chapter 10

Taxonomy is the science of classifying organisms into groups, or taxa, facilitating identification, classification, and nomenclature.
Hierarchical Order: The species is the basic unit. In eukaryotes, this is a group capable of producing fertile offspring; in prokaryotes, it refers to a group of closely related strains (genetic variants).
Classification Basis: Development from general to specific characteristics, including microscopic examination, culture, biochemical tests, and nucleic acid analysis.
Phylogeny: Evolutionary relatedness represented by the three-domain system introduced by Carl Woese et al., based on rRNA sequences.

Microscopic Morphology: Observation of size, shape, and staining (e.g., Gram stain, acid-fast, endospore, capsule). Gram stains can provide enough information to begin therapy.
Culture Characteristics:
- Serratia marcescens: Produces red pigment at $22^\circ\text{C}$ .
- Pseudomonas aeruginosa: Produces green pigment and a distinct fruity odor.
- Differential Media: Streptococcus pyogenes shows $\beta$ -hemolytic colonies on blood agar; E. coli forms pink colonies on MacConkey agar due to lactose fermentation.
Metabolic Capabilities: Often utilize pH indicators to track sugar fermentation or urease production. The Catalase test is a primary biochemical diagnostic.
Commercial Tests: Systems like the Enterotube or API test strip allow rapid, standardized identification via a series of simultaneous tests.
Dichotomous Keys: Flowcharts using successive questions about morphological or biochemical traits to differentiate species.
Serology: Uses commercial antibodies to detect specific antigens (proteins/polysaccharides) in the cell wall, capsule, flagella, or pili.

Advantages: Identifying organisms that cannot be grown in culture.
Nucleic Acid Amplification Tests (NAATs): Techniques like Polymerase chain reaction (PCR) amplify specific sequences.
- Used for slow-growing organisms like Mycobacterium tuberculosis ( $3-4$ hours vs. up to $6$ weeks for culture).
Sequencing Ribosomal RNA Genes: Highly conserved genes with little variation. Sequencing $16S$ rDNA (or $18S$ in eukaryotes) and comparing against databases identifies nearest relatives.

Serological Typing: Distinguishes organisms like $E. coli$ by antigenic types of flagella, capsules, or lipopolysaccharides (e.g., $E. coli\,O157:H7$ where "O" is the lipopolysaccharide and "H" is the flagella).
Molecular Typing: Uses DNA fingerprinting to distinguish phenotypically identical strains by comparing Restriction Fragment Length Polymorphisms (RFLPs) via gel electrophoresis. Useful for tracing outbreaks.
Antibiograms: Identification based on antibiotic susceptibility; clearing zones around antimicrobial discs on an inoculated plate indicate susceptibility levels.