Memly's USMLE Step 1 Microbiology: 300 Organism Cards
300 organisms by structure, virulence and how they are identified.
300 cards
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| Front | Back |
|---|---|
| Gram stain principle | Definition: A differential stain separating bacteria by how well the cell wall retains crystal violet after an alcohol wash. Reads out: Gram-positive cells keep the violet dye, gram-negative cells lose it and take up the counterstain. Why it matters: The result is a property of wall structure, so it also predicts susceptibility to agents that act on the wall. |
| Catalase test | Definition: Detection of the enzyme converting hydrogen peroxide to water and oxygen, seen as bubbling. Reads out: Staphylococci are positive and streptococci are negative, which is the first split among gram-positive cocci. |
| Chocolate agar | Definition: Blood agar heated to lyse the red cells, releasing factor V and factor X. Grows: Haemophilus influenzae, which cannot obtain both factors from intact blood agar. |
| Staphylococcus aureus | Classification: Gram-positive cocci in clusters, catalase positive and coagulase positive, beta hemolytic. Virulence: Protein A binding the antibody Fc region, exotoxins including toxic shock syndrome toxin and exfoliative toxin, and enzymes that spread through tissue. Causes: Skin and soft tissue infection, abscess, osteomyelitis, endocarditis, pneumonia, and a rapid-onset food poisoning from preformed toxin. |
| Streptococcus pyogenes | Classification: Gram-positive cocci in chains, catalase negative, beta hemolytic, bacitracin sensitive, Lancefield group A. Virulence: M protein blocking phagocytosis, streptolysin O, and pyrogenic exotoxins acting as superantigens. Causes: Pharyngitis, skin infection, scarlet fever, and the immune-mediated sequelae of rheumatic fever and post-streptococcal glomerulonephritis. |
| Bacillus anthracis | Classification: Gram-positive spore-forming aerobic rod with a polypeptide capsule of D-glutamate. Virulence: A tripartite toxin of protective antigen, edema factor, and lethal factor. Transmission: Spores from animal products by cutaneous contact or inhalation. |
| Clostridium tetani | Classification: Gram-positive spore-forming obligate anaerobe with a terminal spore. Transmission: Spores entering through a puncture wound. Virulence: Tetanospasmin, which blocks release of the inhibitory transmitters glycine and GABA. |
| Neisseria meningitidis | Classification: Gram-negative diplococci, oxidase positive, maltose and glucose fermenting, grown on Thayer-Martin. Virulence: Polysaccharide capsule, IgA protease, and endotoxin from lipooligosaccharide. Transmission: Respiratory droplets, with carriage in the nasopharynx. |
| Enterobacteriaceae common features | Definition: Gram-negative rods that are oxidase negative, ferment glucose, and reduce nitrate. Why it matters: A negative oxidase result on a gram-negative rod points to this family, which is the first branch in enteric identification. |
| Vibrio cholerae | Classification: Comma-shaped gram-negative rod, oxidase positive, growing in alkaline media. Virulence: Cholera toxin. Transmission: Contaminated water, requiring a large inoculum because the organism is acid sensitive. |
| Brucella | Classification: Small gram-negative coccobacillus, facultative intracellular within macrophages. Transmission: Unpasteurized dairy and contact with infected animals. Why it matters: Intracellular survival produces an undulating fever pattern and a prolonged course. |
| Endotoxin | Definition: Lipopolysaccharide in the outer membrane of gram-negative bacteria, released on cell lysis. Mechanism: Lipid A activates macrophages through Toll-like receptor 4, releasing cytokines that drive fever, vasodilation, and coagulation activation. Often confused with: Exotoxin, which is secreted, protein, heat labile, and often has a specific molecular target. |
| Mycobacterium tuberculosis | Classification: Acid-fast rod, obligate aerobe, slow growing on Lowenstein-Jensen medium. Transmission: Airborne droplet nuclei. Virulence: Cord factor, and sulfatides that inhibit phagosome-lysosome fusion, allowing survival inside macrophages. |
| Treponema pallidum | Classification: Spirochete too thin to be seen on Gram stain, visualized by darkfield microscopy, not culturable on artificial media. Transmission: Sexual contact and across the placenta. Why it matters: Its outer membrane carries few surface proteins, which is one explanation offered for its persistence despite an antibody response. |
| Mycoplasma pneumoniae | Classification: The smallest free-living bacteria, with no cell wall and sterols in the membrane, growing slowly on enriched media. Why it matters: Having no peptidoglycan, it is unaffected by agents acting on the cell wall and is invisible on Gram stain. Causes: A gradual-onset pneumonia, often with cold agglutinins. |
| Biofilm | Definition: A community of bacteria embedded in a self-produced polysaccharide matrix on a surface. Formed by: Staphylococcus epidermidis on prosthetic material, Pseudomonas aeruginosa on respiratory surfaces, and viridans streptococci on damaged valves. Why it matters: Organisms inside divide slowly and are shielded from both phagocytes and diffusion, so the state rather than the species explains persistence. |
| Viral genome classification | Definition: Viruses grouped by nucleic acid type, strandedness, and sense, since those determine what must happen before proteins can be made. Why it matters: The grouping predicts whether the virus must carry its own polymerase, which is a structural requirement rather than a naming convention. |
| DNA virus general features | Definition: Most are double stranded, linear or circular, and replicate in the nucleus using host machinery. Exceptions: Poxviruses replicate in the cytoplasm and carry their own polymerase, and parvoviruses are single stranded. Why it matters: The exceptions are the examinable part, since the general rule follows from needing host nuclear enzymes. |
| RNA virus general features | Definition: Most replicate in the cytoplasm and lack proofreading, so mutation rates are far higher than for DNA viruses. Exceptions: Influenza and retroviruses use the nucleus at some stage. Why it matters: High mutation rate underlies antigenic change, quasispecies diversity, and rapid emergence of resistance. |
| Influenza genome segmentation | Definition: Eight separate RNA segments packaged together in one particle. Why it matters: Co-infection of one cell by two strains allows whole segments to be exchanged, which is the mechanism of antigenic shift and of pandemic emergence. |
| Arbovirus transmission | Definition: Transmission by an arthropod vector in which the virus replicates before being passed on. Why it matters: Vector distribution and season determine where and when infection occurs, which is why these infections are geographically bounded. |
| Fungal cell wall | Definition: A wall of chitin and glucans, with ergosterol rather than cholesterol as the principal membrane sterol. Why it matters: Both the wall polysaccharide and the membrane sterol are absent from human cells, which is why they are the two selective targets. |
| Histoplasma capsulatum | Classification: Dimorphic fungus appearing as small yeasts within macrophages. Transmission: Inhaled spores from soil enriched by bird or bat droppings. Where: Associated with river valley regions of North America and with caves. |
| Giardia lamblia | Classification: Flagellated protozoan with trophozoite and cyst forms. Transmission: Cysts in contaminated water, including streams and lakes. Mechanism: Adheres to the small intestinal surface without invading, producing fat malabsorption. |
| Nematodes | Definition: Roundworms with a cylindrical unsegmented body and separate sexes. Why it matters: Most intestinal species are acquired by ingesting eggs or by larvae penetrating skin, so the entry route separates them into two groups. |
| Definitive versus intermediate host | Definition: The definitive host harbours the sexually reproducing stage, while an intermediate host carries larval or asexual stages. Why it matters: For malaria the mosquito is definitive and the human intermediate, which reverses the assumption that the human is the main host. |
| Type I hypersensitivity | Definition: An immediate reaction in which antigen cross-links IgE bound to mast cells, releasing histamine and other mediators. Why it matters: It requires previous sensitization, so the first exposure produces the IgE and a later one produces the reaction. |
| Toll-like receptors | Definition: Innate receptors recognizing conserved microbial patterns such as lipopolysaccharide, flagellin, and unmethylated DNA motifs. Why it matters: They detect classes of organism rather than specific ones, which is why the innate response is immediate but does not improve with repeated exposure. |
| Antibody isotypes | Definition: IgM as the first response and a strong complement activator, IgG the most abundant and the only one crossing the placenta, IgA in secretions, IgE on mast cells, and IgD on naive B cells. Why it matters: The heavy chain constant region rather than the binding site determines what an antibody can do once bound. |
| B cell defects and organism pattern | Definition: Impaired antibody production, associated with recurrent infection by encapsulated bacteria and by enteroviruses. Why it matters: Encapsulated organisms need opsonizing antibody to be cleared, so the defect predicts the organism class. |
About this deck
Microbiology collapses into a list of names unless each organism carries a small set of features that separate it from the one next to it. Catalase splits the gram-positive cocci, coagulase splits the staphylococci, and novobiocin splits what is left. Non-septate hyphae branching at wide angles is a different mold from septate hyphae branching at acute ones. Narrow-based budding with a capsule is a different yeast from broad-based budding without one. Learn the discriminating feature and the name follows. Learn the name first and you have a list. That is how these 300 cards are built. Every one opens with a classification or a definition, and beyond that the fields follow what the organism actually turns on: 83 give the transmission route, and where two organisms are routinely mixed up, the card names the other one and says which single feature separates them. The weighting is 146 cards of bacteriology including 31 on laboratory identification alone, 74 on virology, 30 on parasites, 28 on fungi, and 22 on immunology and host defence patterns. Antimicrobials are not here. Mechanism, spectrum and adverse effects live in the Pharmacology Drug Classes deck, so the two fit together without repeating a card: this deck is the organism, that one is the agent. Cards are tagged by group and by sub-group, so you can drill just the gram negatives, just the DNA viruses, or just the helminths. Import it and the deck joins your spaced-repetition schedule, and what you end up with is the thing the subject is really testing: given a stain, a plate, and a growth condition, being able to say what it is and why.
Frequently asked
- How is each organism card built?
- It opens with the classification, which for a bacterium means the Gram result, shape, arrangement and the key biochemical results. Then the fields that matter for that organism: virulence mechanism, transmission route on 83 cards, what it causes, and on 19 the organism it is most often confused with plus the single feature that separates them.
- Where do the antimicrobials fit?
- In the Pharmacology Drug Classes deck, deliberately. That deck covers mechanism, target, class suffix and adverse effect profile for every antimicrobial class. Keeping the agent and the organism in separate decks means neither one repeats the other, and you can drill either side on its own. The only drug names here are optochin, bacitracin and novobiocin, which appear as identification discs rather than as therapy.
- Does it cover the laboratory identification tests?
- Yes, as its own block of 31 cards: Gram stain and acid-fast staining, catalase and coagulase, hemolysis patterns, the optochin, bacitracin and novobiocin discs, oxidase, urease, indole and citrate, lactose fermentation on MacConkey, and the special media from chocolate agar to charcoal yeast extract. Each says what the test reads out and which organisms it separates.
- Which groups get the most cards?
- Bacteriology 146, made up of 31 laboratory identification, 35 gram-positive, 35 gram-negative, 23 virulence mechanisms and 22 mycobacteria, spirochetes and atypicals. Then virology 74, parasites 30, fungi 28, and immunology 22. Bacteriology is heaviest because that is where the discriminating features are densest.
- How is it organized for studying one group at a time?
- Every card carries a group tag and a finer sub-group tag, across laboratory identification, gram-positive bacteria, gram-negative bacteria, mycobacteria and spirochetes, bacterial virulence, virology, fungi, parasites and immunology. Filter by a tag to drill one group, or by the finer tag for a single block such as DNA viruses, helminths or biochemical tests.
- Can I import the whole deck on the free plan?
- Yes. Importing a saved deck runs no new AI generation and spends no AI credits, so the free plan imports every card. You can study, edit and delete them afterwards.
- Will importing it twice create duplicates?
- No. Cards you already have are skipped and only cards added in a revision come through. Including re-imports after deleting it, one official deck can be imported three times per account.
- Can I edit the cards after importing?
- Yes. Once imported they are your cards: edit either side, delete the ones you already know cold, retag them, or move them into another deck.
No official questions are reproduced, and every card is written by Memly. Compiled 2026-08-21.