamentals of natural logarithms with these basic problems.

Note:

• when there’s ln, there is an invisible base e

• ln (x) is the same as log base e (x)