Taxonomy, Classification, and Nomenclature
Core concepts
Know the Linnaean hierarchy (domain, kingdom, phylum, class, order, family, genus, species) and that binomial nomenclature italicizes genus and species (e.g., Staphylococcus aureus). Understand that clinical microbiology uses phenotypic classification (Gram stain, morphology, biochemical reactions) alongside genotypic classification (16S rRNA sequencing, whole-genome relatedness). Know the major bacterial groups: Gram-positive cocci (staphylococci, streptococci), Gram-positive bacilli (Bacillus, Clostridium, Listeria, Corynebacterium), Gram-negative cocci (Neisseria, Moraxella), Gram-negative bacilli (Enterobacterales, Pseudomonas, Haemophilus), and the atypical groups (Mycoplasma, Chlamydia, Rickettsia).
Fungi are classified into yeasts, molds, and dimorphic fungi. Viruses are classified by genome type (DNA/RNA, single/double stranded, sense) and replication strategy (Baltimore classification). Parasites are grouped into protozoa, helminths, and arthropods.
Traps to expect
- Confusing taxonomic relatedness with phenotypic similarity - Staphylococcus and Streptococcus are both Gram-positive cocci but differ in catalase and arrangement.
- Forgetting that dimorphic fungi are molds in the environment and yeasts in tissue (e.g., Histoplasma, Blastomyces).
- Mixing up species and subspecies/serovar designations.
- Assuming all "atypical" bacteria are Gram-negative - Mycoplasma lacks a cell wall entirely.
Worked example / rule of thumb
A Gram-positive coccus in clusters that is catalase-positive is presumptively Staphylococcus. Rule of thumb: catalase separates staphylococci (positive) from streptococci and enterococci (negative). Then coagulase separates S. aureus (positive) from coagulase-negative staphylococci. This cascade is a classic exam question.